diff --git a/ChangeLog.md b/ChangeLog.md index 64faed4239..b7431fd3aa 100644 --- a/ChangeLog.md +++ b/ChangeLog.md @@ -7,6 +7,7 @@ Features - Added ability to use posts to sequence methods [2555](https://github.com/GMOD/Apollo/pull/2558). - Added system info web service [2557](https://github.com/GMOD/Apollo/pull/2557). - Add "merged from" comment to merged in transcript and gene [2567](https://github.com/GMOD/Apollo/issues/2567). +- Added support for "obsolete", and partials in the interface for GFF3s [2573](https://github.com/GMOD/Apollo/pull/2573). Bug Fixes: diff --git a/grails-app/controllers/org/bbop/apollo/AnnotatorController.groovy b/grails-app/controllers/org/bbop/apollo/AnnotatorController.groovy index 2d57230d76..44f2788095 100644 --- a/grails-app/controllers/org/bbop/apollo/AnnotatorController.groovy +++ b/grails-app/controllers/org/bbop/apollo/AnnotatorController.groovy @@ -236,6 +236,7 @@ class AnnotatorController { feature.name = data.name feature.symbol = data.symbol feature.description = data.description + feature.isObsolete = data.obsolete if(data.containsKey("obsolete")) { feature.isObsolete = data.getBoolean("obsolete") } @@ -328,6 +329,76 @@ class AnnotatorController { render updateFeatureContainer } +/** + * updates shallow properties of gene / feature + * @return + */ + @RestApiMethod(description = "Update partial fmin / famx", path = "/annotator/updatePartials", verb = RestApiVerb.POST) + @RestApiParams(params = [ + @RestApiParam(name = "username", type = "email", paramType = RestApiParamType.QUERY) + , @RestApiParam(name = "password", type = "password", paramType = RestApiParamType.QUERY) + , @RestApiParam(name = "uniquename", type = "string", paramType = RestApiParamType.QUERY, description = "Uniquename (UUID) of the feature we are editing") + , @RestApiParam(name = "data", type = "string", paramType = RestApiParamType.QUERY, description = "Annotation Info object") + ] + ) + @Transactional + def updatePartials() { + log.debug "update partials ${params.data}" + JSONObject data = permissionService.handleInput(request, params) + if (!permissionService.hasPermissions(data, PermissionEnum.WRITE)) { + render status: HttpStatus.UNAUTHORIZED + return + } + Feature feature = Feature.findByUniqueName(data.uniquename) + FeatureLocation featureLocation = feature.featureLocation + + boolean isFminPartial = feature.featureLocation.isFminPartial + boolean isFmaxPartial = feature.featureLocation.isFmaxPartial + + JSONObject originalFeatureJsonObject = featureService.convertFeatureToJSON(feature) + FeatureOperation featureOperation + if(data.containsKey(FeatureStringEnum.IS_FMIN_PARTIAL.value) + && + data.getBoolean(FeatureStringEnum.IS_FMIN_PARTIAL.value) != isFminPartial + ){ + featureOperation = FeatureOperation.SET_PARTIAL_FMIN +// featureLocation.isFminPartial = data.getBoolean(FeatureStringEnum.IS_FMIN_PARTIAL.value) + featureService.setPartialFmin(feature,data.getBoolean(FeatureStringEnum.IS_FMIN_PARTIAL.value).booleanValue(),feature.featureLocation.fmin) + } + else + if(data.containsKey(FeatureStringEnum.IS_FMAX_PARTIAL.value) + && + data.getBoolean(FeatureStringEnum.IS_FMAX_PARTIAL.value) != isFmaxPartial + ){ + featureOperation = FeatureOperation.SET_PARTIAL_FMAX + featureService.setPartialFmax(feature,data.getBoolean(FeatureStringEnum.IS_FMAX_PARTIAL.value).booleanValue(),feature.featureLocation.fmax) + } + else{ + throw new AnnotationException("Partials have not changed, so not doing anything") + } + featureLocation.save(flush: true, failOnError: true,insert:false) + + JSONObject updateFeatureContainer = jsonWebUtilityService.createJSONFeatureContainer(); + // its either a gene or + + User user = permissionService.getCurrentUser(data) + JSONObject currentFeatureJsonObject = featureService.convertFeatureToJSON(feature) + + JSONArray oldFeaturesJsonArray = new JSONArray() + oldFeaturesJsonArray.add(originalFeatureJsonObject) + JSONArray newFeaturesJsonArray = new JSONArray() + newFeaturesJsonArray.add(currentFeatureJsonObject) + featureEventService.addNewFeatureEvent(featureOperation, + feature.name, + feature.uniqueName, + data, + oldFeaturesJsonArray, + newFeaturesJsonArray, + user) + + render updateFeatureContainer + } + @RestApiMethod(description = "Update exon boundaries", path = "/annotator/setExonBoundaries", verb = RestApiVerb.POST) @RestApiParams(params = [ @@ -991,6 +1062,7 @@ class AnnotatorController { if (!compareNullToBlank(feature.symbol,data.symbol)) return FeatureOperation.SET_SYMBOL if (!compareNullToBlank(feature.description,data.description)) return FeatureOperation.SET_DESCRIPTION if (!compareNullToBlank(feature.status,data.status)) return FeatureOperation.SET_STATUS + if(feature.isObsolete != data.obsolete ) return FeatureOperation.SET_OBSOLETE log.warn("Updated generic feature") null diff --git a/grails-app/domain/org/bbop/apollo/FeatureLocation.groovy b/grails-app/domain/org/bbop/apollo/FeatureLocation.groovy index 9da3777c00..9a01f19aa6 100644 --- a/grails-app/domain/org/bbop/apollo/FeatureLocation.groovy +++ b/grails-app/domain/org/bbop/apollo/FeatureLocation.groovy @@ -35,12 +35,7 @@ class FeatureLocation { static belongsTo = [Feature] - static hasMany = [ - featureLocationPublications: Publication - ] - - - public boolean equals(Object other) { + boolean equals(Object other) { if (this.is(other)) return true if (getClass() != other.class) return false FeatureLocation castOther = (FeatureLocation) other; @@ -48,7 +43,7 @@ class FeatureLocation { return ((this.getFeature() == castOther.getFeature()) || (this.getFeature() != null && castOther.getFeature() != null && this.getFeature().equals(castOther.getFeature()))) && (this.getLocgroup() == castOther.getLocgroup()) && (this.getRank() == castOther.getRank()); } - public int hashCode() { + int hashCode() { int result = 17; result = 37 * result + (getFeature() == null ? 0 : this.getFeature().hashCode()); @@ -63,10 +58,10 @@ class FeatureLocation { * We use this as an artificial accessor in case the property has not been calculatd * @return */ - public Integer calculateLength(){ + Integer calculateLength(){ return fmax-fmin } - public FeatureLocation generateClone() { + FeatureLocation generateClone() { FeatureLocation cloned = new FeatureLocation(); cloned.sequence = this.sequence; cloned.feature = this.feature; @@ -79,7 +74,6 @@ class FeatureLocation { cloned.residueInfo = this.residueInfo; cloned.locgroup = this.locgroup; cloned.rank = this.rank; - cloned.featureLocationPublications = this.featureLocationPublications; return cloned; } diff --git a/grails-app/services/org/bbop/apollo/ChadoHandlerService.groovy b/grails-app/services/org/bbop/apollo/ChadoHandlerService.groovy index d03ec1afb4..839dbe03ff 100644 --- a/grails-app/services/org/bbop/apollo/ChadoHandlerService.groovy +++ b/grails-app/services/org/bbop/apollo/ChadoHandlerService.groovy @@ -456,9 +456,9 @@ class ChadoHandlerService { endTime = System.currentTimeMillis() log.debug "Time taken to create Chado featureloc for feature fmin: ${feature.fmin} fmax: ${feature.fmax}: ${endTime - startTime} ms" exportStatisticsMap['featureloc_count'] += 1 - feature.featureLocation.featureLocationPublications.each { featureLocationPublication -> - createChadoFeaturelocPub(chadoFeatureLoc, featureLocationPublication) - } +// feature.featureLocation.featureLocationPublications.each { featureLocationPublication -> +// createChadoFeaturelocPub(chadoFeatureLoc, featureLocationPublication) +// } return chadoFeatureLoc } diff --git a/grails-app/services/org/bbop/apollo/FeatureService.groovy b/grails-app/services/org/bbop/apollo/FeatureService.groovy index fbc59d9db2..7159ffacb5 100644 --- a/grails-app/services/org/bbop/apollo/FeatureService.groovy +++ b/grails-app/services/org/bbop/apollo/FeatureService.groovy @@ -6,6 +6,7 @@ import org.bbop.apollo.alteration.SequenceAlterationInContext import org.bbop.apollo.geneProduct.GeneProduct import org.bbop.apollo.go.GoAnnotation import org.bbop.apollo.gwt.shared.FeatureStringEnum +import org.bbop.apollo.history.FeatureOperation import org.bbop.apollo.sequence.SequenceTranslationHandler import org.bbop.apollo.sequence.Strand import org.bbop.apollo.sequence.TranslationTable @@ -1966,6 +1967,9 @@ public void setTranslationEnd(Transcript transcript, int translationEnd) { if (gsolFeature.symbol) { jsonFeature.put(FeatureStringEnum.SYMBOL.value, gsolFeature.symbol); } + if (gsolFeature.isObsolete) { + jsonFeature.put(FeatureStringEnum.OBSOLETE.value, gsolFeature.isObsolete); + } if (gsolFeature.description) { jsonFeature.put(FeatureStringEnum.DESCRIPTION.value, gsolFeature.description); } @@ -2356,20 +2360,21 @@ public void setTranslationEnd(Transcript transcript, int translationEnd) { @Timed JSONObject convertFeatureLocationToJSON(FeatureLocation gsolFeatureLocation) throws JSONException { - JSONObject jsonFeatureLocation = new JSONObject(); + JSONObject jsonFeatureLocation = new JSONObject() if (gsolFeatureLocation.id) { - jsonFeatureLocation.put(FeatureStringEnum.ID.value, gsolFeatureLocation.id); + jsonFeatureLocation.put(FeatureStringEnum.ID.value, gsolFeatureLocation.id) } - jsonFeatureLocation.put(FeatureStringEnum.FMIN.value, gsolFeatureLocation.getFmin()); - jsonFeatureLocation.put(FeatureStringEnum.FMAX.value, gsolFeatureLocation.getFmax()); - if (gsolFeatureLocation.isIsFminPartial()) { - jsonFeatureLocation.put(FeatureStringEnum.IS_FMIN_PARTIAL.value, true); + jsonFeatureLocation.put(FeatureStringEnum.FMIN.value, gsolFeatureLocation.getFmin()) + jsonFeatureLocation.put(FeatureStringEnum.FMAX.value, gsolFeatureLocation.getFmax()) + if(gsolFeatureLocation.getIsFminPartial()){ + jsonFeatureLocation.put(FeatureStringEnum.IS_FMIN_PARTIAL.value, gsolFeatureLocation.getIsFminPartial()) } - if (gsolFeatureLocation.isIsFmaxPartial()) { - jsonFeatureLocation.put(FeatureStringEnum.IS_FMAX_PARTIAL.value, true); + + if(gsolFeatureLocation.getIsFmaxPartial()){ + jsonFeatureLocation.put(FeatureStringEnum.IS_FMAX_PARTIAL.value, gsolFeatureLocation.getIsFmaxPartial()) } - jsonFeatureLocation.put(FeatureStringEnum.STRAND.value, gsolFeatureLocation.getStrand()); - return jsonFeatureLocation; + jsonFeatureLocation.put(FeatureStringEnum.STRAND.value, gsolFeatureLocation.getStrand()) + return jsonFeatureLocation } @Transactional @@ -3584,4 +3589,38 @@ public void setTranslationEnd(Transcript transcript, int translationEnd) { return false } + + @Transactional + def setPartialFmin(Feature feature,boolean fminPartial,int fmin){ + FeatureLocation featureLocation = feature.featureLocation + if(fmin==featureLocation.fmin){ + featureLocation.isFminPartial = fminPartial + featureLocation.save() + } + + List childFeatures = feature.parentFeatureRelationships*.childFeature + if(childFeatures){ + for(childFeature in childFeatures){ + setPartialFmin(childFeature,fminPartial,fmin) + } + } + } + + @Transactional + def setPartialFmax(Feature feature,boolean fmaxPartial,int fmax){ + FeatureLocation featureLocation = feature.featureLocation + if(fmax==featureLocation.fmax){ + featureLocation.isFmaxPartial = fmaxPartial + featureLocation.save() + } + + List childFeatures = feature.parentFeatureRelationships*.childFeature + if(childFeatures){ + for(childFeature in childFeatures){ + setPartialFmax(childFeature,fmaxPartial,fmax) + } + } + + } + } diff --git a/grails-app/services/org/bbop/apollo/Gff3HandlerService.groovy b/grails-app/services/org/bbop/apollo/Gff3HandlerService.groovy index 2ce8127b23..3f08e1cd81 100644 --- a/grails-app/services/org/bbop/apollo/Gff3HandlerService.groovy +++ b/grails-app/services/org/bbop/apollo/Gff3HandlerService.groovy @@ -1,12 +1,9 @@ package org.bbop.apollo import org.apache.commons.lang.WordUtils -import org.bbop.apollo.geneProduct.GeneProduct -import org.bbop.apollo.go.GoAnnotation import org.bbop.apollo.gwt.shared.FeatureStringEnum import org.bbop.apollo.sequence.Strand import org.grails.plugins.metrics.groovy.Timed -import org.springframework.format.datetime.DateFormatter import java.text.SimpleDateFormat @@ -53,6 +50,9 @@ class Gff3HandlerService { writeObject.attributesToExport.add(FeatureStringEnum.COMMENTS.value); writeObject.attributesToExport.add(FeatureStringEnum.DATE_CREATION.value); writeObject.attributesToExport.add(FeatureStringEnum.DATE_LAST_MODIFIED.value); + writeObject.attributesToExport.add(FeatureStringEnum.IS_FMIN_PARTIAL.value); + writeObject.attributesToExport.add(FeatureStringEnum.IS_FMAX_PARTIAL.value); + writeObject.attributesToExport.add(FeatureStringEnum.OBSOLETE.value); if (!writeObject.file.canWrite()) { throw new IOException("Cannot write GFF3 to: " + writeObject.file.getAbsolutePath()); @@ -355,6 +355,15 @@ class Gff3HandlerService { String productString = geneProductService.convertGeneProductsToGff3String(feature.geneProducts) attributes.put(FeatureStringEnum.GENE_PRODUCT.value, encodeString(productString)) } + if (writeObject.attributesToExport.contains(FeatureStringEnum.IS_FMIN_PARTIAL.value) && feature.featureLocation.isFminPartial) { + attributes.put(FeatureStringEnum.IS_FMIN_PARTIAL.value, feature.featureLocation.isFminPartial.toString()) + } + if (writeObject.attributesToExport.contains(FeatureStringEnum.OBSOLETE.value) && feature.isObsolete) { + attributes.put(FeatureStringEnum.OBSOLETE.value, feature.isObsolete.toString()) + } + if (writeObject.attributesToExport.contains(FeatureStringEnum.IS_FMAX_PARTIAL.value) && feature.featureLocation.isFmaxPartial) { + attributes.put(FeatureStringEnum.IS_FMAX_PARTIAL.value, feature.featureLocation.isFmaxPartial.toString()) + } if (writeObject.attributesToExport.contains(FeatureStringEnum.STATUS.value) && feature.getStatus() != null) { attributes.put(FeatureStringEnum.STATUS.value, encodeString(feature.getStatus().value)); } diff --git a/src/groovy/org/bbop/apollo/history/FeatureOperation.groovy b/src/groovy/org/bbop/apollo/history/FeatureOperation.groovy index 5db6deb084..b5f3d36ffa 100644 --- a/src/groovy/org/bbop/apollo/history/FeatureOperation.groovy +++ b/src/groovy/org/bbop/apollo/history/FeatureOperation.groovy @@ -23,6 +23,7 @@ enum FeatureOperation { SET_TRANSLATION_ENDS, SET_LONGEST_ORF, FLIP_STRAND, + SET_OBSOLETE, REMOVE_CDS, SET_READTHROUGH_STOP_CODON, UNSET_READTHROUGH_STOP_CODON, @@ -32,6 +33,8 @@ enum FeatureOperation { DISSOCIATE_TRANSCRIPT_FROM_GENE, ASSOCIATE_FEATURE_TO_GENE, DISSOCIATE_FEATURE_FROM_GENE, + SET_PARTIAL_FMIN, + SET_PARTIAL_FMAX, // structural data SET_SYMBOL(false), diff --git a/src/gwt/org/bbop/apollo/gwt/client/GeneDetailPanel.java b/src/gwt/org/bbop/apollo/gwt/client/GeneDetailPanel.java index 886a02c4d7..0eac2e470a 100644 --- a/src/gwt/org/bbop/apollo/gwt/client/GeneDetailPanel.java +++ b/src/gwt/org/bbop/apollo/gwt/client/GeneDetailPanel.java @@ -22,7 +22,6 @@ import org.bbop.apollo.gwt.client.rest.AvailableStatusRestService; import org.bbop.apollo.gwt.client.rest.RestService; import org.bbop.apollo.gwt.shared.FeatureStringEnum; -import org.bbop.apollo.gwt.shared.PermissionEnum; import org.gwtbootstrap3.client.ui.*; import org.gwtbootstrap3.extras.bootbox.client.Bootbox; import org.gwtbootstrap3.extras.bootbox.client.callback.ConfirmCallback; @@ -41,7 +40,7 @@ public class GeneDetailPanel extends Composite { interface AnnotationDetailPanelUiBinder extends UiBinder { } - private static AnnotationDetailPanelUiBinder ourUiBinder = GWT.create(AnnotationDetailPanelUiBinder.class); + private static final AnnotationDetailPanelUiBinder ourUiBinder = GWT.create(AnnotationDetailPanelUiBinder.class); @UiField(provided = true) SuggestBox nameField; @UiField @@ -74,6 +73,12 @@ interface AnnotationDetailPanelUiBinder extends UiBinder childAnnotations = internalAnnotationInfo.getChildAnnotations(); if(childAnnotations.size()==1){ @@ -193,6 +213,8 @@ public void setEditable(boolean editable) { descriptionField.setEnabled(editable); synonymsField.setEnabled(editable); deleteAnnotation.setEnabled(editable); + partialMin.setEnabled(editable); + partialMax.setEnabled(editable); if(!editable || this.internalAnnotationInfo==null){ syncNameButton.setEnabled(false); @@ -202,6 +224,29 @@ public void setEditable(boolean editable) { } } + private void updatePartials() { + setEditable(false); + RequestCallback requestCallback = new RequestCallback() { + @Override + public void onResponseReceived(Request request, Response response) { + JSONValue returnValue = JSONParser.parseStrict(response.getText()); + setEditable(true); + MainPanel.annotatorPanel.setSelectedChildUniqueName(null); + } + + @Override + public void onError(Request request, Throwable exception) { + Bootbox.alert("Error updating gene: " + exception); + setEditable(true); + } + }; +// RestService.sendRequest(requestCallback, "annotator/updateFeature/", AnnotationRestService.convertAnnotationInfoToJSONObject(this.internalAnnotationInfo)); + JSONObject data = AnnotationRestService.convertAnnotationInfoToJSONObject(this.internalAnnotationInfo); + data.put(FeatureStringEnum.ORGANISM.getValue(),new JSONString(MainPanel.getInstance().getCurrentOrganism().getId())); + + RestService.sendRequest(requestCallback, "annotator/updatePartials/", data); + + } private void updateGene() { setEditable(false); @@ -236,6 +281,9 @@ public void updateData(AnnotationInfo annotationInfo) { suggestedNameOracle.setOrganismName(MainPanel.getInstance().getCurrentOrganism().getName()); suggestedNameOracle.setFeatureType("sequence:" + annotationInfo.getType()); nameField.setText(internalAnnotationInfo.getName()); + partialMin.setValue(internalAnnotationInfo.getPartialMin()); + partialMax.setValue(internalAnnotationInfo.getPartialMax()); + obsoleteButton.setValue(internalAnnotationInfo.getObsolete()); symbolField.setText(internalAnnotationInfo.getSymbol()); typeField.setText(internalAnnotationInfo.getType()); synonymsField.setText(internalAnnotationInfo.getSynonyms()); diff --git a/src/gwt/org/bbop/apollo/gwt/client/GeneDetailPanel.ui.xml b/src/gwt/org/bbop/apollo/gwt/client/GeneDetailPanel.ui.xml index 315646844d..420a9a4866 100644 --- a/src/gwt/org/bbop/apollo/gwt/client/GeneDetailPanel.ui.xml +++ b/src/gwt/org/bbop/apollo/gwt/client/GeneDetailPanel.ui.xml @@ -1,5 +1,5 @@ @@ -37,6 +37,18 @@ display: inline; } + .location-button{ + background-color: #eee; + width: 280px; + } + + .partial-button{ + display: inline ; + margin-left: 5px; + padding-left: 0; + padding-right: 0; + } + .inputGroup1 { width: 400px; } @@ -52,6 +64,7 @@ ui:field="annotationIdButton" enabled="true" addStyleNames="{style.action-buttons}"/> + Obsolete Location - + + Partial: + 3' + 5' diff --git a/src/gwt/org/bbop/apollo/gwt/client/TranscriptDetailPanel.java b/src/gwt/org/bbop/apollo/gwt/client/TranscriptDetailPanel.java index 127479d8a9..2d77e3c4c9 100644 --- a/src/gwt/org/bbop/apollo/gwt/client/TranscriptDetailPanel.java +++ b/src/gwt/org/bbop/apollo/gwt/client/TranscriptDetailPanel.java @@ -19,10 +19,7 @@ import org.bbop.apollo.gwt.client.rest.AvailableStatusRestService; import org.bbop.apollo.gwt.client.rest.RestService; import org.bbop.apollo.gwt.shared.FeatureStringEnum; -import org.gwtbootstrap3.client.ui.Button; -import org.gwtbootstrap3.client.ui.InputGroupAddon; -import org.gwtbootstrap3.client.ui.ListBox; -import org.gwtbootstrap3.client.ui.TextBox; +import org.gwtbootstrap3.client.ui.*; import org.gwtbootstrap3.extras.bootbox.client.Bootbox; import org.gwtbootstrap3.extras.bootbox.client.callback.ConfirmCallback; @@ -72,6 +69,12 @@ interface AnnotationDetailPanelUiBinder extends UiBinder + Obsolete Location - + + Partial: + 3' + 5' diff --git a/src/gwt/org/bbop/apollo/gwt/client/dto/AnnotationInfo.java b/src/gwt/org/bbop/apollo/gwt/client/dto/AnnotationInfo.java index bc5228664e..d42702b144 100644 --- a/src/gwt/org/bbop/apollo/gwt/client/dto/AnnotationInfo.java +++ b/src/gwt/org/bbop/apollo/gwt/client/dto/AnnotationInfo.java @@ -15,6 +15,9 @@ public class AnnotationInfo { private String type; private Integer min; private Integer max; + private Boolean partialMin = false; + private Boolean partialMax = false; + private Boolean obsolete = false; private Set childAnnotations = new HashSet<>(); // children private List goAnnotations = new ArrayList<>(); // go annotations private String symbol; @@ -302,4 +305,30 @@ public boolean equals(Object o) { public int hashCode() { return Objects.hash(uniqueName, name, type, min, max, childAnnotations, goAnnotations, symbol, description, strand, noteList, dbXrefList, sequence, phase, owner, dateLastModified, dateCreated, referenceAllele, alternateAlleles, variantProperties, commentList, attributeList, status, synonyms); } + + public Boolean getPartialMin() { + return partialMin; + } + + public void setPartialMin(Boolean partialMin) { + this.partialMin = partialMin; + } + + public Boolean getPartialMax() { + return partialMax; + } + + public void setPartialMax(Boolean partialMax) { + this.partialMax = partialMax; + } + + + public Boolean getObsolete() { + return obsolete; + } + + public void setObsolete(Boolean obsolete) { + this.obsolete = obsolete; + } + } diff --git a/src/gwt/org/bbop/apollo/gwt/client/dto/AnnotationInfoConverter.java b/src/gwt/org/bbop/apollo/gwt/client/dto/AnnotationInfoConverter.java index 15b7267a56..f9acda132e 100644 --- a/src/gwt/org/bbop/apollo/gwt/client/dto/AnnotationInfoConverter.java +++ b/src/gwt/org/bbop/apollo/gwt/client/dto/AnnotationInfoConverter.java @@ -1,6 +1,5 @@ package org.bbop.apollo.gwt.client.dto; -import com.google.gwt.core.client.GWT; import com.google.gwt.json.client.JSONArray; import com.google.gwt.json.client.JSONObject; import org.bbop.apollo.gwt.client.VariantDetailPanel; @@ -31,7 +30,6 @@ public static AnnotationInfo convertFromJsonObject(JSONObject object) { public static AnnotationInfo convertFromJsonObject(JSONObject object, boolean processChildren) { AnnotationInfo annotationInfo = new AnnotationInfo(); - GWT.log(object.toString()); annotationInfo.setName(object.get(FeatureStringEnum.NAME.getValue()).isString().stringValue()); annotationInfo.setType(object.get(FeatureStringEnum.TYPE.getValue()).isObject().get(FeatureStringEnum.NAME.getValue()).isString().stringValue()); if (object.get(FeatureStringEnum.SYMBOL.getValue()) != null) { @@ -69,16 +67,19 @@ public static AnnotationInfo convertFromJsonObject(JSONObject object, boolean pr annotationInfo.setCommentList(CommentInfoConverter.convertToCommentFromArray(object.get(FeatureStringEnum.COMMENTS.getValue()).isArray())); } - -// List goAnnotationList = new ArrayList<>(); -// goAnnotationList.add(generateGoAnnotation()); -// goAnnotationList.add(generateGoAnnotation()); -// goAnnotationList.add(generateGoAnnotation()); -// -// annotationInfo.setGoAnnotations(goAnnotationList); - annotationInfo.setMin((int) object.get(FeatureStringEnum.LOCATION.getValue()).isObject().get(FeatureStringEnum.FMIN.getValue()).isNumber().doubleValue()); annotationInfo.setMax((int) object.get(FeatureStringEnum.LOCATION.getValue()).isObject().get(FeatureStringEnum.FMAX.getValue()).isNumber().doubleValue()); + + if(object.get(FeatureStringEnum.LOCATION.getValue()).isObject().containsKey(FeatureStringEnum.IS_FMIN_PARTIAL.getValue())){ + annotationInfo.setPartialMin(object.get(FeatureStringEnum.LOCATION.getValue()).isObject().get(FeatureStringEnum.IS_FMIN_PARTIAL.getValue()).isBoolean().booleanValue()); + } + if(object.get(FeatureStringEnum.LOCATION.getValue()).isObject().containsKey(FeatureStringEnum.IS_FMAX_PARTIAL.getValue())) { + annotationInfo.setPartialMax(object.get(FeatureStringEnum.LOCATION.getValue()).isObject().get(FeatureStringEnum.IS_FMAX_PARTIAL.getValue()).isBoolean().booleanValue()); + } + + if (object.get(FeatureStringEnum.OBSOLETE.getValue()) != null) { + annotationInfo.setObsolete(object.get(FeatureStringEnum.OBSOLETE.getValue()).isBoolean().booleanValue()); + } annotationInfo.setStrand((int) object.get(FeatureStringEnum.LOCATION.getValue()).isObject().get(FeatureStringEnum.STRAND.getValue()).isNumber().doubleValue()); annotationInfo.setUniqueName(object.get(FeatureStringEnum.UNIQUENAME.getValue()).isString().stringValue()); annotationInfo.setSequence(object.get(FeatureStringEnum.SEQUENCE.getValue()).isString().stringValue()); diff --git a/src/gwt/org/bbop/apollo/gwt/client/rest/AnnotationRestService.java b/src/gwt/org/bbop/apollo/gwt/client/rest/AnnotationRestService.java index e7c81cc9fe..07ced6607e 100644 --- a/src/gwt/org/bbop/apollo/gwt/client/rest/AnnotationRestService.java +++ b/src/gwt/org/bbop/apollo/gwt/client/rest/AnnotationRestService.java @@ -43,6 +43,9 @@ public static JSONObject convertAnnotationInfoToJSONObject(AnnotationInfo annota } jsonObject.put(FeatureStringEnum.FMIN.getValue(), annotationInfo.getMin() != null ? new JSONNumber(annotationInfo.getMin()) : null); jsonObject.put(FeatureStringEnum.FMAX.getValue(), annotationInfo.getMax() != null ? new JSONNumber(annotationInfo.getMax()) : null); + jsonObject.put(FeatureStringEnum.IS_FMIN_PARTIAL.getValue(), JSONBoolean.getInstance(annotationInfo.getPartialMin()) ); + jsonObject.put(FeatureStringEnum.IS_FMAX_PARTIAL.getValue(), JSONBoolean.getInstance(annotationInfo.getPartialMax()) ); + jsonObject.put(FeatureStringEnum.OBSOLETE.getValue(), JSONBoolean.getInstance(annotationInfo.getObsolete()) ); jsonObject.put(FeatureStringEnum.STRAND.getValue(), annotationInfo.getStrand() != null ? new JSONNumber(annotationInfo.getStrand()) : null); return jsonObject; @@ -62,6 +65,8 @@ static JSONObject generateLocationObject(AnnotationInfo annotationInfo){ JSONObject locationObject = new JSONObject(); locationObject.put(FeatureStringEnum.FMIN.getValue(), annotationInfo.getMin() != null ? new JSONNumber(annotationInfo.getMin()) : null); locationObject.put(FeatureStringEnum.FMAX.getValue(), annotationInfo.getMax() != null ? new JSONNumber(annotationInfo.getMax()) : null); + locationObject.put(FeatureStringEnum.IS_FMIN_PARTIAL.getValue(), JSONBoolean.getInstance(annotationInfo.getPartialMin()) ); + locationObject.put(FeatureStringEnum.IS_FMAX_PARTIAL.getValue(), JSONBoolean.getInstance(annotationInfo.getPartialMax()) ); locationObject.put(FeatureStringEnum.STRAND.getValue(), annotationInfo.getStrand() != null ? new JSONNumber(annotationInfo.getStrand()) : null); return locationObject; } diff --git a/src/gwt/org/bbop/apollo/gwt/shared/FeatureStringEnum.java b/src/gwt/org/bbop/apollo/gwt/shared/FeatureStringEnum.java index 4ac0e3d2ec..906fd41ef8 100644 --- a/src/gwt/org/bbop/apollo/gwt/shared/FeatureStringEnum.java +++ b/src/gwt/org/bbop/apollo/gwt/shared/FeatureStringEnum.java @@ -64,6 +64,7 @@ public enum FeatureStringEnum { CONFIRM, FMIN, FMAX, + OBSOLETE, IS_FMIN_PARTIAL, IS_FMAX_PARTIAL, STRAND, diff --git a/web-app/js/restapidoc/restapidoc.json b/web-app/js/restapidoc/restapidoc.json index b863a413ae..b165cbb65b 100644 --- a/web-app/js/restapidoc/restapidoc.json +++ b/web-app/js/restapidoc/restapidoc.json @@ -2,14 +2,14 @@ "basePath": "Fill with basePath config", "apis": [ { - "jsondocId": "ef8dc20d-baf5-495f-a537-0ad54c2bfe43", + "jsondocId": "40b3dc30-efaf-4079-9de3-4b7db741b8eb", "methods": [ { "headers": [], "pathparameters": [], "queryparameters": [ { - "jsondocId": "d708667c-8609-4472-9f9a-3edbe9bc2783", + "jsondocId": "2866635d-ee69-4066-828f-f057ec8fa8e0", "name": "username", "format": "", "description": "", @@ -18,7 +18,7 @@ "allowedvalues": [] }, { - "jsondocId": "4b1f296f-e3cf-405a-9d49-1347855170bc", + "jsondocId": "75c84276-bb31-40e2-9bd6-c78a1f8cc2e3", "name": "password", "format": "", "description": "", @@ -27,7 +27,7 @@ "allowedvalues": [] }, { - "jsondocId": "bd9b5d0d-25c5-4f9d-94bf-b714f803ab40", + "jsondocId": "998f6789-df1c-4680-acb6-10bfb8da3b24", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -36,7 +36,7 @@ "allowedvalues": [] }, { - "jsondocId": "be0938e0-ded3-4ba9-9255-fb470b7f32a4", + "jsondocId": "6144ed3e-feca-429a-8d8a-48f379570532", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -45,21 +45,21 @@ "allowedvalues": [] }, { - "jsondocId": "e720fea5-1767-47bb-8d00-b79615337c3c", + "jsondocId": "47ed7a81-1721-455f-99c9-1d19668f3b63", "name": "features", "format": "", - "description": "JSONArray containing JSON objects with {'uniquename':'ABCD-1234','status':'existing-status-string'}. Available status found here: /availableStatus/ ", + "description": "JSONArray of JSON feature objects ('uniquename' required) JSONArray described by https://github.com/GMOD/Apollo/blob/master/grails-app/domain/org/bbop/apollo/Feature.groovy", "type": "JSONArray", "required": "true", "allowedvalues": [] } ], "verb": "POST", - "description": "Set status of a feature", - "methodName": "setStatus", - "jsondocId": "dda6be1d-d4ec-4c87-9d17-23468dc9018b", + "description": "Get comments", + "methodName": "getComments", + "jsondocId": "589dfd48-4725-4c66-ba34-00c7e60eea8e", "bodyobject": { - "jsondocId": "e7799ac5-f0ed-464b-8f13-3db0cd5574f4", + "jsondocId": "ee3f9219-fde4-48b1-873c-6d5360330bdc", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -67,9 +67,9 @@ "object": "annotation editor" }, "apierrors": [], - "path": "/annotationEditor/setStatus", + "path": "/annotationEditor/getComments", "response": { - "jsondocId": "60ad651f-6a09-43aa-8585-25feb8b2d278", + "jsondocId": "20f3dc80-2b82-4779-828a-2590d2bc22cb", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -82,7 +82,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "84fb4efb-dc69-41af-8299-f06d6fe9aa39", + "jsondocId": "fc3c1b91-7f14-45a0-badb-e88ceaaa50da", "name": "username", "format": "", "description": "", @@ -91,7 +91,7 @@ "allowedvalues": [] }, { - "jsondocId": "6d2291e2-e55a-4ebd-aa32-c57cf537a8e2", + "jsondocId": "7501a08b-50fe-4ce6-9875-42822182947d", "name": "password", "format": "", "description": "", @@ -100,7 +100,7 @@ "allowedvalues": [] }, { - "jsondocId": "8f07ac55-7c92-4aca-b0d5-09339989e1e0", + "jsondocId": "8095ed35-106b-4a90-aa1b-aa854ba46571", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -109,7 +109,7 @@ "allowedvalues": [] }, { - "jsondocId": "4265efb5-6c8c-4e0e-9df4-7b5ae55aa67d", + "jsondocId": "378eee85-6e9d-46cd-86f5-ca3b8f4e40db", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -118,21 +118,21 @@ "allowedvalues": [] }, { - "jsondocId": "6055bf2e-3fcf-43cc-93b4-7421dc9258b8", + "jsondocId": "e91dd016-f593-4792-94b5-e5c0afd36bf0", "name": "features", "format": "", - "description": "JSONArray of JSON feature objects ('uniquename' required) JSONArray described by https://github.com/GMOD/Apollo/blob/master/grails-app/domain/org/bbop/apollo/Feature.groovy", + "description": "JSONArray containing JSON objects with {'uniquename':'ABCD-1234','description':'some descriptive test'}", "type": "JSONArray", "required": "true", "allowedvalues": [] } ], "verb": "POST", - "description": "Get comments", - "methodName": "getComments", - "jsondocId": "74d29bed-431f-429b-969e-7b934de37320", + "description": "Set description for a feature", + "methodName": "setDescription", + "jsondocId": "6f5dd511-57cb-4b37-953e-747095fb9dae", "bodyobject": { - "jsondocId": "4a257321-9e24-4cb3-91c2-720351ec3a1f", + "jsondocId": "83ac27e9-7039-4f19-af97-217c1deb8199", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -140,9 +140,9 @@ "object": "annotation editor" }, "apierrors": [], - "path": "/annotationEditor/getComments", + "path": "/annotationEditor/setDescription", "response": { - "jsondocId": "0af118e6-394d-4620-98fb-d8f428925ec4", + "jsondocId": "3f6fa28b-d86d-45d0-8348-68143bc737dc", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -155,7 +155,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "cab75ef8-ebcf-4c66-b593-a12013a47cf3", + "jsondocId": "bfdf12f3-eab3-4c24-9b55-97563f989416", "name": "username", "format": "", "description": "", @@ -164,7 +164,7 @@ "allowedvalues": [] }, { - "jsondocId": "f659f791-ad15-4939-8ee2-5d264b805b81", + "jsondocId": "e03f185f-f336-426e-98b0-c470b1bd0607", "name": "password", "format": "", "description": "", @@ -173,7 +173,7 @@ "allowedvalues": [] }, { - "jsondocId": "2ff308fe-524d-4348-8f7b-2223a41a8087", + "jsondocId": "cb85e345-8288-4f08-a6b9-d9bfd031e2a9", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -182,7 +182,7 @@ "allowedvalues": [] }, { - "jsondocId": "17c9fc87-880d-4c13-8bf0-6f70117c6c3f", + "jsondocId": "da895699-ed0f-4319-a310-c122936b4751", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -191,21 +191,21 @@ "allowedvalues": [] }, { - "jsondocId": "1e8b4793-545b-4555-8c5d-b713869df5e7", + "jsondocId": "035f9a32-d96f-4a4f-80fc-5e162c565f6c", "name": "features", "format": "", - "description": "JSONArray containing JSON objects with {'uniquename':'ABCD-1234','description':'some descriptive test'}", + "description": "JSONArray containing JSON objects with {'uniquename':'ABCD-1234','symbol':'Pax6a'}", "type": "JSONArray", "required": "true", "allowedvalues": [] } ], "verb": "POST", - "description": "Set description for a feature", - "methodName": "setDescription", - "jsondocId": "e3d3cc0a-ee59-497c-9e18-c2da4701610a", + "description": "Set symbol of a feature", + "methodName": "setSymbol", + "jsondocId": "6698f0f3-7c83-41b5-9174-a923abeaf48a", "bodyobject": { - "jsondocId": "85a1f23a-d189-481f-af1b-4b5b33bcb3ea", + "jsondocId": "dc3a81c2-e441-47c7-b8b0-9e299f988562", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -213,9 +213,9 @@ "object": "annotation editor" }, "apierrors": [], - "path": "/annotationEditor/setDescription", + "path": "/annotationEditor/setSymbol", "response": { - "jsondocId": "28b4a87f-3169-4e23-ac68-126f1690af41", + "jsondocId": "5b88cda6-f74b-47df-959f-06aac949e162", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -228,7 +228,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "51f7b596-96d3-4d9e-b836-6c5c1c28a565", + "jsondocId": "210d3b5b-0aa1-4c94-baed-e8bd0b019006", "name": "username", "format": "", "description": "", @@ -237,7 +237,7 @@ "allowedvalues": [] }, { - "jsondocId": "c3ea3a80-2644-485f-baca-204d71f8c284", + "jsondocId": "b7cd4062-77d0-4de0-b670-f731ea8a22ea", "name": "password", "format": "", "description": "", @@ -246,7 +246,7 @@ "allowedvalues": [] }, { - "jsondocId": "5fb27891-987b-4ce4-b3ef-ac4b04b26de2", + "jsondocId": "c72f8940-2faa-418d-9231-0e97c41971b6", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -255,7 +255,7 @@ "allowedvalues": [] }, { - "jsondocId": "3c4430bd-8694-468d-b645-3e873bee8590", + "jsondocId": "7d70f341-3a37-450e-8ab1-b44bbda7f9c1", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -264,21 +264,21 @@ "allowedvalues": [] }, { - "jsondocId": "c083e34c-3659-4a27-be6e-5ce629927899", + "jsondocId": "29de3ae2-112e-4603-8382-b7f5ba1784b2", "name": "features", "format": "", - "description": "JSONArray containing JSON objects with {'uniquename':'ABCD-1234','non_reserved_properties':[{'tag':'clockwork','value':'orange'},{'tag':'color','value':'purple'}]}. Available status found here: /availableStatus/ ", + "description": "JSONArray containing JSON objects with {'uniquename':'ABCD-1234','name':'gene01'}", "type": "JSONArray", "required": "true", "allowedvalues": [] } ], "verb": "POST", - "description": "Add attribute (key,value pair) to feature", - "methodName": "addAttribute", - "jsondocId": "9f26de7c-10a1-4244-843b-438f0be82a14", + "description": "Set name of a feature", + "methodName": "setName", + "jsondocId": "d5c0c9f1-7520-49e5-aa6c-12a4845986d1", "bodyobject": { - "jsondocId": "259d1b07-1cc0-4c65-bbbc-0ebae4e96858", + "jsondocId": "60d793d6-6e2c-468a-b373-17a88778e4de", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -286,9 +286,9 @@ "object": "annotation editor" }, "apierrors": [], - "path": "/annotationEditor/addAttribute", + "path": "/annotationEditor/setName", "response": { - "jsondocId": "fea32482-c083-48b7-a4a7-f33cdb7791c9", + "jsondocId": "675ca127-118e-4f83-9c29-5ad33af6b401", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -301,7 +301,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "6b9a26b0-4c1b-4149-88ed-986d95cd177a", + "jsondocId": "7610920a-7b5f-439f-9df0-0961169bab71", "name": "username", "format": "", "description": "", @@ -310,7 +310,7 @@ "allowedvalues": [] }, { - "jsondocId": "8a11a069-ee52-426d-b9ee-4075dd414718", + "jsondocId": "b9aac20c-9c9f-4836-8266-9b07f0094aaa", "name": "password", "format": "", "description": "", @@ -319,7 +319,7 @@ "allowedvalues": [] }, { - "jsondocId": "d6ba3530-db67-4e81-8d0f-ce63d5e63457", + "jsondocId": "1b2610b6-d84c-4eb0-b00c-07f5cfdf1cfd", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -328,7 +328,7 @@ "allowedvalues": [] }, { - "jsondocId": "4d01be9b-19d5-404e-a0b4-32506ca36c40", + "jsondocId": "b505c804-fa81-4446-b0ef-35ed05fe7da8", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -337,21 +337,21 @@ "allowedvalues": [] }, { - "jsondocId": "50b05a30-1346-40fa-80a0-2526f8374d53", - "name": "features", + "jsondocId": "18a58a0d-ad9c-4c1f-9d5e-3af0273832ab", + "name": "feature", "format": "", - "description": "JSONArray containing JSON objects with {'uniquename':'ABCD-1234','name':'gene01'}", - "type": "JSONArray", + "description": "object containing JSON objects with {'uniquename':'ABCD-1234','dbxrefs': [{'db': 'PMID', 'accession': '19448641'}]}.", + "type": "JSONObject", "required": "true", "allowedvalues": [] } ], "verb": "POST", - "description": "Set name of a feature", - "methodName": "setName", - "jsondocId": "a9be0a25-d32d-4275-a121-0986c314209d", + "description": "Get attribute (key/value) pairs for a feature", + "methodName": "getAttributes", + "jsondocId": "b605c3a6-475d-417e-8d43-17ce5f821321", "bodyobject": { - "jsondocId": "71622584-b500-4dec-8263-17bfb1e08692", + "jsondocId": "e817ea77-9a4f-4da4-a614-ed204fe3151a", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -359,9 +359,9 @@ "object": "annotation editor" }, "apierrors": [], - "path": "/annotationEditor/setName", + "path": "/annotationEditor/getAttributes", "response": { - "jsondocId": "94edbeed-b523-4ebe-bf73-c9a909d05ad9", + "jsondocId": "9762568f-2d9f-4e62-9915-6fefb1dad5c8", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -374,7 +374,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "11b04501-4a26-4b50-bbe0-499244e89dac", + "jsondocId": "f9604153-e48a-40a0-8cfd-55637d17adc4", "name": "username", "format": "", "description": "", @@ -383,7 +383,7 @@ "allowedvalues": [] }, { - "jsondocId": "d73cbc92-4562-4f45-8ad0-8a302ce7c8e8", + "jsondocId": "582fc200-348a-4440-8cb7-915ffecad3e2", "name": "password", "format": "", "description": "", @@ -392,7 +392,7 @@ "allowedvalues": [] }, { - "jsondocId": "c2ebfea4-fcc6-4861-be1f-1d6d08da67a9", + "jsondocId": "64f05eb2-c346-4ce9-a6f2-2bfa127fd39a", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -401,7 +401,7 @@ "allowedvalues": [] }, { - "jsondocId": "a36113c1-55db-4d4f-baba-e03aef714439", + "jsondocId": "424f2649-9fd7-4496-8e8f-7d63a2f2bbb7", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -410,21 +410,21 @@ "allowedvalues": [] }, { - "jsondocId": "d6aeb842-ce0a-4aa8-aa31-e228686dcf50", - "name": "feature", + "jsondocId": "05b4c9e7-1840-4bf8-9e92-0cfb468fc814", + "name": "features", "format": "", - "description": "object containing JSON objects with {'uniquename':'ABCD-1234','dbxrefs': [{'db': 'PMID', 'accession': '19448641'}]}.", - "type": "JSONObject", + "description": "JSONArray containing JSON objects with {'uniquename':'ABCD-1234','status':'existing-status-string'}. Available status found here: /availableStatus/ ", + "type": "JSONArray", "required": "true", "allowedvalues": [] } ], "verb": "POST", - "description": "Get attribute (key/value) pairs for a feature", - "methodName": "getAttributes", - "jsondocId": "758b6860-2805-4f4a-a187-0c12843de597", + "description": "Set status of a feature", + "methodName": "setStatus", + "jsondocId": "95a47323-4e21-4b49-914e-d7094c5f1896", "bodyobject": { - "jsondocId": "ba62906f-632b-438f-924a-7eb20bdbab6f", + "jsondocId": "1d2f853f-77f8-4681-b59a-44ffb0df25a6", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -432,9 +432,9 @@ "object": "annotation editor" }, "apierrors": [], - "path": "/annotationEditor/getAttributes", + "path": "/annotationEditor/setStatus", "response": { - "jsondocId": "2c4a0bd7-ee1d-40c3-ab52-c4fee9eac5b8", + "jsondocId": "008a95ae-ba76-4406-a601-d348378b5305", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -447,7 +447,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "bc266444-de7a-49bf-a742-22283b8986da", + "jsondocId": "f0581246-3cae-42d6-9b95-a5760332e4a7", "name": "username", "format": "", "description": "", @@ -456,7 +456,7 @@ "allowedvalues": [] }, { - "jsondocId": "c0512827-3037-4a44-9c1f-5906804de7e2", + "jsondocId": "04e536e7-748e-42bc-8bef-88773c80e2ea", "name": "password", "format": "", "description": "", @@ -465,16 +465,7 @@ "allowedvalues": [] }, { - "jsondocId": "68ff05ef-0f71-4016-847d-5ca2916bd76c", - "name": "organism", - "format": "", - "description": "(optional) Organism ID or common name", - "type": "string", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "5642412f-c341-4a5e-9f89-bb52c900bc1e", + "jsondocId": "fb7f10a0-f627-42d8-957f-5b93c5c2e275", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -483,39 +474,30 @@ "allowedvalues": [] }, { - "jsondocId": "ef0528ff-42be-4ee9-bd00-2623395a1c02", - "name": "suppressHistory", - "format": "", - "description": "Suppress the history of this operation", - "type": "boolean", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "b065deff-4ed2-45a8-b169-32089034c2b7", - "name": "suppressEvents", + "jsondocId": "df31a8c6-8290-442f-b840-c7dec192c3f9", + "name": "organism", "format": "", - "description": "Suppress instant update of the user interface", - "type": "boolean", + "description": "(optional) Organism ID or common name", + "type": "string", "required": "true", "allowedvalues": [] }, { - "jsondocId": "3f248ce0-8e30-48fa-866c-501210106a8c", + "jsondocId": "3ad1583b-5095-4425-9f85-8f51a86cdf1a", "name": "features", "format": "", - "description": "JSONArray of JSON feature objects described by https://github.com/GMOD/Apollo/blob/master/grails-app/domain/org/bbop/apollo/Feature.groovy", + "description": "JSONArray containing JSON objects with {'uniquename':'ABCD-1234','non_reserved_properties':[{'tag':'clockwork','value':'orange'},{'tag':'color','value':'purple'}]}. Available status found here: /availableStatus/ ", "type": "JSONArray", "required": "true", "allowedvalues": [] } ], "verb": "POST", - "description": "Add an exon", - "methodName": "addExon", - "jsondocId": "3d5044d3-e28e-4d3c-b675-0ce05e981a61", + "description": "Add attribute (key,value pair) to feature", + "methodName": "addAttribute", + "jsondocId": "86519883-1735-4848-b8de-c3914dffd8a4", "bodyobject": { - "jsondocId": "cdc1a9fb-0a40-43ba-8032-3c6ca97888b5", + "jsondocId": "4fc4ae4c-0574-4997-a79a-2816c18a4b79", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -523,9 +505,9 @@ "object": "annotation editor" }, "apierrors": [], - "path": "/annotationEditor/addExon", + "path": "/annotationEditor/addAttribute", "response": { - "jsondocId": "362f5310-9ab4-4413-b49d-d8d21ea4f7b6", + "jsondocId": "64c92afd-e41f-43f8-96d3-7ee69a98eb6b", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -538,7 +520,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "91ce8090-d3f2-48ae-9333-e33e333c7909", + "jsondocId": "bd680b8d-ac74-497c-b8e8-c67ceb1a1314", "name": "username", "format": "", "description": "", @@ -547,7 +529,7 @@ "allowedvalues": [] }, { - "jsondocId": "2d77ec15-37ad-45fb-8de3-60d767f7ec8f", + "jsondocId": "0b0e06d3-f8c4-4d5e-82d6-0c586bf03aad", "name": "password", "format": "", "description": "", @@ -556,21 +538,30 @@ "allowedvalues": [] }, { - "jsondocId": "15b566e9-d282-439f-8536-723a3c6400c4", + "jsondocId": "0cff7dfa-e5aa-4b35-b53b-225f62137b3f", + "name": "sequence", + "format": "", + "description": "Sequence name", + "type": "string", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "09adcdcf-594d-4f72-9cdd-8e2e883f4216", "name": "features", "format": "", - "description": "JSONArray of features objects to export defined by a unique name {'uniquename':'ABC123'}", + "description": "JSONArray of JSON feature objects unique names.", "type": "JSONArray", "required": "true", "allowedvalues": [] } ], "verb": "POST", - "description": "Get gff3", - "methodName": "getGff3", - "jsondocId": "5d94056f-adaa-4763-8966-fc60747c04f2", + "description": "Gets history for features", + "methodName": "getHistoryForFeatures", + "jsondocId": "8029b651-bc31-4e01-863b-22a2de97bfa3", "bodyobject": { - "jsondocId": "e260eaad-20a5-42eb-83f4-321d44cbece4", + "jsondocId": "c8743e19-2278-4065-a1a5-d6e2691cfc29", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -578,9 +569,36 @@ "object": "annotation editor" }, "apierrors": [], - "path": "/annotationEditor/getGff3", + "path": "/annotationEditor/getHistoryForFeatures", + "response": { + "jsondocId": "976d31dc-85ef-4562-bb0d-73b752ea7bb9", + "mapValueObject": "", + "mapKeyObject": "", + "object": "annotation editor" + }, + "produces": ["application/json"], + "consumes": ["application/json"] + }, + { + "headers": [], + "pathparameters": [], + "queryparameters": [], + "verb": "POST", + "description": "Returns a translation table as JSON", + "methodName": "getTranslationTable", + "jsondocId": "14b40007-f872-454e-b776-657e34fa6e74", + "bodyobject": { + "jsondocId": "4626c5da-24e8-4fb5-9a87-b753c16e1b01", + "mapValueObject": "", + "mapKeyObject": "", + "multiple": "Unknow", + "map": "", + "object": "annotation editor" + }, + "apierrors": [], + "path": "/annotationEditor/getTranslationTable", "response": { - "jsondocId": "91d94109-01d9-4858-b3c9-70b586ea5584", + "jsondocId": "eb74359a-edf5-4c0a-9f25-f5ac982fff14", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -593,7 +611,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "c4fe5482-1a31-451d-a46a-56be6946121a", + "jsondocId": "0a1f3ae1-9721-411e-b250-25f1e118e249", "name": "username", "format": "", "description": "", @@ -602,7 +620,7 @@ "allowedvalues": [] }, { - "jsondocId": "0a6fcf65-06f7-4991-9019-d0067f66115b", + "jsondocId": "f03e31d7-ee44-4ba1-b5d7-a2bff947825b", "name": "password", "format": "", "description": "", @@ -611,57 +629,57 @@ "allowedvalues": [] }, { - "jsondocId": "c9b71acf-4774-4692-8eed-f678941166a8", + "jsondocId": "feee2aa1-375c-44b9-87d3-d0d9e332519f", + "name": "organism", + "format": "", + "description": "(optional) Organism ID or common name", + "type": "string", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "4fde881b-27fe-4637-8b71-fea298135f90", "name": "sequence", "format": "", - "description": "Sequence name", + "description": "(optional) Sequence name", "type": "string", "required": "true", "allowedvalues": [] }, { - "jsondocId": "dbcf3e37-e6d9-4acd-991b-0d853395bfa4", + "jsondocId": "f6efa8ce-d80d-4cfb-995b-6de3f7b6298c", + "name": "suppressHistory", + "format": "", + "description": "Suppress the history of this operation", + "type": "boolean", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "92236db2-bdd4-4596-ab57-15336d15503d", + "name": "suppressEvents", + "format": "", + "description": "Suppress instant update of the user interface", + "type": "boolean", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "286532be-e619-4c7e-865f-9a2b07642a65", "name": "features", "format": "", - "description": "JSONArray of JSON feature objects unique names.", + "description": "JSONArray of JSON feature objects described by https://github.com/GMOD/Apollo/blob/master/grails-app/domain/org/bbop/apollo/Feature.groovy", "type": "JSONArray", "required": "true", "allowedvalues": [] } ], "verb": "POST", - "description": "Gets history for features", - "methodName": "getHistoryForFeatures", - "jsondocId": "3c0fda48-1a85-4f0d-b959-3e68b15266a3", - "bodyobject": { - "jsondocId": "4f9aea58-4e9f-42f9-8d62-0f32b3209318", - "mapValueObject": "", - "mapKeyObject": "", - "multiple": "Unknow", - "map": "", - "object": "annotation editor" - }, - "apierrors": [], - "path": "/annotationEditor/getHistoryForFeatures", - "response": { - "jsondocId": "3768b6f3-1639-4aa2-b2c2-ca72779b638b", - "mapValueObject": "", - "mapKeyObject": "", - "object": "annotation editor" - }, - "produces": ["application/json"], - "consumes": ["application/json"] - }, - { - "headers": [], - "pathparameters": [], - "queryparameters": [], - "verb": "POST", - "description": "Returns a translation table as JSON", - "methodName": "getTranslationTable", - "jsondocId": "2214a1fe-c22a-46fa-8709-fba9bd7f596a", + "description": "Add non-coding genomic feature", + "methodName": "addFeature", + "jsondocId": "e7ae73f0-99a8-4291-9a6d-6519ddcd24ac", "bodyobject": { - "jsondocId": "30e35084-e704-42b2-b52d-9c722c0f317f", + "jsondocId": "e97816e5-9485-40bc-9057-86627178dc5d", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -669,9 +687,9 @@ "object": "annotation editor" }, "apierrors": [], - "path": "/annotationEditor/getTranslationTable", + "path": "/annotationEditor/addFeature", "response": { - "jsondocId": "ca0a2098-8438-448a-b38d-2b882615d5e3", + "jsondocId": "de86f535-820a-4744-b305-1d3334b55e36", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -684,7 +702,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "eadc7fea-3ba2-4344-ab88-365466c58c8d", + "jsondocId": "91f3fd88-0e12-4e89-a036-fd401e81f0b3", "name": "username", "format": "", "description": "", @@ -693,7 +711,7 @@ "allowedvalues": [] }, { - "jsondocId": "211c4ce5-f79a-4911-9e5b-3c9d0c01b614", + "jsondocId": "264dbde4-ee26-4687-98d0-ea0cfca37144", "name": "password", "format": "", "description": "", @@ -702,7 +720,7 @@ "allowedvalues": [] }, { - "jsondocId": "c0388730-7c2b-4628-9827-7366bd9d5ea5", + "jsondocId": "c1eaa993-f6bc-40a7-8d13-80ddfc0d88d0", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -711,7 +729,7 @@ "allowedvalues": [] }, { - "jsondocId": "5fc6a998-a9c2-4161-8b91-c1956c47fbdf", + "jsondocId": "ab6fa725-afba-47d2-b88e-f7c7c30c32b7", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -720,7 +738,7 @@ "allowedvalues": [] }, { - "jsondocId": "34c77dea-33ae-4216-8aa6-5e6ba2e9c2ff", + "jsondocId": "cdbb0aa1-9baf-4f99-ab27-1d245046ff2c", "name": "suppressHistory", "format": "", "description": "Suppress the history of this operation", @@ -729,7 +747,7 @@ "allowedvalues": [] }, { - "jsondocId": "d0ffcfc4-152d-43a2-9856-aa50b7e782e9", + "jsondocId": "e88e84b8-100c-49b6-9b6c-1809e358e85a", "name": "suppressEvents", "format": "", "description": "Suppress instant update of the user interface", @@ -738,7 +756,7 @@ "allowedvalues": [] }, { - "jsondocId": "f991a9bf-7456-4d4e-9ad2-88f4bcf114c3", + "jsondocId": "df5ab782-a60b-4da8-a3f4-ad6fc71b9aad", "name": "features", "format": "", "description": "JSONArray of JSON feature objects described by https://github.com/GMOD/Apollo/blob/master/grails-app/domain/org/bbop/apollo/Feature.groovy", @@ -748,11 +766,11 @@ } ], "verb": "POST", - "description": "Add non-coding genomic feature", - "methodName": "addFeature", - "jsondocId": "e11ec439-eede-4a6e-b100-aa865f8c5a84", + "description": "Set Shine_Dalgarno_sequence feature boundaries", + "methodName": "setShineDalgarnoBoundaries", + "jsondocId": "15efb270-108c-4b8b-aee9-4343af1c7140", "bodyobject": { - "jsondocId": "d5a46b6e-e61e-4f4d-a51b-b082c343bd4f", + "jsondocId": "1a270f0d-fc4e-4945-adc8-08b0e8e852be", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -760,9 +778,9 @@ "object": "annotation editor" }, "apierrors": [], - "path": "/annotationEditor/addFeature", + "path": "/annotationEditor/setShineDalgarnoBoundaries", "response": { - "jsondocId": "c9350481-870a-4865-9d09-d1ca4f8eac81", + "jsondocId": "09a09b82-42af-4ac3-9f86-66e7037f1a47", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -775,7 +793,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "2414212d-5e55-4809-9cfe-f3a8d494fa9a", + "jsondocId": "baa55f8f-c878-43f5-a3e7-74504b9215e8", "name": "username", "format": "", "description": "", @@ -784,7 +802,7 @@ "allowedvalues": [] }, { - "jsondocId": "e34e6e68-c427-42dc-8e71-7756619a1c9b", + "jsondocId": "f567e225-cf3b-4f4e-a52d-12a6ce27ef05", "name": "password", "format": "", "description": "", @@ -793,7 +811,7 @@ "allowedvalues": [] }, { - "jsondocId": "7f5653fb-296c-488e-92c4-00bbed9bfe1b", + "jsondocId": "2ab9b557-7c8f-4a6c-a91d-07e1cca02f8b", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -802,7 +820,7 @@ "allowedvalues": [] }, { - "jsondocId": "22d2d84d-9b80-434f-8a70-0d17cd98e60d", + "jsondocId": "5e33ec0d-500d-46f8-b8b8-c05a99baf20a", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -811,7 +829,7 @@ "allowedvalues": [] }, { - "jsondocId": "8547b8d7-bf2d-4f95-b1ef-ef2cfd4b6670", + "jsondocId": "50388f70-5888-43df-91c7-a12be270034a", "name": "suppressHistory", "format": "", "description": "Suppress the history of this operation", @@ -820,7 +838,7 @@ "allowedvalues": [] }, { - "jsondocId": "976225af-fcd1-43b5-9b71-00371fc6ca27", + "jsondocId": "644b04de-d529-4bfc-82b7-9a11c1977cee", "name": "suppressEvents", "format": "", "description": "Suppress instant update of the user interface", @@ -829,7 +847,7 @@ "allowedvalues": [] }, { - "jsondocId": "919662be-d3e7-490c-9fb4-bfb030330199", + "jsondocId": "2dba5cc5-3064-4a35-a3b7-9fa185c0811b", "name": "features", "format": "", "description": "JSONArray of JSON feature objects described by https://github.com/GMOD/Apollo/blob/master/grails-app/domain/org/bbop/apollo/Feature.groovy", @@ -839,11 +857,11 @@ } ], "verb": "POST", - "description": "Set Shine_Dalgarno_sequence feature boundaries", - "methodName": "setShineDalgarnoBoundaries", - "jsondocId": "fa5c7aeb-3172-41be-9fb2-f84f947bc3e6", + "description": "Add an exon", + "methodName": "addExon", + "jsondocId": "da8d5d83-4497-46bb-b2e4-38e1ed9207f2", "bodyobject": { - "jsondocId": "59e4e353-4456-411a-bfe6-9e2724dad1bc", + "jsondocId": "1016a973-bdcd-4b53-99f3-70bed9e3e33b", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -851,9 +869,9 @@ "object": "annotation editor" }, "apierrors": [], - "path": "/annotationEditor/setShineDalgarnoBoundaries", + "path": "/annotationEditor/addExon", "response": { - "jsondocId": "0b70d42f-0d3d-45c2-87b0-010af58cf511", + "jsondocId": "7ad1d4e7-dd3a-422b-b8ca-4f8dcdcaab85", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -866,7 +884,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "09daa7d5-5924-45d9-ba4e-42dad95d652d", + "jsondocId": "8c253f9d-2236-4084-94a9-23b52fc09061", "name": "username", "format": "", "description": "", @@ -875,7 +893,7 @@ "allowedvalues": [] }, { - "jsondocId": "8c0023a4-bf82-49f9-8a52-af84dbaa1723", + "jsondocId": "d15e7160-172d-4b25-a56f-b79d75abf44b", "name": "password", "format": "", "description": "", @@ -884,7 +902,7 @@ "allowedvalues": [] }, { - "jsondocId": "03a1cc56-8325-482e-a4e9-21d67aaa57e8", + "jsondocId": "89d8a1f7-d06b-4697-8301-b3f81284103d", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -893,7 +911,7 @@ "allowedvalues": [] }, { - "jsondocId": "e1cb7173-09f8-4ac0-ae3a-6902cc023a70", + "jsondocId": "c0a599a9-da13-47d5-ba44-2cb227df730c", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -902,7 +920,7 @@ "allowedvalues": [] }, { - "jsondocId": "743892ae-8a9c-46a0-83c4-c763e43dae35", + "jsondocId": "b086940d-9e3e-452f-b202-57bb0a9a2726", "name": "features", "format": "", "description": "JSONArray of JSON feature objects ('uniquename' required) that include an added 'comments' JSONArray described by https://github.com/GMOD/Apollo/blob/master/grails-app/domain/org/bbop/apollo/Feature.groovy", @@ -914,9 +932,9 @@ "verb": "POST", "description": "Add comments", "methodName": "addComments", - "jsondocId": "0b18cbfb-9076-435c-b656-bc7e18177b77", + "jsondocId": "c6b76b3a-5089-4749-8fc9-389edc39015d", "bodyobject": { - "jsondocId": "7dff68bf-ff8f-4f2f-827f-82ecde2a7c67", + "jsondocId": "243ad358-fb9f-4f83-8494-901107db9df9", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -926,7 +944,7 @@ "apierrors": [], "path": "/annotationEditor/addComments", "response": { - "jsondocId": "f17757c1-1d4a-4cd6-b993-8b989b9ef42c", + "jsondocId": "a28e8c06-a918-4389-b95a-39bd4a4fa25c", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -939,7 +957,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "fc9b8f3e-77fa-4a8b-8659-8137ec199afb", + "jsondocId": "5987c1f0-d9e4-465d-b835-80a4fda72bf4", "name": "username", "format": "", "description": "", @@ -948,7 +966,7 @@ "allowedvalues": [] }, { - "jsondocId": "9a758aec-a294-4a5e-828f-21485fcd7172", + "jsondocId": "01bee81d-8e05-49ce-9b12-eb148fb0a022", "name": "password", "format": "", "description": "", @@ -957,7 +975,7 @@ "allowedvalues": [] }, { - "jsondocId": "1466c4d1-3b84-44be-af88-0641c9060b66", + "jsondocId": "5069f4e0-d906-448f-8d71-23052d888c5c", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -966,7 +984,7 @@ "allowedvalues": [] }, { - "jsondocId": "d5faa521-afb2-4095-8664-dd313b2fb3c4", + "jsondocId": "ee4ff945-f075-46df-89fd-245b49431e3a", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -975,7 +993,7 @@ "allowedvalues": [] }, { - "jsondocId": "89609eb4-9685-41ac-8c5b-edd2e791e883", + "jsondocId": "26342e86-0645-4f06-8177-2a6024830d26", "name": "features", "format": "", "description": "JSONArray of JSON feature objects ('uniquename' required) that include an added 'comments' JSONArray described by https://github.com/GMOD/Apollo/blob/master/grails-app/domain/org/bbop/apollo/Feature.groovy", @@ -987,9 +1005,9 @@ "verb": "POST", "description": "Delete comments", "methodName": "deleteComments", - "jsondocId": "7778a25b-4b75-4080-a501-88b56561afc1", + "jsondocId": "75ac951d-059b-4dba-b548-e441877f0785", "bodyobject": { - "jsondocId": "6fae84cf-9827-4382-a027-4655aa0241f4", + "jsondocId": "cc767d01-08fa-4b6c-8f4c-63a0d2a63bb1", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -999,7 +1017,7 @@ "apierrors": [], "path": "/annotationEditor/deleteComments", "response": { - "jsondocId": "b1d30600-feaa-4237-8e02-edca88dcbc21", + "jsondocId": "ccaa6083-02a5-4776-8048-12367b9a7225", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -1012,7 +1030,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "39b3e323-ffe1-4444-96ef-a9b8bf74f0f7", + "jsondocId": "76a0b2e5-c888-478b-bc1f-0316c727a503", "name": "username", "format": "", "description": "", @@ -1021,7 +1039,7 @@ "allowedvalues": [] }, { - "jsondocId": "9e6083f4-a291-4bc9-b8a4-3327b6a41c31", + "jsondocId": "507d721f-9ec8-495e-9d7f-6938d56e54b2", "name": "password", "format": "", "description": "", @@ -1030,7 +1048,7 @@ "allowedvalues": [] }, { - "jsondocId": "8ce5167f-2798-4cb1-af4d-5d928870d0d5", + "jsondocId": "866c4b38-c248-49df-8b49-0eccef2b7c83", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -1039,7 +1057,7 @@ "allowedvalues": [] }, { - "jsondocId": "844ac54c-f95d-4241-aafe-8404d29c0214", + "jsondocId": "c2660452-2c0b-493e-9f26-4f9b7f70e39e", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -1048,7 +1066,7 @@ "allowedvalues": [] }, { - "jsondocId": "c607960b-c49b-46d8-b9e3-a7e8fb624233", + "jsondocId": "9a601704-b99d-498a-b587-1a625a600bc9", "name": "features", "format": "", "description": "JSONArray of JSON feature objects ('uniquename' required) that include an added 'old_comments','new_comments' JSONArray described by https://github.com/GMOD/Apollo/blob/master/grails-app/domain/org/bbop/apollo/Feature.groovy", @@ -1060,9 +1078,9 @@ "verb": "POST", "description": "Update comments", "methodName": "updateComments", - "jsondocId": "31148940-a61c-4c1e-abcc-8e030d2f5e85", + "jsondocId": "80b88a3c-fc88-46f3-a054-9b3e8ce5f69c", "bodyobject": { - "jsondocId": "d8c4ed6a-6949-4bda-8b0d-07379c16b10b", + "jsondocId": "ebd72024-2970-4bf6-95b3-021762207900", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -1072,7 +1090,7 @@ "apierrors": [], "path": "/annotationEditor/updateComments", "response": { - "jsondocId": "aa25906f-ffa1-46e9-a6f2-70a98c8f76f3", + "jsondocId": "e0296cd3-6401-423b-883e-f167c2f0807f", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -1085,7 +1103,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "dc9f24b8-f8e3-41d7-be4f-2103e7ea4be3", + "jsondocId": "a21a5844-3a15-4ce1-9935-e4c45e9c72e0", "name": "username", "format": "", "description": "", @@ -1094,7 +1112,7 @@ "allowedvalues": [] }, { - "jsondocId": "eeb6ab07-3cec-48de-a154-c3c076c9f25b", + "jsondocId": "a0603ef9-870b-4b3b-a89a-710bb2007af5", "name": "password", "format": "", "description": "", @@ -1103,7 +1121,7 @@ "allowedvalues": [] }, { - "jsondocId": "2edfb443-f039-4382-8d39-7e7712a80801", + "jsondocId": "6e2e6a18-4473-4a53-b15a-df946bb7efed", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -1112,7 +1130,7 @@ "allowedvalues": [] }, { - "jsondocId": "ef5094ae-aeab-4c21-b1a7-272855193bec", + "jsondocId": "8b48981e-ae26-4d52-b2b9-1430a0e571f9", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -1121,7 +1139,7 @@ "allowedvalues": [] }, { - "jsondocId": "a63886ad-c826-4d81-9889-90020a90c45c", + "jsondocId": "ffe6c07d-54ad-4a2b-932a-ec1e1a3527d6", "name": "suppressHistory", "format": "", "description": "Suppress the history of this operation", @@ -1130,7 +1148,7 @@ "allowedvalues": [] }, { - "jsondocId": "bef03cbb-d772-421e-b52b-43f9b7489c0a", + "jsondocId": "6700b7cf-8e90-419f-9e86-3622fa2c6153", "name": "suppressEvents", "format": "", "description": "Suppress instant update of the user interface", @@ -1139,7 +1157,7 @@ "allowedvalues": [] }, { - "jsondocId": "ab431f1b-cc47-4269-b22a-70cc10b5b64d", + "jsondocId": "5b7ef2ff-b80c-4813-9633-69c9cb55581c", "name": "features", "format": "", "description": "JSONArray of JSON feature objects described by https://github.com/GMOD/Apollo/blob/master/grails-app/domain/org/bbop/apollo/Feature.groovy", @@ -1151,9 +1169,9 @@ "verb": "POST", "description": "Add transcript", "methodName": "addTranscript", - "jsondocId": "482a4b09-bf2b-4f50-9455-de387fb81314", + "jsondocId": "443a4dd4-9b3f-4d8b-b802-f3861f61471f", "bodyobject": { - "jsondocId": "807895dd-9781-4e1d-a0c6-e33e65069442", + "jsondocId": "9d9bcd61-ddc7-402e-a1c1-18e722915292", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -1163,7 +1181,7 @@ "apierrors": [], "path": "/annotationEditor/addTranscript", "response": { - "jsondocId": "f6bcdea2-7fde-4ae4-a5ed-aa7625eeda1e", + "jsondocId": "4710e9c2-c38d-418a-8780-78771db07d7d", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -1176,7 +1194,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "1c7c1217-2161-46b2-b8b9-6179b10b866e", + "jsondocId": "a7c67d54-d5fc-43df-8fb9-98c28ed7fae9", "name": "username", "format": "", "description": "", @@ -1185,7 +1203,7 @@ "allowedvalues": [] }, { - "jsondocId": "f3c63bde-fac9-492c-855d-e6846a2b1b36", + "jsondocId": "6041b497-1df9-4ee6-b4ed-78bc224d43bf", "name": "password", "format": "", "description": "", @@ -1194,7 +1212,7 @@ "allowedvalues": [] }, { - "jsondocId": "f68b4274-6616-4873-842a-5ace938367b6", + "jsondocId": "220b9e87-e987-4fe3-bf24-d97a4bae2dac", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -1203,7 +1221,7 @@ "allowedvalues": [] }, { - "jsondocId": "8c5a8fc9-6aeb-44c5-9977-b94f2c4e56a6", + "jsondocId": "e5692f6f-0933-4785-ab27-351f6f3e3146", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -1212,7 +1230,7 @@ "allowedvalues": [] }, { - "jsondocId": "66c86fa3-19c3-4a02-a188-b80a072b9152", + "jsondocId": "80430a7f-2d1a-4679-8b7d-df6db50c7afb", "name": "suppressHistory", "format": "", "description": "Suppress the history of this operation", @@ -1221,7 +1239,7 @@ "allowedvalues": [] }, { - "jsondocId": "65d55d25-4cb6-42bf-ba30-5f260f34a6c4", + "jsondocId": "633b89ba-133f-4ee9-b27b-3df00f22ad81", "name": "suppressEvents", "format": "", "description": "Suppress instant update of the user interface", @@ -1230,7 +1248,7 @@ "allowedvalues": [] }, { - "jsondocId": "be5d68c7-3e80-4c8a-a7ad-ca28352c335e", + "jsondocId": "e76bad9f-baed-48e4-97f8-65980818f168", "name": "features", "format": "", "description": "JSONArray containing a single JSONObject feature that contains 'uniquename'", @@ -1242,9 +1260,9 @@ "verb": "POST", "description": "Duplicate transcript", "methodName": "duplicateTranscript", - "jsondocId": "44d9da8a-dc38-46b6-b48e-86cb3e20b1b6", + "jsondocId": "1eee5926-8f2a-424b-bc80-feee337b98d1", "bodyobject": { - "jsondocId": "d0b9ef4c-7544-4239-8e99-94d96658bcbe", + "jsondocId": "9f43d86d-9aaa-4dfb-b8c2-73b64e3ac914", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -1254,7 +1272,7 @@ "apierrors": [], "path": "/annotationEditor/duplicateTranscript", "response": { - "jsondocId": "67951544-7f4d-4f2f-9742-ec89fc1e90ac", + "jsondocId": "76a33db2-804f-42f5-814d-91e17c89e6cc", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -1267,7 +1285,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "7e03c7d7-9564-4014-bc11-662d4e011229", + "jsondocId": "d4afc8b0-73c1-46f1-8d13-505de444431c", "name": "username", "format": "", "description": "", @@ -1276,7 +1294,7 @@ "allowedvalues": [] }, { - "jsondocId": "ef3c2b93-b2d0-4b50-9515-02e913dd32a6", + "jsondocId": "3be25e49-4e9a-4f54-a594-fd45ae09c403", "name": "password", "format": "", "description": "", @@ -1285,7 +1303,7 @@ "allowedvalues": [] }, { - "jsondocId": "0c84137a-3900-4758-846e-75f77bed9efb", + "jsondocId": "cc64798f-78de-446e-80b8-7a455f6514d2", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -1294,7 +1312,7 @@ "allowedvalues": [] }, { - "jsondocId": "2cdd103a-26e5-4579-b213-5f2d5a44bd8c", + "jsondocId": "efb75e7d-043c-40c0-acbb-e026b3e2f426", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -1303,7 +1321,7 @@ "allowedvalues": [] }, { - "jsondocId": "29d57981-192d-40fd-acee-ef5348bedcd2", + "jsondocId": "91067e97-3bb6-4a97-8421-a3eda3a7a81c", "name": "features", "format": "", "description": "JSONArray containing a single JSONObject feature that contains {'uniquename':'ABCD-1234','location':{'fmin':12}}", @@ -1315,9 +1333,9 @@ "verb": "POST", "description": "Set translation start", "methodName": "setTranslationStart", - "jsondocId": "e52ca834-c124-4173-ba65-f5e574aa8009", + "jsondocId": "1bb43420-23c9-4d33-8b3c-98be4aae4bee", "bodyobject": { - "jsondocId": "be5e8364-1437-4a69-9509-122ee03ca109", + "jsondocId": "736933ec-5961-46b3-8395-2f5c445c0c27", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -1327,7 +1345,7 @@ "apierrors": [], "path": "/annotationEditor/setTranslationStart", "response": { - "jsondocId": "5bd8cd95-0466-4b71-9a26-b436d5287a20", + "jsondocId": "4fd8e10c-3851-4f87-9849-eb7d91404eb7", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -1340,7 +1358,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "ef6c209e-95a1-4f73-b248-3a11ffb86139", + "jsondocId": "1e7a4a5a-f171-4aa8-ae8a-d9c80e556b03", "name": "username", "format": "", "description": "", @@ -1349,7 +1367,7 @@ "allowedvalues": [] }, { - "jsondocId": "c7dedcdd-7c14-44b7-b8fe-72de15c029b7", + "jsondocId": "d19cc7c3-0972-474d-b1dd-2735092288fb", "name": "password", "format": "", "description": "", @@ -1358,7 +1376,7 @@ "allowedvalues": [] }, { - "jsondocId": "231c828c-9fa9-403d-acd8-d42c3da1a127", + "jsondocId": "7461ba96-c636-4dd8-ac20-ff28bfd2b5d7", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -1367,7 +1385,7 @@ "allowedvalues": [] }, { - "jsondocId": "b85c4029-ce0f-4c46-966a-e0fdbe335d62", + "jsondocId": "8ffbb929-c410-4a47-a6ac-cc19f8764b00", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -1376,7 +1394,7 @@ "allowedvalues": [] }, { - "jsondocId": "b633b4fe-500a-438e-8d56-4a9115973831", + "jsondocId": "827df21e-d8b3-4179-b258-d214090b748e", "name": "features", "format": "", "description": "JSONArray containing a single JSONObject feature that contains {'uniquename':'ABCD-1234','location':{'fmax':12}}", @@ -1388,9 +1406,9 @@ "verb": "POST", "description": "Set translation end", "methodName": "setTranslationEnd", - "jsondocId": "f655b4ce-c53f-42ab-ab23-f53ec3dab240", + "jsondocId": "337ec1dc-cf51-464a-9540-66580dea614b", "bodyobject": { - "jsondocId": "9943c236-bf47-470e-9190-f46b314633b2", + "jsondocId": "e8b8e52c-80e6-4b6b-8d2c-6efc6088c19d", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -1400,7 +1418,7 @@ "apierrors": [], "path": "/annotationEditor/setTranslationEnd", "response": { - "jsondocId": "0713243e-75de-4ed0-adf3-6d246bda6650", + "jsondocId": "3bad35a7-ab69-494b-bf4f-72467832b56d", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -1413,7 +1431,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "7b313815-a702-4502-821e-a020a8ebd4b1", + "jsondocId": "90d42861-c570-44b5-9283-b0c4d4453edc", "name": "username", "format": "", "description": "", @@ -1422,7 +1440,7 @@ "allowedvalues": [] }, { - "jsondocId": "f3526b2f-525a-4ca5-a093-c20934da50bf", + "jsondocId": "7a575e98-6627-4539-8994-4d272caf6259", "name": "password", "format": "", "description": "", @@ -1431,7 +1449,7 @@ "allowedvalues": [] }, { - "jsondocId": "7aa5bada-0b15-4890-a64a-7cde58469f36", + "jsondocId": "ccf1e7c0-453d-49b7-8f50-41c7f19be5b3", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -1440,7 +1458,7 @@ "allowedvalues": [] }, { - "jsondocId": "6e6a21eb-7ae2-4125-a54f-5499f63b1fc9", + "jsondocId": "980a5122-fb33-417a-9083-7a56f7291aa7", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -1449,7 +1467,7 @@ "allowedvalues": [] }, { - "jsondocId": "220ace03-ea95-4ff5-81ab-0a95597b47cd", + "jsondocId": "cc19a9e9-c91c-4ad1-b0be-6f81c5daafff", "name": "features", "format": "", "description": "JSONArray containing a single JSONObject feature that contains {'uniquename':'ABCD-1234'}", @@ -1461,9 +1479,9 @@ "verb": "POST", "description": "Set longest ORF", "methodName": "setLongestOrf", - "jsondocId": "a9ee733c-b98b-45bc-a5ba-9b80857c2766", + "jsondocId": "824296ca-2aa7-43c0-b571-b5dcdaac209c", "bodyobject": { - "jsondocId": "c3a282ff-ceee-471a-8208-7cc67a736a84", + "jsondocId": "1b7a1882-6900-44d5-9a94-4f6baa07c55b", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -1473,7 +1491,7 @@ "apierrors": [], "path": "/annotationEditor/setLongestOrf", "response": { - "jsondocId": "bac42291-7981-4e87-bf42-d84860f81c6c", + "jsondocId": "619652d8-8b20-421e-91f3-ad42aeea4cc4", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -1486,7 +1504,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "45a6e8dd-a0ba-4cd4-ac2a-d1a4908a382a", + "jsondocId": "93b0d77e-765c-4de9-9df4-43ea842fdf79", "name": "username", "format": "", "description": "", @@ -1495,7 +1513,7 @@ "allowedvalues": [] }, { - "jsondocId": "ff072183-bea4-4ee7-9aac-ef14e7a59fb4", + "jsondocId": "fadff113-0aa3-45d5-bfb0-28bf63bef86e", "name": "password", "format": "", "description": "", @@ -1504,7 +1522,7 @@ "allowedvalues": [] }, { - "jsondocId": "6965be6c-d267-4bd8-9e3d-4d9250ce5880", + "jsondocId": "d979ff5f-ff90-4d17-ab03-3953c608ac9f", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -1513,7 +1531,7 @@ "allowedvalues": [] }, { - "jsondocId": "79ad2f58-bc24-48b3-abdc-be6d4ae5ed6a", + "jsondocId": "468fa73a-055c-44e9-bfbc-6f2d9c2ee051", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -1522,7 +1540,7 @@ "allowedvalues": [] }, { - "jsondocId": "837fdae5-7d25-43b7-b8a0-e979616da054", + "jsondocId": "2a993478-f301-4f84-b02f-a08bb727e794", "name": "features", "format": "", "description": "JSONArray containing feature objects with the location object defined {'uniquename':'ABCD-1234','location':{'fmin':2,'fmax':12}}", @@ -1534,9 +1552,9 @@ "verb": "POST", "description": "Set boundaries of genomic feature", "methodName": "setBoundaries", - "jsondocId": "da82ebc1-997b-4f6b-88fe-7992765ee77b", + "jsondocId": "2fc7f199-1e3a-45ed-8f43-f684305ed890", "bodyobject": { - "jsondocId": "ff588d49-4a1c-4d63-8ce5-40793482f824", + "jsondocId": "6dda8af8-b630-40d3-9b67-bd2c5790cd21", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -1546,7 +1564,7 @@ "apierrors": [], "path": "/annotationEditor/setBoundaries", "response": { - "jsondocId": "a06d3c8d-ed52-4282-8ad1-ac2234cc6694", + "jsondocId": "2e6d596d-a2dc-4ac4-bc83-98a5d49129e2", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -1559,7 +1577,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "dc509651-2791-479f-aa27-6d3bf7cf79ca", + "jsondocId": "d002bc70-31f6-4ee5-8612-bba4d36fc973", "name": "username", "format": "", "description": "", @@ -1568,7 +1586,7 @@ "allowedvalues": [] }, { - "jsondocId": "c29f93fd-a313-458c-933c-494a70b01fae", + "jsondocId": "19e6e5a2-e1b1-4832-9fb1-9e41ca4151b1", "name": "password", "format": "", "description": "", @@ -1577,7 +1595,7 @@ "allowedvalues": [] }, { - "jsondocId": "815e66a9-ffe7-42d8-ae83-e15760aab19f", + "jsondocId": "a9a3c769-197b-49d1-b585-80ae4661622c", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -1586,7 +1604,7 @@ "allowedvalues": [] }, { - "jsondocId": "873a46ce-45f8-455d-a1a5-1f2766e9f044", + "jsondocId": "71342952-b049-4320-93c6-175247cf9843", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -1598,9 +1616,9 @@ "verb": "POST", "description": "Get all annotated features for a sequence", "methodName": "getFeatures", - "jsondocId": "bfaeee66-b417-4f04-bc62-48167f506461", + "jsondocId": "93be8939-de53-41b9-b4ab-0b1d6856d9bb", "bodyobject": { - "jsondocId": "16220a0e-f5db-4f41-b385-edb5686de23a", + "jsondocId": "2ca9662a-04ad-478a-8faa-23c218da8ba4", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -1610,7 +1628,7 @@ "apierrors": [], "path": "/annotationEditor/getFeatures", "response": { - "jsondocId": "19f53728-c9c6-4875-815d-b451f5676c96", + "jsondocId": "aa63db15-3a85-4817-99f4-ca136cbb7e03", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -1623,7 +1641,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "696b1b9c-839c-44a6-92f5-f9bc32faee1b", + "jsondocId": "7683d54d-b16f-4588-b3d4-e539a0a3b584", "name": "username", "format": "", "description": "", @@ -1632,7 +1650,7 @@ "allowedvalues": [] }, { - "jsondocId": "a8b0707a-92f8-4e69-be02-6d7a7d680e7e", + "jsondocId": "5f126bb7-63c7-4363-b11c-a7c99dd0604b", "name": "password", "format": "", "description": "", @@ -1641,7 +1659,7 @@ "allowedvalues": [] }, { - "jsondocId": "4e41fd18-3ad4-4792-8a57-4499ba30a32d", + "jsondocId": "36ccd60c-8b4e-4600-b23c-b89d01158d58", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -1650,7 +1668,7 @@ "allowedvalues": [] }, { - "jsondocId": "d08a4417-eedd-4302-81cd-459fc5089e9d", + "jsondocId": "d0579580-67a2-45fa-947d-7200fcab44fb", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -1662,9 +1680,9 @@ "verb": "POST", "description": "Get sequence alterations for a given sequence", "methodName": "getSequenceAlterations", - "jsondocId": "f08274e6-d026-4e06-bed2-dbee9a1c1b80", + "jsondocId": "f1d08485-52df-4d8e-83b8-060ac72f7c41", "bodyobject": { - "jsondocId": "a3734918-7b77-4bcc-a1e0-95d983e78abb", + "jsondocId": "a302046e-3966-455d-b013-7b2746b8cc36", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -1674,7 +1692,7 @@ "apierrors": [], "path": "/annotationEditor/getSequenceAlterations", "response": { - "jsondocId": "b8e78c2d-f14b-43d1-affd-0f0e4a01d323", + "jsondocId": "4e354e7e-c442-484a-8098-b5014bc04102", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -1687,7 +1705,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "1d917db6-befc-474c-85e7-b0f37d40e2ed", + "jsondocId": "ee8eda0e-e27e-4d4e-8ef2-71f7ddc38d54", "name": "username", "format": "", "description": "", @@ -1696,7 +1714,7 @@ "allowedvalues": [] }, { - "jsondocId": "78647334-cd67-4225-809e-9962c8b3e2d0", + "jsondocId": "82052ab2-6cb6-4f56-b803-eb57b7e5bf55", "name": "password", "format": "", "description": "", @@ -1705,7 +1723,7 @@ "allowedvalues": [] }, { - "jsondocId": "e38cec58-0175-4689-b337-f298b06700c5", + "jsondocId": "52b405f6-4450-461f-8df5-09752ad08fe2", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -1714,7 +1732,7 @@ "allowedvalues": [] }, { - "jsondocId": "124b4ee8-140e-4f40-99d4-820231a4e480", + "jsondocId": "0934c885-e32f-4f82-99b8-c1f74a073e81", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -1723,7 +1741,7 @@ "allowedvalues": [] }, { - "jsondocId": "91e0d175-fa91-4a37-b64f-d580209b3dbf", + "jsondocId": "4b9a98e3-9c82-4ebd-ae77-ada93212e95b", "name": "features", "format": "", "description": "JSONArray containing JSON objects with {'uniquename':'ABCD-1234','non_reserved_properties':[{'tag':'clockwork','value':'orange'},{'tag':'color','value':'purple'}]}. Available status found here: /availableStatus/ ", @@ -1735,9 +1753,9 @@ "verb": "POST", "description": "Delete attribute (key,value pair) for feature", "methodName": "deleteAttribute", - "jsondocId": "c9c87652-9c01-4fb1-bfd6-4bc3a3a53a04", + "jsondocId": "1568b71b-b7eb-4208-8036-153461dca54d", "bodyobject": { - "jsondocId": "5b3297f2-b5af-4f6e-abea-af467f735366", + "jsondocId": "573bede4-2976-424c-bd1d-2babd0551434", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -1747,7 +1765,7 @@ "apierrors": [], "path": "/annotationEditor/deleteAttribute", "response": { - "jsondocId": "4c01bab9-a7a9-4e47-bb6a-0aa64722b250", + "jsondocId": "0fa7ca88-4f3a-4ea4-b43b-5133b0285628", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -1760,7 +1778,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "ccffb198-d0d7-4b4c-80c4-e81d6362cce9", + "jsondocId": "be5ac50e-d761-4904-9ab3-ce6f6bd2f228", "name": "username", "format": "", "description": "", @@ -1769,7 +1787,7 @@ "allowedvalues": [] }, { - "jsondocId": "83f378f1-7725-4e5c-97d3-d578830cd5af", + "jsondocId": "8f96470c-989b-49b7-ae58-bc1cf16949f0", "name": "password", "format": "", "description": "", @@ -1778,7 +1796,7 @@ "allowedvalues": [] }, { - "jsondocId": "9b00e183-1a04-40be-be82-697f6ac1b63b", + "jsondocId": "8ff6faf9-52a2-4d98-ac04-f0b60c5c56dc", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -1787,7 +1805,7 @@ "allowedvalues": [] }, { - "jsondocId": "25892ad1-7c33-4af8-a8a7-814744296e9d", + "jsondocId": "df8d9bb9-1333-453a-a20a-544b4e3751f9", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -1796,7 +1814,7 @@ "allowedvalues": [] }, { - "jsondocId": "a9aee9ae-7e53-408d-982c-4ea29cb2d980", + "jsondocId": "9aa8b96c-cf76-4661-999d-0e059d32ef0f", "name": "features", "format": "", "description": "JSONArray containing JSON objects with {'uniquename':'ABCD-1234','old_non_reserved_properties':[{'color': 'red'}], 'new_non_reserved_properties': [{'color': 'green'}]}.", @@ -1808,9 +1826,9 @@ "verb": "POST", "description": "Update attribute (key,value pair) for feature", "methodName": "updateAttribute", - "jsondocId": "123be85a-f510-4520-896e-b4d87005b690", + "jsondocId": "12259ad0-fd09-40c5-a917-03bde238bde8", "bodyobject": { - "jsondocId": "a5651590-c603-4930-9011-e9fb4030d6c2", + "jsondocId": "be470c5a-db54-4b29-ac79-6ee2cd96e8cc", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -1820,7 +1838,7 @@ "apierrors": [], "path": "/annotationEditor/updateAttribute", "response": { - "jsondocId": "521c8407-dcf2-4d8a-927e-47e79cc37780", + "jsondocId": "6d04e8af-a3b6-4534-8cde-5f566d84237d", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -1833,7 +1851,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "073cd9ec-5ff4-4f32-ad1f-9b2c2b809130", + "jsondocId": "9b553b89-edf2-40b1-9060-cfc6ba007f93", "name": "username", "format": "", "description": "", @@ -1842,7 +1860,7 @@ "allowedvalues": [] }, { - "jsondocId": "4ec7cf9f-ebb3-4a65-8552-c5b8132ed1af", + "jsondocId": "b71d2bd4-6898-4017-b61a-c836123c966b", "name": "password", "format": "", "description": "", @@ -1851,7 +1869,7 @@ "allowedvalues": [] }, { - "jsondocId": "e0400dce-9ba6-413c-b0ef-8c4dc87e4573", + "jsondocId": "d5437ba1-5a4e-4b69-872e-3537153028fe", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -1860,7 +1878,7 @@ "allowedvalues": [] }, { - "jsondocId": "58066429-d593-45fc-a70d-e2d4b2086587", + "jsondocId": "6575a9f0-c74b-4e17-8686-ff70843365f0", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -1869,7 +1887,7 @@ "allowedvalues": [] }, { - "jsondocId": "5a432caf-3a76-4b82-ba44-e9b18c671c37", + "jsondocId": "2639d959-c624-4077-9c5f-66994fee6b22", "name": "features", "format": "", "description": "JSONArray containing JSON objects with {'uniquename':'ABCD-1234','dbxrefs': [{'db': 'PMID', 'accession': '19448641'}]}.", @@ -1881,9 +1899,9 @@ "verb": "POST", "description": "Add dbxref (db,id pair) to feature", "methodName": "addDbxref", - "jsondocId": "d8945ba3-2ed0-4875-acf7-c6d28a577231", + "jsondocId": "9fe61847-ffe7-4c8d-bbbc-78fe583b1e51", "bodyobject": { - "jsondocId": "597c9037-7059-4b9f-91bd-6dbc87e7ec84", + "jsondocId": "4d340ba2-d757-422b-be54-9efc247d105b", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -1893,7 +1911,7 @@ "apierrors": [], "path": "/annotationEditor/addDbxref", "response": { - "jsondocId": "d63fe8c9-f38b-4cec-87db-0ecc8cb6ee46", + "jsondocId": "82b760f6-bf0a-403b-a1ca-74c95db8046a", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -1906,7 +1924,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "4671ba53-7df5-4802-be64-f14d25b9e74e", + "jsondocId": "960e3671-43e9-46ae-bcc8-e57c8e8b1f0d", "name": "username", "format": "", "description": "", @@ -1915,7 +1933,7 @@ "allowedvalues": [] }, { - "jsondocId": "36e964f2-0805-4e91-b266-2b0b684d9f35", + "jsondocId": "3ec1a783-49c1-4028-9053-ec9d039ca00f", "name": "password", "format": "", "description": "", @@ -1924,7 +1942,7 @@ "allowedvalues": [] }, { - "jsondocId": "ca5f4a1b-f80e-48fe-a35c-c875c3d4f78d", + "jsondocId": "91de9db5-1b89-48ff-9f34-7ec7e6457665", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -1933,7 +1951,7 @@ "allowedvalues": [] }, { - "jsondocId": "70b00c2c-801b-410d-a8d1-2976d7d58d85", + "jsondocId": "fb326b35-08f2-4b2d-b261-fb81e90d73fd", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -1942,7 +1960,7 @@ "allowedvalues": [] }, { - "jsondocId": "aff87638-81fd-4349-be3a-1a78d7a934f6", + "jsondocId": "9f53cdde-7aca-4d70-985a-ec0f474c642e", "name": "features", "format": "", "description": "JSONArray containing JSON objects with {'uniquename':'ABCD-1234','old_dbxrefs': [{'db': 'PMID', 'accession': '19448641'}], 'new_dbxrefs': [{'db': 'PMID', 'accession': '19448642'}]}.", @@ -1954,9 +1972,9 @@ "verb": "POST", "description": "Update dbxrefs (db,id pairs) for a feature", "methodName": "updateDbxref", - "jsondocId": "916a0c5f-2a4f-422f-b23a-45645475fa11", + "jsondocId": "5ed7153b-a1d2-4683-bd34-8d87cea2d089", "bodyobject": { - "jsondocId": "0d7b8356-88b3-40c0-824f-b6c7228ff5ad", + "jsondocId": "655b1d17-6e02-4dd3-ae7a-53a3f0896861", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -1966,7 +1984,7 @@ "apierrors": [], "path": "/annotationEditor/updateDbxref", "response": { - "jsondocId": "3ab7d9d6-204e-4e2f-a40e-1f8cfea0aae1", + "jsondocId": "35536c03-d800-4561-b53c-41c6d340f2ca", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -1979,7 +1997,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "c4a2af4b-bf7d-4583-a58f-24d7a6ccdb9f", + "jsondocId": "28b09507-d54b-47f0-93e5-7d6fcdcf0bc0", "name": "username", "format": "", "description": "", @@ -1988,7 +2006,7 @@ "allowedvalues": [] }, { - "jsondocId": "ccc15757-4d7f-499d-ba47-eeb80f199987", + "jsondocId": "c8575ac3-f30e-44e1-aa56-1979e8813bf7", "name": "password", "format": "", "description": "", @@ -1997,7 +2015,7 @@ "allowedvalues": [] }, { - "jsondocId": "91020beb-0166-4e33-94d8-39b13e5df642", + "jsondocId": "5c0c53d5-10c9-4c0c-9cd3-be3f958d009f", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -2006,7 +2024,7 @@ "allowedvalues": [] }, { - "jsondocId": "8048a951-4468-4f3d-8594-484448e9b4e0", + "jsondocId": "e4591717-a674-451b-8e37-0abdda9d04da", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -2015,7 +2033,7 @@ "allowedvalues": [] }, { - "jsondocId": "36b5e8b7-7b6a-44ad-a465-0071d7240d3a", + "jsondocId": "6533a6f7-2bfe-4dd3-b36e-9e17c7151de8", "name": "features", "format": "", "description": "JSONArray containing JSON objects with {'uniquename':'ABCD-1234','dbxrefs': [{'db': 'PMID', 'accession': '19448641'}]}.", @@ -2027,9 +2045,9 @@ "verb": "POST", "description": "Delete dbxrefs (db,id pairs) for a feature", "methodName": "deleteDbxref", - "jsondocId": "d0e3ae14-fa48-414c-b3c5-e0b7ace5543d", + "jsondocId": "1a9b8530-c7c8-483b-a191-5d5615e85308", "bodyobject": { - "jsondocId": "316047c9-795f-453a-9471-ce74aae25e10", + "jsondocId": "08a873ce-76e6-44d2-b6de-fa871710c7c3", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -2039,7 +2057,7 @@ "apierrors": [], "path": "/annotationEditor/deleteDbxref", "response": { - "jsondocId": "4355608a-67ee-45e4-928a-4a622b447a13", + "jsondocId": "fda643d0-820a-48c1-bf81-a50a5623d4bd", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -2052,7 +2070,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "dd3253d4-6755-4b98-b36e-3350e24667e5", + "jsondocId": "7a4ef5dd-5918-41a9-a06b-ce0b35ae3a41", "name": "username", "format": "", "description": "", @@ -2061,7 +2079,7 @@ "allowedvalues": [] }, { - "jsondocId": "5d1cfd33-8397-4438-990d-b0357b975318", + "jsondocId": "61ed3e99-1fb9-4ddd-af54-e48ba4981972", "name": "password", "format": "", "description": "", @@ -2070,7 +2088,7 @@ "allowedvalues": [] }, { - "jsondocId": "615b9514-b27b-445c-bb96-e2f34fc45a91", + "jsondocId": "fd64d4e0-fade-4b34-90ce-7a89b5a2f0a2", "name": "array of uniquename features", "format": "", "description": "Uniquename of sequence alteration retrieve stringsgs embedded in a features array.", @@ -2082,9 +2100,9 @@ "verb": "POST", "description": "Get information about a sequence alteration object e.g,. features[{'uniquename':'someunqiuenamestring'}],", "methodName": "getInformation", - "jsondocId": "f5479006-4191-4779-8f22-3399b7dd68da", + "jsondocId": "96d21205-5594-4856-86b6-c2c352236f0d", "bodyobject": { - "jsondocId": "104930af-8de0-47f6-8f2d-b2d8742c45e6", + "jsondocId": "4b1bbd8e-1c6e-4f8a-8da9-1aa076000468", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -2094,7 +2112,7 @@ "apierrors": [], "path": "/annotationEditor/getInformation", "response": { - "jsondocId": "449e02bb-d4d6-409e-9caa-cc499d337cdf", + "jsondocId": "1c532489-f390-42b6-ba5d-cc22989b8a8f", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -2107,7 +2125,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "2c2e34f0-094a-46c4-8520-65f0732e7b77", + "jsondocId": "1d89dae7-42e8-4d80-8296-d7f795e2d213", "name": "username", "format": "", "description": "", @@ -2116,7 +2134,7 @@ "allowedvalues": [] }, { - "jsondocId": "2ed55e7e-d910-4bcd-af87-aedf987b4183", + "jsondocId": "bcdab318-8c0b-4830-a2cc-4c49e3a63afa", "name": "password", "format": "", "description": "", @@ -2125,7 +2143,7 @@ "allowedvalues": [] }, { - "jsondocId": "d560a68b-aa6e-4ac8-bb09-ad67676220a6", + "jsondocId": "8491f00c-6933-4200-90fd-de26827380e0", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -2134,7 +2152,7 @@ "allowedvalues": [] }, { - "jsondocId": "c5fe738b-27cb-477f-a015-7566d1b4d054", + "jsondocId": "830256ac-4c7c-4bad-aa56-7cf5022513e4", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -2143,7 +2161,7 @@ "allowedvalues": [] }, { - "jsondocId": "117d542c-7516-4e5f-ab7b-1838d62db621", + "jsondocId": "19a2bb77-8479-4d03-b7b5-173cb5545732", "name": "features", "format": "", "description": "JSONArray containing JSON objects with {'uniquename':'ABCD-1234','dbxrefs': [{'db': 'PMID', 'accession': '19448641'}]}.", @@ -2155,9 +2173,9 @@ "verb": "POST", "description": "Get dbxrefs (db,id pairs) for a feature", "methodName": "getDbxrefs", - "jsondocId": "4bb195ac-d7d0-4b35-8272-e564b796bac3", + "jsondocId": "4118b4b0-f4e2-4df5-8e63-9cd9800b80ad", "bodyobject": { - "jsondocId": "24298a65-40e2-4fdf-b4eb-18274dfe5631", + "jsondocId": "9f508e65-e321-418a-8518-47eb5dc6e7ba", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -2167,7 +2185,7 @@ "apierrors": [], "path": "/annotationEditor/getDbxrefs", "response": { - "jsondocId": "760429f4-1144-4167-bc99-17d6b8951218", + "jsondocId": "07e87d1b-d5f4-460c-9606-e6cfb14c6bdf", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -2180,7 +2198,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "ae9c6726-f289-4de0-83bc-6bcb7c6687ef", + "jsondocId": "a00aaa80-7b08-41a3-8664-0593c90b572c", "name": "username", "format": "", "description": "", @@ -2189,7 +2207,7 @@ "allowedvalues": [] }, { - "jsondocId": "9ed4a9fb-0017-4677-baf6-a68b17e778c7", + "jsondocId": "eab0ffb2-a8a8-4a90-8228-f7ca09bbfb10", "name": "password", "format": "", "description": "", @@ -2198,7 +2216,7 @@ "allowedvalues": [] }, { - "jsondocId": "8d53232f-c9c7-462e-9819-6b4a2d1db3af", + "jsondocId": "208c5c17-507d-47de-bf7d-5d6a1c681e72", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -2207,7 +2225,7 @@ "allowedvalues": [] }, { - "jsondocId": "3c844282-0b2a-4d19-a4ab-047867bf6995", + "jsondocId": "4b142ecc-be60-401f-9221-10629067b73b", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -2216,7 +2234,7 @@ "allowedvalues": [] }, { - "jsondocId": "59c6ae8f-6e9a-4061-8967-dee7b1d1bac9", + "jsondocId": "578f8247-65a2-4843-aac4-fe2588cf64d5", "name": "features", "format": "", "description": "JSONArray with one feature object {'uniquename':'ABCD-1234'}", @@ -2228,9 +2246,9 @@ "verb": "POST", "description": "Set readthrough stop codon", "methodName": "setReadthroughStopCodon", - "jsondocId": "118b9fde-71e1-4c91-bf97-0d9191a54ff1", + "jsondocId": "7a3721d5-cbd2-4986-8943-0617abe4ee64", "bodyobject": { - "jsondocId": "0e2ca630-31b7-4ab3-8b50-9a4a41294ce8", + "jsondocId": "8debd6c7-791c-469f-b0a3-9971014261db", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -2240,7 +2258,7 @@ "apierrors": [], "path": "/annotationEditor/setReadthroughStopCodon", "response": { - "jsondocId": "c1621fb3-2630-4ba2-8dee-188f5407267a", + "jsondocId": "b590b3cc-81a6-4428-9b23-007615718952", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -2253,7 +2271,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "138d4c16-a2a2-4d0b-ad0c-8ce0e04bbb30", + "jsondocId": "59279af1-1cf8-4e0f-9fc4-ab5d861ef60b", "name": "username", "format": "", "description": "", @@ -2262,7 +2280,7 @@ "allowedvalues": [] }, { - "jsondocId": "6d96d35c-82bd-4e4a-9fba-04241b2310fb", + "jsondocId": "2c9a527e-2520-4c2b-8e16-99102d464ad2", "name": "password", "format": "", "description": "", @@ -2271,7 +2289,7 @@ "allowedvalues": [] }, { - "jsondocId": "9175015f-cf4c-464b-aa24-88650e86722d", + "jsondocId": "a4fb25a6-12ff-49ec-9a72-23f6af939b98", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -2280,7 +2298,7 @@ "allowedvalues": [] }, { - "jsondocId": "f96994c7-46c5-4c65-a733-6b10cba2364c", + "jsondocId": "65fe6610-82a4-4ff7-bf11-0f40b763b561", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -2289,7 +2307,7 @@ "allowedvalues": [] }, { - "jsondocId": "4a9137c4-50ff-43b4-804e-4b4a53574b86", + "jsondocId": "185613a2-1d11-4f87-b400-832255deab4a", "name": "features", "format": "", "description": "JSONArray with Sequence Alteration (Insertion, Deletion, Substituion) objects described by https://github.com/GMOD/Apollo/blob/master/grails-app/domain/org/bbop/apollo/", @@ -2301,9 +2319,9 @@ "verb": "POST", "description": "Add sequence alteration", "methodName": "addSequenceAlteration", - "jsondocId": "ea90debc-416d-46c3-9780-6d76b2196046", + "jsondocId": "3e7b62d3-9546-454c-b5d1-58c19db3a09c", "bodyobject": { - "jsondocId": "09fcbe95-ba11-4b12-9116-fc63bc556a66", + "jsondocId": "b7ca19ff-aceb-45f4-a93b-df4d10c3a893", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -2313,7 +2331,7 @@ "apierrors": [], "path": "/annotationEditor/addSequenceAlteration", "response": { - "jsondocId": "7c377dad-6c93-485c-888e-07ab873e3cea", + "jsondocId": "ae7c657e-908c-42c6-b3f1-d939d9a46386", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -2326,7 +2344,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "895ecc21-a8f9-4ab6-aca7-9b97f33a29c2", + "jsondocId": "011d30f6-04f2-49e0-b912-ad8e15a15c7e", "name": "username", "format": "", "description": "", @@ -2335,7 +2353,7 @@ "allowedvalues": [] }, { - "jsondocId": "95916758-ac4d-4bd9-b3e9-d30e57703ada", + "jsondocId": "24f9c3c0-ee53-4ee9-93b5-60eab86a8f32", "name": "password", "format": "", "description": "", @@ -2344,7 +2362,7 @@ "allowedvalues": [] }, { - "jsondocId": "80b4cbf5-831b-4cd9-ad98-de0b860f7eb9", + "jsondocId": "130881a4-e31a-4fe6-8f22-1585073fcb11", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -2353,7 +2371,7 @@ "allowedvalues": [] }, { - "jsondocId": "3b1b35be-33c5-4d08-85ce-15586c054e6c", + "jsondocId": "998cabc8-fefa-4eee-8fd3-0cc77481c310", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -2362,7 +2380,7 @@ "allowedvalues": [] }, { - "jsondocId": "727fffc1-eec7-478c-b279-63a6f4a64e68", + "jsondocId": "32d147c7-79f3-43b6-828f-334a84d481ef", "name": "features", "format": "", "description": "JSONArray with Sequence Alteration identified by unique names {'uniquename':'ABC123'}", @@ -2374,9 +2392,9 @@ "verb": "POST", "description": "Delete sequence alteration", "methodName": "deleteSequenceAlteration", - "jsondocId": "edca0e66-ce53-461e-a844-9922cda7108e", + "jsondocId": "f5afca2b-f9e9-430c-9ba6-b2d629bbdf2f", "bodyobject": { - "jsondocId": "efcd7a81-3aab-4ca6-93b7-fb66b1403aa3", + "jsondocId": "33d1e527-6407-4882-b55c-b41777a013ee", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -2386,7 +2404,7 @@ "apierrors": [], "path": "/annotationEditor/deleteSequenceAlteration", "response": { - "jsondocId": "64507088-baf0-4a0c-bb2e-920a35198ac0", + "jsondocId": "1aa0e26e-5264-4670-b6a2-c575dd6874ac", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -2399,7 +2417,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "04088503-a773-48be-be98-5ba5c720810d", + "jsondocId": "04616836-7b9d-44cf-9d20-4f16d4a9e25e", "name": "username", "format": "", "description": "", @@ -2408,7 +2426,7 @@ "allowedvalues": [] }, { - "jsondocId": "39988cfe-0a3d-447c-a8b6-7e1ae0359260", + "jsondocId": "d9318307-8ba7-4164-9bc2-2d577b7b2bde", "name": "password", "format": "", "description": "", @@ -2417,7 +2435,7 @@ "allowedvalues": [] }, { - "jsondocId": "0b8e14ca-f4b0-436d-85cc-b3bf5773c4c0", + "jsondocId": "b0f9d3f0-a18c-4dcb-9224-eafb0f7bb121", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -2426,7 +2444,7 @@ "allowedvalues": [] }, { - "jsondocId": "394c3acf-4fe3-449e-947f-92322af5f2aa", + "jsondocId": "80b7c8c3-092a-4a43-84a0-321c6d8b57f9", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -2435,7 +2453,7 @@ "allowedvalues": [] }, { - "jsondocId": "3693f7c1-1b12-4e1b-b57c-f2eea83cc46a", + "jsondocId": "a2c7c449-b78c-406e-879f-b3dde0092926", "name": "features", "format": "", "description": "JSONArray with with objects of features defined as {'uniquename':'ABC123'}", @@ -2447,9 +2465,9 @@ "verb": "POST", "description": "Flip strand", "methodName": "flipStrand", - "jsondocId": "b3b872d8-a4c5-42f3-87b0-a1f336cbb085", + "jsondocId": "861abef5-4f16-4edf-907a-e2e763dc9789", "bodyobject": { - "jsondocId": "4b69bd0f-4861-4804-a020-0057cc104e10", + "jsondocId": "890727b2-dd2a-4ac5-83de-3a46c4c3606a", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -2459,7 +2477,7 @@ "apierrors": [], "path": "/annotationEditor/flipStrand", "response": { - "jsondocId": "e6eafae2-75d3-4753-b553-f2cd62789688", + "jsondocId": "47506fe9-ea3d-42b3-ba0c-8cb594294021", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -2472,7 +2490,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "5ce84d70-5379-455d-9cf2-1d7db8eb043d", + "jsondocId": "cafdf0b6-5932-413d-ae93-79da2762a02e", "name": "username", "format": "", "description": "", @@ -2481,7 +2499,7 @@ "allowedvalues": [] }, { - "jsondocId": "4f1db60c-8d96-4b08-bb91-e2403da46186", + "jsondocId": "1dd49b4b-5bc2-4d9b-a0a7-7359400447c6", "name": "password", "format": "", "description": "", @@ -2490,7 +2508,7 @@ "allowedvalues": [] }, { - "jsondocId": "8fbfea5c-de92-43ec-a3c4-3c0bb157b9f7", + "jsondocId": "e7e19335-ab22-4b31-bf74-3118eb4edbe5", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -2499,7 +2517,7 @@ "allowedvalues": [] }, { - "jsondocId": "4f2a04f0-efca-48b3-90c3-c5f3a8271147", + "jsondocId": "3fa9f471-f750-42fa-9e42-f820bc4687e9", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -2508,7 +2526,7 @@ "allowedvalues": [] }, { - "jsondocId": "cbfc6d0a-9385-4253-b56f-ae6f2a35858b", + "jsondocId": "35b651c0-aea4-4ae9-a72e-a09120c851f5", "name": "features", "format": "", "description": "JSONArray with with two objects of referred to as defined as {'uniquename':'ABC123'}", @@ -2520,9 +2538,9 @@ "verb": "POST", "description": "Merge exons", "methodName": "mergeExons", - "jsondocId": "3083ee99-813f-490f-a3cc-94f15c4c1a76", + "jsondocId": "70884562-0d66-4ca8-88b5-3785e25b4057", "bodyobject": { - "jsondocId": "71139aca-f596-4015-bae4-4cce83976fd7", + "jsondocId": "82d1b08e-a3e8-4bf2-a46a-f10d1c7652b0", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -2532,7 +2550,7 @@ "apierrors": [], "path": "/annotationEditor/mergeExons", "response": { - "jsondocId": "ec760b68-8d1f-4259-af1c-0fc606943a28", + "jsondocId": "7da7581c-8676-48da-9953-e3ebcd4a022d", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -2545,7 +2563,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "3565ac4c-7911-4db2-9560-514636b91cdc", + "jsondocId": "1b52387a-976b-4afa-9a3a-70d7493163a1", "name": "username", "format": "", "description": "", @@ -2554,7 +2572,7 @@ "allowedvalues": [] }, { - "jsondocId": "e9bb76ba-1ece-4d5d-aead-6997bd375c6a", + "jsondocId": "615250bb-478f-4b21-a4c5-7c25cd5b3cdf", "name": "password", "format": "", "description": "", @@ -2563,7 +2581,7 @@ "allowedvalues": [] }, { - "jsondocId": "ff6298ae-aff7-487f-829a-8ac6615f5897", + "jsondocId": "a353f2f1-c2d8-40b6-a022-f1284b63c110", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -2572,7 +2590,7 @@ "allowedvalues": [] }, { - "jsondocId": "89645a13-b657-4cf8-ad1a-f71769885fa6", + "jsondocId": "02a252b5-71ba-4557-8b53-966c8d96d471", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -2581,7 +2599,7 @@ "allowedvalues": [] }, { - "jsondocId": "ef0c2a64-2afe-4ae5-a0f3-0fb781dfa5a7", + "jsondocId": "55c492a8-7b5c-4e58-a94c-32e4eb7cae6b", "name": "features", "format": "", "description": "JSONArray containing feature objects with the location object defined {'uniquename':'ABCD-1234','location':{'fmin':2,'fmax':12}}", @@ -2593,9 +2611,9 @@ "verb": "POST", "description": "Split exons", "methodName": "splitExon", - "jsondocId": "07ad373b-d125-4363-b1cc-14f3032829a7", + "jsondocId": "b2a01dff-a5a2-45de-923d-8ff23ca41556", "bodyobject": { - "jsondocId": "85ec83bf-9850-4559-97e4-b9ee3b270dd6", + "jsondocId": "ec02c206-9bf4-4220-9649-e4b0c8fbb5ab", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -2605,7 +2623,7 @@ "apierrors": [], "path": "/annotationEditor/splitExon", "response": { - "jsondocId": "773b6394-90e2-4876-9539-d2aee27fae33", + "jsondocId": "7fd04526-26ef-4447-9a4b-864b0454cc7b", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -2618,7 +2636,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "4fc5570f-d6c6-4b46-bebd-b3092e4c807a", + "jsondocId": "d2a67203-255a-46b0-9f6e-fc8100e73a7e", "name": "username", "format": "", "description": "", @@ -2627,7 +2645,7 @@ "allowedvalues": [] }, { - "jsondocId": "594f2ab8-766f-4755-b990-654235361104", + "jsondocId": "5e72adee-69db-4909-b55b-435595fbd9d7", "name": "password", "format": "", "description": "", @@ -2636,7 +2654,7 @@ "allowedvalues": [] }, { - "jsondocId": "2581b92c-e6b7-45ab-884b-cb15ce4f0958", + "jsondocId": "b8fc32bd-d488-4303-89b5-38b83078887c", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -2645,7 +2663,7 @@ "allowedvalues": [] }, { - "jsondocId": "aceb7935-ff4a-4ccf-84de-db7f29be6519", + "jsondocId": "326d4ed8-5720-4e72-b2b7-f6a521e29ec6", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -2654,7 +2672,7 @@ "allowedvalues": [] }, { - "jsondocId": "e7f70d53-ef18-4df3-a54e-4155801b283b", + "jsondocId": "70ae7c68-88dc-4352-a30d-4740c4860f76", "name": "features", "format": "", "description": "JSONArray of features objects to delete defined by unique name {'uniquename':'ABC123'}", @@ -2666,9 +2684,9 @@ "verb": "POST", "description": "Delete feature", "methodName": "deleteFeature", - "jsondocId": "1f0ee9d0-aa43-4970-98c4-13e97a20901a", + "jsondocId": "6205e55c-fa51-4d57-95e3-59ab03e058bf", "bodyobject": { - "jsondocId": "262b0659-61b2-49d7-a589-e1cff175f34d", + "jsondocId": "08b63eed-7ac8-4fc5-b2be-cefe61d82a5c", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -2678,7 +2696,7 @@ "apierrors": [], "path": "/annotationEditor/deleteFeature", "response": { - "jsondocId": "f1c2bbdf-22cc-4b37-be45-e54b083db0f4", + "jsondocId": "5302dd0a-5fb5-416e-aa4c-e9838c510e0e", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -2691,7 +2709,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "a027d26b-484d-41e6-9d2c-f7542c5f5678", + "jsondocId": "1fb0f6e5-f6da-4207-b68b-18a9d420136e", "name": "username", "format": "", "description": "", @@ -2700,7 +2718,7 @@ "allowedvalues": [] }, { - "jsondocId": "59311ca7-c23c-4a72-a208-fa2b93b6526f", + "jsondocId": "c1a6ba36-a987-4063-a1ea-3032f5bd32ca", "name": "password", "format": "", "description": "", @@ -2709,7 +2727,7 @@ "allowedvalues": [] }, { - "jsondocId": "77d3e344-b835-4720-a8b3-ec5b929c2154", + "jsondocId": "6c3f4753-163d-4402-8049-780003a9b926", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -2718,7 +2736,7 @@ "allowedvalues": [] }, { - "jsondocId": "4d6ac073-3871-42d9-a819-42ca6ab5de15", + "jsondocId": "0a2bf1c3-f83c-4a9b-8bb3-608f77f77053", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -2727,7 +2745,7 @@ "allowedvalues": [] }, { - "jsondocId": "992b027b-cfb0-469e-b1a7-34916c7dde9a", + "jsondocId": "06f1eda0-a107-44ce-a5dc-ca7a55dde9e5", "name": "sequence", "format": "", "description": "JSONArray of sequence id object to delete defined by {id:} ", @@ -2739,9 +2757,9 @@ "verb": "POST", "description": "Delete variant effects for sequences", "methodName": "deleteVariantEffectsForSequences", - "jsondocId": "593852d1-c78f-45d7-a269-f6c47b5554dd", + "jsondocId": "bc2a6d21-8ed5-46ad-845e-8a97d15ce3ef", "bodyobject": { - "jsondocId": "d1f794a1-686b-4c1a-8260-2fa82a652eb9", + "jsondocId": "baa75c6f-9ca5-48d2-ab0a-a3bf7876ce53", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -2751,7 +2769,7 @@ "apierrors": [], "path": "/annotationEditor/deleteVariantEffectsForSequences", "response": { - "jsondocId": "ed8d36f8-9acd-4218-ad02-b17db6b60c41", + "jsondocId": "3588316d-e752-4638-a383-d69767772a56", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -2764,7 +2782,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "3907ad1a-5038-43b9-b66e-3eb1ceff86db", + "jsondocId": "7327c226-2e1c-491c-818e-78ab66c6e680", "name": "username", "format": "", "description": "", @@ -2773,7 +2791,7 @@ "allowedvalues": [] }, { - "jsondocId": "52f437e5-4ef2-44e5-8e7a-d18d3b94a890", + "jsondocId": "2c9a826f-ebf9-4eac-b635-59976405417e", "name": "password", "format": "", "description": "", @@ -2782,7 +2800,7 @@ "allowedvalues": [] }, { - "jsondocId": "2a8390dd-6e9f-4abb-86e4-ce51c4a11777", + "jsondocId": "e730d799-69e2-47fe-b322-74eb5799c658", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -2791,7 +2809,7 @@ "allowedvalues": [] }, { - "jsondocId": "f205f755-0f47-4899-8fa3-3e0385379341", + "jsondocId": "7148c89e-32e4-4730-bbf1-243f9446c7b2", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -2800,7 +2818,7 @@ "allowedvalues": [] }, { - "jsondocId": "a1849734-ab26-4089-910a-9f54d03f90e0", + "jsondocId": "b3ac0afb-a359-4196-9a7a-62e80124dc93", "name": "sequence", "format": "", "description": "JSONArray of sequence id object to delete defined by {id:} ", @@ -2812,9 +2830,9 @@ "verb": "POST", "description": "Delete features for sequences", "methodName": "deleteFeaturesForSequences", - "jsondocId": "2640f25c-25e2-4d68-85be-aac909365471", + "jsondocId": "46be2a3c-b7b7-46b0-9070-d10e9bd710c8", "bodyobject": { - "jsondocId": "e8c06f46-91a2-43e4-8854-1bf90412c477", + "jsondocId": "74d8b667-a1e3-443f-8b57-a6ff3a9a4106", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -2824,7 +2842,7 @@ "apierrors": [], "path": "/annotationEditor/deleteFeaturesForSequences", "response": { - "jsondocId": "15955ff5-d579-4bcd-9fb1-999c31cd4f8b", + "jsondocId": "6ebf7618-87b1-409c-8dfc-859bc0fcd2f5", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -2837,7 +2855,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "9d971c11-de57-4667-867c-721fc00e06ca", + "jsondocId": "2f243c48-bc14-4865-9635-3b6f09ef7d75", "name": "username", "format": "", "description": "", @@ -2846,7 +2864,7 @@ "allowedvalues": [] }, { - "jsondocId": "a913c835-541b-4c91-a018-ed97272eb461", + "jsondocId": "49993e66-03b4-47ca-b275-0f7a376cd109", "name": "password", "format": "", "description": "", @@ -2855,7 +2873,7 @@ "allowedvalues": [] }, { - "jsondocId": "2fb15dd9-6b2c-411e-a788-133f1b1efc37", + "jsondocId": "333330df-7e97-4b0a-b804-31ede93feb0e", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -2864,7 +2882,7 @@ "allowedvalues": [] }, { - "jsondocId": "3ca24366-fec2-4632-950d-ce0e81a562e5", + "jsondocId": "9eab542c-14b2-453d-b742-68afc1107df8", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -2873,7 +2891,7 @@ "allowedvalues": [] }, { - "jsondocId": "2bb04221-bdf7-4adc-a249-a0eff7d7d17a", + "jsondocId": "18a7529f-82da-4fc4-8622-d6d0bff754fe", "name": "features", "format": "", "description": "JSONArray of features objects, where the first is the parent transcript and the remaining are exons all defined by a unique name {'uniquename':'ABC123'}", @@ -2885,9 +2903,9 @@ "verb": "POST", "description": "Delete exons", "methodName": "deleteExon", - "jsondocId": "85848c26-3512-4630-be5a-02fb9f82f5c6", + "jsondocId": "9a189cc3-d5e0-4ecf-a58b-71571a0a6b2c", "bodyobject": { - "jsondocId": "25bbf923-90a5-4ddd-a6a4-2d837d172589", + "jsondocId": "ecb41087-c13b-471e-bab7-aa1adffe6c08", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -2897,7 +2915,7 @@ "apierrors": [], "path": "/annotationEditor/deleteExon", "response": { - "jsondocId": "c9e98dad-8bd5-49a7-ad7f-9ba1d60d3a89", + "jsondocId": "0e08737f-c6c5-442e-97cf-74f548aaa084", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -2910,7 +2928,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "1155ad20-95b0-4a0d-a31b-9b3174e24c95", + "jsondocId": "20f69aab-a9ff-4259-a748-29660770b58c", "name": "username", "format": "", "description": "", @@ -2919,7 +2937,7 @@ "allowedvalues": [] }, { - "jsondocId": "9d9269dd-f3c9-447f-b325-28f248a26416", + "jsondocId": "7312a765-2f28-4bdf-b5c6-15a1793bb868", "name": "password", "format": "", "description": "", @@ -2928,7 +2946,7 @@ "allowedvalues": [] }, { - "jsondocId": "b82bdcf2-418e-4493-8d66-39c8c91eccde", + "jsondocId": "c0618550-e512-412c-98f6-7ef6171a4348", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -2937,7 +2955,7 @@ "allowedvalues": [] }, { - "jsondocId": "8c36bbbd-ec9c-4be2-abe9-03654ac22b10", + "jsondocId": "12aa66c5-362c-423b-9062-6cccedc74a29", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -2946,7 +2964,7 @@ "allowedvalues": [] }, { - "jsondocId": "c1949a3e-2cb3-49fc-ad98-0fcabab21e74", + "jsondocId": "f13e575f-398d-41c6-a620-90114b65f709", "name": "features", "format": "", "description": "JSONArray containing a single JSONObject feature that contains {'uniquename':'ABCD-1234','location':{'fmin':12}}", @@ -2958,9 +2976,9 @@ "verb": "POST", "description": "Make intron", "methodName": "makeIntron", - "jsondocId": "e43b9b8b-e8f8-4530-8de4-3346dba49026", + "jsondocId": "37e8880b-d3ce-4fb2-acae-4893ce8436dc", "bodyobject": { - "jsondocId": "ce2887e0-5cf9-4423-9fd5-aa6cdbc35060", + "jsondocId": "78f512b8-3ede-463a-8d26-dc227d880d41", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -2970,7 +2988,7 @@ "apierrors": [], "path": "/annotationEditor/makeIntron", "response": { - "jsondocId": "36152a59-f21c-43bd-9bf5-2b24d2b13879", + "jsondocId": "18af8a40-f5fb-4e44-aebf-f2c471dc13f8", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -2983,7 +3001,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "2aa8c5ea-cb9e-44d8-90b7-57bd2ce8ef0f", + "jsondocId": "cf5cf06d-4f96-438d-ab6a-2689aba0a29d", "name": "username", "format": "", "description": "", @@ -2992,7 +3010,7 @@ "allowedvalues": [] }, { - "jsondocId": "a5ca0d02-a57f-4c1d-b5a5-43d9b0b6f7f5", + "jsondocId": "e9aa5f90-a4bf-45ef-8e41-a36566742665", "name": "password", "format": "", "description": "", @@ -3001,7 +3019,7 @@ "allowedvalues": [] }, { - "jsondocId": "6ea017fa-9b51-4cec-aade-8b644c194577", + "jsondocId": "bffc8d93-de84-4c65-b250-9d982eae381e", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -3010,7 +3028,7 @@ "allowedvalues": [] }, { - "jsondocId": "c0232345-3c42-4193-b7d4-e51400d939d0", + "jsondocId": "6912eafd-07c4-4c0c-9dfa-d710776b40be", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -3019,7 +3037,7 @@ "allowedvalues": [] }, { - "jsondocId": "222a22ef-1218-44b4-b027-1a1358f37619", + "jsondocId": "36e540da-f26d-466e-b6fd-f3a089bbf529", "name": "features", "format": "", "description": "JSONArray with with two exon objects referred to their unique names {'uniquename':'ABC123'}", @@ -3031,9 +3049,9 @@ "verb": "POST", "description": "Split transcript", "methodName": "splitTranscript", - "jsondocId": "d1ce4fa5-44c3-44c7-8dc8-07365f99183d", + "jsondocId": "5627c3a6-97d8-4388-9805-cae2b79f29b7", "bodyobject": { - "jsondocId": "cdbad90b-af42-421f-8540-a9a27555a7ec", + "jsondocId": "eb4925f2-26b3-40ef-b32f-3ea7c67ebf97", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -3043,7 +3061,7 @@ "apierrors": [], "path": "/annotationEditor/splitTranscript", "response": { - "jsondocId": "dfd3210c-a74a-4432-91a8-ae2161fd7fd6", + "jsondocId": "7c37e719-a04c-4159-b8a5-9254019b7df0", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -3056,7 +3074,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "66f9ded7-64bb-48c9-874e-180545aca474", + "jsondocId": "b9c52973-2ad2-4161-820d-bb3ae7ed0f3a", "name": "username", "format": "", "description": "", @@ -3065,7 +3083,7 @@ "allowedvalues": [] }, { - "jsondocId": "bf4348ae-8872-42e4-b059-f132c7664f7c", + "jsondocId": "76a0657a-918f-473c-aef4-ab2ba490a57f", "name": "password", "format": "", "description": "", @@ -3074,7 +3092,7 @@ "allowedvalues": [] }, { - "jsondocId": "12e562be-4168-442e-a044-8d08365924b7", + "jsondocId": "38aa814a-2365-4d33-b8bf-02107b95af3e", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -3083,7 +3101,7 @@ "allowedvalues": [] }, { - "jsondocId": "3e3070c7-1eeb-46b1-b577-c9af81cf56cc", + "jsondocId": "04dc5254-0f26-42a5-b1c8-933dd901da4a", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -3092,7 +3110,7 @@ "allowedvalues": [] }, { - "jsondocId": "04d19fa3-06fa-45ff-b47e-0aab921ebfd7", + "jsondocId": "7a89a760-c2c9-424f-a450-352584225d8d", "name": "features", "format": "", "description": "JSONArray with with two transcript objects referred to their unique names {'uniquename':'ABC123'}", @@ -3104,9 +3122,9 @@ "verb": "POST", "description": "Merge transcripts", "methodName": "mergeTranscripts", - "jsondocId": "5b7d0bd2-a0d5-4a00-a8b0-2552171e52dc", + "jsondocId": "c8deb46c-8ce5-4379-bc28-8e012df1fbed", "bodyobject": { - "jsondocId": "d6b727fb-93b0-452a-9b73-de1adfc8ad67", + "jsondocId": "37d86dfc-cfc6-465d-a27e-12ef54e78300", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -3116,7 +3134,7 @@ "apierrors": [], "path": "/annotationEditor/mergeTranscripts", "response": { - "jsondocId": "620a8309-02cc-44c8-a77a-b74fe8b31155", + "jsondocId": "b7120b62-5180-451d-b126-beb8bf2c4f5c", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -3129,7 +3147,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "44080940-0ca3-42e5-8f65-a1929dd69e43", + "jsondocId": "5c24a0e3-e5bd-4832-aa4b-5e84492e961d", "name": "username", "format": "", "description": "", @@ -3138,7 +3156,7 @@ "allowedvalues": [] }, { - "jsondocId": "20e0cf58-2208-4f01-9462-e64325e068cc", + "jsondocId": "abe58c8a-2851-40b4-8516-2dc801094acc", "name": "password", "format": "", "description": "", @@ -3147,7 +3165,7 @@ "allowedvalues": [] }, { - "jsondocId": "3f56eaaa-255f-41dc-bb58-c8208174ae31", + "jsondocId": "c39a80a8-a918-44bd-aa3e-2d77d77d02c4", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -3156,7 +3174,7 @@ "allowedvalues": [] }, { - "jsondocId": "71055471-d260-48cd-951d-63582416cd36", + "jsondocId": "187d7c76-c59f-4588-81aa-6477501ad7db", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -3165,7 +3183,7 @@ "allowedvalues": [] }, { - "jsondocId": "f428c9ae-9023-4d18-bd3d-6622a087bca2", + "jsondocId": "7f96f5ba-27d0-45d2-9f38-bb1e61c3b222", "name": "features", "format": "", "description": "JSONArray of features objects to export defined by a unique name {'uniquename':'ABC123'}", @@ -3177,9 +3195,9 @@ "verb": "POST", "description": "Get sequence for feature", "methodName": "getSequence", - "jsondocId": "5e4861be-8c41-4141-8591-e5ee1ae32503", + "jsondocId": "0df3df9a-55ac-4a9c-8e2b-c7be29a47fe4", "bodyobject": { - "jsondocId": "bf3ca4ca-bf78-48ff-8ed0-0cfeaa23ffe3", + "jsondocId": "1f31d9de-2e4f-41fc-8fa2-70071031c72f", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -3189,7 +3207,7 @@ "apierrors": [], "path": "/annotationEditor/getSequence", "response": { - "jsondocId": "6aa0976b-424a-4fb6-8c05-7d51fd47e196", + "jsondocId": "4b95a0cf-c6a1-4751-b898-0433900f7c42", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -3198,7 +3216,7 @@ "consumes": ["application/json"] }, { - "jsondocId": "42cba0c1-5f3c-40d3-8293-8444f779ff04", + "jsondocId": "13f4de7c-659d-4243-a8b5-c000d7f7e787", "bodyobject": null, "apierrors": [], "path": "/annotationEditor/getSequenceSearchTools", @@ -3206,7 +3224,7 @@ "pathparameters": [], "queryparameters": [], "response": { - "jsondocId": "01e493f5-dec5-46e4-b6d0-1afd570489e1", + "jsondocId": "22747cb0-58b2-4c39-8cf2-d67302aefe21", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -3221,7 +3239,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "8eaff0a6-0cf0-4590-baf0-ff815a538938", + "jsondocId": "dee2b99f-edb4-4896-a559-810260fbeb1e", "name": "username", "format": "", "description": "", @@ -3230,7 +3248,7 @@ "allowedvalues": [] }, { - "jsondocId": "7873eb63-839c-4082-9efc-b96e5c6b2798", + "jsondocId": "caffce20-0c65-4a94-a9a4-da2d1169f20a", "name": "password", "format": "", "description": "", @@ -3242,9 +3260,9 @@ "verb": "POST", "description": "Get canned comments", "methodName": "getCannedComments", - "jsondocId": "66f3eb19-b5ad-4992-95ef-0d91969fbcf9", + "jsondocId": "749c12b0-f2b4-4fae-8140-8498562a39a3", "bodyobject": { - "jsondocId": "31ed139b-f29d-48c9-b05c-dac8f9bf7f26", + "jsondocId": "338e71eb-b63c-4c13-9b49-58ba7cbac59d", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -3254,7 +3272,7 @@ "apierrors": [], "path": "/annotationEditor/getCannedComments", "response": { - "jsondocId": "a5e8d11b-3c4d-444c-b2ec-174ac6d9e18a", + "jsondocId": "d0e669d0-0ab4-4313-8eb7-53e458de1636", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -3267,7 +3285,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "5d55aeed-9e41-4abf-9223-d080f2af47df", + "jsondocId": "d9f52d71-4335-4540-9bac-54ce2bce0fc5", "name": "username", "format": "", "description": "", @@ -3276,7 +3294,7 @@ "allowedvalues": [] }, { - "jsondocId": "55447cf1-24c3-4100-bf9b-fa90b1bba413", + "jsondocId": "54491afc-c867-4bae-a658-adac3e4df4a3", "name": "password", "format": "", "description": "", @@ -3288,9 +3306,9 @@ "verb": "POST", "description": "Get canned keys", "methodName": "getCannedKeys", - "jsondocId": "2b5e0307-b630-4d75-8ea7-043d2479ce4c", + "jsondocId": "3fef55f6-a6dc-4ea8-862b-2e1fe14ed5fd", "bodyobject": { - "jsondocId": "0be5e796-791f-45f2-9ebf-b1d976103e38", + "jsondocId": "186c1bd8-798c-412c-acee-56dbe35b61ff", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -3300,7 +3318,7 @@ "apierrors": [], "path": "/annotationEditor/getCannedKeys", "response": { - "jsondocId": "37006778-5455-41b0-9ca3-3e50cd157f13", + "jsondocId": "52e5a667-f63d-4756-9d69-3ae5bfe9d96d", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -3313,7 +3331,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "d4dbd156-b360-4a86-8dc1-a8b93670a5da", + "jsondocId": "b2d14b60-98ba-4d74-8926-3fec47afa863", "name": "username", "format": "", "description": "", @@ -3322,7 +3340,7 @@ "allowedvalues": [] }, { - "jsondocId": "2c040b64-1b4e-446f-9a56-608cb520fe5c", + "jsondocId": "675aaa74-2676-4ee7-97a6-d327237c24fa", "name": "password", "format": "", "description": "", @@ -3334,9 +3352,9 @@ "verb": "POST", "description": "Get canned values", "methodName": "getCannedValues", - "jsondocId": "69020588-16c1-44cf-862e-5eab6bbf22fd", + "jsondocId": "782d433d-647e-4256-85f0-fa1445ad630b", "bodyobject": { - "jsondocId": "5a675cc6-59ae-4d86-b27e-ab90f87bd631", + "jsondocId": "edbdaf77-de7a-4a43-8c1d-be5d0353db68", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -3346,7 +3364,7 @@ "apierrors": [], "path": "/annotationEditor/getCannedValues", "response": { - "jsondocId": "aed425a8-1fce-4027-8715-0c8e1bb18cf0", + "jsondocId": "e3f277b6-4aa1-4159-91c8-cc44b21ac670", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -3359,7 +3377,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "cc258255-7530-42fc-b501-24636b6d8e3f", + "jsondocId": "65c0b8a0-2792-48c0-a639-9dac186fbf19", "name": "username", "format": "", "description": "", @@ -3368,7 +3386,7 @@ "allowedvalues": [] }, { - "jsondocId": "a8b63561-30b6-4d22-9071-a3798920259a", + "jsondocId": "617afcb7-76e9-4487-860e-050bdd25d226", "name": "password", "format": "", "description": "", @@ -3377,7 +3395,7 @@ "allowedvalues": [] }, { - "jsondocId": "26960c69-ccf0-4faf-b3b7-0dff99c62322", + "jsondocId": "33c2dc00-00b6-4e28-8ab7-f5ec9306de72", "name": "organismId", "format": "", "description": "", @@ -3386,7 +3404,7 @@ "allowedvalues": [] }, { - "jsondocId": "bad4b816-492f-450c-82b0-d985d4c942c0", + "jsondocId": "ff6a7467-057e-434d-8dfa-a2c2f2f0dbba", "name": "type", "format": "", "description": "", @@ -3398,9 +3416,9 @@ "verb": "POST", "description": "Get available statuses", "methodName": "getAvailableStatuses", - "jsondocId": "3eeaa511-ceb3-441b-9443-475f7605a013", + "jsondocId": "b199df2d-3acc-4e6c-a5bb-0982dbfaec03", "bodyobject": { - "jsondocId": "4ac81a47-57c3-4ac8-be73-b2f03914718c", + "jsondocId": "e7b90202-210c-45d8-8b79-2cd263d15b61", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -3410,7 +3428,7 @@ "apierrors": [], "path": "/annotationEditor/getAvailableStatuses", "response": { - "jsondocId": "335a360e-f4ce-4bdb-8ae2-8efa298a4cec", + "jsondocId": "ba7c7050-610c-4d63-851d-5896958cf301", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -3422,7 +3440,7 @@ "headers": [], "pathparameters": [], "queryparameters": [{ - "jsondocId": "0137edcc-ddb7-4e9b-a118-9cd24ba5e8ea", + "jsondocId": "0e1ce2c6-5ed6-4284-9153-c97b5562d521", "name": "search", "format": "", "description": "{'key':'blat_prot','residues':'ATACTAGAGATAC':'database_id':'abc123'}", @@ -3433,9 +3451,9 @@ "verb": "POST", "description": "Search sequences", "methodName": "searchSequence", - "jsondocId": "914a6336-f22e-43c1-a224-dc61d8e05330", + "jsondocId": "0b47a4c6-eb2f-4be1-87a2-1fc0c182a83a", "bodyobject": { - "jsondocId": "d3414e93-0e84-4ba9-b5d2-1b025135e9c4", + "jsondocId": "12d190f0-35b2-4915-990f-6f765399d03e", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -3445,7 +3463,7 @@ "apierrors": [], "path": "/annotationEditor/searchSequences", "response": { - "jsondocId": "eabf640e-8a24-4495-82a0-38e3d79a33a7", + "jsondocId": "deda3a52-1cad-48f0-a915-aeedc0153303", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -3458,7 +3476,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "3129d7a5-cb11-4d17-a8d6-64f423f4ef78", + "jsondocId": "379d61ba-a483-402c-bf62-7e056c53529b", "name": "username", "format": "", "description": "", @@ -3467,7 +3485,7 @@ "allowedvalues": [] }, { - "jsondocId": "eb703cad-70bf-49c9-bb1b-2ace12d47ece", + "jsondocId": "d2c2d36a-79a2-4c44-b60e-299740f7f81b", "name": "password", "format": "", "description": "", @@ -3476,30 +3494,21 @@ "allowedvalues": [] }, { - "jsondocId": "69aa17df-bbe3-4c28-bf6b-1b0719ea7699", - "name": "days", - "format": "", - "description": "(Required) Number of past days to retrieve annotations from.", - "type": "Integer", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "54ebb0b8-f7c8-4893-a7ce-c7de75cb59d7", - "name": "status", + "jsondocId": "bf838104-0fa5-446d-92e9-f1a6a96afa30", + "name": "features", "format": "", - "description": "(optional: default allow all) Pipe-separated list of filters (e.g., 'Finished|Published'). Use 'None' if you want annotations without a status. ", - "type": "String", + "description": "JSONArray of features objects to export defined by a unique name {'uniquename':'ABC123'}", + "type": "JSONArray", "required": "true", "allowedvalues": [] } ], "verb": "POST", - "description": "Get genes created or updated in the past, Returns JSON hash gene_name:organism", - "methodName": "getRecentAnnotations", - "jsondocId": "bc86a74b-7872-4c26-8745-db9775db74ae", + "description": "Get gff3", + "methodName": "getGff3", + "jsondocId": "dd9bf29b-3056-46ee-a3d0-524ff31623e4", "bodyobject": { - "jsondocId": "6d8e1225-6097-49ee-9fd3-977d119a1283", + "jsondocId": "7c6c3b33-dbc2-45fd-b921-139d5d360362", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -3507,9 +3516,9 @@ "object": "annotation editor" }, "apierrors": [], - "path": "/annotationEditor/getRecentAnnotations", + "path": "/annotationEditor/getGff3", "response": { - "jsondocId": "2c8a5be9-a043-4cdc-bbd0-891f657b109a", + "jsondocId": "4fa4710c-9278-4e15-8b3f-be424002c0e5", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -3522,7 +3531,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "0283886b-2d5f-4cb6-83ac-05c90b90c2ff", + "jsondocId": "1dc7c5b9-860a-4380-b63b-20a298f6352d", "name": "username", "format": "", "description": "", @@ -3531,7 +3540,7 @@ "allowedvalues": [] }, { - "jsondocId": "9c789acf-825e-4a49-9f34-9618a256c46f", + "jsondocId": "0d557490-37b6-466b-9194-44ccb25010b2", "name": "password", "format": "", "description": "", @@ -3540,39 +3549,30 @@ "allowedvalues": [] }, { - "jsondocId": "8a0e6c42-f18e-4c3d-bc61-5db6fc7c871c", - "name": "sequence", - "format": "", - "description": "(optional) Sequence name", - "type": "string", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "2a2996e5-6383-4739-b06d-1301a9475d48", - "name": "organism", + "jsondocId": "30ea1bb9-1f24-4639-8952-3a4402998611", + "name": "days", "format": "", - "description": "(optional) Organism ID or common name", - "type": "string", + "description": "(Required) Number of past days to retrieve annotations from.", + "type": "Integer", "required": "true", "allowedvalues": [] }, { - "jsondocId": "2fa5acd3-c5a4-49ea-b6c9-bcd34f02a830", - "name": "features", + "jsondocId": "a191aad6-7a91-43d0-a69b-99261119ca97", + "name": "status", "format": "", - "description": "JSONArray containing JSON objects with {'uniquename':'ABCD-1234','symbol':'Pax6a'}", - "type": "JSONArray", + "description": "(optional: default allow all) Pipe-separated list of filters (e.g., 'Finished|Published'). Use 'None' if you want annotations without a status. ", + "type": "String", "required": "true", "allowedvalues": [] } ], "verb": "POST", - "description": "Set symbol of a feature", - "methodName": "setSymbol", - "jsondocId": "8971f4fd-0181-42d5-9a6c-b5548982ec8a", + "description": "Get genes created or updated in the past, Returns JSON hash gene_name:organism", + "methodName": "getRecentAnnotations", + "jsondocId": "d9485014-e8c9-4408-8e0e-be863d0ff629", "bodyobject": { - "jsondocId": "fa7e8d80-74de-4573-b913-5409c1eed3ee", + "jsondocId": "eb4380e8-692f-416c-b299-a03f4753ec21", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -3580,9 +3580,9 @@ "object": "annotation editor" }, "apierrors": [], - "path": "/annotationEditor/setSymbol", + "path": "/annotationEditor/getRecentAnnotations", "response": { - "jsondocId": "2e474aa6-d6fc-4ecb-8852-f316fbf82c71", + "jsondocId": "26ae61cb-416e-4df1-811d-c92f9bd679ca", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -3595,7 +3595,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "6b9e1605-8283-4868-bd23-d2758209b807", + "jsondocId": "37012ad7-4e2d-4f60-a2df-57a26b0754f9", "name": "username", "format": "", "description": "", @@ -3604,7 +3604,7 @@ "allowedvalues": [] }, { - "jsondocId": "069fed37-18c4-4968-999e-937bab3fd4c3", + "jsondocId": "4c6665ad-afd6-4b10-96a1-7fbc6516c138", "name": "password", "format": "", "description": "", @@ -3613,7 +3613,7 @@ "allowedvalues": [] }, { - "jsondocId": "4d541ca7-8d19-4e7f-843d-2ebbd6e04ff8", + "jsondocId": "a30e802e-8118-4c62-9085-f01f713b838e", "name": "organism", "format": "", "description": "(optional) Organism ID or common name", @@ -3622,7 +3622,7 @@ "allowedvalues": [] }, { - "jsondocId": "6f630435-ccc8-47ed-8f84-20eee68fd0d7", + "jsondocId": "72f262a2-3798-4e68-9d47-e30497fcce10", "name": "sequence", "format": "", "description": "(optional) Sequence name", @@ -3631,7 +3631,7 @@ "allowedvalues": [] }, { - "jsondocId": "6eb4c699-e720-4d53-8a97-07d6a25761be", + "jsondocId": "b44ae2e0-4952-4f02-ba8f-f9e05127e156", "name": "suppressHistory", "format": "", "description": "Suppress the history of this operation", @@ -3640,7 +3640,7 @@ "allowedvalues": [] }, { - "jsondocId": "0b72f82d-3754-4ff5-a887-16d7aecd72ae", + "jsondocId": "1a04c249-c8ab-4814-89e4-b22eb484d031", "name": "suppressEvents", "format": "", "description": "Suppress instant update of the user interface", @@ -3649,7 +3649,7 @@ "allowedvalues": [] }, { - "jsondocId": "e20e6f4b-8889-44d0-917c-4037fec941a2", + "jsondocId": "0cc1178c-7d77-4a40-8754-26c217c29aac", "name": "features", "format": "", "description": "JSONArray of JSON feature objects described by https://github.com/GMOD/Apollo/blob/master/grails-app/domain/org/bbop/apollo/Feature.groovy", @@ -3661,9 +3661,9 @@ "verb": "POST", "description": "Set exon feature boundaries", "methodName": "setExonBoundaries", - "jsondocId": "27c3b3bd-e982-4d14-8b5d-6446c32cb10d", + "jsondocId": "bcdb6ae1-7927-4acb-8912-1e6346531518", "bodyobject": { - "jsondocId": "98fc0a45-4e9e-45c4-97dd-e42d30d00778", + "jsondocId": "9202f884-6ff0-4fd3-9abe-a4fcf96bb6d5", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -3673,7 +3673,7 @@ "apierrors": [], "path": "/annotationEditor/setExonBoundaries", "response": { - "jsondocId": "c8dec860-1e7a-4ce0-9720-e0a192174063", + "jsondocId": "e3ccef17-2af1-41de-9c0f-cdff610bf309", "mapValueObject": "", "mapKeyObject": "", "object": "annotation editor" @@ -3686,7 +3686,7 @@ "description": "Methods for running the annotation engine" }, { - "jsondocId": "93e56f77-a288-45a7-a7f4-46ec384be453", + "jsondocId": "2022c635-0605-4239-9a00-840f823deb0b", "methods": [ { "headers": [], @@ -3695,12 +3695,12 @@ "verb": "GET", "description": "Get system info", "methodName": "system", - "jsondocId": "3a8ee22b-5a92-4572-88fc-366e205ad858", + "jsondocId": "fe7d0d17-1a4f-4f5d-a447-f12761bbcb6b", "bodyobject": null, "apierrors": [], "path": "/system", "response": { - "jsondocId": "7ec45406-037f-4277-a0ab-79549da8addd", + "jsondocId": "4a91ac10-b7dd-4d14-9bcf-6f2ade507664", "mapValueObject": "", "mapKeyObject": "", "object": "annotator" @@ -3713,7 +3713,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "5e7eed31-59f6-46cb-8aaf-6e8e3cbbfcb5", + "jsondocId": "a3e90bc4-52e1-4bb6-a0e3-3366a853cab0", "name": "username", "format": "", "description": "", @@ -3722,7 +3722,7 @@ "allowedvalues": [] }, { - "jsondocId": "6899c108-f9ac-4c33-beab-2f3e8d7cf70c", + "jsondocId": "cf63c84f-aa71-4f0c-ba57-1cbbfb1e7bdc", "name": "password", "format": "", "description": "", @@ -3731,7 +3731,7 @@ "allowedvalues": [] }, { - "jsondocId": "52babcaf-0d75-4203-a091-d07eefb011bd", + "jsondocId": "d3a037c4-c16b-4f17-928e-5d63c2a488dc", "name": "uniquename", "format": "", "description": "Uniquename (UUID) of the feature we are editing", @@ -3740,7 +3740,7 @@ "allowedvalues": [] }, { - "jsondocId": "3ab9c168-a73e-460f-a133-0e5bb26dd32e", + "jsondocId": "2304a83c-dd79-46f9-87d5-977c9524ab38", "name": "name", "format": "", "description": "Updated feature name", @@ -3749,7 +3749,7 @@ "allowedvalues": [] }, { - "jsondocId": "eca4cb2a-e912-42f0-adc4-4fd21ffe1c10", + "jsondocId": "b80e4d47-b5eb-4454-a172-ff8f8eade169", "name": "symbol", "format": "", "description": "Updated feature symbol", @@ -3758,7 +3758,7 @@ "allowedvalues": [] }, { - "jsondocId": "0f8d47bf-5d08-4c35-9594-2f4d8c089571", + "jsondocId": "9cfbf643-2e3a-4051-b59d-b17fee278115", "name": "synonyms", "format": "", "description": "Updated synonyms pipe (|) separated", @@ -3767,7 +3767,7 @@ "allowedvalues": [] }, { - "jsondocId": "b3c35ae4-98c6-4da7-bcf7-ee048599020c", + "jsondocId": "1037c989-9017-4b87-91cc-2f07fc5fc8b4", "name": "description", "format": "", "description": "Updated feature description", @@ -3776,7 +3776,7 @@ "allowedvalues": [] }, { - "jsondocId": "3e370cb9-7549-4085-a585-c6766b1aea5f", + "jsondocId": "04a20311-2b43-4b01-b04c-914da355c161", "name": "status", "format": "", "description": "Updated status", @@ -3785,7 +3785,7 @@ "allowedvalues": [] }, { - "jsondocId": "aeab5401-1750-4a0d-91e3-106ceb0f0502", + "jsondocId": "c977044d-d8fa-49ef-b3d2-1598f523a2dc", "name": "obsolete", "format": "", "description": "Updated if obsolete", @@ -3797,9 +3797,9 @@ "verb": "POST", "description": "Update shallow feature properties", "methodName": "updateFeature", - "jsondocId": "65bb9b3d-aa51-4217-a780-d9486f21ad47", + "jsondocId": "ffe6f145-f4d2-4f79-bdd9-a663fef99823", "bodyobject": { - "jsondocId": "fd6ac38f-4682-4b36-823d-f79efc89b1dc", + "jsondocId": "27a6d683-27aa-4c38-b5ad-511b89638aab", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -3809,7 +3809,7 @@ "apierrors": [], "path": "/annotator/updateFeature", "response": { - "jsondocId": "e442cc2c-7560-47e9-a96f-bd4986649fd5", + "jsondocId": "adb743da-3d42-4a3f-9848-386b24db6871", "mapValueObject": "", "mapKeyObject": "", "object": "annotator" @@ -3822,7 +3822,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "a126a011-b610-4e46-9780-e7e8a26b3154", + "jsondocId": "f637e0ca-babd-44f6-b3c3-d7a7084e3580", "name": "username", "format": "", "description": "", @@ -3831,7 +3831,7 @@ "allowedvalues": [] }, { - "jsondocId": "d99599c8-c307-475a-b05e-e16b7a28d60d", + "jsondocId": "f7ea13c2-79a3-4510-86b7-6dabdf025843", "name": "password", "format": "", "description": "", @@ -3840,34 +3840,98 @@ "allowedvalues": [] }, { - "jsondocId": "c15e3194-0bfe-4cfe-9b9c-503e3837b9ad", + "jsondocId": "7d111e47-c842-4ba9-8b6b-2bca5f8d7f6f", "name": "uniquename", "format": "", - "description": "Uniquename (UUID) of the exon we are editing", + "description": "Uniquename (UUID) of the feature we are editing", "type": "string", "required": "true", "allowedvalues": [] }, { - "jsondocId": "b7e1ddf3-89b1-44ab-8601-4dd269c53b76", - "name": "fmin", - "format": "", - "description": "fmin for Exon Location", - "type": "int", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "5532c317-1819-426b-bcaa-6e0cb480e442", - "name": "fmax", + "jsondocId": "cfef76fb-b582-40dd-8544-751e85b42d99", + "name": "data", "format": "", - "description": "fmax for Exon Location", - "type": "int", + "description": "Annotation Info object", + "type": "string", + "required": "true", + "allowedvalues": [] + } + ], + "verb": "POST", + "description": "Update partial fmin / famx", + "methodName": "updatePartials", + "jsondocId": "c9f5b576-7427-48f9-a5c4-cdddd59517f6", + "bodyobject": { + "jsondocId": "b35b8cf9-fd27-4244-97fb-9625445c7f6a", + "mapValueObject": "", + "mapKeyObject": "", + "multiple": "Unknow", + "map": "", + "object": "annotator" + }, + "apierrors": [], + "path": "/annotator/updatePartials", + "response": { + "jsondocId": "a6380d1c-740c-4392-a29c-06e787ebc4bb", + "mapValueObject": "", + "mapKeyObject": "", + "object": "annotator" + }, + "produces": ["application/json"], + "consumes": ["application/json"] + }, + { + "headers": [], + "pathparameters": [], + "queryparameters": [ + { + "jsondocId": "72735de0-da15-4ff0-8c76-9fe22d337821", + "name": "username", + "format": "", + "description": "", + "type": "email", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "150774c9-6333-40f4-b449-b58a1842ffd4", + "name": "password", + "format": "", + "description": "", + "type": "password", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "f923ed39-c797-4bb7-9858-d545cf0d4f4c", + "name": "uniquename", + "format": "", + "description": "Uniquename (UUID) of the exon we are editing", + "type": "string", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "c1ce2d0c-b3d4-4763-a0d6-5cc779e9acdc", + "name": "fmin", + "format": "", + "description": "fmin for Exon Location", + "type": "int", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "f2a6eb20-ae9c-48d3-a06d-15ef4a64cc4e", + "name": "fmax", + "format": "", + "description": "fmax for Exon Location", + "type": "int", "required": "true", "allowedvalues": [] }, { - "jsondocId": "0eeab808-78e6-47d1-b6f6-ee1b0dbaa476", + "jsondocId": "65ca2b90-2c25-4e4d-bf8b-b9bf66c9911a", "name": "strand", "format": "", "description": "strand for Feature Location 1 or -1", @@ -3879,9 +3943,9 @@ "verb": "POST", "description": "Update exon boundaries", "methodName": "setExonBoundaries", - "jsondocId": "1b1f10e0-1d94-43a2-9db9-a9341d131d93", + "jsondocId": "846026c9-44bc-4995-a2f6-28bbbdef0041", "bodyobject": { - "jsondocId": "a916e3a0-a15f-4ce9-8a45-90a83ce9bbd0", + "jsondocId": "e208a09d-9f24-4fa1-8a1b-835468fb3ed0", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -3891,7 +3955,7 @@ "apierrors": [], "path": "/annotator/setExonBoundaries", "response": { - "jsondocId": "30b4acdf-6d84-45bf-8725-9a510ec1cb7a", + "jsondocId": "4a4fc8b0-2ddb-4e14-a4dd-2696f44d6ba7", "mapValueObject": "", "mapKeyObject": "", "object": "annotator" @@ -3904,7 +3968,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "6a1dc0e2-4289-49e7-8232-bbb081d08abc", + "jsondocId": "520fd025-ad50-4c4c-87bd-f376d53b8edd", "name": "username", "format": "", "description": "", @@ -3913,7 +3977,7 @@ "allowedvalues": [] }, { - "jsondocId": "e81f2492-b8d2-4f9c-8ca9-016c5f04a383", + "jsondocId": "a63cf351-3934-4d23-bb40-f797a044c488", "name": "password", "format": "", "description": "", @@ -3922,7 +3986,7 @@ "allowedvalues": [] }, { - "jsondocId": "d43dd5aa-20a4-4172-a23b-73d2d8d06eda", + "jsondocId": "b1992afc-baf4-421c-a8dc-c6b0b1518c6f", "name": "id", "format": "", "description": "Group ID (or specify the name)", @@ -3931,7 +3995,7 @@ "allowedvalues": [] }, { - "jsondocId": "7e78a30a-3020-4517-ada7-ce5cc5360c8b", + "jsondocId": "eac51904-6035-411a-b938-67028eb1fb28", "name": "name", "format": "", "description": "Group name", @@ -3943,9 +4007,9 @@ "verb": "POST", "description": "Get annotators report for group", "methodName": "getAnnotatorsReportForGroup", - "jsondocId": "ca9b3344-7528-40ae-a3ff-ad3656f5f50a", + "jsondocId": "79118be1-4055-4d62-8eb2-8462b413320c", "bodyobject": { - "jsondocId": "b96565bb-4559-4e0f-879e-e36deaaf6013", + "jsondocId": "b504964a-0f60-420e-82ac-bd757690df37", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -3955,7 +4019,7 @@ "apierrors": [], "path": "/group/getAnnotatorsReportForGroup", "response": { - "jsondocId": "d270a191-da4d-4655-8fa4-b5cbb2869730", + "jsondocId": "79a5c9d0-dad5-4c2a-84be-451a5146933b", "mapValueObject": "", "mapKeyObject": "", "object": "annotator" @@ -3968,14 +4032,14 @@ "description": "Methods for running the annotation engine" }, { - "jsondocId": "39dc5fa2-c3f6-4f54-8645-c40a000c5be4", + "jsondocId": "0415aaa6-6337-443c-a842-b3a66949c810", "methods": [ { "headers": [], "pathparameters": [], "queryparameters": [ { - "jsondocId": "6f1e6088-8162-4881-8688-0f06d21910aa", + "jsondocId": "a12d85c6-463e-4649-8f5d-8d4f2e635e2a", "name": "username", "format": "", "description": "", @@ -3984,7 +4048,7 @@ "allowedvalues": [] }, { - "jsondocId": "e6208a3b-02ec-48ff-b581-d62d8bad655e", + "jsondocId": "1b755f0f-e6e8-4751-a278-81ff17ccd8d7", "name": "password", "format": "", "description": "", @@ -3993,7 +4057,7 @@ "allowedvalues": [] }, { - "jsondocId": "cbccbf5f-112d-4830-837e-212e6c126cc0", + "jsondocId": "ee28e501-e065-4585-9879-9491d3fd1c4b", "name": "id", "format": "", "description": "Status ID to update (or specify the old_value)", @@ -4002,7 +4066,7 @@ "allowedvalues": [] }, { - "jsondocId": "75aa2d1e-d290-476b-b14c-1df7e1152b7e", + "jsondocId": "7eeba3bc-b73b-4e2b-a519-45a2e8a404d5", "name": "old_value", "format": "", "description": "Status name to update", @@ -4011,7 +4075,7 @@ "allowedvalues": [] }, { - "jsondocId": "b5b90dc3-bfd1-478e-b14e-eb4fe980ec41", + "jsondocId": "a7522f26-6190-471a-bb2a-a075c5cbfe67", "name": "new_value", "format": "", "description": "Status name to change to (the only editable option)", @@ -4023,9 +4087,9 @@ "verb": "POST", "description": "Update status", "methodName": "updateStatus", - "jsondocId": "cf317fda-dd10-4785-98e2-bed6dea99f42", + "jsondocId": "3d7a81ef-c944-4f9f-8468-e522ea51db76", "bodyobject": { - "jsondocId": "1ff432da-ca66-4017-a159-f12be76c8ee8", + "jsondocId": "eeb1eb8b-8c85-4774-af33-d3da1580c99a", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -4035,7 +4099,7 @@ "apierrors": [], "path": "/availableStatus/updateStatus", "response": { - "jsondocId": "ec1c4d07-152e-46e5-8e80-d43d83131f56", + "jsondocId": "98d93cb7-ac0c-4f00-a326-f011a7655e53", "mapValueObject": "", "mapKeyObject": "", "object": "available status" @@ -4048,7 +4112,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "1075afb9-e2f6-4445-82d9-ef2628391ce0", + "jsondocId": "fc73f6fa-2cac-4ff4-9c13-3f602a21f2be", "name": "username", "format": "", "description": "", @@ -4057,7 +4121,7 @@ "allowedvalues": [] }, { - "jsondocId": "8ae5b339-5976-43ea-9571-2df9adffb831", + "jsondocId": "fcc22562-63e8-4029-8311-2bfb1cc30442", "name": "password", "format": "", "description": "", @@ -4066,7 +4130,7 @@ "allowedvalues": [] }, { - "jsondocId": "69cbc0d9-d3e7-4cd1-9d1c-9ae2d1b93aef", + "jsondocId": "a401d3e4-b343-4864-af05-bc4789be4e74", "name": "value", "format": "", "description": "Status name to add", @@ -4078,9 +4142,9 @@ "verb": "POST", "description": "Create status", "methodName": "createStatus", - "jsondocId": "1d31ebbd-81c9-4a04-8dce-718dde44cb5a", + "jsondocId": "ea0746e4-a895-4b58-ae67-6fa384757a9b", "bodyobject": { - "jsondocId": "6d214103-7d1b-4f88-9b41-67c2b4898a89", + "jsondocId": "a2c85a7d-b0e9-4386-b4d7-ae5b2d8a42d4", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -4090,7 +4154,7 @@ "apierrors": [], "path": "/availableStatus/createStatus", "response": { - "jsondocId": "2ab879e0-b7c6-4da3-a5b1-9349c63ceaf1", + "jsondocId": "5c0aca54-d0c8-449b-acd5-5d2487267c90", "mapValueObject": "", "mapKeyObject": "", "object": "available status" @@ -4103,7 +4167,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "36635301-47ef-40f4-b33e-0dd1bc542361", + "jsondocId": "98f85dfd-bb56-474e-862d-adc325cf4704", "name": "username", "format": "", "description": "", @@ -4112,7 +4176,7 @@ "allowedvalues": [] }, { - "jsondocId": "f1d6b7c4-e897-4f02-b688-2565b0969fe1", + "jsondocId": "a2502fec-0a06-415f-9e95-04b14a66b457", "name": "password", "format": "", "description": "", @@ -4121,7 +4185,7 @@ "allowedvalues": [] }, { - "jsondocId": "fceaee87-5f1b-4fd3-8696-34295d9b54c8", + "jsondocId": "a9788ff4-b9e3-4a8f-8891-8c6dc646cea8", "name": "id", "format": "", "description": "Status ID to remove (or specify the name)", @@ -4130,7 +4194,7 @@ "allowedvalues": [] }, { - "jsondocId": "c586ae73-fe88-4526-948a-d9bb599a95df", + "jsondocId": "2b68f39b-affb-48ea-b900-b287d5bdef7e", "name": "value", "format": "", "description": "Status name to delete", @@ -4142,9 +4206,9 @@ "verb": "POST", "description": "Remove a status", "methodName": "deleteStatus", - "jsondocId": "9785bcca-2220-42e3-babc-bdf52f5b9f4c", + "jsondocId": "e2772f80-f0aa-48f6-bd81-a078b27c87ad", "bodyobject": { - "jsondocId": "b4cc366d-2680-4360-af67-990d214c1038", + "jsondocId": "cb82d878-0d39-4933-a2ce-eccdc99645b2", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -4154,7 +4218,7 @@ "apierrors": [], "path": "/availableStatus/deleteStatus", "response": { - "jsondocId": "3a1a3185-e7a1-4224-9dea-e5a3e6a9df5b", + "jsondocId": "11aac34c-3810-4df5-a7ac-3ee2131e5873", "mapValueObject": "", "mapKeyObject": "", "object": "available status" @@ -4167,7 +4231,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "460dc0f4-54e4-43d4-99b5-93a960bbe09a", + "jsondocId": "93e5cc1a-a549-4883-a8b4-a9b054abd4bd", "name": "username", "format": "", "description": "", @@ -4176,7 +4240,7 @@ "allowedvalues": [] }, { - "jsondocId": "0ddfa402-ebd1-46c3-a924-036d208a9f64", + "jsondocId": "f6662cce-8e4c-4b90-a336-c78fde82016f", "name": "password", "format": "", "description": "", @@ -4185,7 +4249,7 @@ "allowedvalues": [] }, { - "jsondocId": "7624fe6e-14c6-4626-8a78-d482280ed57a", + "jsondocId": "0c031558-225e-4c18-9be7-0e0400791a6d", "name": "id", "format": "", "description": "Status ID to show (or specify a name)", @@ -4194,7 +4258,7 @@ "allowedvalues": [] }, { - "jsondocId": "00a8edfc-27d9-4394-ad12-cbdeeba5148e", + "jsondocId": "a0e10643-39e9-4f44-8b59-e4fbcd12d182", "name": "name", "format": "", "description": "Status name to show", @@ -4206,9 +4270,9 @@ "verb": "POST", "description": "Returns a JSON array of all statuses, or optionally, gets information about a specific status", "methodName": "showStatus", - "jsondocId": "4702b210-08b9-4364-a441-2f0f29f4485d", + "jsondocId": "4e362969-cd50-430f-9a54-ef03d161d3a4", "bodyobject": { - "jsondocId": "82c52449-cd17-44cd-889c-efa10029eb26", + "jsondocId": "bcbae027-d092-425a-af45-c09d0e644255", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -4218,7 +4282,7 @@ "apierrors": [], "path": "/availableStatus/showStatus", "response": { - "jsondocId": "f3e32e9b-3fe5-4ab9-925a-1c1353686419", + "jsondocId": "6776ffda-ffa2-4096-bf5d-6dc2e66bc4ad", "mapValueObject": "", "mapKeyObject": "", "object": "available status" @@ -4231,14 +4295,14 @@ "description": "Methods for managing available statuses" }, { - "jsondocId": "7fad93a0-5ddf-4f4d-8ac9-63428fe04a33", + "jsondocId": "fba6cdc8-6dc7-4371-9c6c-cb84db1ebd44", "methods": [ { "headers": [], "pathparameters": [], "queryparameters": [ { - "jsondocId": "77a7b431-7881-4eb5-935c-71d2b788484f", + "jsondocId": "7d2308d6-85ab-45a6-8a5d-81abfa942e31", "name": "username", "format": "", "description": "", @@ -4247,7 +4311,7 @@ "allowedvalues": [] }, { - "jsondocId": "ee324153-86de-4856-aa6f-3348a72e611d", + "jsondocId": "136a27db-19e7-44ce-af92-4fccd6c0b399", "name": "password", "format": "", "description": "", @@ -4256,7 +4320,7 @@ "allowedvalues": [] }, { - "jsondocId": "9958c7f7-c376-481d-b244-48d2817c4957", + "jsondocId": "923ac6b5-5aa4-4018-9a9b-c79a6db77620", "name": "comment", "format": "", "description": "Canned comment to add", @@ -4265,7 +4329,7 @@ "allowedvalues": [] }, { - "jsondocId": "1a158d15-5403-46c9-b451-d649e887bd3e", + "jsondocId": "fafb4953-5316-4229-aefb-c7c3f6a935c7", "name": "metadata", "format": "", "description": "Optional additional information", @@ -4277,9 +4341,9 @@ "verb": "POST", "description": "Create canned comment", "methodName": "createComment", - "jsondocId": "5a3ec7c9-da1c-4627-a0ca-10e1257e2f5b", + "jsondocId": "2ec6be21-fb17-4d2d-8996-d3a954ae0e82", "bodyobject": { - "jsondocId": "f286d0b9-b033-429e-ae88-419332140648", + "jsondocId": "c56087b9-1f06-41bc-bdf5-f0cd562c8df4", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -4289,7 +4353,7 @@ "apierrors": [], "path": "/cannedComment/createComment", "response": { - "jsondocId": "433e111e-b306-416f-bb4e-1133456ffbd5", + "jsondocId": "30a904c4-fae1-4620-b9ca-147587936820", "mapValueObject": "", "mapKeyObject": "", "object": "canned comment" @@ -4302,7 +4366,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "53092d1e-8f29-4c06-b154-1b037cc57c9c", + "jsondocId": "b20c2ad7-e75e-4ad4-b2a3-21a21d2ff065", "name": "username", "format": "", "description": "", @@ -4311,7 +4375,7 @@ "allowedvalues": [] }, { - "jsondocId": "c3f7bb73-0f04-4727-8265-dee7355b403c", + "jsondocId": "828f0262-a499-4186-9e16-b69329983361", "name": "password", "format": "", "description": "", @@ -4320,7 +4384,7 @@ "allowedvalues": [] }, { - "jsondocId": "7e5e0411-accb-4473-a109-060cff575f16", + "jsondocId": "20745df7-3dda-413c-92f5-627adb95c9f1", "name": "id", "format": "", "description": "Canned comment ID to update (or specify the old_comment)", @@ -4329,7 +4393,7 @@ "allowedvalues": [] }, { - "jsondocId": "1c558526-ad7c-4029-8e39-87065d0c4b8b", + "jsondocId": "1ee36ee4-9388-4710-a4a6-92342239e479", "name": "old_comment", "format": "", "description": "Canned comment to update", @@ -4338,7 +4402,7 @@ "allowedvalues": [] }, { - "jsondocId": "6f7346b9-23ca-473b-b2fe-7fd764dfa923", + "jsondocId": "31c798fc-32fb-4e82-9180-0b0f8bb027d6", "name": "new_comment", "format": "", "description": "Canned comment to change to (the only editable option)", @@ -4347,7 +4411,7 @@ "allowedvalues": [] }, { - "jsondocId": "e8b8c7f2-def8-4e8b-8dce-73dd313220bf", + "jsondocId": "8c7e2441-d3e5-4480-b2eb-706670827d44", "name": "metadata", "format": "", "description": "Optional additional information", @@ -4359,9 +4423,9 @@ "verb": "POST", "description": "Update canned comment", "methodName": "updateComment", - "jsondocId": "4eca4ca5-841a-42ff-bc94-85185cb2cdf5", + "jsondocId": "80c867ea-1d64-4e9e-9b10-1381904f2e43", "bodyobject": { - "jsondocId": "6915a086-0bb7-4ac8-94d0-c025909672d8", + "jsondocId": "39c17587-85fc-49fe-9f08-dc02fe841470", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -4371,7 +4435,7 @@ "apierrors": [], "path": "/cannedComment/updateComment", "response": { - "jsondocId": "3f2986a8-335d-4508-9dc9-8419fa412be7", + "jsondocId": "50fd2c78-66cb-437e-b8cf-5d054a2ea86c", "mapValueObject": "", "mapKeyObject": "", "object": "canned comment" @@ -4384,7 +4448,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "3f3bf4ef-d35a-4726-b4dd-9f94de38c9d7", + "jsondocId": "eab103b1-187f-43f6-b090-01031cd0ef98", "name": "username", "format": "", "description": "", @@ -4393,7 +4457,7 @@ "allowedvalues": [] }, { - "jsondocId": "f177c5eb-3aee-4f20-b53e-c94f7b2ca4cd", + "jsondocId": "2ada3b75-1e32-4bcd-bf62-77fe0f0da6ee", "name": "password", "format": "", "description": "", @@ -4402,7 +4466,7 @@ "allowedvalues": [] }, { - "jsondocId": "8b6a6fa1-f5df-4171-8b24-f157c61ebccc", + "jsondocId": "ff8a1ebb-b726-40d2-aac0-253823829b4a", "name": "id", "format": "", "description": "Canned comment ID to remove (or specify the name)", @@ -4411,7 +4475,7 @@ "allowedvalues": [] }, { - "jsondocId": "5f347a13-3ed5-4196-bea4-05b1252e5838", + "jsondocId": "74c2acf8-b6de-445a-9559-8ea620657b9b", "name": "comment", "format": "", "description": "Canned comment to delete", @@ -4423,9 +4487,9 @@ "verb": "POST", "description": "Remove a canned comment", "methodName": "deleteComment", - "jsondocId": "db992007-d491-449e-87b4-ba18fd37994b", + "jsondocId": "24b78616-fd88-434b-b5ef-4621e9ae5f79", "bodyobject": { - "jsondocId": "7b797346-0b67-4592-b771-32fe726df63e", + "jsondocId": "4c704803-6dc6-4bd4-b6f5-857870863710", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -4435,7 +4499,7 @@ "apierrors": [], "path": "/cannedComment/deleteComment", "response": { - "jsondocId": "a83d1a6f-68d7-4fc9-95d1-9cd60f87e9cd", + "jsondocId": "3158a3de-e1ad-4484-a31e-9c57587dda7b", "mapValueObject": "", "mapKeyObject": "", "object": "canned comment" @@ -4448,7 +4512,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "cf619555-e503-414a-9fab-f76275dec030", + "jsondocId": "b1db8181-e143-4a77-988a-45c58942116d", "name": "username", "format": "", "description": "", @@ -4457,7 +4521,7 @@ "allowedvalues": [] }, { - "jsondocId": "2521ad71-43a6-46fa-9404-6bbea756ee57", + "jsondocId": "dba981c9-b03e-400b-9bd4-68b6be951440", "name": "password", "format": "", "description": "", @@ -4466,7 +4530,7 @@ "allowedvalues": [] }, { - "jsondocId": "355239e2-2b44-419f-9bdd-42746b683d79", + "jsondocId": "2ca696b9-de71-4b20-bc68-af8ae6c6b37d", "name": "id", "format": "", "description": "Comment ID to show (or specify a comment)", @@ -4475,7 +4539,7 @@ "allowedvalues": [] }, { - "jsondocId": "9673acb8-efa4-4566-85ca-7397e0bf934d", + "jsondocId": "cc4dcf1a-3e2f-43e0-b165-62293ce067a3", "name": "comment", "format": "", "description": "Comment to show", @@ -4487,9 +4551,9 @@ "verb": "POST", "description": "Returns a JSON array of all canned comments, or optionally, gets information about a specific canned comment", "methodName": "showComment", - "jsondocId": "b2bb5ff6-9dcc-4850-902e-4ef8dac2d892", + "jsondocId": "f1d24822-075e-4bf1-816e-1a53011bed90", "bodyobject": { - "jsondocId": "ebb5c018-94c7-4e06-a558-f7072d9848bb", + "jsondocId": "1536c868-ffd7-4480-884a-3a4ae976a3ec", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -4499,7 +4563,7 @@ "apierrors": [], "path": "/cannedComment/showComment", "response": { - "jsondocId": "3f6d2507-34f2-493f-bf97-ed5abbfd60d6", + "jsondocId": "79a14b44-fb3e-4897-a04f-76258eb07f8a", "mapValueObject": "", "mapKeyObject": "", "object": "canned comment" @@ -4512,14 +4576,14 @@ "description": "Methods for managing canned comments" }, { - "jsondocId": "68d14168-0079-45af-8ba5-7648a5307e24", + "jsondocId": "e1ed15f0-dda3-46e8-8a70-435cd4b6ff46", "methods": [ { "headers": [], "pathparameters": [], "queryparameters": [ { - "jsondocId": "1836e733-3bc6-4fd9-9475-469e0a996801", + "jsondocId": "787ac495-476d-402d-b7e6-85f747ae103d", "name": "username", "format": "", "description": "", @@ -4528,7 +4592,7 @@ "allowedvalues": [] }, { - "jsondocId": "7b734527-7537-474f-befb-0474e1956411", + "jsondocId": "4c62b5c6-4243-43bd-9472-e8336f2f0172", "name": "password", "format": "", "description": "", @@ -4537,7 +4601,7 @@ "allowedvalues": [] }, { - "jsondocId": "f7d352e1-4688-45e6-93ac-e628c4faf995", + "jsondocId": "84972523-537c-43c7-bfdc-24fa85d20404", "name": "id", "format": "", "description": "Canned key ID to update (or specify the old_key)", @@ -4546,7 +4610,7 @@ "allowedvalues": [] }, { - "jsondocId": "ce3bd758-ccb3-4a22-822b-6fdbc199e7d6", + "jsondocId": "198b5eb0-236f-48b1-a27c-376fa85eed79", "name": "old_key", "format": "", "description": "Canned key to update", @@ -4555,7 +4619,7 @@ "allowedvalues": [] }, { - "jsondocId": "af2dab41-f054-40cc-a646-9e0f2b705640", + "jsondocId": "701207f8-1fcf-430c-9f85-0563d3d07f02", "name": "new_key", "format": "", "description": "Canned key to change to (the only editable option)", @@ -4564,7 +4628,7 @@ "allowedvalues": [] }, { - "jsondocId": "e0ddc9d9-ba89-46b3-9efd-e7d321057b77", + "jsondocId": "ecd6816f-6eea-40b7-8fdf-036e75727829", "name": "metadata", "format": "", "description": "Optional additional information", @@ -4576,9 +4640,9 @@ "verb": "POST", "description": "Update canned key", "methodName": "updateKey", - "jsondocId": "7ce16901-ca9f-4116-b790-03eed0695f0e", + "jsondocId": "be448d99-0118-4119-8252-96edde5f28f5", "bodyobject": { - "jsondocId": "bbffe845-3505-475b-bf7e-68841e69a47a", + "jsondocId": "02bf6a3d-3523-4114-b9ba-f981f1b864b0", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -4588,7 +4652,7 @@ "apierrors": [], "path": "/cannedKey/updateKey", "response": { - "jsondocId": "eb515641-455e-4209-9b27-eb79421dfd78", + "jsondocId": "04b68b91-dc0f-4a36-996b-2edd70c863b7", "mapValueObject": "", "mapKeyObject": "", "object": "canned key" @@ -4601,7 +4665,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "8af4a0a5-733c-4e23-bc02-0c3f3985c2c2", + "jsondocId": "9df218f8-10eb-41a6-af62-b46e1e4e2117", "name": "username", "format": "", "description": "", @@ -4610,7 +4674,7 @@ "allowedvalues": [] }, { - "jsondocId": "7c005364-b49c-4173-be65-a5d2069446c1", + "jsondocId": "14f75ae5-4f61-4a43-acb0-e3a0dbebc699", "name": "password", "format": "", "description": "", @@ -4619,7 +4683,7 @@ "allowedvalues": [] }, { - "jsondocId": "8ccf4bb9-3df9-4cd8-b4ce-0ce6714ee755", + "jsondocId": "e55230d0-db06-4050-9cf4-5df09054f9fb", "name": "key", "format": "", "description": "Canned key to add", @@ -4628,7 +4692,7 @@ "allowedvalues": [] }, { - "jsondocId": "d50c3d07-d8c5-4af7-aa05-5822148164bc", + "jsondocId": "cbd19489-794d-4c49-9fa2-ac58ed0f80ca", "name": "metadata", "format": "", "description": "Optional additional information", @@ -4640,9 +4704,9 @@ "verb": "POST", "description": "Create canned key", "methodName": "createKey", - "jsondocId": "5d8ba961-2423-4b44-b710-4e6fcb394211", + "jsondocId": "9e9c6e3e-cc3a-4afb-b83d-0760f3b2fb3b", "bodyobject": { - "jsondocId": "bf827053-b1bb-4f1a-aa0a-f29bfe3da2bb", + "jsondocId": "78348546-5127-478f-bce9-8a0836f678f3", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -4652,7 +4716,7 @@ "apierrors": [], "path": "/cannedKey/createKey", "response": { - "jsondocId": "a09d92bc-e513-4096-aeeb-0789cabebe77", + "jsondocId": "f0a90c7b-57d3-4ce4-ba00-f4d74e49b097", "mapValueObject": "", "mapKeyObject": "", "object": "canned key" @@ -4665,7 +4729,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "bb326663-d511-43fb-8b50-0281b0ba6bd2", + "jsondocId": "93f420e1-2616-4439-a0b9-81feed924ffc", "name": "username", "format": "", "description": "", @@ -4674,7 +4738,7 @@ "allowedvalues": [] }, { - "jsondocId": "187dcbb1-c5c1-4716-a2af-033a8be1398b", + "jsondocId": "52222434-0241-4c38-9e19-8b0f64472d59", "name": "password", "format": "", "description": "", @@ -4683,7 +4747,7 @@ "allowedvalues": [] }, { - "jsondocId": "4783d1af-8cee-4fd4-b5d9-cf7008465bb7", + "jsondocId": "802b9747-c497-48dd-8fac-94b7688cb4d4", "name": "id", "format": "", "description": "Canned key ID to remove (or specify the name)", @@ -4692,7 +4756,7 @@ "allowedvalues": [] }, { - "jsondocId": "84f37225-bb86-4e16-a8d8-374e008af50d", + "jsondocId": "7a5cefcb-be3d-4b23-a142-85e57b5cd946", "name": "key", "format": "", "description": "Canned key to delete", @@ -4704,9 +4768,9 @@ "verb": "POST", "description": "Remove a canned key", "methodName": "deleteKey", - "jsondocId": "1b46dc8c-f3e6-41dc-8c76-9b2f61c36b48", + "jsondocId": "e9cf7f77-fb0c-45c4-b999-3f336c4febeb", "bodyobject": { - "jsondocId": "8871b661-9e60-4214-9c31-014a5d100119", + "jsondocId": "a21d274d-ecc3-46e3-9c59-77d27cb488c3", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -4716,7 +4780,7 @@ "apierrors": [], "path": "/cannedKey/deleteKey", "response": { - "jsondocId": "565a5789-4b90-44c1-b8ca-ff8426889755", + "jsondocId": "45021cf1-afac-4ea6-b597-1129ca791be3", "mapValueObject": "", "mapKeyObject": "", "object": "canned key" @@ -4729,7 +4793,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "ef25935b-44c5-4a5e-a116-ab7b8c9a30ff", + "jsondocId": "ca20a99b-e24f-4529-94d2-d9fa311cce39", "name": "username", "format": "", "description": "", @@ -4738,7 +4802,7 @@ "allowedvalues": [] }, { - "jsondocId": "69f7e297-e38f-418a-9d42-029ba5e566f1", + "jsondocId": "569af098-72f1-4ba1-b264-1e3f34a04a09", "name": "password", "format": "", "description": "", @@ -4747,7 +4811,7 @@ "allowedvalues": [] }, { - "jsondocId": "9d27a357-09a0-45fd-9213-dabd29f52e09", + "jsondocId": "8d3d16e3-faa7-4d1d-b16f-8a09079dd695", "name": "id", "format": "", "description": "Key ID to show (or specify a key)", @@ -4756,7 +4820,7 @@ "allowedvalues": [] }, { - "jsondocId": "b9398b77-413a-4ff2-b083-31cb0f1d8e2a", + "jsondocId": "07d6209c-03f7-4c80-b296-0fda40f40f4a", "name": "key", "format": "", "description": "Key to show", @@ -4768,9 +4832,9 @@ "verb": "POST", "description": "Returns a JSON array of all canned keys, or optionally, gets information about a specific canned key", "methodName": "showKey", - "jsondocId": "980a958f-d261-410f-a4f0-e1976e32835f", + "jsondocId": "ad5d0ab4-7616-4f20-a86e-ee2b1b9f1229", "bodyobject": { - "jsondocId": "9e56b8c0-c98b-4523-a858-7ebe8b764142", + "jsondocId": "a7378e01-8a9c-499c-9ae3-e7a620e19aa5", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -4780,7 +4844,7 @@ "apierrors": [], "path": "/cannedKey/showKey", "response": { - "jsondocId": "001e78f3-29ad-46d1-862b-0cd44d42a698", + "jsondocId": "61c63246-358a-43e5-bfd8-5106cdbfb9f5", "mapValueObject": "", "mapKeyObject": "", "object": "canned key" @@ -4793,14 +4857,14 @@ "description": "Methods for managing canned keys" }, { - "jsondocId": "9c5b75b1-99ce-4a11-967a-284aa8b31472", + "jsondocId": "dd4d2cd6-1c87-43bf-897b-4198d62d0714", "methods": [ { "headers": [], "pathparameters": [], "queryparameters": [ { - "jsondocId": "7df4fd83-3a0e-4ac4-ba02-4353c76bac74", + "jsondocId": "3005c853-5fee-468c-8603-f75081cad7a1", "name": "username", "format": "", "description": "", @@ -4809,7 +4873,7 @@ "allowedvalues": [] }, { - "jsondocId": "bb5a29f8-5cc8-45a7-a004-466f15a43dbd", + "jsondocId": "0912f82b-adcb-4b1e-8410-8ca1a759191d", "name": "password", "format": "", "description": "", @@ -4818,16 +4882,34 @@ "allowedvalues": [] }, { - "jsondocId": "793ad678-7878-4422-8927-f0bb195d3b6f", - "name": "value", + "jsondocId": "ad5eeca6-48a8-45ee-9ece-48e4aad9ad00", + "name": "id", "format": "", - "description": "Canned value to add", + "description": "Canned value ID to update (or specify the old_value)", + "type": "long", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "f26f2713-a1f0-49c8-886a-7772b933d710", + "name": "old_value", + "format": "", + "description": "Canned value to update", + "type": "string", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "631db315-fd12-4231-9854-e18532ce97ca", + "name": "new_value", + "format": "", + "description": "Canned value to change to (the only editable option)", "type": "string", "required": "true", "allowedvalues": [] }, { - "jsondocId": "6f17d19b-7d08-4be2-b829-e4213ecbe147", + "jsondocId": "895996dc-5925-4a06-8303-b36c02ca3eee", "name": "metadata", "format": "", "description": "Optional additional information", @@ -4837,11 +4919,11 @@ } ], "verb": "POST", - "description": "Create canned value", - "methodName": "createValue", - "jsondocId": "74f08fcc-2df9-4eb7-823b-4655d0a31c62", + "description": "Update canned value", + "methodName": "updateValue", + "jsondocId": "fca569ee-2733-4f20-a054-ee04745bdbe6", "bodyobject": { - "jsondocId": "d7869c13-1b67-447e-8a79-226682e6c4f1", + "jsondocId": "ca811858-2db3-4701-9a6c-b134ef936f1b", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -4849,9 +4931,9 @@ "object": "canned value" }, "apierrors": [], - "path": "/cannedValue/createValue", + "path": "/cannedValue/updateValue", "response": { - "jsondocId": "2862af9b-4762-4e71-af58-388c6946525b", + "jsondocId": "5cc56ca6-d569-453d-a77d-e50792d3667f", "mapValueObject": "", "mapKeyObject": "", "object": "canned value" @@ -4864,7 +4946,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "5a7d32dc-5da4-474d-9eac-280fc4a70c35", + "jsondocId": "97133d38-d717-4f7b-954a-626efee08cb6", "name": "username", "format": "", "description": "", @@ -4873,7 +4955,7 @@ "allowedvalues": [] }, { - "jsondocId": "264b8236-b066-46f1-b7e6-56896c2e456f", + "jsondocId": "fd569cb6-7bb8-4267-b015-493ee4a974fc", "name": "password", "format": "", "description": "", @@ -4882,34 +4964,16 @@ "allowedvalues": [] }, { - "jsondocId": "d409f480-d6ca-4082-a4fd-db76868605c7", - "name": "id", - "format": "", - "description": "Canned value ID to update (or specify the old_value)", - "type": "long", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "fac25668-6539-4351-9a6e-b6470e445a5b", - "name": "old_value", - "format": "", - "description": "Canned value to update", - "type": "string", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "f8d56649-bba5-4966-90ff-730ba69d8137", - "name": "new_value", + "jsondocId": "bb284a4e-c6ac-4299-bb9e-cf0dba242636", + "name": "value", "format": "", - "description": "Canned value to change to (the only editable option)", + "description": "Canned value to add", "type": "string", "required": "true", "allowedvalues": [] }, { - "jsondocId": "65bff33a-d2c9-4594-afd4-5dc36d77740b", + "jsondocId": "f068627d-dba5-46d1-b5bf-5a859dfda955", "name": "metadata", "format": "", "description": "Optional additional information", @@ -4919,11 +4983,11 @@ } ], "verb": "POST", - "description": "Update canned value", - "methodName": "updateValue", - "jsondocId": "64cc3608-dfc1-4d02-af52-45cd543ba9b7", + "description": "Create canned value", + "methodName": "createValue", + "jsondocId": "18f6f238-58c3-4156-abfe-59ddaa1356d1", "bodyobject": { - "jsondocId": "8d094ad6-7c50-451e-aa78-9b2d7db0aac3", + "jsondocId": "b77acf45-4d25-477f-9443-fd68618e7ad8", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -4931,9 +4995,9 @@ "object": "canned value" }, "apierrors": [], - "path": "/cannedValue/updateValue", + "path": "/cannedValue/createValue", "response": { - "jsondocId": "a3a83bb6-ab66-4c5e-832a-07fe8a65626e", + "jsondocId": "10b0183e-2275-49f7-a94c-0c7ceb8022e2", "mapValueObject": "", "mapKeyObject": "", "object": "canned value" @@ -4946,7 +5010,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "386b911f-c239-45e5-98f2-84cee3003fe1", + "jsondocId": "3c46cef2-c671-4e5b-a973-72b3f3e358a6", "name": "username", "format": "", "description": "", @@ -4955,7 +5019,7 @@ "allowedvalues": [] }, { - "jsondocId": "9baf73c2-4813-4396-8bd6-0193bec1b39a", + "jsondocId": "d40acfa0-f834-4f21-81e4-b4be81d026fe", "name": "password", "format": "", "description": "", @@ -4964,7 +5028,7 @@ "allowedvalues": [] }, { - "jsondocId": "5496bfa1-d788-4261-a42c-799032cf19ee", + "jsondocId": "4d4dc427-3ca1-48d3-be7f-484179ae6541", "name": "id", "format": "", "description": "Canned value ID to remove (or specify the name)", @@ -4973,7 +5037,7 @@ "allowedvalues": [] }, { - "jsondocId": "b6b804a2-5b7c-4c79-a267-db37dd54715e", + "jsondocId": "b553a6cb-726c-4c80-ac50-03bdf86a3ee2", "name": "value", "format": "", "description": "Canned value to delete", @@ -4985,9 +5049,9 @@ "verb": "POST", "description": "Remove a canned value", "methodName": "deleteValue", - "jsondocId": "e4b9b1ab-b840-4ab0-9ca6-d5d0b37c30da", + "jsondocId": "cec688d9-3df6-4f89-9377-0ce24b7ca684", "bodyobject": { - "jsondocId": "b2f2bae9-47c3-4a32-9e8d-46ffe0998a8b", + "jsondocId": "78474b8c-441d-4b0b-984e-d36da03cf8dc", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -4997,7 +5061,7 @@ "apierrors": [], "path": "/cannedValue/deleteValue", "response": { - "jsondocId": "c91e61aa-6184-46fb-9385-53e761d3c956", + "jsondocId": "5f494ece-56d5-485a-ab7b-444f20d5fa0b", "mapValueObject": "", "mapKeyObject": "", "object": "canned value" @@ -5010,7 +5074,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "61475eba-2610-4972-bfd8-87bcaeed4c3e", + "jsondocId": "9afd5ef1-0eed-4cc8-96ab-0abe7e698a6b", "name": "username", "format": "", "description": "", @@ -5019,7 +5083,7 @@ "allowedvalues": [] }, { - "jsondocId": "b0556ed8-fa63-4d61-8f7b-166206988303", + "jsondocId": "e7f1b968-38c3-408e-8b91-cc5671dc7107", "name": "password", "format": "", "description": "", @@ -5028,7 +5092,7 @@ "allowedvalues": [] }, { - "jsondocId": "a4175ba8-65ab-4f76-b4e2-9704e4e2d2ac", + "jsondocId": "cf2c7720-4678-4da2-ade0-6934fc6e4123", "name": "id", "format": "", "description": "Value ID to show (or specify a value)", @@ -5037,7 +5101,7 @@ "allowedvalues": [] }, { - "jsondocId": "4a49b95e-6280-49cc-8cf8-847ffbc2cc3f", + "jsondocId": "cb32a368-e1ba-4695-8469-ba7a66b55756", "name": "value", "format": "", "description": "Value to show", @@ -5049,9 +5113,9 @@ "verb": "POST", "description": "Returns a JSON array of all canned values, or optionally, gets information about a specific canned value", "methodName": "showValue", - "jsondocId": "fc70e14b-b12a-4439-a6a2-2e74b305c519", + "jsondocId": "45d74ebc-f69d-4c09-94f8-58a301241dba", "bodyobject": { - "jsondocId": "feb2548d-ea29-438f-aa0f-2850a8524a58", + "jsondocId": "e046ca38-61d8-48b5-b865-7603f14e5f0d", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -5061,7 +5125,7 @@ "apierrors": [], "path": "/cannedValue/showValue", "response": { - "jsondocId": "e2115e8a-0991-48a3-bdd7-192a550ba693", + "jsondocId": "a04ca348-5109-42f1-b934-ac10278a28ab", "mapValueObject": "", "mapKeyObject": "", "object": "canned value" @@ -5074,14 +5138,14 @@ "description": "Methods for managing canned values" }, { - "jsondocId": "9e57e5eb-6ad3-4653-b0f4-1c60c86f8234", + "jsondocId": "394d7548-36a5-4f55-b1df-1d779f0992e2", "methods": [ { "headers": [], "pathparameters": [], "queryparameters": [ { - "jsondocId": "1cf9e7e5-12e4-49ae-95e6-7c1f55f1e3cb", + "jsondocId": "9ad2e304-0e07-4d67-9b89-5f7de0bd5d6b", "name": "username", "format": "", "description": "", @@ -5090,7 +5154,7 @@ "allowedvalues": [] }, { - "jsondocId": "6ecb9345-a160-4770-b75f-08d050468f51", + "jsondocId": "feb7e1c8-3062-401c-8b8b-b0a0c4ca5b51", "name": "password", "format": "", "description": "", @@ -5099,7 +5163,7 @@ "allowedvalues": [] }, { - "jsondocId": "8adb7672-753f-49d7-b2ce-03f8772185da", + "jsondocId": "f6484551-beaa-498d-ab97-74045ddd7417", "name": "uniqueName", "format": "", "description": "Feature name to query on", @@ -5111,9 +5175,9 @@ "verb": "POST", "description": "Load Go Annotations for feature", "methodName": "index", - "jsondocId": "9b3b8a08-4f5c-4ea3-be2a-012ba193037a", + "jsondocId": "4acad00b-2f00-499f-8ef4-b3f3bdaa3336", "bodyobject": { - "jsondocId": "eba5b5da-be5b-4db3-99ae-74f1c83025af", + "jsondocId": "cec48b6d-d8c4-4bbb-b564-b37231a37f75", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -5123,7 +5187,7 @@ "apierrors": [], "path": "/goAnnotation", "response": { - "jsondocId": "8c77707c-54b1-4bc8-98a4-a33bfa3def67", + "jsondocId": "b34b1452-eca4-4bb7-94a0-b4f70067561f", "mapValueObject": "", "mapKeyObject": "", "object": "go annotation" @@ -5136,7 +5200,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "4708a03a-4cc6-43df-bb42-02dc88af26fd", + "jsondocId": "960ce222-0133-4dd1-a8e0-d4f8702de94a", "name": "username", "format": "", "description": "", @@ -5145,7 +5209,7 @@ "allowedvalues": [] }, { - "jsondocId": "3ca71a42-ffd5-400f-a378-24fcf7a1763b", + "jsondocId": "420dc071-9ac6-43d0-b91d-ad2e50d5d12e", "name": "password", "format": "", "description": "", @@ -5154,7 +5218,7 @@ "allowedvalues": [] }, { - "jsondocId": "d467eb40-808f-4a0a-8be7-09306d0ed1bd", + "jsondocId": "1490fa22-96b7-4b6f-b02d-f20dc98a832d", "name": "id", "format": "", "description": "GO Annotation ID to update (required)", @@ -5163,7 +5227,7 @@ "allowedvalues": [] }, { - "jsondocId": "f810659d-8452-4bfa-aeb7-5f64269b5fc9", + "jsondocId": "3b3dcc4d-39f6-4b5f-b65a-f0aaec3a63f3", "name": "feature", "format": "", "description": "uniqueName of feature to query on", @@ -5172,7 +5236,7 @@ "allowedvalues": [] }, { - "jsondocId": "1718513e-45fc-49a2-9896-bef81838f0c8", + "jsondocId": "562c8ec5-1716-4d8f-a807-6de64239478e", "name": "goTerm", "format": "", "description": "GO CURIE", @@ -5181,7 +5245,7 @@ "allowedvalues": [] }, { - "jsondocId": "1dfcc7ef-6e40-4b40-b5dc-c487f9e8326f", + "jsondocId": "82891aba-9e38-488f-9e93-f15c277a2b4b", "name": "goTermLabel", "format": "", "description": "GO Term Label", @@ -5190,7 +5254,7 @@ "allowedvalues": [] }, { - "jsondocId": "1ab9a19b-23e4-4cd6-8e9a-63601a8a8201", + "jsondocId": "caec2ee9-61f0-4ec6-bbdd-c7eb66d20cd7", "name": "aspect", "format": "", "description": "(required) BP, MF, CC", @@ -5199,7 +5263,7 @@ "allowedvalues": [] }, { - "jsondocId": "4d334082-7fde-4968-828d-d5239cca6978", + "jsondocId": "cd573f13-6e4b-435d-a340-0e4ae0524608", "name": "geneRelationship", "format": "", "description": "Gene relationship (RO) CURIE", @@ -5208,7 +5272,7 @@ "allowedvalues": [] }, { - "jsondocId": "b04622b8-3c1d-401f-afcc-ee9e410ec1b5", + "jsondocId": "03df8a86-d7a6-47ef-8322-17a822250370", "name": "evidenceCode", "format": "", "description": "Evidence (ECO) CURIE", @@ -5217,7 +5281,7 @@ "allowedvalues": [] }, { - "jsondocId": "eee16a4e-2ae9-45ff-8b01-ba643dc60597", + "jsondocId": "338a7d08-9f76-418b-b8ce-5caa5df3779c", "name": "evidenceCodeLabel", "format": "", "description": "Evidence (ECO) Label", @@ -5226,7 +5290,7 @@ "allowedvalues": [] }, { - "jsondocId": "69096017-29d3-4e84-91fb-48a451e2c73f", + "jsondocId": "ce71a18f-ae81-49a7-b3d4-5dd2a9c6b447", "name": "negate", "format": "", "description": "Negate evidence (default false)", @@ -5235,7 +5299,7 @@ "allowedvalues": [] }, { - "jsondocId": "569f900b-d3b5-4a91-9774-98e42dc775b8", + "jsondocId": "a3eabdfe-7bf9-423d-aded-17e00ea29f9d", "name": "withOrFrom", "format": "", "description": "JSON Array of with or from CURIE strings, e.g., {[\"UniProtKB:12312]]\"]}", @@ -5244,7 +5308,7 @@ "allowedvalues": [] }, { - "jsondocId": "97401ee8-11d6-4d41-abc6-49b2dfd299aa", + "jsondocId": "6c1d3379-2857-4615-9c03-aad3fdc0a20b", "name": "references", "format": "", "description": "JSON Array of reference CURIE strings, e.g., {[\"PMID:12312]]\"]}", @@ -5256,9 +5320,9 @@ "verb": "POST", "description": "Update existing Go Annotations for feature", "methodName": "update", - "jsondocId": "e90d861c-4991-4182-b6c4-07c4827d621a", + "jsondocId": "4773bc36-8fc1-4ffe-9da5-829a5b769616", "bodyobject": { - "jsondocId": "8ca6b157-ba88-4836-9aab-d1974de5bd82", + "jsondocId": "887fd5c0-4740-4070-9ea9-8a50c2299590", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -5268,7 +5332,7 @@ "apierrors": [], "path": "/goAnnotation/update", "response": { - "jsondocId": "b2b2b58c-d28b-44fa-adfe-95ca33f1dc48", + "jsondocId": "45e09309-9ba4-41a2-8c0b-d2e2455e559a", "mapValueObject": "", "mapKeyObject": "", "object": "go annotation" @@ -5281,7 +5345,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "15842032-2145-41bc-8fbd-374a3bd7fce6", + "jsondocId": "862662fe-47bd-4d15-8c69-231afdea0219", "name": "username", "format": "", "description": "", @@ -5290,7 +5354,7 @@ "allowedvalues": [] }, { - "jsondocId": "d37218c6-ee5d-40c3-8d4b-f957b3e52f3a", + "jsondocId": "f5bd5fe9-9899-47c9-a2c0-a9a339d5b848", "name": "password", "format": "", "description": "", @@ -5299,7 +5363,7 @@ "allowedvalues": [] }, { - "jsondocId": "55e276ab-f086-4d56-b765-6a3724cda7cf", + "jsondocId": "ee6e1648-a739-4649-88eb-550b1ffed7a3", "name": "id", "format": "", "description": "GO Annotation ID to delete (required)", @@ -5308,7 +5372,7 @@ "allowedvalues": [] }, { - "jsondocId": "2576d093-6061-47c7-a024-70ca5ecf26a6", + "jsondocId": "c7af955e-afc8-410e-aff9-1713f80d6ee4", "name": "uniqueName", "format": "", "description": "Gene uniqueName to remove feature from", @@ -5320,9 +5384,9 @@ "verb": "POST", "description": "Delete existing Go Annotations for feature", "methodName": "delete", - "jsondocId": "7efcec33-5b84-486d-b0be-a323f4817c39", + "jsondocId": "0640d56d-58ee-46a6-8722-62117f0ce611", "bodyobject": { - "jsondocId": "d023db6f-5c82-4996-877d-e84690d01262", + "jsondocId": "bd05e25c-e34d-4fd7-a678-3db5cecd978d", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -5332,7 +5396,7 @@ "apierrors": [], "path": "/goAnnotation/delete", "response": { - "jsondocId": "36df2555-e365-491b-91b5-49176643d377", + "jsondocId": "82b0ce38-8932-49d9-9d44-8df48e13f5aa", "mapValueObject": "", "mapKeyObject": "", "object": "go annotation" @@ -5345,7 +5409,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "78582f92-fd02-43cd-ac31-0078d26424dc", + "jsondocId": "71a51ef6-30dc-4872-85f1-d167c3a1345e", "name": "username", "format": "", "description": "", @@ -5354,7 +5418,7 @@ "allowedvalues": [] }, { - "jsondocId": "f14e346e-9209-4b9a-9b58-886db3e08341", + "jsondocId": "7938fdde-75d7-4d28-8675-ced907a247e8", "name": "password", "format": "", "description": "", @@ -5363,7 +5427,7 @@ "allowedvalues": [] }, { - "jsondocId": "3db4aad6-a1dc-4f58-9d7c-a051faddcb6c", + "jsondocId": "d7a649b7-a41a-40c0-8f77-6fb9d3e85144", "name": "feature", "format": "", "description": "uniqueName of feature feature to query on", @@ -5372,7 +5436,7 @@ "allowedvalues": [] }, { - "jsondocId": "51842a84-2a4f-4b6e-9b58-36d8263243a0", + "jsondocId": "6154386a-f5d4-48d8-a21a-43ff17daac22", "name": "goTerm", "format": "", "description": "GO CURIE", @@ -5381,7 +5445,7 @@ "allowedvalues": [] }, { - "jsondocId": "9787613b-7d89-4656-b7e1-b5fbda99aa80", + "jsondocId": "64985b4b-87f9-49f7-a32e-a6d78c401931", "name": "goTermLabel", "format": "", "description": "GO Term Label", @@ -5390,7 +5454,7 @@ "allowedvalues": [] }, { - "jsondocId": "815232ea-5466-46b5-9a7d-b6baba1ecc83", + "jsondocId": "5362b0af-04b3-4aed-9795-87a7baa04425", "name": "aspect", "format": "", "description": "(required) BP, MF, CC", @@ -5399,7 +5463,7 @@ "allowedvalues": [] }, { - "jsondocId": "1daa918c-ad8f-4027-b1d8-a977f549e1e3", + "jsondocId": "49bd2967-6a8b-4987-82dd-dd36f885983a", "name": "geneRelationship", "format": "", "description": "Gene relationship (RO) CURIE", @@ -5408,7 +5472,7 @@ "allowedvalues": [] }, { - "jsondocId": "a7e9a038-9276-4012-b8e2-dd255cd6589a", + "jsondocId": "352e42f7-47c2-473d-aab6-04e855ce5ca3", "name": "evidenceCode", "format": "", "description": "Evidence (ECO) CURIE", @@ -5417,7 +5481,7 @@ "allowedvalues": [] }, { - "jsondocId": "bd7b4d1c-c185-4450-b2ad-0c9290506147", + "jsondocId": "9ad967b2-7963-4e57-909c-9d6adc326b41", "name": "evidenceCodeLAbel", "format": "", "description": "Evidence (ECO) Label", @@ -5426,7 +5490,7 @@ "allowedvalues": [] }, { - "jsondocId": "fd10cf1a-18d7-4bcf-b862-c1e9005ce246", + "jsondocId": "f5a58163-8220-4811-a22b-1e366b887bde", "name": "negate", "format": "", "description": "Negate evidence (default false)", @@ -5435,7 +5499,7 @@ "allowedvalues": [] }, { - "jsondocId": "9e3e9d0c-4d62-43f7-b598-c4ef4e0a3117", + "jsondocId": "18ad379e-bde9-483f-8e5c-290f8582110d", "name": "withOrFrom", "format": "", "description": "JSON Array of with or from CURIE strings, e.g., {[\"UniProtKB:12312]]\"]}", @@ -5444,7 +5508,7 @@ "allowedvalues": [] }, { - "jsondocId": "caa6b4ef-6fa9-4d40-bed6-2441ffcb3246", + "jsondocId": "e27a83a4-513e-4fde-8fa4-26a6a70a43a3", "name": "references", "format": "", "description": "JSON Array of reference CURIE strings, e.g., {[\"PMID:12312]]\"]}", @@ -5456,9 +5520,9 @@ "verb": "POST", "description": "Save New Go Annotations for feature", "methodName": "save", - "jsondocId": "f76752f8-d9c5-4288-ba5c-8a81fb187923", + "jsondocId": "b68ff9a5-f2d9-4432-b5e8-60fee8b9cead", "bodyobject": { - "jsondocId": "cfafe535-0b3a-4d22-846f-b79ed36aa37a", + "jsondocId": "7bb070f2-b4d5-495a-b9a7-139a57a46307", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -5468,7 +5532,7 @@ "apierrors": [], "path": "/goAnnotation/save", "response": { - "jsondocId": "aaadeff1-7b0e-4b1f-a22f-72ef30192d11", + "jsondocId": "fe505e3b-60e8-4ee6-a018-1ddb337b6fe5", "mapValueObject": "", "mapKeyObject": "", "object": "go annotation" @@ -5481,14 +5545,14 @@ "description": "Methods for managing go annotations" }, { - "jsondocId": "0174f02a-ec1d-4d94-82e5-6a44d5cf3be2", + "jsondocId": "50843faa-35bb-438f-9b5b-afe1efbb35ef", "methods": [ { "headers": [], "pathparameters": [], "queryparameters": [ { - "jsondocId": "777b6edf-626f-4d3f-a0f4-8f0dea0d7158", + "jsondocId": "949bb17d-c391-434d-ba72-e295e27997d4", "name": "username", "format": "", "description": "", @@ -5497,7 +5561,7 @@ "allowedvalues": [] }, { - "jsondocId": "ca86cc70-142b-42a4-bed1-c0fb14ef5857", + "jsondocId": "64190ce5-5523-49c3-a6a6-ba00c8a1f589", "name": "password", "format": "", "description": "", @@ -5506,7 +5570,7 @@ "allowedvalues": [] }, { - "jsondocId": "80427296-fea9-4fd8-a02a-90dc6e56b46d", + "jsondocId": "f74f2e9c-8926-4a03-a77d-2d43caf52405", "name": "uniqueName", "format": "", "description": "Gene name to query on", @@ -5518,9 +5582,9 @@ "verb": "POST", "description": "Load gene product for feature", "methodName": "index", - "jsondocId": "ebdbdfb4-2b05-4149-953e-52eef2badc73", + "jsondocId": "61aa081f-2b1b-4950-8af6-83872aca822d", "bodyobject": { - "jsondocId": "6b4ced77-5926-4370-86f4-a9da8f24ed26", + "jsondocId": "61c3da2b-9f75-43c1-ac37-cdbb91c4b6b7", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -5530,7 +5594,7 @@ "apierrors": [], "path": "/geneProduct", "response": { - "jsondocId": "c8d96df2-f28a-428d-89f8-55ad3e6306a6", + "jsondocId": "8de6a541-62a4-4821-807f-2d4ad2022960", "mapValueObject": "", "mapKeyObject": "", "object": "gene product" @@ -5543,7 +5607,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "53f50934-a950-41b2-84b2-414d43037b8b", + "jsondocId": "4884397b-acf8-441a-b8a0-2a954a3902e8", "name": "username", "format": "", "description": "", @@ -5552,7 +5616,7 @@ "allowedvalues": [] }, { - "jsondocId": "2d01dbf2-b296-491d-9a5a-a8748a16d163", + "jsondocId": "0ac4d509-b989-4145-ab35-47e13f75653a", "name": "password", "format": "", "description": "", @@ -5561,7 +5625,7 @@ "allowedvalues": [] }, { - "jsondocId": "09f2e115-3615-40fd-8ba6-ce284966fa52", + "jsondocId": "f355e0f1-6285-458a-a973-fa5fa2316809", "name": "id", "format": "", "description": "GO Annotation ID to update (required)", @@ -5570,7 +5634,7 @@ "allowedvalues": [] }, { - "jsondocId": "d39425b7-4536-488a-9f3e-a39596235cbc", + "jsondocId": "73c4611f-0d80-42c0-bbdb-bb3256567591", "name": "feature", "format": "", "description": "uniqueName of feature to query on", @@ -5579,7 +5643,7 @@ "allowedvalues": [] }, { - "jsondocId": "ef7415ae-14d9-40bd-985b-a8de3de0897d", + "jsondocId": "5802aa90-ded2-4c20-9bdd-525208e0e6b4", "name": "productName", "format": "", "description": "gene product name", @@ -5588,7 +5652,7 @@ "allowedvalues": [] }, { - "jsondocId": "fb2954be-38ef-4df5-9abb-410e50a0f412", + "jsondocId": "276e0994-34cd-4806-b6e2-47f1fb9eb0ea", "name": "alternate", "format": "", "description": "(default false) alternate", @@ -5597,7 +5661,7 @@ "allowedvalues": [] }, { - "jsondocId": "44a47337-7558-423f-b925-e09bddbc8d6e", + "jsondocId": "1052dd31-83db-4c85-aa19-7ff3510afe92", "name": "evidenceCode", "format": "", "description": "Evidence (ECO) CURIE", @@ -5606,7 +5670,7 @@ "allowedvalues": [] }, { - "jsondocId": "a47371f8-ba7e-47fc-88bd-4160cdef35ef", + "jsondocId": "2aa2c5ae-7a17-4c31-9420-139156e9edac", "name": "evidenceCodeLabel", "format": "", "description": "Evidence (ECO) Label", @@ -5615,7 +5679,7 @@ "allowedvalues": [] }, { - "jsondocId": "ad5743fb-8ad8-4a88-a7e9-f0758df9d308", + "jsondocId": "2dd37708-155d-4ef6-bc6c-bebc5676edf7", "name": "negate", "format": "", "description": "Negate evidence (default false)", @@ -5624,7 +5688,7 @@ "allowedvalues": [] }, { - "jsondocId": "0134c485-317c-438b-9faa-32b9139067b7", + "jsondocId": "e74bb7c5-c297-406b-8cf4-06804f33bedc", "name": "withOrFrom", "format": "", "description": "JSON Array of with or from CURIE strings, e.g., {[\"UniProtKB:12312\"]}", @@ -5633,7 +5697,7 @@ "allowedvalues": [] }, { - "jsondocId": "0913b32f-f33e-4094-a34f-11a2d95874d3", + "jsondocId": "ab8feb20-eee6-4f10-b13a-acdae9121a8c", "name": "references", "format": "", "description": "JSON Array of reference CURIE strings, e.g., {[\"PMID:12312\"]}", @@ -5642,7 +5706,7 @@ "allowedvalues": [] }, { - "jsondocId": "a55d68ad-88b7-4838-92af-69cf8a7abaad", + "jsondocId": "3b86b6a9-32c9-4f93-9631-24485fa4cb74", "name": "notes", "format": "", "description": "JSON Array of notes strings, e.g., {[\"This is a note\"]}", @@ -5654,9 +5718,9 @@ "verb": "POST", "description": "Update existing gene products for feature", "methodName": "update", - "jsondocId": "cd44c6e4-3b9b-469d-a03e-f35ff5b7b859", + "jsondocId": "c08c3b1c-7077-4fe2-9ef2-2964baafa379", "bodyobject": { - "jsondocId": "3021e36c-4b6f-4203-9713-1d42099b7e4a", + "jsondocId": "4eaff83b-776f-44e8-9284-85d0318ba174", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -5666,7 +5730,7 @@ "apierrors": [], "path": "/geneProduct/update", "response": { - "jsondocId": "0ddccc45-55fb-4779-99cf-58d50a0c1687", + "jsondocId": "2d5d46b8-c7e6-48e2-9d8e-99c242b6178d", "mapValueObject": "", "mapKeyObject": "", "object": "gene product" @@ -5679,7 +5743,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "08886161-86ad-4b5c-ad60-ded274f595fa", + "jsondocId": "b6aa9003-e36f-4a73-b117-02de43853e14", "name": "username", "format": "", "description": "", @@ -5688,7 +5752,7 @@ "allowedvalues": [] }, { - "jsondocId": "a1de8c94-b1bc-4129-bd6d-cdea60fc101d", + "jsondocId": "b825f555-d6cf-4f25-a7b0-701584eca411", "name": "password", "format": "", "description": "", @@ -5697,7 +5761,7 @@ "allowedvalues": [] }, { - "jsondocId": "a7cfedc9-e730-46d9-8d5a-a605a62244e8", + "jsondocId": "3112c7b6-8668-4edf-95d8-63955fea8fa9", "name": "id", "format": "", "description": "GO Annotation ID to delete (required)", @@ -5706,7 +5770,7 @@ "allowedvalues": [] }, { - "jsondocId": "69fce41e-c976-4342-9221-1959f902cfc7", + "jsondocId": "211769bd-a933-4531-aa86-b2705345ed1a", "name": "uniqueName", "format": "", "description": "Feature uniqueName to remove feature from", @@ -5718,9 +5782,9 @@ "verb": "POST", "description": "Delete existing gene product for feature", "methodName": "delete", - "jsondocId": "b8e7f695-7dae-41fc-98e7-7caf463306ca", + "jsondocId": "bbe5a4bc-6652-485a-bcea-c02b6ef61caa", "bodyobject": { - "jsondocId": "c70a32ce-7e7c-434e-b16b-364ab4fa5034", + "jsondocId": "619285aa-616b-41b5-9cca-3a8a5e60df16", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -5730,7 +5794,7 @@ "apierrors": [], "path": "/geneProduct/delete", "response": { - "jsondocId": "3380697e-9ed7-4338-82a0-1250838db88a", + "jsondocId": "69727a03-35f7-4ee9-9a4a-32df4fa8cc34", "mapValueObject": "", "mapKeyObject": "", "object": "gene product" @@ -5743,7 +5807,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "392b086e-faec-4adc-95f5-b38ca30c79f8", + "jsondocId": "0a217f5d-d577-4c64-a7ea-a610537c28ab", "name": "username", "format": "", "description": "", @@ -5752,7 +5816,7 @@ "allowedvalues": [] }, { - "jsondocId": "215a7f7d-add0-48c5-8f24-81d8a152a025", + "jsondocId": "39023862-f9a3-4572-b374-a93ce9aea8ff", "name": "password", "format": "", "description": "", @@ -5761,7 +5825,7 @@ "allowedvalues": [] }, { - "jsondocId": "2576140e-be49-49f0-9f23-b622f5f33781", + "jsondocId": "999f1ff7-9e36-48db-9798-cb74c8f1aea7", "name": "feature", "format": "", "description": "uniqueName of gene feature to query on", @@ -5770,7 +5834,7 @@ "allowedvalues": [] }, { - "jsondocId": "82006b86-ba3b-43f3-8e0c-4c7a33f06f47", + "jsondocId": "ced13dd7-7e1d-421c-b3f1-2da5d8f08724", "name": "productName", "format": "", "description": "Name of gene product", @@ -5779,7 +5843,7 @@ "allowedvalues": [] }, { - "jsondocId": "5d903cc8-e028-465e-a11e-896cd0025be3", + "jsondocId": "4868c590-ae51-4461-af56-615514c46493", "name": "alternate", "format": "", "description": "Alternate (default false)", @@ -5788,7 +5852,7 @@ "allowedvalues": [] }, { - "jsondocId": "782f9909-ba96-4c56-801e-19244ed1c0bb", + "jsondocId": "fa364dc6-a52d-4918-a091-998633ab5d00", "name": "evidenceCode", "format": "", "description": "Evidence (ECO) CURIE", @@ -5797,7 +5861,7 @@ "allowedvalues": [] }, { - "jsondocId": "7b2a3da5-3052-4651-bca6-4af5f2b478b7", + "jsondocId": "b73bfca8-909e-4922-ab50-6f08822f06c1", "name": "evidenceCodeLAbel", "format": "", "description": "Evidence (ECO) Label", @@ -5806,7 +5870,7 @@ "allowedvalues": [] }, { - "jsondocId": "feaa9c43-5e40-4b41-86c1-4d19a7f0cf00", + "jsondocId": "2f70855d-f6af-4d87-a0a3-42df3326052c", "name": "negate", "format": "", "description": "Negate evidence (default false)", @@ -5815,7 +5879,7 @@ "allowedvalues": [] }, { - "jsondocId": "e0a4be59-ea56-4be8-bba5-78e07766852e", + "jsondocId": "1d59022e-cb99-4055-92f3-3aa50cf0b2e1", "name": "withOrFrom", "format": "", "description": "JSON Array of with or from CURIE strings, e.g., {[\"UniProtKB:12312]]\"]}", @@ -5824,7 +5888,7 @@ "allowedvalues": [] }, { - "jsondocId": "1407b865-3646-4441-b9b9-56861babb602", + "jsondocId": "34cacb10-dc63-4025-89d5-a66fd76f9b3c", "name": "references", "format": "", "description": "JSON Array of reference CURIE strings, e.g., {[\"PMID:12312]]\"]}", @@ -5833,7 +5897,7 @@ "allowedvalues": [] }, { - "jsondocId": "0d52cfcd-ede4-461f-85db-a012d57bf424", + "jsondocId": "59d46471-ad56-440b-9c8b-6f6d512642d4", "name": "notes", "format": "", "description": "JSON Array of reference CURIE strings, e.g., {[\"PMID:12312]]\"]}", @@ -5845,9 +5909,9 @@ "verb": "POST", "description": "Save New gene product for feature", "methodName": "save", - "jsondocId": "612e69d6-57a4-4b07-a416-b256e0d19a6f", + "jsondocId": "a7016708-e2a4-49cf-bf20-7e39bcd3e67d", "bodyobject": { - "jsondocId": "520d94d6-ad7b-449d-967b-fbbdd3f5ab6e", + "jsondocId": "71a903aa-d956-4022-8c87-52cfe2ffc4e3", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -5857,7 +5921,7 @@ "apierrors": [], "path": "/geneProduct/save", "response": { - "jsondocId": "e054e451-49d4-4087-b992-37b555465721", + "jsondocId": "5147bbb0-fac6-4762-bd9c-67f380bec42d", "mapValueObject": "", "mapKeyObject": "", "object": "gene product" @@ -5870,7 +5934,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "67fd4e08-c83b-463a-a0da-24096527c346", + "jsondocId": "e377c67e-ec49-47cd-ae5d-4b1d95a578ce", "name": "organism", "format": "", "description": "Organism name", @@ -5879,7 +5943,7 @@ "allowedvalues": [] }, { - "jsondocId": "0cc64a4d-c7a3-4227-8ad4-e369f65c8750", + "jsondocId": "8404083d-143c-4a7d-86ef-7ebbdcb36df9", "name": "query", "format": "", "description": "Query value", @@ -5891,12 +5955,12 @@ "verb": "GET", "description": "Returns a JSON array of all suggested gene product names", "methodName": "search", - "jsondocId": "4113fd45-9e69-48f1-8cf5-d212212f2dd1", + "jsondocId": "92286296-020f-462e-927d-022dce5ee9cd", "bodyobject": null, "apierrors": [], "path": "/geneProduct/search", "response": { - "jsondocId": "99c5130b-599b-4d4e-9ac2-ff50d55746d1", + "jsondocId": "ff49bfd5-1653-423f-bc30-1f83ddf7792b", "mapValueObject": "", "mapKeyObject": "", "object": "gene product" @@ -5909,14 +5973,14 @@ "description": "Methods for managing gene product annotaitons" }, { - "jsondocId": "329ebf9f-462f-499e-97ec-b23f223ade5f", + "jsondocId": "6cb7d340-bac6-4abb-bd45-1476f67ffa89", "methods": [ { "headers": [], "pathparameters": [], "queryparameters": [ { - "jsondocId": "13b9cc9a-db21-480e-88d4-0cd515f1c51e", + "jsondocId": "bdeeb0cd-fb77-4ebf-9c00-084056c196cd", "name": "username", "format": "", "description": "", @@ -5925,7 +5989,7 @@ "allowedvalues": [] }, { - "jsondocId": "1f997b42-ab9b-46f9-88aa-5cd22168f1de", + "jsondocId": "3adee372-7f03-47bf-87b5-1805d15335fa", "name": "password", "format": "", "description": "", @@ -5934,7 +5998,7 @@ "allowedvalues": [] }, { - "jsondocId": "8414a407-a1d7-46ce-b630-cca0575f7ed6", + "jsondocId": "ecfd0a47-8f87-448e-baa9-47fb3a01dcb4", "name": "name", "format": "", "description": "Group name to add, or a comma-delimited list of names", @@ -5946,9 +6010,9 @@ "verb": "POST", "description": "Create group", "methodName": "createGroup", - "jsondocId": "b3259193-1f39-4072-ac4c-f078252545bc", + "jsondocId": "31008251-b24a-4be7-a4b2-60b8596bd190", "bodyobject": { - "jsondocId": "b8133655-6cdb-41e1-97a2-031e56de394e", + "jsondocId": "3fda0bef-bd02-40a4-b8f3-d97e87983db8", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -5958,7 +6022,71 @@ "apierrors": [], "path": "/group/createGroup", "response": { - "jsondocId": "5600391f-80fc-4dcb-a10e-1f7633e592f9", + "jsondocId": "9eec08ab-be13-4749-a4e3-bc6b7ce8af8a", + "mapValueObject": "", + "mapKeyObject": "", + "object": "group" + }, + "produces": ["application/json"], + "consumes": ["application/json"] + }, + { + "headers": [], + "pathparameters": [], + "queryparameters": [ + { + "jsondocId": "d3ad231f-f6f6-48fc-9e25-21e0a8a4815a", + "name": "username", + "format": "", + "description": "", + "type": "email", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "9a428d27-2c20-419d-85cd-a3f08fd5a282", + "name": "password", + "format": "", + "description": "", + "type": "password", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "68c130ee-799c-420c-a890-aa0e7fa0ef9b", + "name": "id", + "format": "", + "description": "Group ID (or specify the name)", + "type": "long", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "5ee88948-99f1-4e61-a6ca-85c8f8ddcca1", + "name": "name", + "format": "", + "description": "Group name", + "type": "string", + "required": "true", + "allowedvalues": [] + } + ], + "verb": "POST", + "description": "Get organism permissions for group", + "methodName": "getOrganismPermissionsForGroup", + "jsondocId": "4af72380-4802-43a7-b092-9e4d4a09748c", + "bodyobject": { + "jsondocId": "41f2daae-013f-41a4-9a7c-ba3d38cd1f1b", + "mapValueObject": "", + "mapKeyObject": "", + "multiple": "Unknow", + "map": "", + "object": "group" + }, + "apierrors": [], + "path": "/group/getOrganismPermissionsForGroup", + "response": { + "jsondocId": "9d6d564e-7ffb-4d41-8301-1e78af7d6a81", "mapValueObject": "", "mapKeyObject": "", "object": "group" @@ -5971,7 +6099,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "da726ab7-2b83-48aa-89cb-6273fe42f765", + "jsondocId": "60f83cea-5e62-45cf-b29d-a63a331f2630", "name": "username", "format": "", "description": "", @@ -5980,7 +6108,7 @@ "allowedvalues": [] }, { - "jsondocId": "d55a1506-9b5a-474a-922e-db180fe65618", + "jsondocId": "5c684026-06cd-4bff-ad3e-9c8eb0bb06c8", "name": "password", "format": "", "description": "", @@ -5989,7 +6117,7 @@ "allowedvalues": [] }, { - "jsondocId": "3d68dfab-dc24-48cc-ae84-8a1d84f209c6", + "jsondocId": "5bf4e324-a86a-409f-8b27-4c2bbc6ed2c1", "name": "groupId", "format": "", "description": "Optional only load a specific groupId", @@ -6001,9 +6129,9 @@ "verb": "POST", "description": "Load all groups", "methodName": "loadGroups", - "jsondocId": "56453161-98c1-48c4-a6a9-0cceaa97a9c6", + "jsondocId": "22bbf450-3aa5-4618-8eca-a6ac1b6aa73d", "bodyobject": { - "jsondocId": "a1772dbc-d918-4052-adfb-5606a67aba84", + "jsondocId": "3b07ff05-2667-43ee-a207-2446c4d09bdd", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -6013,7 +6141,7 @@ "apierrors": [], "path": "/group/loadGroups", "response": { - "jsondocId": "162af8fe-8053-4932-be65-a90b452355a1", + "jsondocId": "09e29070-04cb-4fe8-9364-a549b0bbd316", "mapValueObject": "", "mapKeyObject": "", "object": "group" @@ -6026,7 +6154,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "8de884e7-7184-44cd-84f7-b376b6a92cf0", + "jsondocId": "8a61a47c-e986-4de8-abfd-285bbd6e8748", "name": "username", "format": "", "description": "", @@ -6035,7 +6163,7 @@ "allowedvalues": [] }, { - "jsondocId": "1917914a-aeac-4320-9c40-555fb51373b7", + "jsondocId": "0e5bbbac-19fc-4dce-bccf-ce7999a42df8", "name": "password", "format": "", "description": "", @@ -6044,7 +6172,7 @@ "allowedvalues": [] }, { - "jsondocId": "d1a0b518-e567-4659-b118-5cd54be6abd0", + "jsondocId": "2efb644f-bfe5-4b7a-8255-f1da4594e22d", "name": "id", "format": "", "description": "Group ID to remove (or specify the name)", @@ -6053,7 +6181,7 @@ "allowedvalues": [] }, { - "jsondocId": "31d7e9a1-7769-44dc-ba9f-92e3076e4c8a", + "jsondocId": "bcee7ba4-4b11-4dfa-aeb9-6da5a79c5564", "name": "name", "format": "", "description": "Group name or comma-delimited list of names to remove", @@ -6065,9 +6193,9 @@ "verb": "POST", "description": "Delete a group", "methodName": "deleteGroup", - "jsondocId": "63efe32a-a5fe-462b-915c-f50fb6f79fec", + "jsondocId": "05aeb608-a9a1-4da8-ac2e-3cd802983460", "bodyobject": { - "jsondocId": "027133c0-81d4-4da5-ac55-a4343c5f414a", + "jsondocId": "8920b636-c39b-4324-ad40-52615ddffc13", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -6077,7 +6205,7 @@ "apierrors": [], "path": "/group/deleteGroup", "response": { - "jsondocId": "d8400b91-e143-4569-847e-840bdeed5978", + "jsondocId": "e7352bc8-684f-42f1-b40d-0a463cc7faf5", "mapValueObject": "", "mapKeyObject": "", "object": "group" @@ -6090,7 +6218,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "bfd290b5-3171-4e0d-8282-ebb979db1cd5", + "jsondocId": "4980f62f-fdb1-4157-bb5a-0a0fb27a2964", "name": "username", "format": "", "description": "", @@ -6099,7 +6227,7 @@ "allowedvalues": [] }, { - "jsondocId": "66874ae2-eef6-459c-bd17-5042a4a11674", + "jsondocId": "1b735a5e-c194-4a3f-bf52-9af7985165a4", "name": "password", "format": "", "description": "", @@ -6108,7 +6236,7 @@ "allowedvalues": [] }, { - "jsondocId": "40e3e9e4-e08c-4bb2-b54b-c779b8a1a139", + "jsondocId": "c8782332-d22d-4319-8fb1-67843109ce90", "name": "id", "format": "", "description": "Group ID to update", @@ -6117,7 +6245,7 @@ "allowedvalues": [] }, { - "jsondocId": "83ce97f3-8418-4074-b3db-9d6d49998cb3", + "jsondocId": "a6869050-ebd1-49b7-99f5-e0ae274ebc6b", "name": "name", "format": "", "description": "Group name to change to (the only editable optoin)", @@ -6129,9 +6257,9 @@ "verb": "POST", "description": "Update group", "methodName": "updateGroup", - "jsondocId": "48fcb5b8-bb68-4320-ac3e-198121bc139d", + "jsondocId": "696591bd-83b7-4712-b4d9-fd261853acbb", "bodyobject": { - "jsondocId": "02c84e82-c4c8-4d54-8b9a-2f82b7ae0523", + "jsondocId": "2bd9b54f-ac71-4446-bcc1-8dbc66ef2537", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -6141,7 +6269,7 @@ "apierrors": [], "path": "/group/updateGroup", "response": { - "jsondocId": "e97f8814-aa18-44a1-a921-14878fc58878", + "jsondocId": "0443f3c6-14ec-4943-bf37-53c4096ea9e7", "mapValueObject": "", "mapKeyObject": "", "object": "group" @@ -6154,7 +6282,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "d5f8de6d-131d-413f-a3c0-1e13c513013e", + "jsondocId": "3eaf73e7-9012-4742-9730-7140605fe1bd", "name": "username", "format": "", "description": "", @@ -6163,7 +6291,7 @@ "allowedvalues": [] }, { - "jsondocId": "69192a0f-bdde-469d-ad8e-124b033d36c2", + "jsondocId": "a30ade82-9a3c-49be-b97e-f409d45ff23b", "name": "password", "format": "", "description": "", @@ -6172,7 +6300,7 @@ "allowedvalues": [] }, { - "jsondocId": "50cda721-a812-4d4e-bf5a-440d952a6af9", + "jsondocId": "9ebcc812-4ffc-4499-a564-b5ac9bbe88c4", "name": "groupId", "format": "", "description": "Group ID to modify permissions for (must provide this or 'name')", @@ -6181,7 +6309,7 @@ "allowedvalues": [] }, { - "jsondocId": "bf3f1ba2-e68b-46a0-ad34-484d2f222f18", + "jsondocId": "25654baa-6125-44f6-88cc-2616df14525f", "name": "name", "format": "", "description": "Group name to modify permissions for (must provide this or 'groupId')", @@ -6190,7 +6318,7 @@ "allowedvalues": [] }, { - "jsondocId": "0569d02e-2ed0-4106-a568-67918c431f6f", + "jsondocId": "4ed4f5a3-d1e5-4540-9d26-f64b9083815a", "name": "organism", "format": "", "description": "Organism common name", @@ -6199,7 +6327,7 @@ "allowedvalues": [] }, { - "jsondocId": "520bca9d-2153-45ff-a78a-862eb4165a41", + "jsondocId": "e6e4609e-1379-4a68-9bf2-91ab9f0cdddb", "name": "ADMINISTRATE", "format": "", "description": "Indicate if user has administrative and all lesser (including user/group) privileges for the organism", @@ -6208,7 +6336,7 @@ "allowedvalues": [] }, { - "jsondocId": "9525ce48-fe4b-4d82-ace8-c961db504264", + "jsondocId": "65cce9b4-390d-4a66-a3bc-34747f2ab40d", "name": "WRITE", "format": "", "description": "Indicate if user has write and all lesser privileges for the organism", @@ -6217,7 +6345,7 @@ "allowedvalues": [] }, { - "jsondocId": "f43a5cd4-6742-4d14-b315-1542fc128515", + "jsondocId": "c55c16cd-da2d-4cb9-af3c-59322d8aa70e", "name": "EXPORT", "format": "", "description": "Indicate if user has export and all lesser privileges for the organism", @@ -6226,7 +6354,7 @@ "allowedvalues": [] }, { - "jsondocId": "f43ad662-4381-4683-9857-16107d766926", + "jsondocId": "600d2036-ed06-4244-9442-64f7db96aa1c", "name": "READ", "format": "", "description": "Indicate if user has read and all lesser privileges for the organism", @@ -6238,9 +6366,9 @@ "verb": "POST", "description": "Update organism permission", "methodName": "updateOrganismPermission", - "jsondocId": "f34cb6fa-e8d1-4b3c-b171-3bea61b93cf3", + "jsondocId": "9c502aef-e70b-47b1-8b71-ec72f707acbc", "bodyobject": { - "jsondocId": "f7d607a7-c656-4799-a091-a0292f2f6751", + "jsondocId": "3b4e07f0-6a6f-4304-9df6-f80837aa8512", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -6250,7 +6378,7 @@ "apierrors": [], "path": "/group/updateOrganismPermission", "response": { - "jsondocId": "b9e34f45-544a-4a59-85c0-1d7df2e0563c", + "jsondocId": "7f1aab19-6c57-4f69-b2e6-e8314563947a", "mapValueObject": "", "mapKeyObject": "", "object": "group" @@ -6263,7 +6391,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "021cb832-142b-4fca-b337-2a93847900f2", + "jsondocId": "6875be35-7c26-48a8-a968-a8d3e4fd1818", "name": "username", "format": "", "description": "", @@ -6272,7 +6400,7 @@ "allowedvalues": [] }, { - "jsondocId": "e55fa46a-f520-4282-92ff-24f561694331", + "jsondocId": "d1fa56fc-17cc-48e8-bd2d-d563af1a146a", "name": "password", "format": "", "description": "", @@ -6281,7 +6409,7 @@ "allowedvalues": [] }, { - "jsondocId": "fcf1321c-a5e4-4aa0-b2c1-77738261281d", + "jsondocId": "53f653a8-6121-47b3-9d11-7e03aa78bb18", "name": "groupId", "format": "", "description": "Group ID to alter membership of", @@ -6290,7 +6418,7 @@ "allowedvalues": [] }, { - "jsondocId": "5bd77662-a6bf-4e1a-b735-e3005f30b212", + "jsondocId": "48ebc66d-0c60-4c28-862b-cef2acaf994f", "name": "users", "format": "", "description": "A JSON array of strings of emails of users the now belong to the group", @@ -6299,7 +6427,7 @@ "allowedvalues": [] }, { - "jsondocId": "b78d60fa-ca23-49c2-9c24-1495e12eb973", + "jsondocId": "e2ae8652-52aa-4028-85fa-bce0463763d5", "name": "memberships", "format": "", "description": "Bulk memberships (instead of users and groupId) to update of the form: [ {groupId: ,users: [\"user1\", \"user2\", \"user3\"]}, {groupId:, users: [\"user2\", \"user8\"]}]", @@ -6311,9 +6439,9 @@ "verb": "POST", "description": "Update group membership", "methodName": "updateMembership", - "jsondocId": "ad83a17d-6479-4be0-8acb-771b1ecff1bb", + "jsondocId": "6dc1d7fa-023e-41bb-a78a-64ec86a2f744", "bodyobject": { - "jsondocId": "72b729cf-5038-47cf-a979-a2b801045855", + "jsondocId": "80d8fc23-ed7a-4cc3-a44f-4b4cb92927f6", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -6323,7 +6451,7 @@ "apierrors": [], "path": "/group/updateMembership", "response": { - "jsondocId": "d2181b23-8770-4524-b464-1d86aaae060c", + "jsondocId": "c5889871-5749-43c3-abb2-7bcc1c29ecf5", "mapValueObject": "", "mapKeyObject": "", "object": "group" @@ -6336,7 +6464,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "b21348f9-c549-44a6-bf7b-ac5db5aa58d8", + "jsondocId": "63f6ff7d-7930-47d7-8240-a4c7873d01b0", "name": "username", "format": "", "description": "", @@ -6345,7 +6473,7 @@ "allowedvalues": [] }, { - "jsondocId": "a10d170b-b722-4fdf-a7e9-04f12e0f9caf", + "jsondocId": "0b6f23d4-b7f0-4444-a455-05fd8e6d72d3", "name": "password", "format": "", "description": "", @@ -6354,7 +6482,7 @@ "allowedvalues": [] }, { - "jsondocId": "83d5f85e-a3f9-4aff-8843-76fd87aef1b4", + "jsondocId": "d7593d5c-1c13-4e89-97aa-10f7c7e9bb1f", "name": "groupId", "format": "", "description": "Group ID to alter membership of", @@ -6363,7 +6491,7 @@ "allowedvalues": [] }, { - "jsondocId": "a29b1cd0-0c26-42dd-8e48-f68eccbb8855", + "jsondocId": "0a5e95be-0b13-4325-b655-47008540df95", "name": "users", "format": "", "description": "A JSON array of strings of emails of users the now belong to the group", @@ -6375,9 +6503,9 @@ "verb": "POST", "description": "Update group admin", "methodName": "updateGroupAdmin", - "jsondocId": "2199d589-a4f3-422a-a6b7-ee2943bcedf3", + "jsondocId": "8d045a47-294b-4a1d-9744-d93a0d129f6e", "bodyobject": { - "jsondocId": "d5979f60-c9c6-4482-bcb3-88b749413363", + "jsondocId": "05721395-ccaf-4041-806e-0ac879cad18a", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -6387,7 +6515,7 @@ "apierrors": [], "path": "/group/updateGroupAdmin", "response": { - "jsondocId": "1ce3b728-a6e1-4519-bd6b-fc9d27b85e79", + "jsondocId": "323a6d1d-0a06-4ed4-912d-642dd3f4b0a8", "mapValueObject": "", "mapKeyObject": "", "object": "group" @@ -6400,7 +6528,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "b84d6061-8c03-414b-915a-5144dff63322", + "jsondocId": "eb4e036f-0a68-4ccf-812c-87f3a1ec84ad", "name": "username", "format": "", "description": "", @@ -6409,7 +6537,7 @@ "allowedvalues": [] }, { - "jsondocId": "9e0eac12-d274-4202-9de8-5cb0bc971114", + "jsondocId": "19506b05-d2e0-4595-8281-c1b06f5a1cf4", "name": "password", "format": "", "description": "", @@ -6418,7 +6546,7 @@ "allowedvalues": [] }, { - "jsondocId": "ea672d3e-8302-4d42-8857-4013f3c61df4", + "jsondocId": "1d3eb46e-7819-420b-a604-efaebca771e0", "name": "name", "format": "", "description": "Group name", @@ -6430,9 +6558,9 @@ "verb": "POST", "description": "Get group admins, returns group admins as JSONArray", "methodName": "getGroupAdmin", - "jsondocId": "996ca354-2922-4b0b-bb15-fbb6d4220b42", + "jsondocId": "c4474582-49b0-4502-9f84-a33f30bb3cd5", "bodyobject": { - "jsondocId": "28f4d55e-df3c-4d2b-8dcf-47a11ff22976", + "jsondocId": "ec36f7fd-afd1-4352-9856-61b5a32955b0", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -6442,7 +6570,7 @@ "apierrors": [], "path": "/group/getGroupAdmin", "response": { - "jsondocId": "706fda34-6fda-4cec-9c1b-ea9f1451de12", + "jsondocId": "16bf67f6-4778-49c8-816d-0ea900b07bef", "mapValueObject": "", "mapKeyObject": "", "object": "group" @@ -6455,7 +6583,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "9b779b4d-cd60-454e-a764-2c2b992761db", + "jsondocId": "6d55c1d8-06a7-457e-8db2-d3b262c605a3", "name": "username", "format": "", "description": "", @@ -6464,7 +6592,7 @@ "allowedvalues": [] }, { - "jsondocId": "f2152f5a-c823-4614-8a3a-63e366590584", + "jsondocId": "9a6dd710-63f6-4d2a-9a74-ff0c9c37bfba", "name": "password", "format": "", "description": "", @@ -6473,7 +6601,7 @@ "allowedvalues": [] }, { - "jsondocId": "67f94ae0-d45e-411b-9d38-b46637a6ac50", + "jsondocId": "570e9402-5f6d-4506-a75a-a305a95f38c5", "name": "name", "format": "", "description": "Group name", @@ -6485,9 +6613,9 @@ "verb": "POST", "description": "Get creator metadata for group, returns userId as JSONObject", "methodName": "getGroupCreator", - "jsondocId": "35c6cb02-7127-495f-b35d-b61bf87e3ea0", + "jsondocId": "fc065bdf-0be8-4654-a50a-830f3808c466", "bodyobject": { - "jsondocId": "e2dffdb2-39b2-4a2b-a106-c3c6e0795661", + "jsondocId": "e745ccc2-5a56-4903-988d-49c4f1cc231e", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -6497,71 +6625,7 @@ "apierrors": [], "path": "/group/getGroupCreator", "response": { - "jsondocId": "9617095a-7755-49d2-bd35-e210bb1ac777", - "mapValueObject": "", - "mapKeyObject": "", - "object": "group" - }, - "produces": ["application/json"], - "consumes": ["application/json"] - }, - { - "headers": [], - "pathparameters": [], - "queryparameters": [ - { - "jsondocId": "c4bb894f-b5c3-4bdf-bc02-7f7d3c6d5260", - "name": "username", - "format": "", - "description": "", - "type": "email", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "cea632f2-8092-4c50-bd1e-26f7bc3fb793", - "name": "password", - "format": "", - "description": "", - "type": "password", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "5729ac9e-30f9-4c49-821d-1d7d9f88c650", - "name": "id", - "format": "", - "description": "Group ID (or specify the name)", - "type": "long", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "f4d10c5b-1d4e-41be-8d09-f98fa67212ab", - "name": "name", - "format": "", - "description": "Group name", - "type": "string", - "required": "true", - "allowedvalues": [] - } - ], - "verb": "POST", - "description": "Get organism permissions for group", - "methodName": "getOrganismPermissionsForGroup", - "jsondocId": "eb348316-6ef4-44a8-ad12-820651c86c04", - "bodyobject": { - "jsondocId": "895aec1a-5986-49e2-8d8b-81d0ad4c1892", - "mapValueObject": "", - "mapKeyObject": "", - "multiple": "Unknow", - "map": "", - "object": "group" - }, - "apierrors": [], - "path": "/group/getOrganismPermissionsForGroup", - "response": { - "jsondocId": "56de1837-2c7b-4071-bf19-4b1d43252764", + "jsondocId": "83287d23-e08f-4d86-a885-ea75e5454603", "mapValueObject": "", "mapKeyObject": "", "object": "group" @@ -6574,13 +6638,13 @@ "description": "Methods for managing groups" }, { - "jsondocId": "7a0c77ba-7a1f-40ea-8551-df3d9ca78234", + "jsondocId": "8656c031-eb34-49eb-8634-499d5daf6d77", "methods": [{ "headers": [], "pathparameters": [], "queryparameters": [ { - "jsondocId": "7f340fee-570c-43f6-871c-ae3f644ee5ed", + "jsondocId": "77888919-8c90-4d7b-b6f1-9c2c2d872630", "name": "username", "format": "", "description": "", @@ -6589,7 +6653,7 @@ "allowedvalues": [] }, { - "jsondocId": "2c400a85-5cf3-4969-b638-af88e8df0925", + "jsondocId": "1e671ef7-6f28-4894-b4f7-82f235ceec84", "name": "password", "format": "", "description": "", @@ -6598,7 +6662,7 @@ "allowedvalues": [] }, { - "jsondocId": "00387dd0-9dbd-408e-af77-d8941fdabc83", + "jsondocId": "edab8810-464c-4f5d-86b0-9859aeed69c1", "name": "date", "format": "", "description": "Date to query yyyy-MM-dd:HH:mm:ss or yyyy-MM-dd", @@ -6607,7 +6671,7 @@ "allowedvalues": [] }, { - "jsondocId": "72bdeb19-41b8-4e6d-a3ab-a4649dea4c26", + "jsondocId": "dd27b834-c992-4fb2-964d-fedd210e53d7", "name": "afterDate", "format": "", "description": "Search after or on the given date.", @@ -6616,7 +6680,7 @@ "allowedvalues": [] }, { - "jsondocId": "b244b9a5-a142-4204-bac0-12c911d19e24", + "jsondocId": "a455e7b2-1b4b-4bee-b6f8-f23b5a06f7a2", "name": "beforeDate", "format": "", "description": "Search before or on the given date.", @@ -6625,7 +6689,7 @@ "allowedvalues": [] }, { - "jsondocId": "58d71ce3-e44f-4e3e-938c-0f10063171bf", + "jsondocId": "832c977d-6295-46ba-8406-eb1d122a8662", "name": "max", "format": "", "description": "Max to return", @@ -6634,7 +6698,7 @@ "allowedvalues": [] }, { - "jsondocId": "aa1c358e-2fc2-4d0b-8058-7d64abb6fe1c", + "jsondocId": "292d9fdf-2ecf-4552-8699-0b7184ed126c", "name": "sort", "format": "", "description": "Sort parameter (lastUpdated). See FeatureEvent object/table.", @@ -6643,7 +6707,7 @@ "allowedvalues": [] }, { - "jsondocId": "b6b553f4-de0d-4267-a625-003e85a2437f", + "jsondocId": "a5bcd78f-e5a7-44d7-b1a2-f0cc1e9ab05b", "name": "order", "format": "", "description": "desc/asc sort order by sort param", @@ -6655,9 +6719,9 @@ "verb": "POST", "description": "Returns a JSON representation of all current Annotations before or after a given date.", "methodName": "findChanges", - "jsondocId": "ffe19e5c-b6ee-4310-9666-3dcf96aa9de0", + "jsondocId": "4d747dd8-0202-4ea4-9b78-99677ef215f4", "bodyobject": { - "jsondocId": "d3b1e1ab-54da-4b64-a5bc-b2a3527fb122", + "jsondocId": "6853718b-cf81-4450-ab97-a88fcdd0265a", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -6667,7 +6731,7 @@ "apierrors": [], "path": "/featureEvent/findChanges", "response": { - "jsondocId": "8520af5a-322e-4762-9789-064f6212b4c1", + "jsondocId": "90eddb90-d785-4d2a-9247-747f223e0acd", "mapValueObject": "", "mapKeyObject": "", "object": "feature event" @@ -6679,23 +6743,141 @@ "description": "Methods for querying history" }, { - "jsondocId": "5ab53c23-6d6c-4874-9c9b-772332292846", + "jsondocId": "25650484-8155-4e70-bea4-00ca2bf99cc5", "methods": [ { "headers": [], "pathparameters": [], "queryparameters": [ { - "jsondocId": "981c05f6-03b5-4d32-a66d-e134c0f94c2f", - "name": "uuid", + "jsondocId": "1ff8e551-a105-40d1-8a94-c26c0b22d716", + "name": "username", "format": "", - "description": "UUID that holds the key to the stored download.", + "description": "", + "type": "email", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "4c874e84-471f-40a0-9c28-aa5547e48135", + "name": "password", + "format": "", + "description": "", + "type": "password", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "c3955fdf-4ac7-4650-8b70-94a0d6b2e130", + "name": "type", + "format": "", + "description": "Type of annotated genomic features to export 'FASTA','GFF3','CHADO'.", + "type": "string", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "8230f9f3-fcc6-49de-b8f2-2941cddff959", + "name": "seqType", + "format": "", + "description": "Type of output sequence 'peptide','cds','cdna','genomic'.", "type": "string", "required": "true", "allowedvalues": [] }, { - "jsondocId": "4943a122-c6eb-4944-92fd-21b810070501", + "jsondocId": "8f7751e6-d710-4821-8675-919780ae84d9", + "name": "format", + "format": "", + "description": "'gzip' or 'text'", + "type": "string", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "7046f1d5-5d81-46a1-854f-848118370556", + "name": "sequences", + "format": "", + "description": "Names of references sequences to add (default is all).", + "type": "string", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "0e5e4b9f-4833-4b62-b091-e6c9eb528a7e", + "name": "organism", + "format": "", + "description": "Name of organism that sequences belong to (will default to last organism).", + "type": "string", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "87e03b71-9d05-4e68-ac5b-681480e5aa21", + "name": "output", + "format": "", + "description": "Output method 'file','text'", + "type": "string", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "09856014-f24b-4e39-b2eb-1682dbec12bd", + "name": "exportAllSequences", + "format": "", + "description": "Export all reference sequences for an organism (over-rides 'sequences')", + "type": "boolean", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "0f80172e-1372-4ea8-809b-29c461a6aa7c", + "name": "region", + "format": "", + "description": "Highlighted genomic region to export in form sequence:min..max e.g., chr3:1001..1034", + "type": "String", + "required": "true", + "allowedvalues": [] + } + ], + "verb": "POST", + "description": "Write out genomic data. An example script is used in the https://github.com/GMOD/Apollo/blob/master/docs/web_services/examples/groovy/get_gff3.groovy", + "methodName": "write", + "jsondocId": "dea6b204-c404-4837-a60a-1a1ea2ecf04f", + "bodyobject": { + "jsondocId": "76165a95-cb12-4605-9897-db445d5ed63b", + "mapValueObject": "", + "mapKeyObject": "", + "multiple": "Unknow", + "map": "", + "object": "i o service" + }, + "apierrors": [], + "path": "/IOService/write", + "response": { + "jsondocId": "8c8470a6-82d7-4281-a3e5-3f07f6e1488c", + "mapValueObject": "", + "mapKeyObject": "", + "object": "i o service" + }, + "produces": ["application/json"], + "consumes": ["application/json"] + }, + { + "headers": [], + "pathparameters": [], + "queryparameters": [ + { + "jsondocId": "28c97066-238b-4d21-9fde-b4769dc9a05f", + "name": "uuid", + "format": "", + "description": "UUID that holds the key to the stored download.", + "type": "string", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "a61df171-12d0-473d-bc98-30d135d5c4dd", "name": "format", "format": "", "description": "'gzip' or 'text'", @@ -6707,9 +6889,9 @@ "verb": "POST", "description": "This is used to retrieve the a download link once the write operation was initialized using output: file.", "methodName": "download", - "jsondocId": "22f21606-4609-4270-b93d-529b85aa4d09", + "jsondocId": "9e8be6dc-9ccd-4568-8383-1e12cb68e6bd", "bodyobject": { - "jsondocId": "e67c1d37-fe36-4b4a-b55c-866d248e895f", + "jsondocId": "e4a32446-13f5-484b-a3d3-7b21e82ce7f5", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -6719,20 +6901,27 @@ "apierrors": [], "path": "/IOService/download", "response": { - "jsondocId": "4c26361c-10d4-4382-829e-c2adb8b35fb1", + "jsondocId": "137e7535-d37a-49e9-b48c-261c91e43f5c", "mapValueObject": "", "mapKeyObject": "", "object": "i o service" }, "produces": ["application/json"], "consumes": ["application/json"] - }, + } + ], + "name": "IO Services", + "description": "Methods for bulk importing and exporting sequence data" + }, + { + "jsondocId": "d341ce07-1165-4388-aa5a-2196e598014a", + "methods": [ { "headers": [], "pathparameters": [], "queryparameters": [ { - "jsondocId": "43a91be3-f2c7-47e0-9693-12271e629417", + "jsondocId": "26cb77c0-e315-4a81-9692-fe8a6c9752a8", "name": "username", "format": "", "description": "", @@ -6741,7 +6930,7 @@ "allowedvalues": [] }, { - "jsondocId": "34be309a-d3b1-448a-98c6-c0e2781b62a2", + "jsondocId": "9465e82a-deac-4a07-90c0-9279737dd1e5", "name": "password", "format": "", "description": "", @@ -6750,114 +6939,126 @@ "allowedvalues": [] }, { - "jsondocId": "ed6c2bab-d85c-41f1-ba28-047ee4c1147d", - "name": "type", + "jsondocId": "d68b2c0b-9603-42c0-ba41-569ddbc070fd", + "name": "id", "format": "", - "description": "Type of annotated genomic features to export 'FASTA','GFF3','CHADO'.", - "type": "string", + "description": "Pass an Organism ID or commonName that corresponds to the organism to be removed", + "type": "string or number", "required": "true", "allowedvalues": [] }, { - "jsondocId": "3b5a6a8a-fd2b-42ee-a914-be88cf2dc1f7", - "name": "seqType", + "jsondocId": "d1db4d6a-8043-4a51-8962-0141e460766d", + "name": "organism", "format": "", - "description": "Type of output sequence 'peptide','cds','cdna','genomic'.", - "type": "string", + "description": "Pass an Organism ID or commonName that corresponds to the organism to be removed", + "type": "string or number", "required": "true", "allowedvalues": [] }, { - "jsondocId": "e340264c-cbb7-4ca2-bb66-405555ae9685", - "name": "format", + "jsondocId": "d0270911-c087-4d70-b028-b0bca5f65996", + "name": "returnAllOrganisms", "format": "", - "description": "'gzip' or 'text'", - "type": "string", + "description": "(optional) Return all organisms (true / false) (default true)", + "type": "boolean", "required": "true", "allowedvalues": [] - }, + } + ], + "verb": "POST", + "description": "Remove an organism", + "methodName": "deleteOrganism", + "jsondocId": "e962cdad-10a9-451b-9970-622ba9f39b97", + "bodyobject": { + "jsondocId": "8190011e-6f24-4822-9324-f3b6892abaec", + "mapValueObject": "", + "mapKeyObject": "", + "multiple": "Unknow", + "map": "", + "object": "organism" + }, + "apierrors": [], + "path": "/organism/deleteOrganism", + "response": { + "jsondocId": "5348ca0c-d551-4b95-82f5-64138f8af24c", + "mapValueObject": "", + "mapKeyObject": "", + "object": "organism" + }, + "produces": ["application/json"], + "consumes": ["application/json"] + }, + { + "headers": [], + "pathparameters": [], + "queryparameters": [ { - "jsondocId": "5f5da394-4244-4514-819a-d1eacff2eb21", - "name": "sequences", + "jsondocId": "91cc5abe-7b6f-49f1-8533-b0850d825410", + "name": "username", "format": "", - "description": "Names of references sequences to add (default is all).", - "type": "string", + "description": "", + "type": "email", "required": "true", "allowedvalues": [] }, { - "jsondocId": "85faf07d-efe8-4e39-9599-28f5d06cbe77", - "name": "organism", + "jsondocId": "ddb2ee91-b907-44b4-b47a-141995c223f8", + "name": "password", "format": "", - "description": "Name of organism that sequences belong to (will default to last organism).", - "type": "string", + "description": "", + "type": "password", "required": "true", "allowedvalues": [] }, { - "jsondocId": "aab8ec6e-331b-4416-8f77-98a1cbc47bd4", - "name": "output", + "jsondocId": "21d7e276-7b00-4a51-9e72-13de0e2e7c8e", + "name": "organism", "format": "", - "description": "Output method 'file','text'", + "description": "ID or commonName that can be used to uniquely identify an organism", "type": "string", "required": "true", "allowedvalues": [] }, { - "jsondocId": "d502497a-dd25-4af5-b590-9cac9db1c3ed", - "name": "exportAllSequences", - "format": "", - "description": "Export all reference sequences for an organism (over-rides 'sequences')", - "type": "boolean", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "71818e48-5d92-4db9-b0a4-b119d1a9fedd", - "name": "region", + "jsondocId": "f1aaf745-ec09-45a6-a3a5-3ddc04a737f8", + "name": "id", "format": "", - "description": "Highlighted genomic region to export in form sequence:min..max e.g., chr3:1001..1034", - "type": "String", + "description": "ID or commonName that can be used to uniquely identify an organism", + "type": "string", "required": "true", "allowedvalues": [] } ], "verb": "POST", - "description": "Write out genomic data. An example script is used in the https://github.com/GMOD/Apollo/blob/master/docs/web_services/examples/groovy/get_gff3.groovy", - "methodName": "write", - "jsondocId": "857f0f96-c42e-43ba-ba45-92bfd0e9cff0", + "description": "Delete an organism along with its data directory and returns a JSON object containing properties of the deleted organism", + "methodName": "deleteOrganismWithSequence", + "jsondocId": "777ed852-9c94-4f33-8ca4-13e4f54bc9aa", "bodyobject": { - "jsondocId": "82d13e4d-395d-44ed-a47a-a5ce38cc2533", + "jsondocId": "0a7a08ed-78f8-4334-a26b-98bdd8d7a56d", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", "map": "", - "object": "i o service" + "object": "organism" }, "apierrors": [], - "path": "/IOService/write", + "path": "/organism/deleteOrganismWithSequence", "response": { - "jsondocId": "c80ec0c1-1ffb-42f8-8fcf-b5698761edea", + "jsondocId": "4320eb1c-d665-4556-8431-dc25294a2ff8", "mapValueObject": "", "mapKeyObject": "", - "object": "i o service" + "object": "organism" }, "produces": ["application/json"], "consumes": ["application/json"] - } - ], - "name": "IO Services", - "description": "Methods for bulk importing and exporting sequence data" - }, - { - "jsondocId": "70b3422f-12a9-4065-966e-f34156c1429c", - "methods": [ + }, { "headers": [], "pathparameters": [], "queryparameters": [ { - "jsondocId": "a811c564-f277-4528-82ee-06b9d9ac2b58", + "jsondocId": "b970a9f4-1dba-4d81-8ac6-b5078197be9c", "name": "username", "format": "", "description": "", @@ -6866,7 +7067,7 @@ "allowedvalues": [] }, { - "jsondocId": "dbdd5124-5acc-4e79-b442-bafb40c2bfb5", + "jsondocId": "c534f9c5-4041-4be9-aba4-05698eb47056", "name": "password", "format": "", "description": "", @@ -6875,21 +7076,30 @@ "allowedvalues": [] }, { - "jsondocId": "eca49665-a47a-4ceb-9f5c-d11bf3006c7f", + "jsondocId": "b597dcf0-a7d8-4693-ae1a-0f3397a25788", "name": "organism", "format": "", - "description": "Common name or ID for the organism", + "description": "ID or commonName that can be used to uniquely identify an organism.", + "type": "string", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "90a8de32-04af-4e9f-8d28-027fc6790cc9", + "name": "sequences", + "format": "", + "description": "(optional) Comma-delimited sequence names on that organism if only certain sequences should be deleted.", "type": "string", "required": "true", "allowedvalues": [] } ], "verb": "POST", - "description": "Finds sequences for a given organism and returns a JSON object including the username, organism and a JSONArray of sequences", - "methodName": "getSequencesForOrganism", - "jsondocId": "4d474106-c6d8-48ab-b432-dd736b55cac0", + "description": "Remove features from an organism", + "methodName": "deleteOrganismFeatures", + "jsondocId": "f7e6778a-aedc-4007-a69a-4a85ad66aae7", "bodyobject": { - "jsondocId": "5a2a5530-457f-47af-8a33-18fde7f92168", + "jsondocId": "782c6d12-0e14-424f-9047-8e5a31cc022c", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -6897,9 +7107,9 @@ "object": "organism" }, "apierrors": [], - "path": "/organism/getSequencesForOrganism", + "path": "/organism/deleteOrganismFeatures", "response": { - "jsondocId": "588f8dc9-bb2c-4f68-85bc-df1e6b11fddf", + "jsondocId": "df4cf0d5-5369-4ec9-831b-3231cd7548a1", "mapValueObject": "", "mapKeyObject": "", "object": "organism" @@ -6912,7 +7122,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "1be55059-3f49-47d7-8cfa-e40ef0da6abe", + "jsondocId": "d58165de-fad4-4c1b-8dd5-22bfa2b55b37", "name": "username", "format": "", "description": "", @@ -6921,7 +7131,7 @@ "allowedvalues": [] }, { - "jsondocId": "2f7f8ef0-2ede-45b7-9859-726a48123ec1", + "jsondocId": "12d3f988-d80c-4d74-a9d8-a4b8c75f59e3", "name": "password", "format": "", "description": "", @@ -6930,25 +7140,7 @@ "allowedvalues": [] }, { - "jsondocId": "62ef649c-62b3-4a51-97de-1d0b0c3dd9be", - "name": "id", - "format": "", - "description": "unique id of organism to change", - "type": "long", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "e11d6fa9-121a-4a3f-bddd-7b84a5a5102c", - "name": "directory", - "format": "", - "description": "filesystem path for the organisms data directory (required)", - "type": "string", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "9ee8d3ad-a838-4bb0-aa1a-336c85bf0d82", + "jsondocId": "8a340c6a-a593-4645-9591-53ab1b6f0bff", "name": "species", "format": "", "description": "species name", @@ -6957,7 +7149,7 @@ "allowedvalues": [] }, { - "jsondocId": "412a2c94-c94a-4092-ad53-66e7e55bf9ca", + "jsondocId": "445a073c-2ec6-4041-bc83-9d3d395140f2", "name": "genus", "format": "", "description": "species genus", @@ -6966,16 +7158,16 @@ "allowedvalues": [] }, { - "jsondocId": "f60e6972-2548-4741-a757-e73d19d4ff45", + "jsondocId": "d6bb7b10-9f06-4501-befc-9ec8b19876ca", "name": "blatdb", "format": "", - "description": "filesystem path for a BLAT database (e.g. a .2bit file)", + "description": "filesystem path for a BLAT database (e.g. a .2bit file) if not uploaded", "type": "string", "required": "true", "allowedvalues": [] }, { - "jsondocId": "2839c2bf-b97b-4279-832b-29b40e79205d", + "jsondocId": "2c004a1e-626d-49e3-9a6b-126ad214902b", "name": "publicMode", "format": "", "description": "a flag for whether the organism appears as in the public genomes list", @@ -6984,16 +7176,16 @@ "allowedvalues": [] }, { - "jsondocId": "2a7cdf2f-c7a6-443e-a092-92e89a6e65f8", - "name": "name", + "jsondocId": "457ab5c0-7f0b-4602-96b9-4e77460cddfe", + "name": "commonName", "format": "", - "description": "a common name used for the organism", + "description": "commonName for an organism", "type": "string", "required": "true", "allowedvalues": [] }, { - "jsondocId": "09bbd110-cb31-4e98-a399-fdd27756d66e", + "jsondocId": "167465c4-6953-4d7a-87ae-26e0392a5c14", "name": "nonDefaultTranslationTable", "format": "", "description": "non-default translation table", @@ -7002,7 +7194,7 @@ "allowedvalues": [] }, { - "jsondocId": "4d91ea9b-af0a-4647-a2b7-bbb8e7299815", + "jsondocId": "097fe6d4-f3e4-43e7-8079-a4b90c4e50f6", "name": "metadata", "format": "", "description": "organism metadata", @@ -7011,7 +7203,7 @@ "allowedvalues": [] }, { - "jsondocId": "25ce688e-d00f-4b94-89cb-aa7ffbdea278", + "jsondocId": "3825a044-d405-4007-9e7e-5b6919b38bcc", "name": "organismData", "format": "", "description": "zip or tar.gz compressed data directory (if other options not used). Blat data should include a .2bit suffix and be in a directory 'searchDatabaseData'", @@ -7020,30 +7212,30 @@ "allowedvalues": [] }, { - "jsondocId": "c5bc9fbc-c9e8-45a3-be01-16203ed70879", - "name": "noReloadSequences", + "jsondocId": "9f3d5ab1-f7cf-4560-be53-42e8a6641490", + "name": "sequenceData", "format": "", - "description": "(default false) If set to true, then sequences will not be reloaded if the organism directory changes.", - "type": "boolean", + "description": "FASTA file (optionally compressed) to automatically upload with", + "type": "file", "required": "true", "allowedvalues": [] }, { - "jsondocId": "175a80a3-f0cc-44cc-a321-44f03d92acb0", - "name": "returnAllOrganisms", + "jsondocId": "9c8a105d-44af-4659-93cd-32b9616c3a3e", + "name": "searchDatabaseData", "format": "", - "description": "(optional) Return all organisms (true / false) (default true)", - "type": "boolean", + "description": "2bit file for blat search (optional)", + "type": "file", "required": "true", "allowedvalues": [] } ], "verb": "POST", "description": "Adds an organism returning a JSON array of all organisms", - "methodName": "updateOrganismInfo", - "jsondocId": "d9b0bfa4-7096-4a10-a567-888811553983", + "methodName": "addOrganismWithSequence", + "jsondocId": "63721673-faaf-42af-8c3f-7fae42d10fd5", "bodyobject": { - "jsondocId": "c6163dcd-3599-4231-bf2a-1e0ec09d6041", + "jsondocId": "d06c60fe-fb43-4cd2-8a52-d239a30effbc", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -7051,9 +7243,9 @@ "object": "organism" }, "apierrors": [], - "path": "/organism/updateOrganismInfo", + "path": "/organism/addOrganismWithSequence", "response": { - "jsondocId": "633e7531-8c24-444e-978e-ac9f0e342928", + "jsondocId": "5e440b0c-2e59-4cc4-97e5-912ccf2998b6", "mapValueObject": "", "mapKeyObject": "", "object": "organism" @@ -7066,7 +7258,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "71297de3-f87f-4b4e-b7b6-2fa79f98c229", + "jsondocId": "4b9350c2-d9da-448c-92c9-103e5ea348b8", "name": "username", "format": "", "description": "", @@ -7075,7 +7267,7 @@ "allowedvalues": [] }, { - "jsondocId": "55058149-c0d5-42a3-8c74-869dadcc5106", + "jsondocId": "98d9054a-419d-4118-ac51-43e649929eaf", "name": "password", "format": "", "description": "", @@ -7084,30 +7276,30 @@ "allowedvalues": [] }, { - "jsondocId": "3e5f4d7f-3c68-4150-9d90-45f28e21a5d4", - "name": "id", + "jsondocId": "020063ca-8ffa-4f19-a02a-a7acc4456539", + "name": "organism", "format": "", - "description": "unique id of organism to change", - "type": "long", + "description": "ID or commonName that can be used to uniquely identify an organism", + "type": "string", "required": "true", "allowedvalues": [] }, { - "jsondocId": "7c04ac3c-ffcd-4164-a5b4-0eef723bae7f", - "name": "metadata", + "jsondocId": "1fa9824b-e553-4806-a866-ae8d4c0b752f", + "name": "trackLabel", "format": "", - "description": "organism metadata", + "description": "Name of track", "type": "string", "required": "true", "allowedvalues": [] } ], "verb": "POST", - "description": "Update organism metadata", - "methodName": "updateOrganismMetadata", - "jsondocId": "08d065b7-6dad-4c1a-bd1c-ca81e7d4331c", + "description": "Removes an added track from an existing organism returning a JSON object containing all tracks for the current organism.", + "methodName": "removeTrackFromOrganism", + "jsondocId": "151723bd-fb44-4a89-9243-a3740e5a459e", "bodyobject": { - "jsondocId": "f8dce519-0259-4d13-a20f-b5d39a809caf", + "jsondocId": "4bb426cd-853d-41bc-94d6-dcb69d4d8f18", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -7115,9 +7307,9 @@ "object": "organism" }, "apierrors": [], - "path": "/organism/updateOrganismMetadata", + "path": "/organism/removeTrackFromOrganism", "response": { - "jsondocId": "6a223f20-41b2-4ab3-a090-e6331d4edfca", + "jsondocId": "d1d50709-df37-4955-975b-b1b17f650382", "mapValueObject": "", "mapKeyObject": "", "object": "organism" @@ -7130,7 +7322,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "e3a93124-db36-4190-b471-592ef95dc0c8", + "jsondocId": "312be520-9822-4965-b51d-46c503c0c36a", "name": "username", "format": "", "description": "", @@ -7139,7 +7331,7 @@ "allowedvalues": [] }, { - "jsondocId": "31ec58a1-85af-459f-9e74-2da07bee5373", + "jsondocId": "317d252a-8a51-4b63-96be-4ba8326e1e7e", "name": "password", "format": "", "description": "", @@ -7148,85 +7340,57 @@ "allowedvalues": [] }, { - "jsondocId": "d772731f-bf08-4144-94d2-6de5cc3dcc94", + "jsondocId": "22b33e9d-b288-4992-9fdd-d3511efd59ab", "name": "organism", "format": "", "description": "ID or commonName that can be used to uniquely identify an organism", "type": "string", "required": "true", "allowedvalues": [] - } - ], - "verb": "POST", - "description": "Get creator metadata for organism, returns userId as String", - "methodName": "getOrganismCreator", - "jsondocId": "4465ef06-d791-4d95-9c65-d39351c9b094", - "bodyobject": { - "jsondocId": "f5cb80ef-d1c5-4c72-bca5-2f4ab4a88cfd", - "mapValueObject": "", - "mapKeyObject": "", - "multiple": "Unknow", - "map": "", - "object": "organism" - }, - "apierrors": [], - "path": "/organism/getOrganismCreator", - "response": { - "jsondocId": "13cd0950-62da-48e9-96b1-48d1879c83e2", - "mapValueObject": "", - "mapKeyObject": "", - "object": "organism" - }, - "produces": ["application/json"], - "consumes": ["application/json"] - }, - { - "headers": [], - "pathparameters": [], - "queryparameters": [ + }, { - "jsondocId": "bce50d47-cbad-4b5c-aa0a-817042217f86", - "name": "username", + "jsondocId": "513a4c53-05b1-4d42-84ce-120ff9419214", + "name": "trackData", "format": "", - "description": "", - "type": "email", + "description": "zip or tar.gz compressed track data", + "type": "string", "required": "true", "allowedvalues": [] }, { - "jsondocId": "3f7cdb43-7999-416b-9032-65c95da488a4", - "name": "password", + "jsondocId": "a3dc85d4-8393-4899-9cb0-fd3b86821379", + "name": "trackFile", "format": "", - "description": "", - "type": "password", + "description": "track file (*.bam, *.vcf, *.bw, *gff)", + "type": "string", "required": "true", "allowedvalues": [] }, { - "jsondocId": "f6b05b9a-fca1-49ad-92b5-6d24a55682b8", - "name": "showPublicOnly", + "jsondocId": "9061832b-e3fb-45c5-9f87-fc8cc6834ea6", + "name": "trackFileIndex", "format": "", - "description": "", - "type": "boolean", + "description": "index (*.bai, *.tbi)", + "type": "string", "required": "true", "allowedvalues": [] }, { - "jsondocId": "94ff05b6-840d-4421-93c0-1afa2c1a2ded", - "name": "organism", + "jsondocId": "185e1208-943a-46da-ba9a-17c7be08fd75", + "name": "trackConfig", "format": "", - "description": "(optional) ID or commonName that can be used to uniquely identify an organism", + "description": "Track configuration (JBrowse JSON)", "type": "string", "required": "true", "allowedvalues": [] } ], "verb": "POST", - "description": "Returns a JSON array of all organisms, or optionally, gets information about a specific organism", - "methodName": "findAllOrganisms", - "jsondocId": "1c615bd5-4438-4b28-95bc-e01f323ea94f", + "description": "Adds a track to an existing organism returning a JSON object containing all tracks for the current organism.", + "methodName": "addTrackToOrganism", + "jsondocId": "97eb37d1-bd69-4a53-98e9-447798c63054", "bodyobject": { - "jsondocId": "76507419-4b56-4c10-aace-31986dd29fa4", + "jsondocId": "7ebe80c9-0dbc-4a96-ba58-a723d4741b11", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -7234,9 +7398,9 @@ "object": "organism" }, "apierrors": [], - "path": "/organism/findAllOrganisms", + "path": "/organism/addTrackToOrganism", "response": { - "jsondocId": "91284c40-f64f-4292-bbb8-b8af255b705c", + "jsondocId": "b7b4d079-8c29-4df6-8a13-54d4a94e11e6", "mapValueObject": "", "mapKeyObject": "", "object": "organism" @@ -7249,7 +7413,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "d5fe4ead-8301-4298-9e63-3aa412066e40", + "jsondocId": "2d710558-8433-447c-8579-f63349f0beb3", "name": "username", "format": "", "description": "", @@ -7258,7 +7422,7 @@ "allowedvalues": [] }, { - "jsondocId": "f837228a-73a4-4c18-96dc-344ade857e6e", + "jsondocId": "f8e5e232-11bc-4b37-9230-57cd49826c59", "name": "password", "format": "", "description": "", @@ -7267,39 +7431,30 @@ "allowedvalues": [] }, { - "jsondocId": "3f90ea7b-73de-4fa7-a8ae-ab0bbea2435c", - "name": "id", - "format": "", - "description": "Pass an Organism ID or commonName that corresponds to the organism to be removed", - "type": "string or number", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "94046f45-fe5d-4aed-a929-79af3f8c9974", + "jsondocId": "84b302b6-2d9a-41f1-9f1c-78719eafbe34", "name": "organism", "format": "", - "description": "Pass an Organism ID or commonName that corresponds to the organism to be removed", - "type": "string or number", + "description": "ID or commonName that can be used to uniquely identify an organism", + "type": "string", "required": "true", "allowedvalues": [] }, { - "jsondocId": "058a5a6f-88ce-4c63-ba41-3aeb7c8338af", - "name": "returnAllOrganisms", + "jsondocId": "58324222-38d1-4c7a-9144-ea6963955c0a", + "name": "trackLabel", "format": "", - "description": "(optional) Return all organisms (true / false) (default true)", - "type": "boolean", + "description": "Track label corresponding to the track that is to be deleted", + "type": "string", "required": "true", "allowedvalues": [] } ], "verb": "POST", - "description": "Remove an organism", - "methodName": "deleteOrganism", - "jsondocId": "0b750fe2-0f5d-4e54-b0ac-17ce176eaa3a", + "description": "Deletes a track from an existing organism and returns a JSON object of the deleted track's configuration", + "methodName": "deleteTrackFromOrganism", + "jsondocId": "a5102d22-ff2c-480e-ba5f-37abf14cd92c", "bodyobject": { - "jsondocId": "4cbbe307-c2c8-4e44-b091-08844eeb9f1d", + "jsondocId": "62800473-4de4-4d51-8251-d4202b969a8c", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -7307,9 +7462,9 @@ "object": "organism" }, "apierrors": [], - "path": "/organism/deleteOrganism", + "path": "/organism/deleteTrackFromOrganism", "response": { - "jsondocId": "c443491e-2d33-4792-997a-6bc01533a86d", + "jsondocId": "06e15160-0173-4186-8afa-d1f2ed990a5b", "mapValueObject": "", "mapKeyObject": "", "object": "organism" @@ -7322,7 +7477,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "e0a17022-562d-4460-8ad2-efae7f43fedd", + "jsondocId": "f6b59ac2-b4c4-4d92-be13-ac249c60e771", "name": "username", "format": "", "description": "", @@ -7331,7 +7486,7 @@ "allowedvalues": [] }, { - "jsondocId": "3bfdb966-a016-4057-a299-8f842396348c", + "jsondocId": "80755462-5565-406c-8b7d-a70c2edaf996", "name": "password", "format": "", "description": "", @@ -7340,7 +7495,7 @@ "allowedvalues": [] }, { - "jsondocId": "86944b9b-7b1d-4ecd-86df-7cce51c3773a", + "jsondocId": "62b30ce8-67d1-43ae-99f7-2f88d0d3b216", "name": "organism", "format": "", "description": "ID or commonName that can be used to uniquely identify an organism", @@ -7349,21 +7504,21 @@ "allowedvalues": [] }, { - "jsondocId": "4235ae56-8221-4e9c-9c00-8f0d71a8fc44", - "name": "id", + "jsondocId": "6193aaa7-041c-42ce-a062-5bcafb3d4d3c", + "name": "trackConfig", "format": "", - "description": "ID or commonName that can be used to uniquely identify an organism", + "description": "Track configuration (JBrowse JSON)", "type": "string", "required": "true", "allowedvalues": [] } ], "verb": "POST", - "description": "Delete an organism along with its data directory and returns a JSON object containing properties of the deleted organism", - "methodName": "deleteOrganismWithSequence", - "jsondocId": "198bd0e5-5ec6-4265-aebb-50cd99d6543d", + "description": "Update a track in an existing organism returning a JSON object containing old and new track configurations", + "methodName": "updateTrackForOrganism", + "jsondocId": "1b9bf2b5-4a83-4736-9fea-c000d9fc0305", "bodyobject": { - "jsondocId": "3e5fce88-625b-41dc-b51a-71b70d643ba1", + "jsondocId": "1dcdfe4d-7cf6-481d-a34c-1f2d7c32a267", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -7371,9 +7526,9 @@ "object": "organism" }, "apierrors": [], - "path": "/organism/deleteOrganismWithSequence", + "path": "/organism/updateTrackForOrganism", "response": { - "jsondocId": "7414187f-0a9b-48ac-b635-f91a5da86667", + "jsondocId": "5d66c451-1372-47c6-8c2d-606a4ff7ece4", "mapValueObject": "", "mapKeyObject": "", "object": "organism" @@ -7386,7 +7541,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "8a42867e-2653-4542-b33c-d2fd30fe51cc", + "jsondocId": "45b8c77c-a981-48ed-8450-b907f08517e3", "name": "username", "format": "", "description": "", @@ -7395,7 +7550,7 @@ "allowedvalues": [] }, { - "jsondocId": "8db27ff5-80ab-4ad5-931c-92c2c8269ed4", + "jsondocId": "ee3c4bcd-aa79-413c-988c-a1868a8a258c", "name": "password", "format": "", "description": "", @@ -7404,166 +7559,84 @@ "allowedvalues": [] }, { - "jsondocId": "18854c07-c6ff-458a-8bb3-4854977c4ea6", - "name": "organism", + "jsondocId": "d4286098-c2a1-4857-9e34-ffc000cf8493", + "name": "directory", "format": "", - "description": "ID or commonName that can be used to uniquely identify an organism.", + "description": "Filesystem path for the organisms data directory (required)", "type": "string", "required": "true", "allowedvalues": [] }, { - "jsondocId": "f8c54309-14f8-4330-93e7-ded9805a6541", - "name": "sequences", + "jsondocId": "05dc2430-7a59-45ae-baa8-d1a74e879346", + "name": "commonName", "format": "", - "description": "(optional) Comma-delimited sequence names on that organism if only certain sequences should be deleted.", + "description": "A name used for the organism", "type": "string", "required": "true", "allowedvalues": [] - } - ], - "verb": "POST", - "description": "Remove features from an organism", - "methodName": "deleteOrganismFeatures", - "jsondocId": "210daeae-45ab-40fb-afeb-34acf05f055f", - "bodyobject": { - "jsondocId": "4456e0db-7291-4b53-98c5-e84f072e499e", - "mapValueObject": "", - "mapKeyObject": "", - "multiple": "Unknow", - "map": "", - "object": "organism" - }, - "apierrors": [], - "path": "/organism/deleteOrganismFeatures", - "response": { - "jsondocId": "01025870-8f4b-4920-9ffc-3e3ea9801b35", - "mapValueObject": "", - "mapKeyObject": "", - "object": "organism" - }, - "produces": ["application/json"], - "consumes": ["application/json"] - }, - { - "headers": [], - "pathparameters": [], - "queryparameters": [ - { - "jsondocId": "4fb36262-8d6a-4759-b95f-a4a8d20c671d", - "name": "username", - "format": "", - "description": "", - "type": "email", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "4a936608-f71d-477b-ab93-4fa3e1d0215e", - "name": "password", - "format": "", - "description": "", - "type": "password", - "required": "true", - "allowedvalues": [] }, { - "jsondocId": "e20395d9-70bc-4a71-8a0a-1e1192938ef2", + "jsondocId": "05b8e821-512e-4e13-90b5-8bd523e132de", "name": "species", "format": "", - "description": "species name", + "description": "(optional) Species name", "type": "string", "required": "true", "allowedvalues": [] }, { - "jsondocId": "21ec1014-3155-44b1-a2ca-b93790c63fb5", + "jsondocId": "440172b2-55e3-4c51-be2e-050000024a22", "name": "genus", "format": "", - "description": "species genus", + "description": "(optional) Species genus", "type": "string", "required": "true", "allowedvalues": [] }, { - "jsondocId": "eb778396-bd9b-43b9-a6ed-4498dba8ddb9", + "jsondocId": "f1b2e865-4d98-4d40-8dba-26d0d5b9d9fe", "name": "blatdb", "format": "", - "description": "filesystem path for a BLAT database (e.g. a .2bit file) if not uploaded", + "description": "(optional) Filesystem path for a BLAT database (e.g. a .2bit file)", "type": "string", "required": "true", "allowedvalues": [] }, { - "jsondocId": "8fe9fedd-03ec-4688-86b4-ed6002c0d936", + "jsondocId": "0c61593f-6210-4fe3-aa20-c6796fc3c113", "name": "publicMode", "format": "", - "description": "a flag for whether the organism appears as in the public genomes list", + "description": "(optional) A flag for whether the organism appears as in the public genomes list (default false)", "type": "boolean", "required": "true", "allowedvalues": [] }, { - "jsondocId": "e64cc03d-19e8-420d-8eb9-97211295b834", - "name": "commonName", - "format": "", - "description": "commonName for an organism", - "type": "string", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "dc5cbab4-b669-4ada-8def-80a1b7408ee3", - "name": "nonDefaultTranslationTable", - "format": "", - "description": "non-default translation table", - "type": "string", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "0925e5ef-53a8-4619-98c2-ac11cc74da52", + "jsondocId": "f82bf93a-ff46-400a-808e-003231fd1664", "name": "metadata", "format": "", - "description": "organism metadata", + "description": "(optional) Organism metadata", "type": "string", "required": "true", "allowedvalues": [] }, { - "jsondocId": "590ba9f2-738e-4aab-9ff0-00197b1c39c2", - "name": "organismData", - "format": "", - "description": "zip or tar.gz compressed data directory (if other options not used). Blat data should include a .2bit suffix and be in a directory 'searchDatabaseData'", - "type": "file", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "4e63bc6d-521a-4f1d-bef7-a993806dee04", - "name": "sequenceData", - "format": "", - "description": "FASTA file (optionally compressed) to automatically upload with", - "type": "file", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "f84ff68e-8703-4b2c-8ee5-63b029b03d66", - "name": "searchDatabaseData", + "jsondocId": "aac57ef8-4e1e-47fe-8d5f-c85ffad467b2", + "name": "returnAllOrganisms", "format": "", - "description": "2bit file for blat search (optional)", - "type": "file", + "description": "(optional) Return all organisms (true / false) (default true)", + "type": "boolean", "required": "true", "allowedvalues": [] } ], "verb": "POST", "description": "Adds an organism returning a JSON array of all organisms", - "methodName": "addOrganismWithSequence", - "jsondocId": "1da70a97-f517-4593-9e71-b7a909cd4f97", + "methodName": "addOrganism", + "jsondocId": "849b4a31-aa30-4e7c-a6ea-b177302dad37", "bodyobject": { - "jsondocId": "77b04369-53de-467d-92a4-30de9fbdf5e6", + "jsondocId": "fc0e654c-27bc-4b6a-b62d-1e8f5119e3cc", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -7571,9 +7644,9 @@ "object": "organism" }, "apierrors": [], - "path": "/organism/addOrganismWithSequence", + "path": "/organism/addOrganism", "response": { - "jsondocId": "f7a36617-0247-442e-b910-10f8a10c9edd", + "jsondocId": "ff58d9bb-ef71-4414-8019-6a39893059a5", "mapValueObject": "", "mapKeyObject": "", "object": "organism" @@ -7586,7 +7659,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "1579cfec-405d-43d4-9b43-eee6dd62770b", + "jsondocId": "6002feac-d15d-4aed-90fe-7c3e3de426fc", "name": "username", "format": "", "description": "", @@ -7595,7 +7668,7 @@ "allowedvalues": [] }, { - "jsondocId": "f79b2db3-459a-405d-b211-b4630fcb505c", + "jsondocId": "29b063b0-3b59-4df8-95f6-dbdb1674be6c", "name": "password", "format": "", "description": "", @@ -7604,30 +7677,21 @@ "allowedvalues": [] }, { - "jsondocId": "fd4e20b3-cb79-4949-8f79-f16cacb2042f", + "jsondocId": "60ebf199-5558-408b-9e4a-824ec7c8198c", "name": "organism", "format": "", - "description": "ID or commonName that can be used to uniquely identify an organism", - "type": "string", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "a4f81f99-bb06-437a-bc6c-cd2b4a11142c", - "name": "trackLabel", - "format": "", - "description": "Name of track", + "description": "Common name or ID for the organism", "type": "string", "required": "true", "allowedvalues": [] } ], "verb": "POST", - "description": "Removes an added track from an existing organism returning a JSON object containing all tracks for the current organism.", - "methodName": "removeTrackFromOrganism", - "jsondocId": "1248cf4b-3e46-4868-9628-c2a153e0af9a", + "description": "Finds sequences for a given organism and returns a JSON object including the username, organism and a JSONArray of sequences", + "methodName": "getSequencesForOrganism", + "jsondocId": "2876c35d-3e50-46e8-b16c-e813eab6552b", "bodyobject": { - "jsondocId": "9467e8e8-d9bb-4995-9fd2-928341915f2c", + "jsondocId": "e6b2fdae-eee5-473a-9ccf-c115cc7bbe4c", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -7635,9 +7699,9 @@ "object": "organism" }, "apierrors": [], - "path": "/organism/removeTrackFromOrganism", + "path": "/organism/getSequencesForOrganism", "response": { - "jsondocId": "88d0a11d-9585-4bbe-a9e2-171838311b09", + "jsondocId": "3a333166-1836-4167-8f4c-e9daf8e2bd31", "mapValueObject": "", "mapKeyObject": "", "object": "organism" @@ -7650,7 +7714,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "73243b3a-eea0-446a-aa2c-286ee9617b6c", + "jsondocId": "d98e092e-660c-4fac-b52d-5081c52e25ed", "name": "username", "format": "", "description": "", @@ -7659,66 +7723,129 @@ "allowedvalues": [] }, { - "jsondocId": "b6ed2203-1502-4e22-8e6b-ad2d3d035736", - "name": "password", + "jsondocId": "ad07d2be-1bf7-40cb-bd24-1f35aa8a4265", + "name": "password", + "format": "", + "description": "", + "type": "password", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "1748237e-a5f9-4288-8192-9162affb0bab", + "name": "id", + "format": "", + "description": "unique id of organism to change", + "type": "long", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "6794b694-54b0-4573-8cf6-9d22b96dae79", + "name": "directory", + "format": "", + "description": "filesystem path for the organisms data directory (required)", + "type": "string", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "68c4e1ba-dbe0-403a-a4c8-1efea47407ea", + "name": "species", + "format": "", + "description": "species name", + "type": "string", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "32a1c9f0-a219-4014-803f-4b3124a687f2", + "name": "genus", + "format": "", + "description": "species genus", + "type": "string", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "d083897c-b758-4a26-b91f-46da949f8906", + "name": "blatdb", + "format": "", + "description": "filesystem path for a BLAT database (e.g. a .2bit file)", + "type": "string", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "de70060e-4ceb-4643-b6c9-138a6b90eaec", + "name": "publicMode", + "format": "", + "description": "a flag for whether the organism appears as in the public genomes list", + "type": "boolean", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "36a7022b-3d48-48f0-86fc-69d63862a3f1", + "name": "name", "format": "", - "description": "", - "type": "password", + "description": "a common name used for the organism", + "type": "string", "required": "true", "allowedvalues": [] }, { - "jsondocId": "9cba260a-05d2-4322-8644-00fb84c99adc", - "name": "organism", + "jsondocId": "12485c36-eed3-4323-9ecd-ea40c221b144", + "name": "nonDefaultTranslationTable", "format": "", - "description": "ID or commonName that can be used to uniquely identify an organism", + "description": "non-default translation table", "type": "string", "required": "true", "allowedvalues": [] }, { - "jsondocId": "f6c04771-5190-47e9-bd70-5a0296ed9dd0", - "name": "trackData", + "jsondocId": "e361315f-e76f-49fa-ac0a-3db27cdab087", + "name": "metadata", "format": "", - "description": "zip or tar.gz compressed track data", + "description": "organism metadata", "type": "string", "required": "true", "allowedvalues": [] }, { - "jsondocId": "2680f7a4-0287-4cb1-aca6-a9a74fdf21b4", - "name": "trackFile", + "jsondocId": "bdb08f11-42ca-4874-ab1e-5cf1a1250247", + "name": "organismData", "format": "", - "description": "track file (*.bam, *.vcf, *.bw, *gff)", - "type": "string", + "description": "zip or tar.gz compressed data directory (if other options not used). Blat data should include a .2bit suffix and be in a directory 'searchDatabaseData'", + "type": "file", "required": "true", "allowedvalues": [] }, { - "jsondocId": "37ecadaf-1ba7-410d-9d44-9f98ad2bcc0e", - "name": "trackFileIndex", + "jsondocId": "845bfe24-59a1-4244-bc8f-4e5ac1ffbce3", + "name": "noReloadSequences", "format": "", - "description": "index (*.bai, *.tbi)", - "type": "string", + "description": "(default false) If set to true, then sequences will not be reloaded if the organism directory changes.", + "type": "boolean", "required": "true", "allowedvalues": [] }, { - "jsondocId": "06aa27e1-8a11-4814-8177-a5f17162db5e", - "name": "trackConfig", + "jsondocId": "bbd9e011-4a83-412e-a0e8-6b42b1723a6a", + "name": "returnAllOrganisms", "format": "", - "description": "Track configuration (JBrowse JSON)", - "type": "string", + "description": "(optional) Return all organisms (true / false) (default true)", + "type": "boolean", "required": "true", "allowedvalues": [] } ], "verb": "POST", - "description": "Adds a track to an existing organism returning a JSON object containing all tracks for the current organism.", - "methodName": "addTrackToOrganism", - "jsondocId": "a2b1960f-9ef8-4955-bb64-fe7dcbf4a5f0", + "description": "Adds an organism returning a JSON array of all organisms", + "methodName": "updateOrganismInfo", + "jsondocId": "7b1cf75d-11be-4dc0-aeb9-02f9fc9f88d5", "bodyobject": { - "jsondocId": "3d759f29-5267-4b41-96be-2ad28d07b51c", + "jsondocId": "af32a8c6-333e-4b9e-aa95-a5f8ab6ee9a4", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -7726,9 +7853,9 @@ "object": "organism" }, "apierrors": [], - "path": "/organism/addTrackToOrganism", + "path": "/organism/updateOrganismInfo", "response": { - "jsondocId": "d277b623-f99a-45b8-aac8-e807dd422c89", + "jsondocId": "e3558ca0-7d60-4bab-8bd5-8680f0e7e9b7", "mapValueObject": "", "mapKeyObject": "", "object": "organism" @@ -7741,7 +7868,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "d4e351ef-b5e3-42fc-85c3-482473340b68", + "jsondocId": "a9bd3b76-47dd-4fd3-bc6c-503228250d22", "name": "username", "format": "", "description": "", @@ -7750,7 +7877,7 @@ "allowedvalues": [] }, { - "jsondocId": "fd8521bf-b262-43f5-8cbc-b573e995b51c", + "jsondocId": "74c75a0f-f38f-4f21-83eb-790f03ecc4d7", "name": "password", "format": "", "description": "", @@ -7759,30 +7886,30 @@ "allowedvalues": [] }, { - "jsondocId": "b49f74b0-4b07-4355-84f8-91ffc1256cb7", - "name": "organism", + "jsondocId": "f1651f6e-e9d8-4114-aaf3-7d401a7af804", + "name": "id", "format": "", - "description": "ID or commonName that can be used to uniquely identify an organism", - "type": "string", + "description": "unique id of organism to change", + "type": "long", "required": "true", "allowedvalues": [] }, { - "jsondocId": "d0c188c8-4df0-463c-82ed-ba9d4b52a69a", - "name": "trackLabel", + "jsondocId": "70ae75e6-a5fe-4e89-ad13-3d4b17fd9d10", + "name": "metadata", "format": "", - "description": "Track label corresponding to the track that is to be deleted", + "description": "organism metadata", "type": "string", "required": "true", "allowedvalues": [] } ], "verb": "POST", - "description": "Deletes a track from an existing organism and returns a JSON object of the deleted track's configuration", - "methodName": "deleteTrackFromOrganism", - "jsondocId": "57c8ec88-683e-4b9e-b041-af11e556b354", + "description": "Update organism metadata", + "methodName": "updateOrganismMetadata", + "jsondocId": "43bc564f-ca85-4022-8750-c412e09b3821", "bodyobject": { - "jsondocId": "1edff763-8d0b-44ea-a2e6-2d719956b970", + "jsondocId": "ec4afac7-2d75-4b77-affe-7b99248117d8", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -7790,9 +7917,9 @@ "object": "organism" }, "apierrors": [], - "path": "/organism/deleteTrackFromOrganism", + "path": "/organism/updateOrganismMetadata", "response": { - "jsondocId": "36674d9b-9229-46b8-8188-850c220a842e", + "jsondocId": "9bac1bd8-be0e-4e87-8ec1-9b513eb0ac53", "mapValueObject": "", "mapKeyObject": "", "object": "organism" @@ -7805,7 +7932,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "061ab26b-d5f2-42d4-8a72-a5be68b74dfc", + "jsondocId": "94d44d86-27fe-4a40-8309-0e6ce2b7f2df", "name": "username", "format": "", "description": "", @@ -7814,7 +7941,7 @@ "allowedvalues": [] }, { - "jsondocId": "7e957d9c-e39f-4891-8882-9e29c0aa9780", + "jsondocId": "81df898a-7d5e-4a64-ad97-1774513cb99d", "name": "password", "format": "", "description": "", @@ -7823,30 +7950,21 @@ "allowedvalues": [] }, { - "jsondocId": "52fec630-c5ae-455b-98c7-0f1571018b4c", + "jsondocId": "118f8a96-4f1c-4c1b-8ec4-d796ccd42150", "name": "organism", "format": "", "description": "ID or commonName that can be used to uniquely identify an organism", "type": "string", "required": "true", "allowedvalues": [] - }, - { - "jsondocId": "e81c7266-6695-49f0-bf36-aa771825df66", - "name": "trackConfig", - "format": "", - "description": "Track configuration (JBrowse JSON)", - "type": "string", - "required": "true", - "allowedvalues": [] } ], "verb": "POST", - "description": "Update a track in an existing organism returning a JSON object containing old and new track configurations", - "methodName": "updateTrackForOrganism", - "jsondocId": "c14b04a7-67b8-44fc-9ccf-6e310e59bcb2", + "description": "Get creator metadata for organism, returns userId as String", + "methodName": "getOrganismCreator", + "jsondocId": "919f6397-d3f5-4800-92ae-4631d3ca56bb", "bodyobject": { - "jsondocId": "af16e6a2-7f67-490d-b517-68b148d8cffa", + "jsondocId": "c9a8b2ea-5bd3-4ad1-a9e0-4b589fdc13ba", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -7854,9 +7972,9 @@ "object": "organism" }, "apierrors": [], - "path": "/organism/updateTrackForOrganism", + "path": "/organism/getOrganismCreator", "response": { - "jsondocId": "40c38a8f-77ed-4319-af59-198a193300ac", + "jsondocId": "cb3f4004-0ff5-46c1-adce-362a647c18f1", "mapValueObject": "", "mapKeyObject": "", "object": "organism" @@ -7869,7 +7987,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "0d3beec4-da8e-4182-9388-ae5a01212ed1", + "jsondocId": "57e557ef-9763-4983-b313-53cbfc64b170", "name": "username", "format": "", "description": "", @@ -7878,7 +7996,7 @@ "allowedvalues": [] }, { - "jsondocId": "92414373-2b51-4f03-b3cc-59fd47d30b09", + "jsondocId": "775c2a1f-e2c3-452c-a0ce-318a46b2a1d4", "name": "password", "format": "", "description": "", @@ -7887,84 +8005,30 @@ "allowedvalues": [] }, { - "jsondocId": "7fb12f94-0b21-4657-981f-f8e926863137", - "name": "directory", - "format": "", - "description": "Filesystem path for the organisms data directory (required)", - "type": "string", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "dca62985-e289-4bde-96a2-b93a48ffb803", - "name": "commonName", - "format": "", - "description": "A name used for the organism", - "type": "string", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "96ad5411-8117-4eb5-b0e1-ac5bca1d0e8a", - "name": "species", - "format": "", - "description": "(optional) Species name", - "type": "string", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "097641de-1207-4654-a1c3-dba1890a107b", - "name": "genus", - "format": "", - "description": "(optional) Species genus", - "type": "string", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "1b102755-e106-4f69-b4b8-ecd00d7505c6", - "name": "blatdb", - "format": "", - "description": "(optional) Filesystem path for a BLAT database (e.g. a .2bit file)", - "type": "string", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "801732a2-39ce-45cf-a849-3eb57402ac40", - "name": "publicMode", + "jsondocId": "67114c08-be62-4cff-8ec2-14be183170c6", + "name": "showPublicOnly", "format": "", - "description": "(optional) A flag for whether the organism appears as in the public genomes list (default false)", + "description": "", "type": "boolean", "required": "true", "allowedvalues": [] }, { - "jsondocId": "0b6a1e5c-bf81-4d41-a9d4-932f30d1039d", - "name": "metadata", + "jsondocId": "9b6b396f-b5a9-4e3f-8d4f-41de2d912e29", + "name": "organism", "format": "", - "description": "(optional) Organism metadata", + "description": "(optional) ID or commonName that can be used to uniquely identify an organism", "type": "string", "required": "true", "allowedvalues": [] - }, - { - "jsondocId": "c5885869-4e62-4148-8dbe-56665dde9015", - "name": "returnAllOrganisms", - "format": "", - "description": "(optional) Return all organisms (true / false) (default true)", - "type": "boolean", - "required": "true", - "allowedvalues": [] } ], "verb": "POST", - "description": "Adds an organism returning a JSON array of all organisms", - "methodName": "addOrganism", - "jsondocId": "e5f4d039-7471-460b-a554-8d4aa06145a6", + "description": "Returns a JSON array of all organisms, or optionally, gets information about a specific organism", + "methodName": "findAllOrganisms", + "jsondocId": "8f91bf09-f416-4a6a-8835-ffc3556748a9", "bodyobject": { - "jsondocId": "1c57df21-5a16-4ab4-849f-1b382f16c579", + "jsondocId": "1d59feea-ecd7-429f-b745-6fb090cd9595", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -7972,9 +8036,9 @@ "object": "organism" }, "apierrors": [], - "path": "/organism/addOrganism", + "path": "/organism/findAllOrganisms", "response": { - "jsondocId": "30598d1f-e4d4-4ca4-88a9-9acef281db1e", + "jsondocId": "89aa3695-89f8-48cb-8537-abc533cd0f3f", "mapValueObject": "", "mapKeyObject": "", "object": "organism" @@ -7987,14 +8051,14 @@ "description": "Methods for managing organisms" }, { - "jsondocId": "a2bcc341-e528-4b0f-a2a1-91015b714f45", + "jsondocId": "d26920d5-beac-4827-b704-c49310c8938e", "methods": [ { "headers": [], "pathparameters": [], "queryparameters": [ { - "jsondocId": "94e600ba-e078-422c-926c-753c76d8533d", + "jsondocId": "6d6ba072-b688-4701-bbb1-6e2e97c343dd", "name": "username", "format": "", "description": "", @@ -8003,7 +8067,7 @@ "allowedvalues": [] }, { - "jsondocId": "2c0469b9-63fe-44c2-bf1e-890af2e13470", + "jsondocId": "aa7c52a0-f9b2-4eca-beb2-ee4b3c6f4342", "name": "password", "format": "", "description": "", @@ -8012,7 +8076,7 @@ "allowedvalues": [] }, { - "jsondocId": "bc79ed26-1408-4f82-903d-2f37aa963af5", + "jsondocId": "dcd80a75-d44f-4403-baf9-c5cdbf280d5f", "name": "uniqueName", "format": "", "description": "Feature name to query on", @@ -8024,9 +8088,9 @@ "verb": "POST", "description": "Load Annotations for feature", "methodName": "index", - "jsondocId": "e9cc5d2b-3792-4ea4-95a5-776683f8ffed", + "jsondocId": "4a2c96b9-6f21-4a76-86ad-0829601aa3fa", "bodyobject": { - "jsondocId": "c1842739-621e-456e-854e-829b573f5698", + "jsondocId": "dd7f17aa-7c4b-4084-ad4c-0162c9e065eb", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -8036,7 +8100,7 @@ "apierrors": [], "path": "/provenance", "response": { - "jsondocId": "d0f2a506-1910-4e4e-9dde-59bac3c9f117", + "jsondocId": "5b159ae5-231e-4cb6-9318-9c7870851fc6", "mapValueObject": "", "mapKeyObject": "", "object": "provenance" @@ -8049,7 +8113,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "879c5194-223d-4407-b002-1aa19222694a", + "jsondocId": "c58abaa5-d8af-4bfd-9ca4-3794b7333e99", "name": "username", "format": "", "description": "", @@ -8058,7 +8122,7 @@ "allowedvalues": [] }, { - "jsondocId": "21c3e6c5-d590-4f90-901c-fd69bfe40a48", + "jsondocId": "1f7fa969-bb25-4a33-92ed-f6807176c698", "name": "password", "format": "", "description": "", @@ -8067,7 +8131,7 @@ "allowedvalues": [] }, { - "jsondocId": "b32c3f41-bcef-413e-8767-67fe0cbd95a7", + "jsondocId": "4099bb5c-c1f1-4251-b8c7-a5bb0fc03413", "name": "id", "format": "", "description": "GO Annotation ID to update (required)", @@ -8076,7 +8140,7 @@ "allowedvalues": [] }, { - "jsondocId": "b2fdd732-f1d8-40d7-a3b7-f13fc3ba3548", + "jsondocId": "7053d616-e410-4150-9eb6-15c5ad863325", "name": "feature", "format": "", "description": "uniqueName of feature to query on", @@ -8085,7 +8149,7 @@ "allowedvalues": [] }, { - "jsondocId": "4663248a-270b-47da-98ef-1acc26c3ac32", + "jsondocId": "4e3eeede-cfd3-4c8c-a428-c25c9d0584e2", "name": "field", "format": "", "description": "field type annotated", @@ -8094,7 +8158,7 @@ "allowedvalues": [] }, { - "jsondocId": "c66ccd61-bab0-4ab9-84f5-cb2a104c0b43", + "jsondocId": "671c4f21-1ece-48cb-8072-93e1b68dfb5c", "name": "evidenceCode", "format": "", "description": "Evidence (ECO) CURIE", @@ -8103,7 +8167,7 @@ "allowedvalues": [] }, { - "jsondocId": "5d64dfa7-2dd1-437d-b81d-5aa1fad54ed7", + "jsondocId": "b291d143-ce45-4cca-9ce3-fe603805c753", "name": "evidenceCodeLabel", "format": "", "description": "Evidence (ECO) Label", @@ -8112,7 +8176,7 @@ "allowedvalues": [] }, { - "jsondocId": "876ab46a-c5e5-4171-a4da-a41b58896aa3", + "jsondocId": "3fbed764-3b0f-4729-a4a4-8e2b88349b72", "name": "withOrFrom", "format": "", "description": "JSON Array of with or from CURIE strings, e.g., {[\"UniProtKB:12312]]\"]}", @@ -8121,7 +8185,7 @@ "allowedvalues": [] }, { - "jsondocId": "7e8bdada-04cb-4938-8d49-e773f14998c3", + "jsondocId": "3867879d-036a-4a75-84d6-e261fbcedda9", "name": "notes", "format": "", "description": "JSON Array of notes {[\"A simple note\"]}", @@ -8130,7 +8194,7 @@ "allowedvalues": [] }, { - "jsondocId": "7b83ebc1-54be-491b-979f-40d49645073c", + "jsondocId": "ecc85f7d-baf0-4654-a11c-70b886a29d4e", "name": "references", "format": "", "description": "JSON Array of reference CURIE strings, e.g., {[\"PMID:12312\"]}", @@ -8142,9 +8206,9 @@ "verb": "POST", "description": "Update existing annotations for feature", "methodName": "update", - "jsondocId": "707e9a75-0394-4aa8-843e-f4ad8b6369c2", + "jsondocId": "99a8a781-7518-4dda-a81c-adba73d85c79", "bodyobject": { - "jsondocId": "1a13d59a-85c9-4e3d-bab4-35237bd68335", + "jsondocId": "53c78b5f-912b-430a-bfb6-7ffcb0cc08e8", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -8154,7 +8218,7 @@ "apierrors": [], "path": "/provenance/update", "response": { - "jsondocId": "a7a51dd5-9e98-4405-a672-200ad483c6e8", + "jsondocId": "205d3b02-6ef8-430f-8de9-93b25740e5b1", "mapValueObject": "", "mapKeyObject": "", "object": "provenance" @@ -8167,7 +8231,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "02801f1a-2643-4fed-a9f9-8a5b07250f12", + "jsondocId": "a35ce4d2-eb45-4c69-8540-fe93a66c858e", "name": "username", "format": "", "description": "", @@ -8176,7 +8240,7 @@ "allowedvalues": [] }, { - "jsondocId": "a80b1b43-f359-41a1-a98d-605f9d0bfa1c", + "jsondocId": "0bf5fb5f-aeb0-4217-8eff-e8690b0e66e8", "name": "password", "format": "", "description": "", @@ -8185,7 +8249,7 @@ "allowedvalues": [] }, { - "jsondocId": "8d65220f-24c1-4272-8ea0-93f4ee0d0871", + "jsondocId": "c10ea5e0-ccd3-4885-be2c-c22b14442af4", "name": "id", "format": "", "description": "GO Annotation ID to delete (required)", @@ -8194,7 +8258,7 @@ "allowedvalues": [] }, { - "jsondocId": "222d74bf-42e3-403d-a1fb-7ad1672c50f6", + "jsondocId": "4ff443ca-abda-48c0-b60a-5503872be448", "name": "uniqueName", "format": "", "description": "Feature uniqueName to remove feature from", @@ -8206,9 +8270,9 @@ "verb": "POST", "description": "Delete existing annotations for feature", "methodName": "delete", - "jsondocId": "726f7ddf-1721-4274-9813-b3a80c3b4e4d", + "jsondocId": "ea9eb771-8cbb-490f-afce-c62a30a62cc8", "bodyobject": { - "jsondocId": "043522c2-0240-4185-97a3-d2b8d5b4193f", + "jsondocId": "7e08c1e4-89d0-46b7-acb1-151659147a0c", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -8218,7 +8282,7 @@ "apierrors": [], "path": "/provenance/delete", "response": { - "jsondocId": "dcddbbe6-ca89-4e37-8ed4-91122f32c0e0", + "jsondocId": "c786555a-c6d4-4aea-b27e-9ab0e9ee49f0", "mapValueObject": "", "mapKeyObject": "", "object": "provenance" @@ -8231,7 +8295,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "d041aa28-cf87-4f30-aace-bd577ab0450e", + "jsondocId": "fd2b337d-de30-4276-b9bd-d1997b52a415", "name": "username", "format": "", "description": "", @@ -8240,7 +8304,7 @@ "allowedvalues": [] }, { - "jsondocId": "159ceab6-a38f-405f-b3b7-d70951de6941", + "jsondocId": "45bb3017-fa8c-471f-9219-eaa86ee35d74", "name": "password", "format": "", "description": "", @@ -8249,7 +8313,7 @@ "allowedvalues": [] }, { - "jsondocId": "ee944341-ab80-4806-9918-2743e56152bc", + "jsondocId": "c65f3582-dbf6-46f4-8657-79b39e56e455", "name": "feature", "format": "", "description": "Feature uniqueName to query on", @@ -8258,7 +8322,7 @@ "allowedvalues": [] }, { - "jsondocId": "9402e9ed-3f80-43e5-97c2-232d523f2db1", + "jsondocId": "477e8145-1c2b-4cc6-b2ca-0e724276ced1", "name": "field", "format": "", "description": "Field type to annotate ", @@ -8267,7 +8331,7 @@ "allowedvalues": [] }, { - "jsondocId": "de7890d4-97a8-4150-8c25-4c44268d62cc", + "jsondocId": "e0bf2812-3b70-4024-98f2-299a1fe4a440", "name": "evidenceCode", "format": "", "description": "Evidence (ECO) CURIE", @@ -8276,7 +8340,7 @@ "allowedvalues": [] }, { - "jsondocId": "6f5f4e5e-8ab6-4565-86bb-e8124a56ba8f", + "jsondocId": "de27555d-ab8e-4f65-b456-6be698b2f79d", "name": "evidenceCodeLabel", "format": "", "description": "Evidence (ECO) Label", @@ -8285,7 +8349,7 @@ "allowedvalues": [] }, { - "jsondocId": "b2ced7bc-eab0-4e25-b9cf-cc7868729ced", + "jsondocId": "fe7e7fcc-9a2b-47c6-a4dd-44b733479eca", "name": "withOrFrom", "format": "", "description": "JSON Array of with or from CURIE strings, e.g., {[\"UniProtKB:12312]]\"]}", @@ -8294,7 +8358,7 @@ "allowedvalues": [] }, { - "jsondocId": "2bd2e7e2-e7ea-47a9-893f-0c0851e2c05a", + "jsondocId": "19a2719b-abe6-404d-8f1c-ebe0fb689b69", "name": "notes", "format": "", "description": "JSON Array of notes {[\"A simple note\"]}", @@ -8303,7 +8367,7 @@ "allowedvalues": [] }, { - "jsondocId": "34958d65-5435-4a5e-976c-0a34a89498e5", + "jsondocId": "6b59e06d-7b0c-4705-a540-39ecc12ab869", "name": "references", "format": "", "description": "JSON Array of reference CURIE strings, e.g., {[\"PMID:12312\"]}", @@ -8315,9 +8379,9 @@ "verb": "POST", "description": "Save New Go Annotations for feature", "methodName": "save", - "jsondocId": "662dc959-65c1-4711-80ce-79d9e3b85cdd", + "jsondocId": "05e90102-8437-48a0-ba06-b4c2522b89ae", "bodyobject": { - "jsondocId": "3b0b6c30-9a63-400b-84f0-b93252aa25ce", + "jsondocId": "8cc496aa-2ed9-4973-9e77-b49e333bd9b9", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -8327,7 +8391,7 @@ "apierrors": [], "path": "/provenance/save", "response": { - "jsondocId": "32acb629-94b8-424b-83da-42a4ef0714b4", + "jsondocId": "4321ee0d-1107-4951-b0d7-712a0be1a92e", "mapValueObject": "", "mapKeyObject": "", "object": "provenance" @@ -8340,14 +8404,14 @@ "description": "Methods for managing provenance annotations" }, { - "jsondocId": "2f89a6ac-de40-4e6b-b4eb-5b6fcc3f0f6a", + "jsondocId": "31ed3beb-ab39-40dd-8c6a-cb40f097959d", "methods": [ { "headers": [], "pathparameters": [], "queryparameters": [ { - "jsondocId": "7dd9b01a-91a9-4c5a-b8be-751a26bcf6db", + "jsondocId": "36f30f9d-b6d4-40c0-a8ac-e28fb3e00f7d", "name": "organismString", "format": "", "description": "Organism common name or ID(required)", @@ -8356,7 +8420,7 @@ "allowedvalues": [] }, { - "jsondocId": "0b6873f3-a588-48b1-8e55-88ea41bf5efa", + "jsondocId": "9e2c27d0-1ec2-4e14-8b79-a96d27b5f9a3", "name": "sequenceName", "format": "", "description": "Sequence name(required)", @@ -8365,7 +8429,7 @@ "allowedvalues": [] }, { - "jsondocId": "ee166ebc-ca48-446f-a0dc-73ce3bd9aaa8", + "jsondocId": "38ebd6b1-2dfa-4acc-99f4-4c3a2e032eac", "name": "fmin", "format": "", "description": "Minimum range(required)", @@ -8374,7 +8438,7 @@ "allowedvalues": [] }, { - "jsondocId": "ff7dec76-ef77-449c-bb4b-8bb7ff912cde", + "jsondocId": "30a4e570-35fe-4526-b9a2-00121d22bbfe", "name": "fmax", "format": "", "description": "Maximum range (required)", @@ -8383,7 +8447,7 @@ "allowedvalues": [] }, { - "jsondocId": "60a410be-981f-4922-8c0a-030d32072c68", + "jsondocId": "1fa23238-eb8f-4938-90fd-37ba1f83879a", "name": "ignoreCache", "format": "", "description": "(default false). Use cache for request if available.", @@ -8395,12 +8459,12 @@ "verb": "GET", "description": "Get sequence data within a range (also works as post)", "methodName": "sequenceByLocation", - "jsondocId": "eed8e5fa-5483-47fe-936c-400bce153aa3", + "jsondocId": "1fc2e4c1-5f66-4f05-984d-afcf55d82a31", "bodyobject": null, "apierrors": [], "path": "/sequence//:..?ignoreCache=", "response": { - "jsondocId": "6ae20500-7518-4136-988a-94e16e717d60", + "jsondocId": "4261507d-583e-4330-8574-1e2e413a48b0", "mapValueObject": "", "mapKeyObject": "", "object": "sequence" @@ -8413,7 +8477,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "6ec49234-4900-4b86-9cae-bdc828c97863", + "jsondocId": "d71cf086-9236-4277-a7f9-3dbdcaa8c27e", "name": "organismString", "format": "", "description": "Organism common name or ID (required)", @@ -8422,7 +8486,7 @@ "allowedvalues": [] }, { - "jsondocId": "9d0518e2-38d9-40e0-a662-ed20fc817dce", + "jsondocId": "9e91836e-cf06-4207-84dc-4b6c42f18fb4", "name": "sequenceName", "format": "", "description": "Sequence name (required)", @@ -8431,7 +8495,7 @@ "allowedvalues": [] }, { - "jsondocId": "b9ea2105-81e1-41e4-9760-02bfd8d82c3f", + "jsondocId": "b4c39f68-0af6-47a3-901d-f03d6be83214", "name": "featureName", "format": "", "description": "The uniqueName (UUID) or given name of the feature (typically transcript) of the element to retrieve sequence from", @@ -8440,7 +8504,7 @@ "allowedvalues": [] }, { - "jsondocId": "7d940091-3a22-48e0-99f9-94c391308550", + "jsondocId": "f26af50d-0ab5-45ab-a350-700be998b037", "name": "type", "format": "", "description": "(default genomic) Return type: genomic, cds, cdna, peptide", @@ -8449,7 +8513,7 @@ "allowedvalues": [] }, { - "jsondocId": "e2144081-6397-4c7a-bf76-4bf8cd721939", + "jsondocId": "b04acd4c-4ce6-417b-a6c0-60f383818b6b", "name": "ignoreCache", "format": "", "description": "(default false). Use cache for request if available.", @@ -8461,12 +8525,12 @@ "verb": "GET", "description": "Get sequence data as for a selected name (also works as post)", "methodName": "sequenceByName", - "jsondocId": "8da4d43c-561e-4bfd-9465-399ebf9488ba", + "jsondocId": "e24bb880-f246-4209-956c-e231832a8e03", "bodyobject": null, "apierrors": [], "path": "/sequence///.?ignoreCache=", "response": { - "jsondocId": "f9a12ea6-002e-4c42-a42a-ac21f6ab90c5", + "jsondocId": "93eff44f-1a79-42e0-8e59-4199177d71fd", "mapValueObject": "", "mapKeyObject": "", "object": "sequence" @@ -8479,7 +8543,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "295ed1cd-0faf-42fe-aa57-c02a6fa76f29", + "jsondocId": "b8c00ef7-82ee-4a84-8b39-c8961a6695c7", "name": "organismName", "format": "", "description": "Organism common name (required)", @@ -8488,7 +8552,7 @@ "allowedvalues": [] }, { - "jsondocId": "03d6c55d-86e5-4d89-bfe0-4388c76f6cb5", + "jsondocId": "dca4e96e-43c9-47e8-a480-91cdf23abddc", "name": "sequenceName", "format": "", "description": "Sequence name (required)", @@ -8497,7 +8561,7 @@ "allowedvalues": [] }, { - "jsondocId": "15d0a47c-1ed1-49fa-8bdc-a52cf036386c", + "jsondocId": "ba089758-d8db-435d-b53d-fa6256aedf9a", "name": "username", "format": "", "description": "username (optional)", @@ -8506,7 +8570,7 @@ "allowedvalues": [] }, { - "jsondocId": "4c8eb54e-45ef-4b30-bc7d-f031850ef56f", + "jsondocId": "66968172-901b-4267-acc0-1992022f07e4", "name": "password", "format": "", "description": "password (required)", @@ -8518,12 +8582,12 @@ "verb": "GET", "description": "Remove sequence cache for an organism and sequence", "methodName": "clearSequenceCache", - "jsondocId": "3af10e28-c28c-4f8d-8c35-8c442a5a3a29", + "jsondocId": "87a6531a-a3ff-468c-8f27-113329ad3d5e", "bodyobject": null, "apierrors": [], "path": "/sequence/cache/clear//", "response": { - "jsondocId": "486c41f0-2f42-4bed-bfe5-7681327ea47f", + "jsondocId": "f3e18600-d359-4fa5-9fba-4537f002de42", "mapValueObject": "", "mapKeyObject": "", "object": "sequence" @@ -8536,7 +8600,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "a34225ee-0f4b-4598-bac3-b4303d639e3e", + "jsondocId": "cb7c2ec6-8709-4470-88f7-21d89c533044", "name": "organismName", "format": "", "description": "Organism common name (required) or 'ALL' if admin", @@ -8545,7 +8609,7 @@ "allowedvalues": [] }, { - "jsondocId": "4a49c3d6-ca03-48ba-b798-35b293d8871e", + "jsondocId": "e3cd11ce-b2ed-4dbf-b967-629321c2e9f6", "name": "username", "format": "", "description": "username (optional)", @@ -8554,7 +8618,7 @@ "allowedvalues": [] }, { - "jsondocId": "34bc339c-f1d5-4ab9-8b4d-d927e66bb6eb", + "jsondocId": "007b7efc-f295-4e51-b4f7-a4270386dc43", "name": "password", "format": "", "description": "password (required)", @@ -8566,12 +8630,12 @@ "verb": "GET", "description": "Remove sequence cache for an organism", "methodName": "clearOrganismCache", - "jsondocId": "d913a720-53ad-49b3-8a6d-297cbf694a77", + "jsondocId": "9cf6cb94-fc73-4f31-a3c9-83eca407a7e2", "bodyobject": null, "apierrors": [], "path": "/sequence/cache/clear/", "response": { - "jsondocId": "0f9c1b14-561e-4273-8e4b-3d123851973e", + "jsondocId": "c66af81f-eae7-4978-be49-24d95cf9ec62", "mapValueObject": "", "mapKeyObject": "", "object": "sequence" @@ -8584,14 +8648,78 @@ "description": "Methods for retrieving sequence data" }, { - "jsondocId": "435b3d7f-b0bf-40e9-b848-099ef788f40d", + "jsondocId": "300c9da7-986c-43b3-9658-ea655b453f9a", "methods": [ { "headers": [], "pathparameters": [], "queryparameters": [ { - "jsondocId": "b7e3a84d-0111-4a6c-ae13-3c49ce730552", + "jsondocId": "90cbf495-c711-4fbf-9ee9-5b757ef73933", + "name": "username", + "format": "", + "description": "", + "type": "email", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "1160d5c6-4b63-40c5-9a0d-c6212cb03912", + "name": "password", + "format": "", + "description": "", + "type": "password", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "6063087c-90c5-4af0-be52-27f1a7d92be0", + "name": "id", + "format": "", + "description": "Name ID to show (or specify a name)", + "type": "long", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "630fb798-1351-4781-b8c8-31a12753ba6c", + "name": "name", + "format": "", + "description": "Name to show", + "type": "string", + "required": "true", + "allowedvalues": [] + } + ], + "verb": "POST", + "description": "Returns a JSON array of all suggested names, or optionally, gets information about a specific suggested name", + "methodName": "showName", + "jsondocId": "9333e91e-ea05-40b2-a421-ba0378746256", + "bodyobject": { + "jsondocId": "08d24203-0a9d-4704-84f3-8f8d04065036", + "mapValueObject": "", + "mapKeyObject": "", + "multiple": "Unknow", + "map": "", + "object": "suggested name" + }, + "apierrors": [], + "path": "/suggestedName/showName", + "response": { + "jsondocId": "a57142a8-63b6-43e9-b32f-3061af4a4044", + "mapValueObject": "", + "mapKeyObject": "", + "object": "suggested name" + }, + "produces": ["application/json"], + "consumes": ["application/json"] + }, + { + "headers": [], + "pathparameters": [], + "queryparameters": [ + { + "jsondocId": "7c70376d-b75f-42f0-92b9-517d8baca053", "name": "featureType", "format": "", "description": "Feature type", @@ -8600,7 +8728,7 @@ "allowedvalues": [] }, { - "jsondocId": "1b1dd6f7-4dd5-4e30-ab19-27b959ce004a", + "jsondocId": "94118fc3-e319-46a2-ba58-85d2ed339581", "name": "organism", "format": "", "description": "Organism name", @@ -8609,7 +8737,7 @@ "allowedvalues": [] }, { - "jsondocId": "b9e4e9b5-f470-4317-aec8-d0e107c7d468", + "jsondocId": "8a9afe2a-3ed5-49f6-85e2-2b16f4fdde25", "name": "query", "format": "", "description": "Query value", @@ -8621,12 +8749,12 @@ "verb": "GET", "description": "Returns a JSON array of all suggested names, or optionally, gets information about a specific suggested name", "methodName": "search", - "jsondocId": "d8fd5b46-15b8-40d1-af7b-701461032b69", + "jsondocId": "b7ea1735-b693-40ad-9026-c67d8e5c82bc", "bodyobject": null, "apierrors": [], "path": "/suggestedName/search", "response": { - "jsondocId": "b85365b2-f96d-4952-9bc2-5916fb2175f7", + "jsondocId": "0923121a-0203-4fdf-9193-475c3b0d0911", "mapValueObject": "", "mapKeyObject": "", "object": "suggested name" @@ -8639,7 +8767,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "c9d32f8e-6542-4d44-b212-aef49dbd43b0", + "jsondocId": "84fd8674-aa6d-44b5-b9b1-54671b4a69ca", "name": "username", "format": "", "description": "", @@ -8648,7 +8776,7 @@ "allowedvalues": [] }, { - "jsondocId": "b2dae751-492c-459a-ada7-56316f54d3b7", + "jsondocId": "0b9cfa48-26fb-4001-b101-b78864e4a599", "name": "password", "format": "", "description": "", @@ -8657,30 +8785,21 @@ "allowedvalues": [] }, { - "jsondocId": "59dde89c-cd3c-40df-a67a-96b01292f8f2", - "name": "id", - "format": "", - "description": "Name ID to show (or specify a name)", - "type": "long", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "8136e1a5-7004-4aa2-b9f0-768e611532a2", - "name": "name", + "jsondocId": "6a39799c-e5f8-4f5c-a74a-2798f8a2d6e3", + "name": "names", "format": "", - "description": "Name to show", + "description": "A comma-delimited list of names to add", "type": "string", "required": "true", "allowedvalues": [] } ], "verb": "POST", - "description": "Returns a JSON array of all suggested names, or optionally, gets information about a specific suggested name", - "methodName": "showName", - "jsondocId": "5c5d8137-87d8-4136-9e78-3b3a29017bc2", + "description": "A comma-delimited list of names", + "methodName": "addNames", + "jsondocId": "c0d6d450-08d1-479e-9513-d031c145a6dd", "bodyobject": { - "jsondocId": "ada16e4c-ae33-4d75-acba-66296b8e1324", + "jsondocId": "68c3bf52-5c20-4932-857b-4a26b533da22", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -8688,9 +8807,9 @@ "object": "suggested name" }, "apierrors": [], - "path": "/suggestedName/showName", + "path": "/suggestedName/addNames", "response": { - "jsondocId": "329a7f9c-509a-4b5a-8be4-4e72a055b541", + "jsondocId": "e20cfd4c-5bb4-478f-b9af-3aa2186a1c3d", "mapValueObject": "", "mapKeyObject": "", "object": "suggested name" @@ -8703,7 +8822,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "d6053d23-ac49-4b9d-9e8c-11753a30083f", + "jsondocId": "f7eb9c05-6248-4e92-8c89-04064b6aa1b3", "name": "username", "format": "", "description": "", @@ -8712,7 +8831,7 @@ "allowedvalues": [] }, { - "jsondocId": "740e3bd7-22d8-4dd6-83ce-177c70414a64", + "jsondocId": "1e096ffd-6cc5-460a-8257-ab9f927f3208", "name": "password", "format": "", "description": "", @@ -8721,7 +8840,7 @@ "allowedvalues": [] }, { - "jsondocId": "19bdfe9d-97fe-448f-9ff5-4d5cfcdf3f6c", + "jsondocId": "e9ee68d7-2679-4f5c-bef2-9a7acebaad30", "name": "name", "format": "", "description": "Suggested name to add", @@ -8730,7 +8849,7 @@ "allowedvalues": [] }, { - "jsondocId": "6a92c3f4-dbc8-465f-9b09-86f130768cec", + "jsondocId": "9d9d3a52-9f7e-40ff-a2b2-c8b2d631f7f2", "name": "metadata", "format": "", "description": "Optional additional information", @@ -8742,9 +8861,9 @@ "verb": "POST", "description": "Create suggested name", "methodName": "createName", - "jsondocId": "73c8e475-bc88-4b9a-bd09-78fb4d4d7437", + "jsondocId": "e50014e0-57b3-458d-8766-8b2f0b0916ab", "bodyobject": { - "jsondocId": "e55f8e04-3d5f-4c5a-9393-1aae72396b22", + "jsondocId": "4faf19ff-8f07-427c-be13-4f8f136e2a9c", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -8754,7 +8873,7 @@ "apierrors": [], "path": "/suggestedName/createName", "response": { - "jsondocId": "7395c6b7-8d51-472a-b787-907401f28368", + "jsondocId": "6de30d11-8d8f-4ae7-b1cb-a1891c0c8c40", "mapValueObject": "", "mapKeyObject": "", "object": "suggested name" @@ -8767,7 +8886,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "b2a3104c-5cf0-4788-b2d3-ea591cff9af4", + "jsondocId": "d5c0904b-0c06-4989-8193-7055845c5b94", "name": "username", "format": "", "description": "", @@ -8776,7 +8895,7 @@ "allowedvalues": [] }, { - "jsondocId": "debca48a-380a-4eb5-952d-01615319e398", + "jsondocId": "160bfb6c-cd3a-4530-9b67-e77d91247d5c", "name": "password", "format": "", "description": "", @@ -8785,7 +8904,7 @@ "allowedvalues": [] }, { - "jsondocId": "5ed12dba-c21f-4918-ad3e-cdff77ea2566", + "jsondocId": "11398ecc-960f-4acb-b7db-18c679684968", "name": "id", "format": "", "description": "Suggested name ID to update (or specify the old_name)", @@ -8794,7 +8913,7 @@ "allowedvalues": [] }, { - "jsondocId": "ceeeff9f-ee5e-4c4b-b2a1-3a3fe99ba088", + "jsondocId": "5f7ac40d-f7a4-40fa-8eaf-3328f6122915", "name": "old_name", "format": "", "description": "Suggested name to update", @@ -8803,7 +8922,7 @@ "allowedvalues": [] }, { - "jsondocId": "9a9f3131-81c7-4b8d-a0ee-8309e06915f8", + "jsondocId": "1e75c6cd-abaf-49e3-9b9f-482f5bf0d42c", "name": "new_name", "format": "", "description": "Suggested name to change to (the only editable option)", @@ -8812,7 +8931,7 @@ "allowedvalues": [] }, { - "jsondocId": "4f868e2a-8973-4a78-95c1-7ddfaaf3c494", + "jsondocId": "4ac613ec-5c8e-477f-bba6-05d812af50e8", "name": "metadata", "format": "", "description": "Optional additional information", @@ -8824,9 +8943,9 @@ "verb": "POST", "description": "Update suggested name", "methodName": "updateName", - "jsondocId": "76b7c3df-aa04-4d3b-ad7e-6bd01b3fadd5", + "jsondocId": "51fd0c1f-0406-484e-b34b-0dd38d3305c8", "bodyobject": { - "jsondocId": "ebb107c6-2035-4d00-adf7-b027253f4d74", + "jsondocId": "d5992edf-2cd3-4524-bb25-5b76adc79d64", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -8836,7 +8955,7 @@ "apierrors": [], "path": "/suggestedName/updateName", "response": { - "jsondocId": "f4ae4af1-44d7-44e2-a3ef-960861896573", + "jsondocId": "44d8de4c-92a4-41f9-a24f-53ba14941828", "mapValueObject": "", "mapKeyObject": "", "object": "suggested name" @@ -8849,7 +8968,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "f0473384-884a-457b-9c90-49e3617e1ca5", + "jsondocId": "7554891f-39e0-40c8-8ade-b30e87b91cd6", "name": "username", "format": "", "description": "", @@ -8858,7 +8977,7 @@ "allowedvalues": [] }, { - "jsondocId": "e135faaa-3168-4133-a089-7272c7fd892d", + "jsondocId": "0ea4c140-d47e-4f29-a9ca-243bb9d22c79", "name": "password", "format": "", "description": "", @@ -8867,7 +8986,7 @@ "allowedvalues": [] }, { - "jsondocId": "2bc6f2c3-143a-46c1-808f-be8a78667b4b", + "jsondocId": "36fd2a8e-cd34-42c6-a0eb-e5a64903ac6d", "name": "id", "format": "", "description": "Suggested name ID to remove (or specify the name)", @@ -8876,7 +8995,7 @@ "allowedvalues": [] }, { - "jsondocId": "ad952f8b-21dc-4e6d-b762-24ce6a1ad153", + "jsondocId": "e37d7a47-baac-4be4-9e1f-c25bbe3d6705", "name": "name", "format": "", "description": "Suggested name to delete", @@ -8888,9 +9007,9 @@ "verb": "POST", "description": "Remove a suggested name", "methodName": "deleteName", - "jsondocId": "31d6b603-80f3-489c-b0f1-f89a15ed70f5", + "jsondocId": "140866a9-c5f4-43c9-a2ab-b9146a279665", "bodyobject": { - "jsondocId": "c7b25556-4600-45f1-930a-6bfe0a1cff10", + "jsondocId": "f49a4ae7-9587-4dcc-8f18-ac6e4f87b716", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -8900,82 +9019,55 @@ "apierrors": [], "path": "/suggestedName/deleteName", "response": { - "jsondocId": "e0e11ac9-59a4-4221-a1b4-76cf1a3cc307", + "jsondocId": "846dcf8f-0706-4326-b8b2-9da950b211bb", "mapValueObject": "", "mapKeyObject": "", "object": "suggested name" }, "produces": ["application/json"], "consumes": ["application/json"] - }, + } + ], + "name": "Suggested Names Services", + "description": "Methods for managing suggested names" + }, + { + "jsondocId": "3cc42b7e-e838-46aa-92b0-dbeee3636e3c", + "methods": [ { "headers": [], "pathparameters": [], - "queryparameters": [ - { - "jsondocId": "2787f507-6b36-4a85-94d9-dcfb68001c8a", - "name": "username", - "format": "", - "description": "", - "type": "email", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "26111d04-08df-43aa-aae5-3c28e2847bad", - "name": "password", - "format": "", - "description": "", - "type": "password", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "003dec62-c2f1-434c-9fc2-098aeb8221c4", - "name": "names", - "format": "", - "description": "A comma-delimited list of names to add", - "type": "string", - "required": "true", - "allowedvalues": [] - } - ], - "verb": "POST", - "description": "A comma-delimited list of names", - "methodName": "addNames", - "jsondocId": "048af5a8-07ea-4f31-aafd-887c81b93b4f", - "bodyobject": { - "jsondocId": "af4115a3-ac3e-4591-b55e-237a6737b297", - "mapValueObject": "", - "mapKeyObject": "", - "multiple": "Unknow", - "map": "", - "object": "suggested name" - }, + "queryparameters": [{ + "jsondocId": "c6a85d5a-97fe-401c-9e8c-30e7a3970a9a", + "name": "organismName", + "format": "", + "description": "Organism common name (required) or 'ALL' if admin", + "type": "string", + "required": "true", + "allowedvalues": [] + }], + "verb": "GET", + "description": "Remove track cache for an organism", + "methodName": "clearOrganismCache", + "jsondocId": "0452cb55-0058-4013-bcb8-8eb533954d64", + "bodyobject": null, "apierrors": [], - "path": "/suggestedName/addNames", + "path": "/track/cache/clear/", "response": { - "jsondocId": "e2a77746-6924-4026-9080-c8d110dffa04", + "jsondocId": "640f6d61-48a6-46eb-9940-b0060a70b083", "mapValueObject": "", "mapKeyObject": "", - "object": "suggested name" + "object": "track" }, "produces": ["application/json"], - "consumes": ["application/json"] - } - ], - "name": "Suggested Names Services", - "description": "Methods for managing suggested names" - }, - { - "jsondocId": "510b31c3-ee70-4060-b4d8-c68739bfbb79", - "methods": [ + "consumes": [] + }, { "headers": [], "pathparameters": [], "queryparameters": [ { - "jsondocId": "56dc7f45-78c6-4ed0-8187-72d78df3fd1f", + "jsondocId": "b1036edb-6d57-4b63-8ff5-a1346cff6bcd", "name": "organismName", "format": "", "description": "Organism common name (required)", @@ -8984,7 +9076,7 @@ "allowedvalues": [] }, { - "jsondocId": "6e8682f2-9f05-4610-a7fa-fe9b0b83e9bf", + "jsondocId": "1b90eb79-3c63-4d66-b903-5c751fd02ab7", "name": "trackName", "format": "", "description": "Track name (required)", @@ -8996,12 +9088,12 @@ "verb": "GET", "description": "Remove track cache for an organism and track", "methodName": "clearTrackCache", - "jsondocId": "30a841f6-1bb3-47b7-9f86-93db2a9e3392", + "jsondocId": "ee53b2e4-2a6f-4f47-8532-81e43be043b2", "bodyobject": null, "apierrors": [], "path": "/track/cache/clear//", "response": { - "jsondocId": "9510a9bb-58ab-4609-aa9c-02380e32001b", + "jsondocId": "912936d8-b16b-42de-97f8-34cd9d1fe573", "mapValueObject": "", "mapKeyObject": "", "object": "track" @@ -9013,7 +9105,7 @@ "headers": [], "pathparameters": [], "queryparameters": [{ - "jsondocId": "a29ca5f6-9c9f-4182-b274-99957cef43b6", + "jsondocId": "aae3ac51-d716-4dac-9310-1837fed07959", "name": "organismName", "format": "", "description": "Organism common name (required)", @@ -9024,12 +9116,12 @@ "verb": "GET", "description": "List all tracks for an organism", "methodName": "getTracks", - "jsondocId": "a61f01a1-b588-444c-86e0-ce88de95e0e0", + "jsondocId": "bc082a69-5f44-4347-8dbd-931c2f6b9ce9", "bodyobject": null, "apierrors": [], "path": "/track/list/", "response": { - "jsondocId": "1e2fefe3-4a42-4c04-a938-e7e8c8d271aa", + "jsondocId": "4d1ee2e5-7ba0-48ff-995b-63107f571924", "mapValueObject": "", "mapKeyObject": "", "object": "track" @@ -9042,7 +9134,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "e7310b53-d288-45a4-a57b-ad420d677fdb", + "jsondocId": "619fe6c8-c411-4f79-84e8-1b2cad00cbf4", "name": "organismString", "format": "", "description": "Organism common name or ID(required)", @@ -9051,7 +9143,7 @@ "allowedvalues": [] }, { - "jsondocId": "f173643b-5db8-4cfa-8b7b-abf44fccaab3", + "jsondocId": "cc9fee09-71c9-4b69-a9c4-91438f0fe557", "name": "trackName", "format": "", "description": "Track name(required)", @@ -9060,7 +9152,7 @@ "allowedvalues": [] }, { - "jsondocId": "5ded49de-ad67-46d5-b9da-93bcf247bfcb", + "jsondocId": "413ed947-2e5f-4b67-8a08-0c3f0a5c6978", "name": "sequence", "format": "", "description": "Sequence name(required)", @@ -9069,7 +9161,7 @@ "allowedvalues": [] }, { - "jsondocId": "101a1b5f-7837-43b0-b9c5-93229c1c1773", + "jsondocId": "bd8fb519-c4ef-4174-a1a2-8707755b6efb", "name": "featureName", "format": "", "description": "If top-level feature 'id' matches, then annotate with 'selected'=1", @@ -9078,7 +9170,7 @@ "allowedvalues": [] }, { - "jsondocId": "8387a835-ad9c-49b4-a9e7-b3e009a0f7a4", + "jsondocId": "3a2eba32-f492-41fa-892b-f25ee4623cd2", "name": "ignoreCache", "format": "", "description": "(default false). Use cache for request if available.", @@ -9087,7 +9179,7 @@ "allowedvalues": [] }, { - "jsondocId": "bd34b92b-07bd-4cc8-98d4-9cdf707c9ae8", + "jsondocId": "22174d4e-f2c8-4064-bb98-34fa482fb46b", "name": "flatten", "format": "", "description": "Brings nested top-level components to the root level. If not provided or 'false' it will not flatten. Default is 'gene'.", @@ -9096,7 +9188,7 @@ "allowedvalues": [] }, { - "jsondocId": "ba60b072-261c-49d0-8297-1f88021b13b6", + "jsondocId": "0c489e59-361f-4d9c-9b73-d6bad9eff8ca", "name": "type", "format": "", "description": ".json or .svg", @@ -9108,12 +9200,12 @@ "verb": "GET", "description": "Get track data as an JSON within but only for the selected name", "methodName": "featuresByName", - "jsondocId": "2ac67a3f-50b4-4903-9e9f-fc859aced014", + "jsondocId": "ce10fb45-4421-4fd6-9eb6-203328f8883f", "bodyobject": null, "apierrors": [], "path": "/track////.?ignoreCache=", "response": { - "jsondocId": "0330201a-6177-4321-b4ef-22c0adf32d33", + "jsondocId": "f81edaa2-abf2-4a31-94ba-59a977760639", "mapValueObject": "", "mapKeyObject": "", "object": "track" @@ -9126,7 +9218,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "8302f205-835e-482d-a93c-fdd2ba24b749", + "jsondocId": "5eeee9cf-f557-4d18-9df4-6c2b0df15417", "name": "organismString", "format": "", "description": "Organism common name or ID(required)", @@ -9135,7 +9227,7 @@ "allowedvalues": [] }, { - "jsondocId": "651e72c8-8ded-4ba5-9d9c-261ec21c8267", + "jsondocId": "179340b9-184f-4615-a19b-765e1260d61d", "name": "trackName", "format": "", "description": "Track name(required)", @@ -9144,7 +9236,7 @@ "allowedvalues": [] }, { - "jsondocId": "eaf7f074-012b-4566-8359-ee3c73bc9203", + "jsondocId": "2ad5d7e9-c3da-4e5a-a979-519735826863", "name": "sequence", "format": "", "description": "Sequence name(required)", @@ -9153,7 +9245,7 @@ "allowedvalues": [] }, { - "jsondocId": "4bdc7309-ae65-4e6d-947d-417c06ba8bd5", + "jsondocId": "7ea09fbc-152b-4e50-949b-1617eb44f27c", "name": "fmin", "format": "", "description": "Minimum range(required)", @@ -9162,7 +9254,7 @@ "allowedvalues": [] }, { - "jsondocId": "80c4dc31-aecb-44d9-b533-666033a252fa", + "jsondocId": "92b4b8de-54ea-4822-a14f-d87a5afecfa5", "name": "fmax", "format": "", "description": "Maximum range (required)", @@ -9171,7 +9263,7 @@ "allowedvalues": [] }, { - "jsondocId": "08d12a6e-09c2-47d3-af61-ba4ef7b5f05b", + "jsondocId": "e4ad0599-d140-485f-b01b-66651038736c", "name": "name", "format": "", "description": "If top-level feature 'name' matches, then annotate with 'selected'=true. Multiple names can be passed in.", @@ -9180,7 +9272,7 @@ "allowedvalues": [] }, { - "jsondocId": "a7674032-bdfc-4fd8-9893-7629b1e795e5", + "jsondocId": "453595c5-6d8d-4c48-94bb-0e7633d3973e", "name": "onlySelected", "format": "", "description": "(default false). If 'selected'!=1 one, then exclude.", @@ -9189,7 +9281,7 @@ "allowedvalues": [] }, { - "jsondocId": "26d7e98c-f866-4c95-b232-e4e6bf23d6ed", + "jsondocId": "fbcd0f65-32cf-4078-85d2-2db79da79e06", "name": "ignoreCache", "format": "", "description": "(default false). Use cache for request if available.", @@ -9198,7 +9290,7 @@ "allowedvalues": [] }, { - "jsondocId": "71a803e7-e134-4932-8438-c1bc90b75874", + "jsondocId": "366f9556-b8ef-4897-aaa2-937ba5be5cf1", "name": "flatten", "format": "", "description": "Brings nested top-level components to the root level. If not provided or 'false' it will not flatten. Default is 'gene'.", @@ -9207,7 +9299,7 @@ "allowedvalues": [] }, { - "jsondocId": "1e41593e-2268-43ff-8e4a-8627f8f61189", + "jsondocId": "5ab9a123-e7a5-4d5a-9ff8-c521ed5b5119", "name": "type", "format": "", "description": ".json or .svg", @@ -9219,40 +9311,12 @@ "verb": "GET", "description": "Get track data as an JSON within an range", "methodName": "featuresByLocation", - "jsondocId": "3a087d09-fccb-4534-a91c-eee5452e171b", + "jsondocId": "2e86089a-500c-428d-97c0-756a261df093", "bodyobject": null, "apierrors": [], "path": "/track///:...?name=&onlySelected=&ignoreCache=", "response": { - "jsondocId": "5dad4370-3c13-42a3-a57c-241f05aa19bc", - "mapValueObject": "", - "mapKeyObject": "", - "object": "track" - }, - "produces": ["application/json"], - "consumes": [] - }, - { - "headers": [], - "pathparameters": [], - "queryparameters": [{ - "jsondocId": "76175171-c3a7-4370-bf67-8d5115440511", - "name": "organismName", - "format": "", - "description": "Organism common name (required) or 'ALL' if admin", - "type": "string", - "required": "true", - "allowedvalues": [] - }], - "verb": "GET", - "description": "Remove track cache for an organism", - "methodName": "clearOrganismCache", - "jsondocId": "fe8ec09e-c149-4480-8b00-0dea92664870", - "bodyobject": null, - "apierrors": [], - "path": "/track/cache/clear/", - "response": { - "jsondocId": "dd56e20d-e7ac-4b7c-9a57-fddd03bbbc0c", + "jsondocId": "7b2db5f0-5555-4147-a769-3124b7366b49", "mapValueObject": "", "mapKeyObject": "", "object": "track" @@ -9265,14 +9329,14 @@ "description": "Methods for retrieving track data" }, { - "jsondocId": "3b259c0f-eed5-4603-90be-fe53952c3123", + "jsondocId": "2937873e-1e8c-464f-9613-19b0173585f1", "methods": [ { "headers": [], "pathparameters": [], "queryparameters": [ { - "jsondocId": "30876d7e-1495-403f-b8e9-dccc32af6257", + "jsondocId": "4015453a-b339-4099-adc2-1b722f20fb92", "name": "username", "format": "", "description": "", @@ -9281,7 +9345,7 @@ "allowedvalues": [] }, { - "jsondocId": "770af04d-8033-4aad-8198-50edc2351f07", + "jsondocId": "0b5da29d-d900-4dd1-9f4b-b619cbb93c37", "name": "password", "format": "", "description": "", @@ -9290,7 +9354,7 @@ "allowedvalues": [] }, { - "jsondocId": "f2195570-8571-4c8d-bdf1-8e1274307009", + "jsondocId": "d17a31d0-aa6b-4cc6-b966-b4723e134784", "name": "userId", "format": "", "description": "User ID to fetch", @@ -9302,9 +9366,9 @@ "verb": "POST", "description": "Get organism permissions for user, returns an array of permission objects", "methodName": "getOrganismPermissionsForUser", - "jsondocId": "d16cd168-b318-4af2-9ecc-297099ce8cba", + "jsondocId": "0c32d8b0-23ab-4f31-a24d-f0442f38ed08", "bodyobject": { - "jsondocId": "cf4e6fb1-a5e6-4f20-a071-de183ac2c903", + "jsondocId": "7f407d8a-d50e-4863-813f-6c214f6bc5f2", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -9314,7 +9378,125 @@ "apierrors": [], "path": "/user/getOrganismPermissionsForUser", "response": { - "jsondocId": "9aa8edb1-7797-45b8-83cd-a9ce844d32e8", + "jsondocId": "7124c739-3293-430e-a5ae-94be040f801d", + "mapValueObject": "", + "mapKeyObject": "", + "object": "user" + }, + "produces": ["application/json"], + "consumes": ["application/json"] + }, + { + "headers": [], + "pathparameters": [], + "queryparameters": [ + { + "jsondocId": "3b3aeae1-85f2-4684-9f0f-71bce37b590b", + "name": "username", + "format": "", + "description": "", + "type": "email", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "77dfb31f-54fa-4d86-80eb-f3438fe9cc7c", + "name": "password", + "format": "", + "description": "", + "type": "password", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "9f498a69-042d-4692-9863-12c8dcb8feff", + "name": "userId", + "format": "", + "description": "User ID to modify permissions for", + "type": "long", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "3cb15755-5754-401b-a8fb-a42127fb5410", + "name": "user", + "format": "", + "description": "(Optional) user email of the user to modify permissions for if User ID is not provided", + "type": "email", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "d8ab284b-eeb8-4d7f-9023-ba368560e875", + "name": "organism", + "format": "", + "description": "Name of organism to update", + "type": "string", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "39dc833d-7029-45e2-85bc-83d22262afaf", + "name": "id", + "format": "", + "description": "Permission ID to update (can get from userId/organism instead)", + "type": "long", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "6c1b1b8a-f012-42b3-9b01-361e045969f0", + "name": "ADMINISTRATE", + "format": "", + "description": "Indicate if user has administrative and all lesser (including user/group) privileges for the organism", + "type": "boolean", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "8768d09d-a639-40b4-a171-454550004391", + "name": "WRITE", + "format": "", + "description": "Indicate if user has write and all lesser privileges for the organism", + "type": "boolean", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "612a53e1-5b4b-44cc-8d9b-6adb4f4cb695", + "name": "EXPORT", + "format": "", + "description": "Indicate if user has export and all lesser privileges for the organism", + "type": "boolean", + "required": "true", + "allowedvalues": [] + }, + { + "jsondocId": "a343697b-aae1-4e6c-8104-5b8ac60c5254", + "name": "READ", + "format": "", + "description": "Indicate if user has read and all lesser privileges for the organism", + "type": "boolean", + "required": "true", + "allowedvalues": [] + } + ], + "verb": "POST", + "description": "Update organism permissions", + "methodName": "updateOrganismPermission", + "jsondocId": "4df8da38-7f0d-4047-a233-5efea5af8b84", + "bodyobject": { + "jsondocId": "4f8d892b-5964-413e-9588-aaa83962bdf3", + "mapValueObject": "", + "mapKeyObject": "", + "multiple": "Unknow", + "map": "", + "object": "user" + }, + "apierrors": [], + "path": "/user/updateOrganismPermission", + "response": { + "jsondocId": "850aff92-4c85-428a-805f-7844b3e2f9e0", "mapValueObject": "", "mapKeyObject": "", "object": "user" @@ -9327,7 +9509,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "53bf112e-3414-4f4e-87d8-68ad0e23afab", + "jsondocId": "4ae215b2-dd6b-43e0-8be1-0126a9785b69", "name": "username", "format": "", "description": "", @@ -9336,7 +9518,7 @@ "allowedvalues": [] }, { - "jsondocId": "c3efd48d-96d1-4a30-985e-b36d411db7f6", + "jsondocId": "fa702bd7-d932-4fd0-af87-05e76acc6fd2", "name": "password", "format": "", "description": "", @@ -9345,7 +9527,7 @@ "allowedvalues": [] }, { - "jsondocId": "70ea1900-385e-4a30-86b4-b5f7210adfc6", + "jsondocId": "db683b6f-c663-4602-9bdb-3a4f76cc9b4d", "name": "userId", "format": "", "description": "Optionally only user a specific userId as an integer database id or a username string", @@ -9354,7 +9536,7 @@ "allowedvalues": [] }, { - "jsondocId": "8f94c714-6df6-44ed-a01b-3341421ebdfd", + "jsondocId": "d85b7ce4-2ea9-4de5-9f25-85b568fc4ceb", "name": "start", "format": "", "description": "(optional) Result start / offset", @@ -9363,7 +9545,7 @@ "allowedvalues": [] }, { - "jsondocId": "2240220e-ea57-448a-ae1e-fb0e97611d5e", + "jsondocId": "29ea0915-fde4-459a-895f-43e0286daffc", "name": "length", "format": "", "description": "(optional) Result length", @@ -9372,7 +9554,7 @@ "allowedvalues": [] }, { - "jsondocId": "ec38fa79-5c27-44c8-bd10-01742b4e2b0f", + "jsondocId": "4b4316d9-a54f-4217-8bab-a1b4f75dd201", "name": "name", "format": "", "description": "(optional) Search name", @@ -9381,7 +9563,7 @@ "allowedvalues": [] }, { - "jsondocId": "ec3d0ca7-196b-4850-b747-971e37c0cf15", + "jsondocId": "4b929003-7514-4d8c-925e-d23813101f5b", "name": "sortColumn", "format": "", "description": "(optional) Sort column, default 'name'", @@ -9390,7 +9572,7 @@ "allowedvalues": [] }, { - "jsondocId": "0f8cd846-38a7-4847-942a-0e55d3562726", + "jsondocId": "e8b3578e-d234-4768-a385-5936fb97bdee", "name": "sortAscending", "format": "", "description": "(optional) Sort column is ascending if true (default false)", @@ -9399,7 +9581,7 @@ "allowedvalues": [] }, { - "jsondocId": "6a48f83a-26a3-4977-b8a2-effe55144a5b", + "jsondocId": "141a9c94-526d-4984-bd71-d4b933b5b2be", "name": "omitEmptyOrganisms", "format": "", "description": "(optional) Omits empty organism permissions from return (default false)", @@ -9408,7 +9590,7 @@ "allowedvalues": [] }, { - "jsondocId": "ccb5de54-e4d4-4044-b20a-e9056b589b67", + "jsondocId": "cf16e5cc-606e-4fcb-b24d-ba511549e554", "name": "showInactiveUsers", "format": "", "description": "(optional) Shows inactive users without permissions (default false)", @@ -9420,9 +9602,9 @@ "verb": "POST", "description": "Load all users and their permissions", "methodName": "loadUsers", - "jsondocId": "9a5c14e1-fe08-4157-b76d-a173e0861371", + "jsondocId": "9cf6373b-1ce7-4ccf-abe8-d67904bd018b", "bodyobject": { - "jsondocId": "44365704-d3f0-45ea-a63d-8f5605ae434d", + "jsondocId": "706eb754-6c97-4bab-a879-6c521bc959d3", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -9432,7 +9614,7 @@ "apierrors": [], "path": "/user/loadUsers", "response": { - "jsondocId": "c7b4cddd-90d0-490c-8983-b46b2ba52283", + "jsondocId": "d2367e91-c359-497d-acdb-b3468a3899f1", "mapValueObject": "", "mapKeyObject": "", "object": "user" @@ -9445,7 +9627,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "b0ee4a1e-1dec-4512-8fe2-c8cf18c84d81", + "jsondocId": "4a04fbfc-fa92-499d-b4d9-7ee592c75657", "name": "username", "format": "", "description": "", @@ -9454,7 +9636,7 @@ "allowedvalues": [] }, { - "jsondocId": "a16acd9b-be7a-4801-9b56-ce78d39b4c92", + "jsondocId": "c5ca70bd-2441-4e41-a1b4-4de0455fd836", "name": "password", "format": "", "description": "", @@ -9463,7 +9645,7 @@ "allowedvalues": [] }, { - "jsondocId": "c9b059aa-8882-4edd-abee-987a58f3c666", + "jsondocId": "ef502e72-746f-4ad0-9ce6-91b106366fd1", "name": "group", "format": "", "description": "Group name", @@ -9472,7 +9654,7 @@ "allowedvalues": [] }, { - "jsondocId": "e6e892d2-7379-4b45-9854-bcef78e9d31d", + "jsondocId": "f9b14fbb-db07-4dbb-95ac-55bd546b363b", "name": "userId", "format": "", "description": "User id", @@ -9481,7 +9663,7 @@ "allowedvalues": [] }, { - "jsondocId": "b150d544-b5e3-42ef-9c97-6e937a7d091a", + "jsondocId": "1dc9a2e2-b189-4244-a4bd-ee0b399697ba", "name": "user", "format": "", "description": "User email/username (supplied if user id unknown)", @@ -9493,9 +9675,9 @@ "verb": "POST", "description": "Add user to group", "methodName": "addUserToGroup", - "jsondocId": "c70615d4-c48b-49b2-9ddb-01827f80be33", + "jsondocId": "d7c25c0e-dc4b-4281-9dfe-a1271fb33a62", "bodyobject": { - "jsondocId": "98048434-e834-4f39-8b0d-b530ef3c6e46", + "jsondocId": "0c9cba76-5410-4571-946f-92d0dd58176e", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -9505,7 +9687,7 @@ "apierrors": [], "path": "/user/addUserToGroup", "response": { - "jsondocId": "d786b264-854f-4050-aed7-650ed4851009", + "jsondocId": "c0484fdf-17f5-45b4-94bf-87662dc3ce19", "mapValueObject": "", "mapKeyObject": "", "object": "user" @@ -9518,7 +9700,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "f499efc1-2017-45db-9a9c-ca03c4b35224", + "jsondocId": "3a4dc746-267c-49bf-8e5c-989b8027a825", "name": "username", "format": "", "description": "", @@ -9527,7 +9709,7 @@ "allowedvalues": [] }, { - "jsondocId": "cf1998d6-4739-4dfb-8b7d-66d292016faf", + "jsondocId": "1a60cded-38da-4a93-b48b-ce13203320c0", "name": "password", "format": "", "description": "", @@ -9536,7 +9718,7 @@ "allowedvalues": [] }, { - "jsondocId": "f4d1e2dc-3a32-49e7-b8d4-a5ca95d823ff", + "jsondocId": "6b8557a0-b604-423f-af7e-6ad852ee3197", "name": "group", "format": "", "description": "Group name", @@ -9545,7 +9727,7 @@ "allowedvalues": [] }, { - "jsondocId": "2c28585b-43b9-4f7f-8f07-7937a5555390", + "jsondocId": "e1a9642c-fbfb-4458-9614-83280cd18c2d", "name": "userId", "format": "", "description": "User id", @@ -9554,7 +9736,7 @@ "allowedvalues": [] }, { - "jsondocId": "2e030d7e-3d1d-4be5-9096-cfaa66bce89d", + "jsondocId": "4a508eab-3d6b-48db-90b0-3ed378393284", "name": "user", "format": "", "description": "User email/username (supplied if user id unknown)", @@ -9566,9 +9748,9 @@ "verb": "POST", "description": "Remove user from group", "methodName": "removeUserFromGroup", - "jsondocId": "28d26ef3-e797-4a6e-96d3-d940284724dd", + "jsondocId": "923e11f1-38ba-4c72-b2c6-79d4d073a547", "bodyobject": { - "jsondocId": "fca07967-d44b-464a-bf5a-8957c4b805c9", + "jsondocId": "c78e10b0-2baf-4e65-8101-7dc8ab24b6ca", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -9578,7 +9760,7 @@ "apierrors": [], "path": "/user/removeUserFromGroup", "response": { - "jsondocId": "06fd0efc-9a64-4ebf-9305-bab095f98ebd", + "jsondocId": "a5fd2741-0365-45a9-b31e-1c78d9fb6e8d", "mapValueObject": "", "mapKeyObject": "", "object": "user" @@ -9591,7 +9773,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "75285a6c-f4ac-4eac-a19f-1ffd4b8aade1", + "jsondocId": "b0e97d3f-fabd-41c1-bd8d-c811830f0514", "name": "username", "format": "", "description": "", @@ -9600,7 +9782,7 @@ "allowedvalues": [] }, { - "jsondocId": "5017f4f2-f24f-4fb5-8b09-c4e33effd618", + "jsondocId": "881d9ffe-5003-47bc-989d-33ba5425981a", "name": "password", "format": "", "description": "", @@ -9609,7 +9791,7 @@ "allowedvalues": [] }, { - "jsondocId": "0aaf960c-cd13-4c23-b047-f876340e1ef3", + "jsondocId": "db3b1974-3826-448e-a211-fe8f77d16ad9", "name": "email", "format": "", "description": "Email of the user to add", @@ -9618,7 +9800,7 @@ "allowedvalues": [] }, { - "jsondocId": "ac045e2e-06bf-4c25-92d7-b77a96f205ae", + "jsondocId": "d5a141a6-2a7c-4fb9-b096-7c72ccb6cfc1", "name": "firstName", "format": "", "description": "First name of user to add", @@ -9627,7 +9809,7 @@ "allowedvalues": [] }, { - "jsondocId": "6cd270fb-b24f-4b8f-aed4-e7a83d229ecb", + "jsondocId": "cc65e5f9-94fd-4381-bcff-6c5fb660dc56", "name": "lastName", "format": "", "description": "Last name of user to add", @@ -9636,7 +9818,7 @@ "allowedvalues": [] }, { - "jsondocId": "9b050fca-22e4-4260-bca8-e62c2b1ac6c7", + "jsondocId": "f9b10b2d-5230-469d-9675-2e73a690ca10", "name": "metadata", "format": "", "description": "User metadata (optional)", @@ -9645,7 +9827,7 @@ "allowedvalues": [] }, { - "jsondocId": "7859b8d2-c625-45e1-8849-21f7fe96a6bd", + "jsondocId": "fcf44991-f5fc-4bf4-9722-6722a95028e9", "name": "role", "format": "", "description": "User role USER / ADMIN (optional: default USER) ", @@ -9654,7 +9836,7 @@ "allowedvalues": [] }, { - "jsondocId": "17107ba5-28a0-4525-a6b2-131ffa091591", + "jsondocId": "f13e87db-f4e2-4c7a-af12-498ba02b06a4", "name": "newPassword", "format": "", "description": "Password of user to add", @@ -9666,9 +9848,9 @@ "verb": "POST", "description": "Create user", "methodName": "createUser", - "jsondocId": "a723766b-f3ff-49f8-8d3d-a1976ba5196b", + "jsondocId": "b84faa9d-be86-4413-9dbc-66a18296adc0", "bodyobject": { - "jsondocId": "8810de14-e3fc-4bf4-9742-057441e62742", + "jsondocId": "99ec8728-cf14-4235-a6de-6eebeaf722f0", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -9678,7 +9860,7 @@ "apierrors": [], "path": "/user/createUser", "response": { - "jsondocId": "936eeb26-3f46-48b0-ab08-fe2df471b61d", + "jsondocId": "862fecb1-6a34-4b4c-a787-2f8a90bb7df8", "mapValueObject": "", "mapKeyObject": "", "object": "user" @@ -9691,7 +9873,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "4bc0e613-0f11-4976-bac1-35854983b4f5", + "jsondocId": "1e89d185-1e4e-4985-920f-4e90c633f40c", "name": "username", "format": "", "description": "", @@ -9700,7 +9882,7 @@ "allowedvalues": [] }, { - "jsondocId": "f24a8924-3cb8-4654-9153-0a5f8b6f3053", + "jsondocId": "c172cef8-359a-4416-96fc-3f42ceceab69", "name": "password", "format": "", "description": "", @@ -9709,7 +9891,7 @@ "allowedvalues": [] }, { - "jsondocId": "0c560c8f-0411-432b-8625-30f60732d960", + "jsondocId": "02fbb3de-11bf-4ec1-8cb2-763c8a135d30", "name": "userId", "format": "", "description": "User ID to delete", @@ -9718,7 +9900,7 @@ "allowedvalues": [] }, { - "jsondocId": "55e67845-0e2a-4dd0-bbcd-ccca4c493463", + "jsondocId": "4b129143-e8a2-4ee0-9651-eee5f9f37f29", "name": "userToDelete", "format": "", "description": "Username (email) to inactivate", @@ -9730,9 +9912,9 @@ "verb": "POST", "description": "Inactivate user, removing all permsissions and setting flag", "methodName": "inactivateUser", - "jsondocId": "2d78c5a0-55ab-41b3-9884-9bd6bc1fa15f", + "jsondocId": "f54f06f5-0c37-402f-a7c9-0b694ffc91b7", "bodyobject": { - "jsondocId": "a72b9f86-5f8d-4a5c-9b02-ce894ef204d1", + "jsondocId": "385c5466-8014-4d5b-a90f-4399474d12d6", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -9742,7 +9924,7 @@ "apierrors": [], "path": "/user/inactivateUser", "response": { - "jsondocId": "e0c93a6f-a0f0-472d-8799-748abdd67cb3", + "jsondocId": "22c9cea7-304d-40a4-85e7-292a686318e3", "mapValueObject": "", "mapKeyObject": "", "object": "user" @@ -9755,7 +9937,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "a0b67670-d1a9-4dc4-a7fe-f6e953c2863b", + "jsondocId": "7532bbda-90af-4e90-b62c-86976e6b2b0a", "name": "username", "format": "", "description": "", @@ -9764,7 +9946,7 @@ "allowedvalues": [] }, { - "jsondocId": "da2aabda-1d3b-4263-9e93-08cdd2894921", + "jsondocId": "e0f3d4fd-a583-409d-8e5c-361c0535535d", "name": "password", "format": "", "description": "", @@ -9773,7 +9955,7 @@ "allowedvalues": [] }, { - "jsondocId": "ee7c692e-e7b5-47c6-9cac-62cfe8d57c45", + "jsondocId": "42b725cd-4491-4457-b9b0-60efb36c1b00", "name": "userId", "format": "", "description": "User ID to delete", @@ -9782,7 +9964,7 @@ "allowedvalues": [] }, { - "jsondocId": "89120e4f-ddfe-49ea-9c12-e26632bb452b", + "jsondocId": "a6fdada9-3e49-4263-8378-6eef9c31c849", "name": "userToActivate", "format": "", "description": "Username (email) to inactivate", @@ -9794,9 +9976,9 @@ "verb": "POST", "description": "Activate user", "methodName": "activateUser", - "jsondocId": "a6266720-a0a8-4898-b351-8565aa8cb782", + "jsondocId": "a9e9e850-1a60-46ed-bd08-e3ed9cbdfb5e", "bodyobject": { - "jsondocId": "639fc761-65d6-4ebb-b238-7049e9dc835f", + "jsondocId": "7e679041-cc8e-462d-96e6-4ceee4546c00", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -9806,7 +9988,7 @@ "apierrors": [], "path": "/user/activateUser", "response": { - "jsondocId": "920ebd95-ba37-44a0-b054-0200a5d35f64", + "jsondocId": "1cd15d98-c54e-42c5-9894-12eb35b0b795", "mapValueObject": "", "mapKeyObject": "", "object": "user" @@ -9819,7 +10001,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "17bc6ed2-02fe-4435-966f-1dd79680c5f5", + "jsondocId": "d7bfc191-65c5-474f-89c3-cc2171e0d3b1", "name": "username", "format": "", "description": "", @@ -9828,7 +10010,7 @@ "allowedvalues": [] }, { - "jsondocId": "e4edbf63-f132-4532-9977-25f1cbd5321b", + "jsondocId": "285e2d68-f487-4fc4-a9a6-05ed534809dc", "name": "password", "format": "", "description": "", @@ -9837,7 +10019,7 @@ "allowedvalues": [] }, { - "jsondocId": "b7155af0-8ea9-413d-a000-2606041d73a2", + "jsondocId": "59973f58-66c4-44c9-9ddd-274e86913cdd", "name": "userId", "format": "", "description": "User ID to delete", @@ -9846,7 +10028,7 @@ "allowedvalues": [] }, { - "jsondocId": "322062a0-e197-40e4-bfd6-a3178aff5f61", + "jsondocId": "afad7638-53f5-4dd0-a6b1-c35aeeb86d23", "name": "userToDelete", "format": "", "description": "Username (email) to delete", @@ -9858,9 +10040,9 @@ "verb": "POST", "description": "Delete user", "methodName": "deleteUser", - "jsondocId": "de68cb57-2e25-4fcf-aa38-11c4832307c1", + "jsondocId": "e88914fa-14c4-4185-9c69-6deeaaa70120", "bodyobject": { - "jsondocId": "a3f0d486-f455-4c22-8440-111aab3ff5b6", + "jsondocId": "d5945c3d-cc9c-4cf3-bca0-239406c4ada2", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -9870,7 +10052,7 @@ "apierrors": [], "path": "/user/deleteUser", "response": { - "jsondocId": "c567d8fe-1b30-405e-98f5-e0dbdfc7da65", + "jsondocId": "b197f33b-2301-4e4e-89db-b1ca97459b55", "mapValueObject": "", "mapKeyObject": "", "object": "user" @@ -9883,7 +10065,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "d2fc58ce-7f94-4e7b-94bd-c91c1bd11b4f", + "jsondocId": "6670d0f6-c73b-405e-8488-1e2b03691c63", "name": "username", "format": "", "description": "", @@ -9892,7 +10074,7 @@ "allowedvalues": [] }, { - "jsondocId": "b2407ca2-2b87-4742-b134-09f05455a4f8", + "jsondocId": "860e114e-8836-41fb-9842-b68d4d042324", "name": "password", "format": "", "description": "", @@ -9901,7 +10083,7 @@ "allowedvalues": [] }, { - "jsondocId": "556ef536-1f4e-46d4-afd8-cf05e668567a", + "jsondocId": "1b21f776-82fe-4224-a6a5-309a7343190b", "name": "userId", "format": "", "description": "User ID to update", @@ -9910,7 +10092,7 @@ "allowedvalues": [] }, { - "jsondocId": "8fb5a20c-cccf-4791-8b34-82c69361f583", + "jsondocId": "784035b4-9d2e-4703-b791-3aa9b725cbbd", "name": "email", "format": "", "description": "Email of the user to update", @@ -9919,7 +10101,7 @@ "allowedvalues": [] }, { - "jsondocId": "15669c0e-5372-47c4-81ac-90da4fc1062b", + "jsondocId": "42432a4b-814b-4c04-b4c8-ca6a40522aea", "name": "firstName", "format": "", "description": "First name of user to update", @@ -9928,7 +10110,7 @@ "allowedvalues": [] }, { - "jsondocId": "e488d819-e667-4a7d-8c41-2580f8b7a207", + "jsondocId": "1383ffde-2ea7-4097-9a61-31e48648c59c", "name": "lastName", "format": "", "description": "Last name of user to update", @@ -9937,7 +10119,7 @@ "allowedvalues": [] }, { - "jsondocId": "431ce22c-6259-4db6-8738-192a861f8d95", + "jsondocId": "c62e90b9-dd85-4771-9663-84b63cbb927d", "name": "metadata", "format": "", "description": "User metadata (optional)", @@ -9946,7 +10128,7 @@ "allowedvalues": [] }, { - "jsondocId": "ff039854-43bf-4bd0-9f1a-2a993eee90af", + "jsondocId": "40cb7445-32d3-4953-a70a-76c9829ec426", "name": "newPassword", "format": "", "description": "Password of user to update", @@ -9958,9 +10140,9 @@ "verb": "POST", "description": "Update user", "methodName": "updateUser", - "jsondocId": "b48f148d-8246-493c-86d7-f008306b80e3", + "jsondocId": "83460772-178a-43d1-a8d7-06a8633f2490", "bodyobject": { - "jsondocId": "e52a5db3-8e33-4b9c-a752-f2a2ec5ad82d", + "jsondocId": "deff9df1-3dc9-4266-a37d-7b6c475c7e88", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -9970,7 +10152,7 @@ "apierrors": [], "path": "/user/updateUser", "response": { - "jsondocId": "ee72f03b-d6d8-494f-9621-db884f9fa797", + "jsondocId": "b50fbcca-9ef3-4a85-bee5-62506faa7906", "mapValueObject": "", "mapKeyObject": "", "object": "user" @@ -9983,7 +10165,7 @@ "pathparameters": [], "queryparameters": [ { - "jsondocId": "19d1b87e-86b3-4018-b62a-9839a550c5af", + "jsondocId": "2672e4a6-d9d0-4758-b04c-81431cc66732", "name": "username", "format": "", "description": "", @@ -9992,7 +10174,7 @@ "allowedvalues": [] }, { - "jsondocId": "a79ac0ab-3265-417b-a463-0fdb1c3a82c1", + "jsondocId": "46da9e86-336c-4118-a9b0-928582785abd", "name": "password", "format": "", "description": "", @@ -10001,7 +10183,7 @@ "allowedvalues": [] }, { - "jsondocId": "616d2790-386c-4a39-883f-991c8893c8ce", + "jsondocId": "c761f8d8-f2d0-4a9b-ba09-f77185e7489c", "name": "email", "format": "", "description": "Email of the user", @@ -10013,9 +10195,9 @@ "verb": "POST", "description": "Get creator metadata for user, returns creator userId as JSONObject", "methodName": "getUserCreator", - "jsondocId": "0e01d8bd-41a2-4a1b-9b69-7ece999b5119", + "jsondocId": "0045193a-9315-4b7b-b4fb-20a65638c1d6", "bodyobject": { - "jsondocId": "d6635a35-7950-415c-b62f-a56aa6e6a613", + "jsondocId": "12b3454a-550e-463b-a85d-43758a568908", "mapValueObject": "", "mapKeyObject": "", "multiple": "Unknow", @@ -10025,125 +10207,7 @@ "apierrors": [], "path": "/user/getUserCreator", "response": { - "jsondocId": "6b698794-9783-4618-8dc7-6cf189432d13", - "mapValueObject": "", - "mapKeyObject": "", - "object": "user" - }, - "produces": ["application/json"], - "consumes": ["application/json"] - }, - { - "headers": [], - "pathparameters": [], - "queryparameters": [ - { - "jsondocId": "27357b37-8839-4bdb-bcf2-b40dfb9d51e5", - "name": "username", - "format": "", - "description": "", - "type": "email", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "c8e658e4-cd87-4c5f-a356-9c3e5e8bb0b5", - "name": "password", - "format": "", - "description": "", - "type": "password", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "0ae81ed3-75dc-4f25-8c91-ed3a0512c7e3", - "name": "userId", - "format": "", - "description": "User ID to modify permissions for", - "type": "long", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "6580cf4f-6087-4338-8923-30f389a9c21a", - "name": "user", - "format": "", - "description": "(Optional) user email of the user to modify permissions for if User ID is not provided", - "type": "email", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "cb00adf7-34b0-4069-bdcf-fe7ff50ef1e5", - "name": "organism", - "format": "", - "description": "Name of organism to update", - "type": "string", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "815da2cd-5ada-4fd4-84c4-429616f0a6bc", - "name": "id", - "format": "", - "description": "Permission ID to update (can get from userId/organism instead)", - "type": "long", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "e03fa67c-732e-465f-9eea-17741834fc31", - "name": "ADMINISTRATE", - "format": "", - "description": "Indicate if user has administrative and all lesser (including user/group) privileges for the organism", - "type": "boolean", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "0cb0552d-53cd-42b5-a0e3-fa1b8dead073", - "name": "WRITE", - "format": "", - "description": "Indicate if user has write and all lesser privileges for the organism", - "type": "boolean", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "2f2b9b72-1295-4ece-9090-9c0f3802133e", - "name": "EXPORT", - "format": "", - "description": "Indicate if user has export and all lesser privileges for the organism", - "type": "boolean", - "required": "true", - "allowedvalues": [] - }, - { - "jsondocId": "c6c9d8d4-0b8c-4755-8b54-2dc7b30a9c3c", - "name": "READ", - "format": "", - "description": "Indicate if user has read and all lesser privileges for the organism", - "type": "boolean", - "required": "true", - "allowedvalues": [] - } - ], - "verb": "POST", - "description": "Update organism permissions", - "methodName": "updateOrganismPermission", - "jsondocId": "08a8c487-8077-4b5a-a018-f595ff959ee0", - "bodyobject": { - "jsondocId": "2456c47d-3c09-42b4-b3d5-581ee71266a1", - "mapValueObject": "", - "mapKeyObject": "", - "multiple": "Unknow", - "map": "", - "object": "user" - }, - "apierrors": [], - "path": "/user/updateOrganismPermission", - "response": { - "jsondocId": "2bd419b0-bd76-45d8-8909-601d0a589e49", + "jsondocId": "8f16b26b-0cc2-4102-9d64-33291112191b", "mapValueObject": "", "mapKeyObject": "", "object": "user" @@ -10156,13 +10220,13 @@ "description": "Methods for managing users" }, { - "jsondocId": "e09ab375-b711-4977-ac2e-c158dccdb663", + "jsondocId": "ce910806-1427-43c5-90cd-ae600a6f03d3", "methods": [{ "headers": [], "pathparameters": [], "queryparameters": [ { - "jsondocId": "2b85217d-71e9-4dbe-a9ca-993f48141807", + "jsondocId": "47b08d01-d36e-40fd-a161-cee12149d73d", "name": "organismString", "format": "", "description": "Organism common name or ID (required)", @@ -10171,7 +10235,7 @@ "allowedvalues": [] }, { - "jsondocId": "371628d4-572f-4d05-97ce-327785db8032", + "jsondocId": "baaf42ad-1add-46b7-bb50-7e51f36d0731", "name": "trackName", "format": "", "description": "Track name by label in trackList.json (required)", @@ -10180,7 +10244,7 @@ "allowedvalues": [] }, { - "jsondocId": "aa2b9b9f-16f3-4c9f-8a0d-3f69dd8f3a25", + "jsondocId": "4f089dfe-54f4-4907-82b4-393ff7fd0625", "name": "sequence", "format": "", "description": "Sequence name (required)", @@ -10189,7 +10253,7 @@ "allowedvalues": [] }, { - "jsondocId": "4f71544f-9310-4731-9a0c-9040637e0274", + "jsondocId": "bb9530e9-5acb-4f0e-89c3-bd8c491a0b11", "name": "fmin", "format": "", "description": "Minimum range (required)", @@ -10198,7 +10262,7 @@ "allowedvalues": [] }, { - "jsondocId": "69b63d2f-9c93-421c-a06b-735df975be33", + "jsondocId": "2b94ede3-7571-4092-861b-dce406f37056", "name": "fmax", "format": "", "description": "Maximum range (required)", @@ -10207,7 +10271,7 @@ "allowedvalues": [] }, { - "jsondocId": "7b00737e-639f-4421-a0d1-e73c30b8a187", + "jsondocId": "fb5eb85c-1065-43e3-86a1-98f65d8a4549", "name": "type", "format": "", "description": ".json (required)", @@ -10216,7 +10280,7 @@ "allowedvalues": [] }, { - "jsondocId": "6b6c0338-afd3-4fd2-a6b5-2958c2a546dc", + "jsondocId": "9db08c6c-54ad-4c81-8c5a-b857e6b9299d", "name": "includeGenotypes", "format": "", "description": "(default: false). If true, will include genotypes associated with variants from VCF.", @@ -10225,7 +10289,7 @@ "allowedvalues": [] }, { - "jsondocId": "041dd511-b252-4ba4-a11c-71101ec05967", + "jsondocId": "98f407b4-c321-4f30-b008-5ce07321e9c8", "name": "ignoreCache", "format": "", "description": "(default: false). Use cache for request, if available.", @@ -10237,12 +10301,12 @@ "verb": "GET", "description": "Get VCF track data for a given range as JSON", "methodName": "featuresByLocation", - "jsondocId": "25e435fd-8a3b-404e-97a7-8a288dce2284", + "jsondocId": "3f77cf9e-2ec8-40f2-af6b-502af827921f", "bodyobject": null, "apierrors": [], "path": "/vcf///:...?includeGenotypes=&ignoreCache=", "response": { - "jsondocId": "75000a7e-1cc7-4f9b-8638-f69dca55f140", + "jsondocId": "6c4076bc-d75a-4d43-9a6c-5c6fd0f48f0f", "mapValueObject": "", "mapKeyObject": "", "object": "vcf"