client: improve description of the parameter 'field' for aggregations…

…, #TASK-7152, #TASK-7134

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisClinicalCommandOptions.java

@@ -238,7 +238,7 @@ public class AggregationStatsCommandOptions {
         @Parameter(names = {"--deleted"}, description = "Boolean to retrieve deleted entries", required = false, help = true, arity = 0)
         public boolean deleted = false; 
 
-        @Parameter(names = {"--field"}, description = "List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size)", required = false, arity = 1)
+        @Parameter(names = {"--field"}, description = "Field to apply aggregation statistics to (or a list of fields separated by semicolons), e.g.: studies;type;numSamples[0..10]:1;format:sum(size)", required = false, arity = 1)
         public String field; 
 
     }
@@ -596,7 +596,7 @@ public class AggregationStatsInterpretationCommandOptions {
         @Parameter(names = {"--release"}, description = "Release when it was created", required = false, arity = 1)
         public String release; 
 
-        @Parameter(names = {"--field"}, description = "List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size)", required = false, arity = 1)
+        @Parameter(names = {"--field"}, description = "Field to apply aggregation statistics to (or a list of fields separated by semicolons), e.g.: studies;type;numSamples[0..10]:1;format:sum(size)", required = false, arity = 1)
         public String field; 
 
     }

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/CohortsCommandOptions.java

@@ -146,7 +146,7 @@ public class AggregationStatsCommandOptions {
         @Parameter(names = {"--release"}, description = "release", required = false, arity = 1)
         public String release; 
 
-        @Parameter(names = {"--field"}, description = "List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size)", required = false, arity = 1)
+        @Parameter(names = {"--field"}, description = "Field to apply aggregation statistics to (or a list of fields separated by semicolons), e.g.: studies;type;numSamples[0..10]:1;format:sum(size)", required = false, arity = 1)
         public String field; 
 
     }

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/DiseasePanelsCommandOptions.java

@@ -154,7 +154,7 @@ public class AggregationStatsCommandOptions {
         @Parameter(names = {"--snapshot"}, description = "Snapshot value (Latest version of the entry in the specified release)", required = false, arity = 1)
         public Integer snapshot; 
 
-        @Parameter(names = {"--field"}, description = "List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size)", required = false, arity = 1)
+        @Parameter(names = {"--field"}, description = "Field to apply aggregation statistics to (or a list of fields separated by semicolons), e.g.: studies;type;numSamples[0..10]:1;format:sum(size)", required = false, arity = 1)
         public String field; 
 
     }

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/FamiliesCommandOptions.java

@@ -162,7 +162,7 @@ public class AggregationStatsCommandOptions {
         @Parameter(names = {"--snapshot"}, description = "Snapshot value (Latest version of the entry in the specified release)", required = false, arity = 1)
         public Integer snapshot; 
 
-        @Parameter(names = {"--field"}, description = "List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size)", required = false, arity = 1)
+        @Parameter(names = {"--field"}, description = "Field to apply aggregation statistics to (or a list of fields separated by semicolons), e.g.: studies;type;numSamples[0..10]:1;format:sum(size)", required = false, arity = 1)
         public String field; 
 
     }

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/FilesCommandOptions.java

@@ -213,7 +213,7 @@ public class AggregationStatsCommandOptions {
         @Parameter(names = {"--release"}, description = "Release when it was created", required = false, arity = 1)
         public String release; 
 
-        @Parameter(names = {"--field"}, description = "List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size)", required = false, arity = 1)
+        @Parameter(names = {"--field"}, description = "Field to apply aggregation statistics to (or a list of fields separated by semicolons), e.g.: studies;type;numSamples[0..10]:1;format:sum(size)", required = false, arity = 1)
         public String field; 
 
     }

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/IndividualsCommandOptions.java

@@ -185,7 +185,7 @@ public class AggregationStatsCommandOptions {
         @Parameter(names = {"--snapshot"}, description = "Snapshot value (Latest version of the entry in the specified release)", required = false, arity = 1)
         public Integer snapshot; 
 
-        @Parameter(names = {"--field"}, description = "List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size)", required = false, arity = 1)
+        @Parameter(names = {"--field"}, description = "Field to apply aggregation statistics to (or a list of fields separated by semicolons), e.g.: studies;type;numSamples[0..10]:1;format:sum(size)", required = false, arity = 1)
         public String field; 
 
     }

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/JobsCommandOptions.java

@@ -158,7 +158,7 @@ public class AggregationStatsCommandOptions {
         @Parameter(names = {"--deleted"}, description = "Boolean to retrieve deleted entries", required = false, help = true, arity = 0)
         public boolean deleted = false; 
 
-        @Parameter(names = {"--field"}, description = "List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size)", required = false, arity = 1)
+        @Parameter(names = {"--field"}, description = "Field to apply aggregation statistics to (or a list of fields separated by semicolons), e.g.: studies;type;numSamples[0..10]:1;format:sum(size)", required = false, arity = 1)
         public String field; 
 
     }

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/SamplesCommandOptions.java

@@ -227,7 +227,7 @@ public class AggregationStatsCommandOptions {
         @Parameter(names = {"--stats-consequence-type-count"}, description = "Sample variant stats ConsequenceTypeCount", required = false, arity = 1)
         public String statsConsequenceTypeCount; 
 
-        @Parameter(names = {"--field"}, description = "List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size)", required = false, arity = 1)
+        @Parameter(names = {"--field"}, description = "Field to apply aggregation statistics to (or a list of fields separated by semicolons), e.g.: studies;type;numSamples[0..10]:1;format:sum(size)", required = false, arity = 1)
         public String field; 
 
     }

opencga-client/src/main/R/R/Clinical-methods.R

@@ -107,7 +107,7 @@ setMethod("clinicalClient", "OpencgaR", function(OpencgaR, annotationSet, clinic
         #' @param internalStatus Filter by internal status.
         #' @param annotation Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0.
         #' @param deleted Boolean to retrieve deleted entries.
-        #' @param field List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size).
+        #' @param field Field to apply aggregation statistics to (or a list of fields separated by semicolons), e.g.: studies;type;numSamples[0..10]:1;format:sum(size).
         aggregationStats=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL, subcategory="clinical",
                 subcategoryId=NULL, action="aggregationStats", params=params, httpMethod="GET", as.queryParam=NULL,
                 ...),
@@ -194,7 +194,7 @@ setMethod("clinicalClient", "OpencgaR", function(OpencgaR, annotationSet, clinic
         #' @param status Filter by status.
         #' @param internalStatus Filter by internal status.
         #' @param release Release when it was created.
-        #' @param field List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size).
+        #' @param field Field to apply aggregation statistics to (or a list of fields separated by semicolons), e.g.: studies;type;numSamples[0..10]:1;format:sum(size).
         aggregationStatsInterpretation=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL,
                 subcategory="clinical/interpretation", subcategoryId=NULL, action="aggregationStats", params=params,
                 httpMethod="GET", as.queryParam=NULL, ...),

opencga-client/src/main/R/R/Cohort-methods.R

@@ -68,7 +68,7 @@ setMethod("cohortClient", "OpencgaR", function(OpencgaR, annotationSet, cohort,
         #' @param samples Cohort sample IDs.
         #' @param numSamples Number of samples.
         #' @param release release.
-        #' @param field List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size).
+        #' @param field Field to apply aggregation statistics to (or a list of fields separated by semicolons), e.g.: studies;type;numSamples[0..10]:1;format:sum(size).
         aggregationStats=fetchOpenCGA(object=OpencgaR, category="cohorts", categoryId=NULL, subcategory=NULL,
                 subcategoryId=NULL, action="aggregationStats", params=params, httpMethod="GET", as.queryParam=NULL,
                 ...),

opencga-client/src/main/R/R/Family-methods.R

@@ -71,7 +71,7 @@ setMethod("familyClient", "OpencgaR", function(OpencgaR, annotationSet, families
         #' @param acl Filter entries for which a user has the provided permissions. Format: acl={user}:{permissions}. Example: acl=john:WRITE,WRITE_ANNOTATIONS will return all entries for which user john has both WRITE and WRITE_ANNOTATIONS permissions. Only study owners or administrators can query by this field. .
         #' @param release Release when it was created.
         #' @param snapshot Snapshot value (Latest version of the entry in the specified release).
-        #' @param field List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size).
+        #' @param field Field to apply aggregation statistics to (or a list of fields separated by semicolons), e.g.: studies;type;numSamples[0..10]:1;format:sum(size).
         aggregationStats=fetchOpenCGA(object=OpencgaR, category="families", categoryId=NULL, subcategory=NULL,
                 subcategoryId=NULL, action="aggregationStats", params=params, httpMethod="GET", as.queryParam=NULL,
                 ...),

opencga-client/src/main/R/R/File-methods.R

@@ -95,7 +95,7 @@ setMethod("fileClient", "OpencgaR", function(OpencgaR, annotationSet, file, file
         #' @param acl Filter entries for which a user has the provided permissions. Format: acl={user}:{permissions}. Example: acl=john:WRITE,WRITE_ANNOTATIONS will return all entries for which user john has both WRITE and WRITE_ANNOTATIONS permissions. Only study owners or administrators can query by this field. .
         #' @param deleted Boolean to retrieve deleted entries.
         #' @param release Release when it was created.
-        #' @param field List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size).
+        #' @param field Field to apply aggregation statistics to (or a list of fields separated by semicolons), e.g.: studies;type;numSamples[0..10]:1;format:sum(size).
         aggregationStats=fetchOpenCGA(object=OpencgaR, category="files", categoryId=NULL, subcategory=NULL,
                 subcategoryId=NULL, action="aggregationStats", params=params, httpMethod="GET", as.queryParam=NULL,
                 ...),

opencga-client/src/main/R/R/Individual-methods.R

@@ -80,7 +80,7 @@ setMethod("individualClient", "OpencgaR", function(OpencgaR, annotationSet, indi
         #' @param acl Filter entries for which a user has the provided permissions. Format: acl={user}:{permissions}. Example: acl=john:WRITE,WRITE_ANNOTATIONS will return all entries for which user john has both WRITE and WRITE_ANNOTATIONS permissions. Only study owners or administrators can query by this field. .
         #' @param release Release when it was created.
         #' @param snapshot Snapshot value (Latest version of the entry in the specified release).
-        #' @param field List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size).
+        #' @param field Field to apply aggregation statistics to (or a list of fields separated by semicolons), e.g.: studies;type;numSamples[0..10]:1;format:sum(size).
         aggregationStats=fetchOpenCGA(object=OpencgaR, category="individuals", categoryId=NULL, subcategory=NULL,
                 subcategoryId=NULL, action="aggregationStats", params=params, httpMethod="GET", as.queryParam=NULL,
                 ...),

opencga-client/src/main/R/R/Job-methods.R

@@ -73,7 +73,7 @@ setMethod("jobClient", "OpencgaR", function(OpencgaR, job, jobs, members, endpoi
         #' @param acl Filter entries for which a user has the provided permissions. Format: acl={user}:{permissions}. Example: acl=john:WRITE,WRITE_ANNOTATIONS will return all entries for which user john has both WRITE and WRITE_ANNOTATIONS permissions. Only study owners or administrators can query by this field. .
         #' @param release Release when it was created.
         #' @param deleted Boolean to retrieve deleted entries.
-        #' @param field List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size).
+        #' @param field Field to apply aggregation statistics to (or a list of fields separated by semicolons), e.g.: studies;type;numSamples[0..10]:1;format:sum(size).
         aggregationStats=fetchOpenCGA(object=OpencgaR, category="jobs", categoryId=NULL, subcategory=NULL,
                 subcategoryId=NULL, action="aggregationStats", params=params, httpMethod="GET", as.queryParam=NULL,
                 ...),

opencga-client/src/main/R/R/Panel-methods.R

@@ -70,7 +70,7 @@ setMethod("panelClient", "OpencgaR", function(OpencgaR, members, panels, endpoin
         #' @param acl Filter entries for which a user has the provided permissions. Format: acl={user}:{permissions}. Example: acl=john:WRITE,WRITE_ANNOTATIONS will return all entries for which user john has both WRITE and WRITE_ANNOTATIONS permissions. Only study owners or administrators can query by this field. .
         #' @param release Release when it was created.
         #' @param snapshot Snapshot value (Latest version of the entry in the specified release).
-        #' @param field List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size).
+        #' @param field Field to apply aggregation statistics to (or a list of fields separated by semicolons), e.g.: studies;type;numSamples[0..10]:1;format:sum(size).
         aggregationStats=fetchOpenCGA(object=OpencgaR, category="panels", categoryId=NULL, subcategory=NULL,
                 subcategoryId=NULL, action="aggregationStats", params=params, httpMethod="GET", as.queryParam=NULL,
                 ...),

opencga-client/src/main/R/R/Sample-methods.R

@@ -91,7 +91,7 @@ setMethod("sampleClient", "OpencgaR", function(OpencgaR, annotationSet, members,
         #' @param statsBiotypeCount Sample variant stats BiotypeCount.
         #' @param statsClinicalSignificanceCount Sample variant stats ClinicalSignificanceCount.
         #' @param statsConsequenceTypeCount Sample variant stats ConsequenceTypeCount.
-        #' @param field List of fields separated by semicolons to apply aggregation statistics, e.g.: studies;type;numSamples[0..10]:1;format:sum(size).
+        #' @param field Field to apply aggregation statistics to (or a list of fields separated by semicolons), e.g.: studies;type;numSamples[0..10]:1;format:sum(size).
         aggregationStats=fetchOpenCGA(object=OpencgaR, category="samples", categoryId=NULL, subcategory=NULL,
                 subcategoryId=NULL, action="aggregationStats", params=params, httpMethod="GET", as.queryParam=NULL,
                 ...),

opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java

@@ -124,7 +124,7 @@ public RestResponse<ClinicalAnalysisAclEntryList> updateAcl(String members, Stri
      *       annotation: Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit
      *            http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0.
      *       deleted: Boolean to retrieve deleted entries.
-     *       field: List of fields separated by semicolons to apply aggregation statistics, e.g.:
+     *       field: Field to apply aggregation statistics to (or a list of fields separated by semicolons), e.g.:
      *            studies;type;numSamples[0..10]:1;format:sum(size).
      * @return a RestResponse object.
      * @throws ClientException ClientException if there is any server error.
@@ -254,7 +254,7 @@ public RestResponse<ObjectMap> distinct(String field, ObjectMap params) throws C
      *       status: Filter by status.
      *       internalStatus: Filter by internal status.
      *       release: Release when it was created.
-     *       field: List of fields separated by semicolons to apply aggregation statistics, e.g.:
+     *       field: Field to apply aggregation statistics to (or a list of fields separated by semicolons), e.g.:
      *            studies;type;numSamples[0..10]:1;format:sum(size).
      * @return a RestResponse object.
      * @throws ClientException ClientException if there is any server error.

opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java

@@ -91,7 +91,7 @@ public RestResponse<CohortAclEntryList> updateAcl(String members, String action,
      *       samples: Cohort sample IDs.
      *       numSamples: Number of samples.
      *       release: release.
-     *       field: List of fields separated by semicolons to apply aggregation statistics, e.g.:
+     *       field: Field to apply aggregation statistics to (or a list of fields separated by semicolons), e.g.:
      *            studies;type;numSamples[0..10]:1;format:sum(size).
      * @return a RestResponse object.
      * @throws ClientException ClientException if there is any server error.

opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java

@@ -104,7 +104,7 @@ public RestResponse<PanelAclEntryList> updateAcl(String members, String action,
      *            permissions. Only study owners or administrators can query by this field. .
      *       release: Release when it was created.
      *       snapshot: Snapshot value (Latest version of the entry in the specified release).
-     *       field: List of fields separated by semicolons to apply aggregation statistics, e.g.:
+     *       field: Field to apply aggregation statistics to (or a list of fields separated by semicolons), e.g.:
      *            studies;type;numSamples[0..10]:1;format:sum(size).
      * @return a RestResponse object.
      * @throws ClientException ClientException if there is any server error.

opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java

@@ -99,7 +99,7 @@ public RestResponse<FamilyAclEntryList> updateAcl(String members, String action,
      *            permissions. Only study owners or administrators can query by this field. .
      *       release: Release when it was created.
      *       snapshot: Snapshot value (Latest version of the entry in the specified release).
-     *       field: List of fields separated by semicolons to apply aggregation statistics, e.g.:
+     *       field: Field to apply aggregation statistics to (or a list of fields separated by semicolons), e.g.:
      *            studies;type;numSamples[0..10]:1;format:sum(size).
      * @return a RestResponse object.
      * @throws ClientException ClientException if there is any server error.

opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java

@@ -115,7 +115,7 @@ public RestResponse<FileAclEntryList> updateAcl(String members, String action, F
      *            permissions. Only study owners or administrators can query by this field. .
      *       deleted: Boolean to retrieve deleted entries.
      *       release: Release when it was created.
-     *       field: List of fields separated by semicolons to apply aggregation statistics, e.g.:
+     *       field: Field to apply aggregation statistics to (or a list of fields separated by semicolons), e.g.:
      *            studies;type;numSamples[0..10]:1;format:sum(size).
      * @return a RestResponse object.
      * @throws ClientException ClientException if there is any server error.