TASK-6442 - Add Resources Management functionality #2535
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…ASK-7047, #TASK-6442
…alyisis resources for the current OpenCGA version, and generate clients, #TASK-7088, #TASK-6442
…o the installation folder, #TASK-7088, #TASK-6442
…lization, and add the flag fetchResourceOnInit in the configuration file, #TASK-7088, #TASK-6442
… #TASK-7088, #TASK-6442
…-7088, #TASK-6442
…ing, #TASK-7125, #TASK-6442
…esource management, #TASK-7127, #TASK-6442
…me some constants, #TASK-7088, #TASK-6442
…ng the ResourceManager, #TASK-7139, #TASK-6442
…TASK-7047, #TASK-6442
| FqnUtils.FQN fqn = FqnUtils.parse(study.getFqn()); | ||
| String organization = fqn.getOrganization(); | ||
| try { | ||
| URI studyUri = ioManager.getStudyUri(organization, Long.toString(project.getUid()), Long.toString(study.getUid())); |
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Isn't this responsibility of the StudyManager?
By this I mean "setting and validating expected values to the object to insert"
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Yes, I agree it should be its responsibility. However, until we create some kind of session between the manager and the dbadaptor, I'd say that's the best place it could be for integrity reasons.
opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/StudyMongoDBAdaptor.java
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opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/StudyManager.java
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| /* | ||
| $ cat resources-3.3.0-SNAPSHOT.json | jq |
| @@ -18,7 +18,8 @@ analysis: | |||
| - "org.opencb.opencga" | |||
| scratchDir: "/tmp/" # Scratch folder for the analysis. | |||
| # Default URL for downloading analysis resources. | |||
| resourceUrl: "http://resources.opencb.org/opencb/opencga/analysis/" | |||
| resourceUrl: "http://resources.opencb.org/opencb/opencga/analysis/resources-test/" | |||
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"resources-test/" is the actual final value, or just a temporary testing change?
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| public class AnalysisResourceList { | ||
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| private String analysisId; |
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Is "analysis" a thing? What is this "analysisId" ? Isn't this a "toolId" ?
The only "analysisId" that we have are the "clinicalAnalysisIds"
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| public class AnalysisResource { | ||
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| private String url; |
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Please, add @DataField annotations to new fields
e.g.
@DataField(description = "I have no idea what this key is for. Wild guess : it's for encryption purposes")
private String key;| import java.util.ArrayList; | ||
| import java.util.List; | ||
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| public class AnalysisResource { |
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There is a naming discrepancy between "Resource" and "AnalysisResource".
Does the ResourceManager manage AnalysisResources? Are there any other non-analysis resources?
Files can be just a "resource : bool"
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| // Mark fetching as started | ||
| try { | ||
| isFetching = true; |
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What if it's being fetched from another node?
| private Configuration configuration; | ||
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| // Flag to track if all resources are fetching | ||
| private boolean isFetching = false; |
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make it "volatile" or "AtomicBoolean"
…changes, #TASK-7139, #TASK-6442
…K-7125, #TASK-6442
…hanges, #TASK-7127, #TASK-6442
…anges, #TASK-7088, #TASK-6442
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