TASK-7610 - Extend Workflows data model #2631
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Task linked: TASK-7610 Extend Workflows data model |
opencga-analysis/src/main/java/org/opencb/opencga/analysis/tools/OpenCgaTool.java
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| @DataField(id = "manager", description = FieldConstants.WORKFLOW_MANAGER_DESCRIPTION) | ||
| private WorkflowSystem manager; | ||
| @DataField(id = "scope", description = FieldConstants.EXTERNAL_TOOL_SCOPE_DESCRIPTION) | ||
| private ExternalToolScope scope; |
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Classic tools already have a "scope". This name is misleading, as it has a totally different meaning.
I don't even know what this scope is for 🤷 (the DataField content doesn't help either)
It's some sort of tool classification by purpose?
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There's a data field explaining what that scope is.
...cga-core/src/main/java/org/opencb/opencga/core/models/externalTool/ExternalToolVariable.java
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...cga-core/src/main/java/org/opencb/opencga/core/models/externalTool/ExternalToolVariable.java
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| public static final String EXTERNAL_TOOL_TYPE_DESCRIPTION = "External tool type. Valid values: TOOL, VARIANT_WALKER or WORKFLOW."; | ||
| public static final String EXTERNAL_TOOL_SCOPE_DESCRIPTION = "External tool scope. Valid values: SECONDARY_ANALYSIS, RESEARCH_ANALYSIS," | ||
| + " CLINICAL_INTERPRETATION_ANALYSIS or OTHER."; | ||
| public static final String EXTERNAL_TOOL_DRAFT_DESCRIPTION = "Flag indicating whether the external tool is a draft or not."; |
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Ok, cool, but what are the implications of a draft tool? Is this just informative, or has an actual meaning internally?
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Tools that are not intended to be published/used yet are marked as "draft", but that's up to you whether you want to trust that or not. We are not restricting anything
opencga-analysis/src/main/java/org/opencb/opencga/analysis/customTool/CustomToolExecutor.java
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opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/ExternalToolManager.java
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| protected String getStudyFqn() throws CatalogException { | ||
| String study = StringUtils.isNotEmpty(this.study) ? this.study : getParams().getString(ParamConstants.STUDY_PARAM); | ||
| if (StringUtils.isEmpty(study)) { | ||
| return ""; |
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if empty, would not call catalog to see if there is any default study? Shouldn't fail if empty? This is different behaviour than the "OpenCgaToolScopeStudy"
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I can't think of a case where that will be empty, but if it is, calls to anything in OpenCGA will use an empty study and should return something either way if there's only one study
...cga-analysis/src/main/java/org/opencb/opencga/analysis/variant/operations/OperationTool.java
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| @Migration(id = "remove_status_name", description = "Remove status name #TASK-5964", version = "3.2.0", | ||
| language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20240612) | ||
| language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20240612, | ||
| deprecatedSince = "4.0.0") |
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hummm... actually, deprecatedSince 5.0.0, right?
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There are a few other migrations with the wrong deprecatiedSince
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