You can use this field to store any other information, keep in mind this is not indexed so you cannot search by attributes.
| | **status**Object status.
| -<<<<<<< HEAD -<<<<<<< HEAD -### Panel -You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-521/opencga-core/src/main/java/org/opencb/opencga/core/models/panel/Panel.java). -| Field | Description | -| :--- | :--- | -| **uuid**Unique 32-character identifier assigned automatically by OpenCGA.
| -| **release**An integer describing the current data release.
| -| **version**OpenCGA version of this panel, this is incremented when the panel is updated.
| -| **~~author~~**Author of the panel.
| -| **status**Panel status can have the values READY or DELETED.
| -| **internal**Internal field to manage the object.
| -| **studyUid**Panel reference to study.
| -| **uid**Panel reference to study.
| - -### ClinicalAnalysisInternal -You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-521/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/ClinicalAnalysisInternal.java). - -| Field | Description | -| :--- | :--- | -| **status**Status of the internal object.
| -| **registrationDate**Registration date of the internal object.
| -| **lastModified**Date of the last modification of the internal object.
| - -### ClinicalAudit -You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/ClinicalAudit.java). -======= ### ClinicalAnalyst You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/ClinicalAnalyst.java). ->>>>>>> release-2.2.x - -| Field | Description | -| :--- | :--- | -| **id**Id to identify the object
| -| **name**Object name
| -| **email**Email of the analyst
| -| **assignedBy**Assigned by field
| -| **date**Date of the clinical analyst
| - -<<<<<<< HEAD -### ClinicalConsentAnnotation -You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-521/opencga-core/src/main/java/org/opencb/opencga/core/models/study/configuration/ClinicalConsentAnnotation.java). - -| Field | Description | -| :--- | :--- | -| **consents**List of ClinicalConsentParam.
| -| **date**Date of the ClinicalConsentAnnotation.
| - -### ClinicalPriorityAnnotation -You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-521/opencga-core/src/main/java/org/opencb/opencga/core/models/study/configuration/ClinicalPriorityAnnotation.java). - -| Field | Description | -| :--- | :--- | -======= -### ClinicalPriorityAnnotation -You can find the Java code [here](https://github.com/opencb/opencga/tree/release-2.2.x/opencga-core/src/main/java/org/opencb/opencga/core/models/study/configuration/ClinicalPriorityAnnotation.java). - -| Field | Description | -| :--- | :--- | ->>>>>>> release-2.2.x -| **id**Object ID is a mandatory parameter when creating a new one, this ID cannot be changed at the moment.
| -| **description**Users may provide a description for the entry.
| -| **rank**ClinicalPriorityAnnotation rank.
| -| **date**ClinicalPriorityAnnotation date.
| -<<<<<<< HEAD - -### FlagAnnotation -You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-521/opencga-core/src/main/java/org/opencb/opencga/core/models/common/FlagAnnotation.java). -======= - -### ClinicalConsentAnnotation -You can find the Java code [here](https://github.com/opencb/opencga/tree/release-2.2.x/opencga-core/src/main/java/org/opencb/opencga/core/models/study/configuration/ClinicalConsentAnnotation.java). - -| Field | Description | -| :--- | :--- | -| **consents**List of ClinicalConsentParam.
| -| **date**Date of the ClinicalConsentAnnotation.
| - -### FlagAnnotation -You can find the Java code [here](https://github.com/opencb/opencga/tree/release-2.2.x/opencga-core/src/main/java/org/opencb/opencga/core/models/common/FlagAnnotation.java). ->>>>>>> release-2.2.x - -| Field | Description | -| :--- | :--- | -| **id**Object ID is a mandatory parameter when creating a new one, this ID cannot be changed at the moment.
| -| **description**Users may provide a description for the entry.
| -| **date**FlagAnnotation date.
| - -<<<<<<< HEAD -### Interpretation -You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-521/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/Interpretation.java). - -| Field | Description | -| :--- | :--- | -| **studyUid**Study identifier.
| -| **uid**Interpretation identifier.
| -| **panels**Interpretation panel list.
| -| **internal**Internal field to manage the object.
| -| **release**An integer describing the current data release.
| -======= -======= ->>>>>>> release-2.2.x -### ClinicalAnalysisQualityControl -You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-1587/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/ClinicalAnalysisQualityControl.java). - -| Field | Description | -| :--- | :--- | -| **summary**ClinicalAnalysisQualityControl summary that can have the values HIGH, MEDIUM, LOW, DISCARD, NEEDS_REVIEW, UNKNOWN.
| -| **comments**List of ClinicalAnalysisQualityControl comments.
| -| **comments**List of ClinicalAnalysisQualityControl files.
| ->>>>>>> release-2.2.x - -<<<<<<< HEAD ### ClinicalComment You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/ClinicalComment.java). @@ -201,7 +82,6 @@ You can find the Java code [here](https://github.com/opencb/biodata/tree/develop | **tags**List of tags for the clinical comment
| | **date**Date of the clinical comment
| -<<<<<<< HEAD ### ClinicalAnalysisQualityControl You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-521/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/ClinicalAnalysisQualityControl.java). @@ -223,30 +103,6 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-52 | **signedBy**Indicates who has signed the report.
| | **signature**Report signature.
| | **date**Report date.
| -======= -======= ->>>>>>> release-2.2.x -### Interpretation -You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-1587/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/Interpretation.java). - -| Field | Description | -| :--- | :--- | -| **studyUid**Study identifier.
| -| **uid**Interpretation identifier.
| -| **panels**Interpretation panel list.
| -| **internal**Internal field for manage the object.
| -| **release**An integer describing the current data release.
| - -### ClinicalAudit -You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/ClinicalAudit.java). - -| Field | Description | -| :--- | :--- | -| **author**Audit author
| -| **action**Enum action that can have the values CREATE_CLINICAL_ANALYSIS, CREATE_INTERPRETATION, UPDATE_CLINICAL_ANALYSIS, DELETE_CLINICAL_ANALYSIS, UPDATE_INTERPRETATION, REVERT_INTERPRETATION, CLEAR_INTERPRETATION, MERGE_INTERPRETATION, SWAP_INTERPRETATION and DELETE_INTERPRETATION
| -| **message**Audit message
| -| **date**Date of the audit
| ->>>>>>> release-2.2.x ### ClinicalAnalysisInternal You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-1587/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/ClinicalAnalysisInternal.java). @@ -270,17 +126,8 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-15 | **signature**Report signature.
| | **date**Report date.
| -<<<<<<< HEAD ### ClinicalAnalyst You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/ClinicalAnalyst.java). -======= -### Panel -<<<<<<< HEAD -You can find the Java code [here](https://github.com/opencb/opencga/tree/release-2.2.x/opencga-core/src/main/java/org/opencb/opencga/core/models/panel/Panel.java). ->>>>>>> release-2.2.x -======= -You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-1587/opencga-core/src/main/java/org/opencb/opencga/core/models/panel/Panel.java). ->>>>>>> release-2.2.x | Field | Description | | :--- | :--- | @@ -290,7 +137,6 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-15 | **assignedBy**Assigned by field
| | **date**Date of the clinical analyst
| -<<<<<<< HEAD ### ClinicalConsentParam You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-521/opencga-core/src/main/java/org/opencb/opencga/core/models/study/configuration/ClinicalConsentParam.java). @@ -300,8 +146,6 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-52 | **name**Name of the .
| | **description**Users may provide a description for the entry.
| | **value**Value of the param that can have the values YES, NO and UNKNOWN.
| - -<<<<<<< HEAD ### Status You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/common/Status.java). @@ -311,90 +155,16 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-52 | Field | Description | | :--- | :--- | -======= -======= -### ClinicalPriorityAnnotation -You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-1587/opencga-core/src/main/java/org/opencb/opencga/core/models/study/configuration/ClinicalPriorityAnnotation.java). - -| Field | Description | -| :--- | :--- | -| **id**Object ID is a mandatory parameter when creating a new one, this ID cannot be changed at the moment.
| -| **description**Users may provide a description for the entry.
| -| **rank**ClinicalPriorityAnnotation rank.
| -| **date**ClinicalPriorityAnnotation date.
| - -### FlagAnnotation -You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-1587/opencga-core/src/main/java/org/opencb/opencga/core/models/common/FlagAnnotation.java). - -| Field | Description | -| :--- | :--- | -| **id**Object ID is a mandatory parameter when creating a new one, this ID cannot be changed at the moment.
| -| **description**Users may provide a description for the entry.
| -| **date**FlagAnnotation date.
| - -### ClinicalComment -You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/ClinicalComment.java). - -| Field | Description | -| :--- | :--- | -| **author**Clinical comment author
| -| **message**Clinical comment message
| -| **tags**List of tags for the clinical comment
| -| **date**Date of the clinical comment
| - ->>>>>>> release-2.2.x -### Disorder -You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/Disorder.java). - -| Field | Description | -| :--- | :--- | -| **id**Id to identify the object
| -| **name**Object name
| -| **description**Users may provide a description for the entry.
| -| **source**Ontology source
| -| **url**Ontology url
| -| **attributes**Dictionary that can be customised by users to store any additional information users may require..
| - -### ClinicalAnalyst -You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/ClinicalAnalyst.java). - -| Field | Description | -| :--- | :--- | -| **id**Id to identify the object
| -| **name**Object name
| -| **email**Email of the analyst
| -| **assignedBy**Assigned by field
| -| **date**Date of the clinical analyst
| - -### ClinicalConsentAnnotation -You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-1587/opencga-core/src/main/java/org/opencb/opencga/core/models/study/configuration/ClinicalConsentAnnotation.java). - -| Field | Description | -| :--- | :--- | -| **consents**List of ClinicalConsentParam.
| -| **date**Date of the ClinicalConsentAnnotation.
| - -### Status -You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/common/Status.java). - - -### InterpretationInternal -You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-1587/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/InterpretationInternal.java). - -| Field | Description | -| :--- | :--- | -| **status**State of the interpretation that can have the values READY, DELETED, NOT_REVIEWED, UNDER_REVIEW, REVIEWED and REJECTED.
| ->>>>>>> release-2.2.x | **status**Status of the internal object.
| | **registrationDate**Registration date of the internal object.
| | **lastModified**Date of the last modification of the internal object.
| -<<<<<<< HEAD + ### InternalStatus You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-521/opencga-core/src/main/java/org/opencb/opencga/core/models/common/InternalStatus.java). -<<<<<<< HEAD + ### InterpretationInternal You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-521/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/InterpretationInternal.java). @@ -407,9 +177,6 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-52 ### InterpretationStatus You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-521/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/InterpretationStatus.java). -======= -======= ->>>>>>> release-2.2.x ### ClinicalConsentParam You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-1587/opencga-core/src/main/java/org/opencb/opencga/core/models/study/configuration/ClinicalConsentParam.java). @@ -425,10 +192,6 @@ You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-15 ### InterpretationStatus -<<<<<<< HEAD You can find the Java code [here](https://github.com/opencb/opencga/tree/release-2.2.x/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/InterpretationStatus.java). ->>>>>>> release-2.2.x -======= -You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-1587/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/InterpretationStatus.java). ->>>>>>> release-2.2.x + diff --git a/docs/data-models/family.md b/docs/data-models/family.md index e901ddb549d..c104f183f77 100644 --- a/docs/data-models/family.md +++ b/docs/data-models/family.md @@ -25,15 +25,8 @@ Family data model hosts information about any family. ## Data Model ### Family -<<<<<<< HEAD -<<<<<<< HEAD -You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-521/opencga-core/src/main/java/org/opencb/opencga/core/models/family/Family.java). -======= -You can find the Java code [here](https://github.com/opencb/opencga/tree/release-2.2.x/opencga-core/src/main/java/org/opencb/opencga/core/models/family/Family.java). ->>>>>>> release-2.2.x -======= You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-1587/opencga-core/src/main/java/org/opencb/opencga/core/models/family/Family.java). ->>>>>>> release-2.2.x + | Field | Description | | :--- | :--- | diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2_4_11/catalog/SignatureFittingsMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2_4_11/catalog/SignatureFittingsMigration.java index 46fcf8aa891..0f3401e0755 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2_4_11/catalog/SignatureFittingsMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2_4_11/catalog/SignatureFittingsMigration.java @@ -53,7 +53,7 @@ protected void run() throws Exception { bulk.add(new UpdateOneModel<>( eq("_id", document.get("_id")), - new Document("$set", new Document("qualityControl.variant", signatures))) + new Document("$set", new Document("qualityControl.variant.signatures", signatures))) ); } }); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2_6_0/storage/AddCellbaseDataRelease.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2_6_0/storage/AddCellbaseDataRelease.java index 8c949dd7214..6d77b8f2be3 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2_6_0/storage/AddCellbaseDataRelease.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2_6_0/storage/AddCellbaseDataRelease.java @@ -36,18 +36,29 @@ protected void run() throws Exception { cellbase.setDataRelease(cellBaseUtils.getDataRelease()); updateCellbase = true; } else { + String serverVersion; + try { + serverVersion = cellBaseUtils.getVersionFromServer(); + } catch (Exception e) { + if (cellBaseUtils.getVersion().equals("v4")) { + logger.debug(e.getMessage(), e); + logger.warn(e.getMessage(), e); + logger.info("DataRelease not supported on version '" + cellBaseUtils.getVersion() + "' . Leaving empty"); + continue; + } + throw e; + } if (cellBaseUtils.supportsDataRelease()) { cellbase.setDataRelease("1"); updateCellbase = true; } else { - String serverVersion = cellBaseUtils.getVersionFromServer(); logger.info("DataRelease not supported on version '" + serverVersion + "' . Leaving empty"); } } } if (updateCellbase) { logger.info("Update cellbase info for project '{}' with '{}'", projectFqn, cellBaseUtils); - variantStorageManager.setCellbaseConfiguration(projectFqn, null, false, null, token); + variantStorageManager.setCellbaseConfiguration(projectFqn, cellbase, false, null, token); } } } diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/auth/authorization/CatalogAuthorizationManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/auth/authorization/CatalogAuthorizationManager.java index f2103bab429..c4d9c3cf84f 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/auth/authorization/CatalogAuthorizationManager.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/auth/authorization/CatalogAuthorizationManager.java @@ -102,6 +102,9 @@ public boolean isPublicRegistration() { @Override public void checkCanEditProject(long projectId, String userId) throws CatalogException { + if (isInstallationAdministrator(userId)) { + return; + } if (projectDBAdaptor.getOwnerId(projectId).equals(userId)) { return; }