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core: add new CVDB index status in Clinical Analysis, #TASK-5610
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47 changes: 47 additions & 0 deletions
47
.../java/org/opencb/opencga/app/migrations/v4/v4_0_0/catalog/ClinicalCvdbIndexMigration.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,47 @@ | ||
| package org.opencb.opencga.app.migrations.v4.v4_0_0.catalog; | ||
|
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| import com.mongodb.client.model.Filters; | ||
| import com.mongodb.client.model.Updates; | ||
| import org.bson.Document; | ||
| import org.bson.conversions.Bson; | ||
| import org.opencb.opencga.catalog.db.api.ClinicalAnalysisDBAdaptor; | ||
| import org.opencb.opencga.catalog.db.mongodb.OrganizationMongoDBAdaptorFactory; | ||
| import org.opencb.opencga.catalog.migration.Migration; | ||
| import org.opencb.opencga.catalog.migration.MigrationTool; | ||
| import org.opencb.opencga.core.models.clinical.ClinicalStatusValue; | ||
| import org.opencb.opencga.core.models.clinical.CvdbIndexStatus; | ||
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| import java.util.Arrays; | ||
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| @Migration(id = "add_cvdb_index_to_clinical_analysis", | ||
| description = "Add CVDB index status to Clinical Analysis #TASK-5610", version = "4.0.0", | ||
| language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20241118) | ||
| public class ClinicalCvdbIndexMigration extends MigrationTool { | ||
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| @Override | ||
| protected void run() throws Exception { | ||
| Bson closedCaseQuery = Filters.and( | ||
| Filters.exists(ClinicalAnalysisDBAdaptor.QueryParams.INTERNAL_CVDB_INDEX.key(), false), | ||
| Filters.eq("status.type", ClinicalStatusValue.ClinicalStatusType.CLOSED) | ||
| ); | ||
| Bson openCaseQuery = Filters.and( | ||
| Filters.exists(ClinicalAnalysisDBAdaptor.QueryParams.INTERNAL_CVDB_INDEX.key(), false), | ||
| Filters.ne("status.type", ClinicalStatusValue.ClinicalStatusType.CLOSED) | ||
| ); | ||
| CvdbIndexStatus pendingCvdbIndexStatus = new CvdbIndexStatus(CvdbIndexStatus.PENDING); | ||
| Document pendingCvdbIndexDoc = convertToDocument(pendingCvdbIndexStatus); | ||
| Bson updateClosedCase = Updates.set(ClinicalAnalysisDBAdaptor.QueryParams.INTERNAL_CVDB_INDEX.key(), pendingCvdbIndexDoc); | ||
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| CvdbIndexStatus noneCvdbIndexStatus = new CvdbIndexStatus(CvdbIndexStatus.NONE); | ||
| Document noneCvdbIndexDoc = convertToDocument(noneCvdbIndexStatus); | ||
| Bson updateOpenCase = Updates.set(ClinicalAnalysisDBAdaptor.QueryParams.INTERNAL_CVDB_INDEX.key(), noneCvdbIndexDoc); | ||
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| for (String collection : Arrays.asList(OrganizationMongoDBAdaptorFactory.CLINICAL_ANALYSIS_COLLECTION, | ||
| OrganizationMongoDBAdaptorFactory.CLINICAL_ANALYSIS_ARCHIVE_COLLECTION, | ||
| OrganizationMongoDBAdaptorFactory.DELETED_CLINICAL_ANALYSIS_COLLECTION)) { | ||
| getMongoCollection(collection).updateMany(closedCaseQuery, updateClosedCase); | ||
| getMongoCollection(collection).updateMany(openCaseQuery, updateOpenCase); | ||
| } | ||
| } | ||
|
|
||
| } |
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56 changes: 56 additions & 0 deletions
56
opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/CvdbIndexStatus.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,56 @@ | ||
| package org.opencb.opencga.core.models.clinical; | ||
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| import org.opencb.opencga.core.models.common.OperationIndexStatus; | ||
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| import java.util.Arrays; | ||
| import java.util.List; | ||
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| public class CvdbIndexStatus extends OperationIndexStatus { | ||
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| public static final String ERROR = "ERROR"; | ||
| public static final String PENDING_REMOVE = "PENDING_REMOVE"; | ||
| public static final String PENDING_OVERWRITE = "PENDING_OVERWRITE"; | ||
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| public static final List<String> STATUS_LIST = Arrays.asList(NONE, PENDING, PENDING_REMOVE, PENDING_OVERWRITE, READY, ERROR); | ||
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| public CvdbIndexStatus(String status, String message) { | ||
| if (isValid(status)) { | ||
| init(status, message); | ||
| } else { | ||
| throw new IllegalArgumentException("Unknown status " + status); | ||
| } | ||
| } | ||
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| public CvdbIndexStatus(String status) { | ||
| this(status, ""); | ||
| } | ||
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| public CvdbIndexStatus() { | ||
| this(NONE, ""); | ||
| } | ||
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| @Override | ||
| public String getId() { | ||
| return super.getId(); | ||
| } | ||
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| @Override | ||
| public String getName() { | ||
| return super.getName(); | ||
| } | ||
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| public static CvdbIndexStatus init() { | ||
| return new CvdbIndexStatus(); | ||
| } | ||
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| public static boolean isValid(String status) { | ||
| return status != null | ||
| && (status.equals(NONE) | ||
| || status.equals(PENDING) | ||
| || status.equals(PENDING_REMOVE) | ||
| || status.equals(PENDING_OVERWRITE) | ||
| || status.equals(READY) | ||
| || status.equals(ERROR)); | ||
| } | ||
|
|
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| } |
48 changes: 48 additions & 0 deletions
48
opencga-core/src/main/java/org/opencb/opencga/core/models/common/OperationIndexStatus.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,48 @@ | ||
| package org.opencb.opencga.core.models.common; | ||
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| import java.util.Arrays; | ||
| import java.util.List; | ||
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| public class OperationIndexStatus extends IndexStatus { | ||
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| public static final String PENDING = "PENDING"; | ||
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| public static final List<String> STATUS_LIST = Arrays.asList(READY, PENDING, NONE); | ||
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| public OperationIndexStatus(String status, String message) { | ||
| if (isValid(status)) { | ||
| init(status, message); | ||
| } else { | ||
| throw new IllegalArgumentException("Unknown status " + status); | ||
| } | ||
| } | ||
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| public OperationIndexStatus(String status) { | ||
| this(status, ""); | ||
| } | ||
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| public OperationIndexStatus() { | ||
| this(NONE, ""); | ||
| } | ||
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| @Override | ||
| public String getId() { | ||
| return super.getId(); | ||
| } | ||
|
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| @Override | ||
| public String getName() { | ||
| return super.getName(); | ||
| } | ||
|
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| public static OperationIndexStatus init() { | ||
| return new OperationIndexStatus(); | ||
| } | ||
|
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| public static boolean isValid(String status) { | ||
| return status != null | ||
| && (status.equals(READY) | ||
| || status.equals(PENDING) | ||
| || status.equals(NONE)); | ||
| } | ||
| } |