Skip to content

Commit

Permalink
Merge pull request #2474 from opencb/TASK-5964
Browse files Browse the repository at this point in the history 
TASK-5964 - Clinical Improvements
  • Loading branch information
@pfurio
pfurio authored Aug 28, 2024
2 parents 35074a6 + 40651f8 commit d624826
Show file tree
Hide file tree
Showing 49 changed files with 1,663 additions and 656 deletions.
13 changes: 11 additions & 2 deletions .../main/java/org/opencb/opencga/app/cli/main/executors/AnalysisClinicalCommandExecutor.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -347,7 +347,7 @@ private RestResponse<ClinicalAnalysis> create() throws Exception {
putNestedIfNotEmpty(beanParams, "disorder.id", commandOptions.disorderId, true);
putNestedIfNotEmpty(beanParams, "proband.id", commandOptions.probandId, true);
putNestedIfNotEmpty(beanParams, "family.id", commandOptions.familyId, true);
putNestedIfNotNull(beanParams, "panelLock", commandOptions.panelLock, true);
putNestedIfNotNull(beanParams, "panelLocked", commandOptions.panelLocked, true);
putNestedIfNotEmpty(beanParams, "analyst.id", commandOptions.analystId, true);
putNestedIfNotEmpty(beanParams, "report.title", commandOptions.reportTitle, true);
putNestedIfNotEmpty(beanParams, "report.overview", commandOptions.reportOverview, true);
Expand All @@ -367,6 +367,7 @@ private RestResponse<ClinicalAnalysis> create() throws Exception {
putNestedIfNotEmpty(beanParams, "responsible.address", commandOptions.responsibleAddress, true);
putNestedIfNotEmpty(beanParams, "responsible.city", commandOptions.responsibleCity, true);
putNestedIfNotEmpty(beanParams, "responsible.postcode", commandOptions.responsiblePostcode, true);
putNestedIfNotEmpty(beanParams, "interpretation.name", commandOptions.interpretationName, true);
putNestedIfNotEmpty(beanParams, "interpretation.description", commandOptions.interpretationDescription, true);
putNestedIfNotEmpty(beanParams, "interpretation.clinicalAnalysisId", commandOptions.interpretationClinicalAnalysisId, true);
putNestedIfNotEmpty(beanParams, "interpretation.creationDate", commandOptions.interpretationCreationDate, true);
Expand Down Expand Up @@ -419,6 +420,7 @@ private RestResponse<ObjectMap> distinct() throws Exception {
queryParams.putIfNotEmpty("dueDate", commandOptions.dueDate);
queryParams.putIfNotEmpty("qualityControlSummary", commandOptions.qualityControlSummary);
queryParams.putIfNotEmpty("release", commandOptions.release);
queryParams.putIfNotNull("snapshot", commandOptions.snapshot);
queryParams.putIfNotEmpty("status", commandOptions.status);
queryParams.putIfNotEmpty("internalStatus", commandOptions.internalStatus);
queryParams.putIfNotEmpty("annotation", commandOptions.annotation);
Expand All @@ -439,6 +441,7 @@ private RestResponse<ObjectMap> distinctInterpretation() throws Exception {
queryParams.putIfNotEmpty("study", commandOptions.study);
queryParams.putIfNotEmpty("id", commandOptions.id);
queryParams.putIfNotEmpty("uuid", commandOptions.uuid);
queryParams.putIfNotEmpty("name", commandOptions.name);
queryParams.putIfNotEmpty("clinicalAnalysisId", commandOptions.clinicalAnalysisId);
queryParams.putIfNotEmpty("analystId", commandOptions.analystId);
queryParams.putIfNotEmpty("methodName", commandOptions.methodName);
Expand Down Expand Up @@ -471,6 +474,7 @@ private RestResponse<Interpretation> searchInterpretation() throws Exception {
queryParams.putIfNotEmpty("study", commandOptions.study);
queryParams.putIfNotEmpty("id", commandOptions.id);
queryParams.putIfNotEmpty("uuid", commandOptions.uuid);
queryParams.putIfNotEmpty("name", commandOptions.name);
queryParams.putIfNotEmpty("clinicalAnalysisId", commandOptions.clinicalAnalysisId);
queryParams.putIfNotEmpty("analystId", commandOptions.analystId);
queryParams.putIfNotEmpty("methodName", commandOptions.methodName);
Expand Down Expand Up @@ -1145,6 +1149,7 @@ private RestResponse<ClinicalAnalysis> search() throws Exception {
queryParams.putIfNotEmpty("dueDate", commandOptions.dueDate);
queryParams.putIfNotEmpty("qualityControlSummary", commandOptions.qualityControlSummary);
queryParams.putIfNotEmpty("release", commandOptions.release);
queryParams.putIfNotNull("snapshot", commandOptions.snapshot);
queryParams.putIfNotEmpty("status", commandOptions.status);
queryParams.putIfNotEmpty("internalStatus", commandOptions.internalStatus);
queryParams.putIfNotEmpty("annotation", commandOptions.annotation);
Expand Down Expand Up @@ -1293,7 +1298,7 @@ private RestResponse<ClinicalAnalysis> update() throws Exception {
putNestedIfNotEmpty(beanParams, "description", commandOptions.description, true);
putNestedIfNotNull(beanParams, "type", commandOptions.type, true);
putNestedIfNotEmpty(beanParams, "disorder.id", commandOptions.disorderId, true);
putNestedIfNotNull(beanParams, "panelLock", commandOptions.panelLock, true);
putNestedIfNotNull(beanParams, "panelLocked", commandOptions.panelLocked, true);
putNestedIfNotEmpty(beanParams, "proband.id", commandOptions.probandId, true);
putNestedIfNotEmpty(beanParams, "family.id", commandOptions.familyId, true);
putNestedIfNotNull(beanParams, "locked", commandOptions.locked, true);
Expand Down Expand Up @@ -1325,6 +1330,7 @@ private RestResponse<ClinicalAnalysis> update() throws Exception {
putNestedIfNotEmpty(beanParams, "priority.id", commandOptions.priorityId, true);
putNestedMapIfNotEmpty(beanParams, "attributes", commandOptions.attributes, true);
putNestedIfNotEmpty(beanParams, "status.id", commandOptions.statusId, true);
putNestedIfNotNull(beanParams, "panelLock", commandOptions.panelLock, true);

clinicalAnalysisUpdateParams = JacksonUtils.getDefaultObjectMapper().copy()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
Expand Down Expand Up @@ -1369,6 +1375,7 @@ private RestResponse<ClinicalAnalysis> info() throws Exception {
queryParams.putIfNotEmpty("exclude", commandOptions.exclude);
queryParams.putIfNotNull("flattenAnnotations", commandOptions.flattenAnnotations);
queryParams.putIfNotEmpty("study", commandOptions.study);
queryParams.putIfNotEmpty("version", commandOptions.version);
queryParams.putIfNotNull("deleted", commandOptions.deleted);
if (queryParams.get("study") == null && OpencgaMain.isShellMode()) {
queryParams.putIfNotEmpty("study", sessionManager.getSession().getCurrentStudy());
Expand Down Expand Up @@ -1404,6 +1411,7 @@ private RestResponse<Interpretation> createInterpretation() throws Exception {
.readValue(new java.io.File(commandOptions.jsonFile), InterpretationCreateParams.class);
} else {
ObjectMap beanParams = new ObjectMap();
putNestedIfNotEmpty(beanParams, "name", commandOptions.name, true);
putNestedIfNotEmpty(beanParams, "description", commandOptions.description, true);
putNestedIfNotEmpty(beanParams, "clinicalAnalysisId", commandOptions.clinicalAnalysisId, true);
putNestedIfNotEmpty(beanParams, "creationDate", commandOptions.creationDate, true);
Expand Down Expand Up @@ -1493,6 +1501,7 @@ private RestResponse<Interpretation> updateInterpretation() throws Exception {
.readValue(new java.io.File(commandOptions.jsonFile), InterpretationUpdateParams.class);
} else {
ObjectMap beanParams = new ObjectMap();
putNestedIfNotEmpty(beanParams, "name", commandOptions.name, true);
putNestedIfNotEmpty(beanParams, "description", commandOptions.description, true);
putNestedIfNotEmpty(beanParams, "analyst.id", commandOptions.analystId, true);
putNestedIfNotEmpty(beanParams, "method.name", commandOptions.methodName, true);
Expand Down
35 changes: 31 additions & 4 deletions ...src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisClinicalCommandOptions.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -241,8 +241,8 @@ public class CreateCommandOptions {
@Parameter(names = {"--family-id"}, description = "The body web service id parameter", required = false, arity = 1)
public String familyId;

@Parameter(names = {"--panel-lock"}, description = "The body web service panelLock parameter", required = false, arity = 1)
public Boolean panelLock;
@Parameter(names = {"--panel-locked"}, description = "The body web service panelLocked parameter", required = false, arity = 1)
public Boolean panelLocked;

@Parameter(names = {"--analyst-id"}, description = "The body web service id parameter", required = false, arity = 1)
public String analystId;
Expand Down Expand Up @@ -301,6 +301,9 @@ public class CreateCommandOptions {
@Parameter(names = {"--responsible-postcode"}, description = "The body web service postcode parameter", required = false, arity = 1)
public String responsiblePostcode;

@Parameter(names = {"--interpretation-name"}, description = "The body web service name parameter", required = false, arity = 1)
public String interpretationName;

@Parameter(names = {"--interpretation-description"}, description = "The body web service description parameter", required = false, arity = 1)
public String interpretationDescription;

Expand Down Expand Up @@ -423,6 +426,9 @@ public class DistinctCommandOptions {
@Parameter(names = {"--release"}, description = "Release when it was created", required = false, arity = 1)
public String release;

@Parameter(names = {"--snapshot"}, description = "Snapshot value (Latest version of the entry in the specified release)", required = false, arity = 1)
public Integer snapshot;

@Parameter(names = {"--status"}, description = "Filter by status", required = false, arity = 1)
public String status;

Expand Down Expand Up @@ -455,6 +461,9 @@ public class DistinctInterpretationCommandOptions {
@Parameter(names = {"--uuid"}, description = "Comma separated list of Interpretation UUIDs up to a maximum of 100", required = false, arity = 1)
public String uuid;

@Parameter(names = {"--name", "-n"}, description = "Comma separated list of Interpretation names up to a maximum of 100", required = false, arity = 1)
public String name;

@Parameter(names = {"--clinical-analysis-id"}, description = "Clinical Analysis id", required = false, arity = 1)
public String clinicalAnalysisId;

Expand Down Expand Up @@ -523,6 +532,9 @@ public class SearchInterpretationCommandOptions {
@Parameter(names = {"--uuid"}, description = "Comma separated list of Interpretation UUIDs up to a maximum of 100", required = false, arity = 1)
public String uuid;

@Parameter(names = {"--name", "-n"}, description = "Comma separated list of Interpretation names up to a maximum of 100", required = false, arity = 1)
public String name;

@Parameter(names = {"--clinical-analysis-id"}, description = "Clinical Analysis id", required = false, arity = 1)
public String clinicalAnalysisId;

Expand Down Expand Up @@ -1740,6 +1752,9 @@ public class SearchCommandOptions {
@Parameter(names = {"--release"}, description = "Release when it was created", required = false, arity = 1)
public String release;

@Parameter(names = {"--snapshot"}, description = "Snapshot value (Latest version of the entry in the specified release)", required = false, arity = 1)
public Integer snapshot;

@Parameter(names = {"--status"}, description = "Filter by status", required = false, arity = 1)
public String status;

Expand Down Expand Up @@ -2027,8 +2042,8 @@ public class UpdateCommandOptions {
@Parameter(names = {"--disorder-id"}, description = "The body web service id parameter", required = false, arity = 1)
public String disorderId;

@Parameter(names = {"--panel-lock"}, description = "The body web service panelLock parameter", required = false, arity = 1)
public Boolean panelLock;
@Parameter(names = {"--panel-locked"}, description = "The body web service panelLocked parameter", required = false, arity = 1)
public Boolean panelLocked;

@Parameter(names = {"--proband-id"}, description = "The body web service id parameter", required = false, arity = 1)
public String probandId;
Expand Down Expand Up @@ -2123,6 +2138,9 @@ public class UpdateCommandOptions {
@Parameter(names = {"--status-id"}, description = "The body web service id parameter", required = false, arity = 1)
public String statusId;

@Parameter(names = {"--panel-lock"}, description = "The body web service panelLock parameter", required = false, arity = 1)
public Boolean panelLock;

}

@Parameters(commandNames = {"annotation-sets-annotations-update"}, commandDescription ="Update annotations from an annotationSet")
Expand Down Expand Up @@ -2172,6 +2190,9 @@ public class InfoCommandOptions {
@Parameter(names = {"--study", "-s"}, description = "Study [[organization@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1)
public String study;

@Parameter(names = {"--version"}, description = "Comma separated list of clinical versions. 'all' to get all the clinical versions. Not supported if multiple clinical ids are provided", required = false, arity = 1)
public String version;

@Parameter(names = {"--deleted"}, description = "Boolean to retrieve deleted entries", required = false, help = true, arity = 0)
public boolean deleted = false;

Expand Down Expand Up @@ -2207,6 +2228,9 @@ public class CreateInterpretationCommandOptions {
@Parameter(names = {"--include-result"}, description = "Flag indicating to include the created or updated document result in the response", required = false, help = true, arity = 0)
public boolean includeResult = false;

@Parameter(names = {"--name", "-n"}, description = "The body web service name parameter", required = false, arity = 1)
public String name;

@Parameter(names = {"--description"}, description = "The body web service description parameter", required = false, arity = 1)
public String description;

Expand Down Expand Up @@ -2344,6 +2368,9 @@ public class UpdateInterpretationCommandOptions {
@Parameter(names = {"--include-result"}, description = "Flag indicating to include the created or updated document result in the response", required = false, help = true, arity = 0)
public boolean includeResult = false;

@Parameter(names = {"--name", "-n"}, description = "The body web service name parameter", required = false, arity = 1)
public String name;

@Parameter(names = {"--description"}, description = "The body web service description parameter", required = false, arity = 1)
public String description;

Expand Down
35 changes: 35 additions & 0 deletions ...ain/java/org/opencb/opencga/app/migrations/v3/v3_2_0/TASK_5964/AddInterpretationName.java
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,35 @@
package org.opencb.opencga.app.migrations.v3.v3_2_0.TASK_5964;

import com.mongodb.client.model.Filters;
import com.mongodb.client.model.Projections;
import com.mongodb.client.model.UpdateOneModel;
import org.bson.Document;
import org.bson.conversions.Bson;
import org.opencb.opencga.catalog.db.mongodb.OrganizationMongoDBAdaptorFactory;
import org.opencb.opencga.catalog.migration.Migration;
import org.opencb.opencga.catalog.migration.MigrationTool;

import java.util.Arrays;

@Migration(id = "add_interpretation_name", description = "Add Interpretation name #TASK-5964", version = "3.2.0",
language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20240610)
public class AddInterpretationName extends MigrationTool {

@Override
protected void run() throws Exception {
// Add new Interpretation name field
Bson nameDoesNotExistQuery = Filters.exists("name", false);
Bson projection = Projections.include("id");
for (String collection : Arrays.asList(OrganizationMongoDBAdaptorFactory.INTERPRETATION_COLLECTION,
OrganizationMongoDBAdaptorFactory.INTERPRETATION_ARCHIVE_COLLECTION,
OrganizationMongoDBAdaptorFactory.DELETED_INTERPRETATION_COLLECTION)) {
migrateCollection(collection, nameDoesNotExistQuery, projection,
(document, bulk) -> {
Document updateDocument = new Document()
.append("name", document.get("id"));
bulk.add(new UpdateOneModel<>(Filters.eq("_id", document.get("_id")), new Document("$set", updateDocument)));
});
}
}

}
Loading

0 comments on commit d624826

Please sign in to comment.