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Merge pull request #2529 from opencb/TASK-7134
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TASK-7134 - Re-implement Aggregations Stats for all Catalog Browsers
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@jtarraga
jtarraga authored Feb 10, 2025
2 parents 8197675 + be93358 commit 20552c9
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Showing 89 changed files with 3,683 additions and 303 deletions.
16 changes: 8 additions & 8 deletions opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -39,17 +39,17 @@ public abstract class OpenCgaCompleter implements Completer {
.map(Candidate::new)
.collect(toList());

private List<Candidate> panelsList = asList( "acl-update","create","distinct","import","search","acl","delete","info","update")
private List<Candidate> panelsList = asList( "acl-update","aggregationstats","create","distinct","import","search","acl","delete","info","update")
.stream()
.map(Candidate::new)
.collect(toList());

private List<Candidate> clinicalList = asList( "acl-update","annotation-sets-load","clinical-configuration-update","create","distinct","interpretation-distinct","interpretation-search","interpretation-info","interpreter-cancer-tiering-run","interpreter-exomiser-run","interpreter-team-run","interpreter-tiering-run","interpreter-zetta-run","load","rga-aggregation-stats","rga-gene-query","rga-gene-summary","rga-index-run","rga-individual-query","rga-individual-summary","rga-variant-query","rga-variant-summary","search","variant-query","acl","delete","update","annotation-sets-annotations-update","info","interpretation-create","interpretation-clear","interpretation-delete","interpretation-revert","interpretation-update","report-update")
private List<Candidate> clinicalList = asList( "acl-update","aggregationstats","annotation-sets-load","clinical-configuration-update","create","distinct","interpretation-aggregation-stats","interpretation-distinct","interpretation-search","interpretation-info","interpreter-cancer-tiering-run","interpreter-exomiser-run","interpreter-team-run","interpreter-tiering-run","interpreter-zetta-run","load","rga-aggregation-stats","rga-gene-query","rga-gene-summary","rga-index-run","rga-individual-query","rga-individual-summary","rga-variant-query","rga-variant-summary","search","variant-query","acl","delete","update","annotation-sets-annotations-update","info","interpretation-create","interpretation-clear","interpretation-delete","interpretation-revert","interpretation-update","report-update")
.stream()
.map(Candidate::new)
.collect(toList());

private List<Candidate> jobsList = asList( "acl-update","create","distinct","retry","search","top","acl","delete","info","update","kill","log-head","log-tail")
private List<Candidate> jobsList = asList( "acl-update","aggregationstats","create","distinct","retry","search","top","acl","delete","info","update","kill","log-head","log-tail")
.stream()
.map(Candidate::new)
.collect(toList());
Expand All @@ -59,12 +59,12 @@ public abstract class OpenCgaCompleter implements Completer {
.map(Candidate::new)
.collect(toList());

private List<Candidate> individualsList = asList( "acl-update","annotation-sets-load","create","distinct","search","acl","delete","info","update","annotation-sets-annotations-update","relatives")
private List<Candidate> individualsList = asList( "acl-update","aggregationstats","annotation-sets-load","create","distinct","search","acl","delete","info","update","annotation-sets-annotations-update","relatives")
.stream()
.map(Candidate::new)
.collect(toList());

private List<Candidate> familiesList = asList( "acl-update","annotation-sets-load","create","distinct","search","acl","delete","info","update","annotation-sets-annotations-update")
private List<Candidate> familiesList = asList( "acl-update","aggregationstats","annotation-sets-load","create","distinct","search","acl","delete","info","update","annotation-sets-annotations-update")
.stream()
.map(Candidate::new)
.collect(toList());
Expand All @@ -74,7 +74,7 @@ public abstract class OpenCgaCompleter implements Completer {
.map(Candidate::new)
.collect(toList());

private List<Candidate> samplesList = asList( "acl-update","annotation-sets-load","create","distinct","load","search","acl","delete","info","update","annotation-sets-annotations-update")
private List<Candidate> samplesList = asList( "acl-update","aggregationstats","annotation-sets-load","create","distinct","load","search","acl","delete","info","update","annotation-sets-annotations-update")
.stream()
.map(Candidate::new)
.collect(toList());
Expand All @@ -99,7 +99,7 @@ public abstract class OpenCgaCompleter implements Completer {
.map(Candidate::new)
.collect(toList());

private List<Candidate> filesList = asList( "acl-update","annotation-sets-load","bioformats","create","distinct","fetch","formats","link","link-run","postlink-run","search","upload","acl","delete","info","unlink","update","annotation-sets-annotations-update","download","grep","head","image","move","refresh","tail","list","tree")
private List<Candidate> filesList = asList( "acl-update","aggregationstats","annotation-sets-load","bioformats","create","distinct","fetch","formats","link","link-run","postlink-run","search","upload","acl","delete","info","unlink","update","annotation-sets-annotations-update","download","grep","head","image","move","refresh","tail","list","tree")
.stream()
.map(Candidate::new)
.collect(toList());
Expand All @@ -109,7 +109,7 @@ public abstract class OpenCgaCompleter implements Completer {
.map(Candidate::new)
.collect(toList());

private List<Candidate> cohortsList = asList( "acl-update","annotation-sets-load","create","distinct","generate","search","acl","delete","info","update","annotation-sets-annotations-update")
private List<Candidate> cohortsList = asList( "acl-update","aggregationstats","annotation-sets-load","create","distinct","generate","search","acl","delete","info","update","annotation-sets-annotations-update")
.stream()
.map(Candidate::new)
.collect(toList());
Expand Down
9 changes: 9 additions & 0 deletions opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java
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Original file line number Diff line number Diff line change
Expand Up @@ -99,6 +99,7 @@ public OpencgaCliOptionsParser() {
jCommander.addCommand("panels", diseasePanelsCommandOptions);
JCommander diseasePanelsSubCommands = jCommander.getCommands().get("panels");
diseasePanelsSubCommands.addCommand("acl-update", diseasePanelsCommandOptions.updateAclCommandOptions);
diseasePanelsSubCommands.addCommand("aggregationstats", diseasePanelsCommandOptions.aggregationStatsCommandOptions);
diseasePanelsSubCommands.addCommand("create", diseasePanelsCommandOptions.createCommandOptions);
diseasePanelsSubCommands.addCommand("distinct", diseasePanelsCommandOptions.distinctCommandOptions);
diseasePanelsSubCommands.addCommand("import", diseasePanelsCommandOptions.importCommandOptions);
Expand All @@ -112,10 +113,12 @@ public OpencgaCliOptionsParser() {
jCommander.addCommand("clinical", analysisClinicalCommandOptions);
JCommander analysisClinicalSubCommands = jCommander.getCommands().get("clinical");
analysisClinicalSubCommands.addCommand("acl-update", analysisClinicalCommandOptions.updateAclCommandOptions);
analysisClinicalSubCommands.addCommand("aggregationstats", analysisClinicalCommandOptions.aggregationStatsCommandOptions);
analysisClinicalSubCommands.addCommand("annotation-sets-load", analysisClinicalCommandOptions.loadAnnotationSetsCommandOptions);
analysisClinicalSubCommands.addCommand("clinical-configuration-update", analysisClinicalCommandOptions.updateClinicalConfigurationCommandOptions);
analysisClinicalSubCommands.addCommand("create", analysisClinicalCommandOptions.createCommandOptions);
analysisClinicalSubCommands.addCommand("distinct", analysisClinicalCommandOptions.distinctCommandOptions);
analysisClinicalSubCommands.addCommand("interpretation-aggregation-stats", analysisClinicalCommandOptions.aggregationStatsInterpretationCommandOptions);
analysisClinicalSubCommands.addCommand("interpretation-distinct", analysisClinicalCommandOptions.distinctInterpretationCommandOptions);
analysisClinicalSubCommands.addCommand("interpretation-search", analysisClinicalCommandOptions.searchInterpretationCommandOptions);
analysisClinicalSubCommands.addCommand("interpretation-info", analysisClinicalCommandOptions.infoInterpretationCommandOptions);
Expand Down Expand Up @@ -151,6 +154,7 @@ public OpencgaCliOptionsParser() {
jCommander.addCommand("jobs", jobsCommandOptions);
JCommander jobsSubCommands = jCommander.getCommands().get("jobs");
jobsSubCommands.addCommand("acl-update", jobsCommandOptions.updateAclCommandOptions);
jobsSubCommands.addCommand("aggregationstats", jobsCommandOptions.aggregationStatsCommandOptions);
jobsSubCommands.addCommand("create", jobsCommandOptions.createCommandOptions);
jobsSubCommands.addCommand("distinct", jobsCommandOptions.distinctCommandOptions);
jobsSubCommands.addCommand("retry", jobsCommandOptions.retryCommandOptions);
Expand Down Expand Up @@ -182,6 +186,7 @@ public OpencgaCliOptionsParser() {
jCommander.addCommand("individuals", individualsCommandOptions);
JCommander individualsSubCommands = jCommander.getCommands().get("individuals");
individualsSubCommands.addCommand("acl-update", individualsCommandOptions.updateAclCommandOptions);
individualsSubCommands.addCommand("aggregationstats", individualsCommandOptions.aggregationStatsCommandOptions);
individualsSubCommands.addCommand("annotation-sets-load", individualsCommandOptions.loadAnnotationSetsCommandOptions);
individualsSubCommands.addCommand("create", individualsCommandOptions.createCommandOptions);
individualsSubCommands.addCommand("distinct", individualsCommandOptions.distinctCommandOptions);
Expand All @@ -197,6 +202,7 @@ public OpencgaCliOptionsParser() {
jCommander.addCommand("families", familiesCommandOptions);
JCommander familiesSubCommands = jCommander.getCommands().get("families");
familiesSubCommands.addCommand("acl-update", familiesCommandOptions.updateAclCommandOptions);
familiesSubCommands.addCommand("aggregationstats", familiesCommandOptions.aggregationStatsCommandOptions);
familiesSubCommands.addCommand("annotation-sets-load", familiesCommandOptions.loadAnnotationSetsCommandOptions);
familiesSubCommands.addCommand("create", familiesCommandOptions.createCommandOptions);
familiesSubCommands.addCommand("distinct", familiesCommandOptions.distinctCommandOptions);
Expand Down Expand Up @@ -227,6 +233,7 @@ public OpencgaCliOptionsParser() {
jCommander.addCommand("samples", samplesCommandOptions);
JCommander samplesSubCommands = jCommander.getCommands().get("samples");
samplesSubCommands.addCommand("acl-update", samplesCommandOptions.updateAclCommandOptions);
samplesSubCommands.addCommand("aggregationstats", samplesCommandOptions.aggregationStatsCommandOptions);
samplesSubCommands.addCommand("annotation-sets-load", samplesCommandOptions.loadAnnotationSetsCommandOptions);
samplesSubCommands.addCommand("create", samplesCommandOptions.createCommandOptions);
samplesSubCommands.addCommand("distinct", samplesCommandOptions.distinctCommandOptions);
Expand Down Expand Up @@ -309,6 +316,7 @@ public OpencgaCliOptionsParser() {
jCommander.addCommand("files", filesCommandOptions);
JCommander filesSubCommands = jCommander.getCommands().get("files");
filesSubCommands.addCommand("acl-update", filesCommandOptions.updateAclCommandOptions);
filesSubCommands.addCommand("aggregationstats", filesCommandOptions.aggregationStatsCommandOptions);
filesSubCommands.addCommand("annotation-sets-load", filesCommandOptions.loadAnnotationSetsCommandOptions);
filesSubCommands.addCommand("bioformats", filesCommandOptions.bioformatsCommandOptions);
filesSubCommands.addCommand("create", filesCommandOptions.createCommandOptions);
Expand Down Expand Up @@ -373,6 +381,7 @@ public OpencgaCliOptionsParser() {
jCommander.addCommand("cohorts", cohortsCommandOptions);
JCommander cohortsSubCommands = jCommander.getCommands().get("cohorts");
cohortsSubCommands.addCommand("acl-update", cohortsCommandOptions.updateAclCommandOptions);
cohortsSubCommands.addCommand("aggregationstats", cohortsCommandOptions.aggregationStatsCommandOptions);
cohortsSubCommands.addCommand("annotation-sets-load", cohortsCommandOptions.loadAnnotationSetsCommandOptions);
cohortsSubCommands.addCommand("create", cohortsCommandOptions.createCommandOptions);
cohortsSubCommands.addCommand("distinct", cohortsCommandOptions.distinctCommandOptions);
Expand Down
77 changes: 77 additions & 0 deletions .../main/java/org/opencb/opencga/app/cli/main/executors/AnalysisClinicalCommandExecutor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -103,6 +103,9 @@ public void execute() throws Exception {
case "acl-update":
queryResponse = updateAcl();
break;
case "aggregationstats":
queryResponse = aggregationStats();
break;
case "annotation-sets-load":
queryResponse = loadAnnotationSets();
break;
Expand All @@ -115,6 +118,9 @@ public void execute() throws Exception {
case "distinct":
queryResponse = distinct();
break;
case "interpretation-aggregation-stats":
queryResponse = aggregationStatsInterpretation();
break;
case "interpretation-distinct":
queryResponse = distinctInterpretation();
break;
Expand Down Expand Up @@ -248,6 +254,48 @@ private RestResponse<ClinicalAnalysisAclEntryList> updateAcl() throws Exception
return openCGAClient.getClinicalAnalysisClient().updateAcl(commandOptions.members, commandOptions.action, clinicalAnalysisAclUpdateParams, queryParams);
}

private RestResponse<FacetField> aggregationStats() throws Exception {
logger.debug("Executing aggregationStats in Analysis - Clinical command line");

AnalysisClinicalCommandOptions.AggregationStatsCommandOptions commandOptions = analysisClinicalCommandOptions.aggregationStatsCommandOptions;

ObjectMap queryParams = new ObjectMap();
queryParams.putIfNotEmpty("study", commandOptions.study);
queryParams.putIfNotEmpty("id", commandOptions.id);
queryParams.putIfNotEmpty("uuid", commandOptions.uuid);
queryParams.putIfNotEmpty("type", commandOptions.type);
queryParams.putIfNotEmpty("disorder", commandOptions.disorder);
queryParams.putIfNotEmpty("files", commandOptions.files);
queryParams.putIfNotEmpty("sample", commandOptions.sample);
queryParams.putIfNotEmpty("individual", commandOptions.individual);
queryParams.putIfNotEmpty("proband", commandOptions.proband);
queryParams.putIfNotEmpty("probandSamples", commandOptions.probandSamples);
queryParams.putIfNotEmpty("family", commandOptions.family);
queryParams.putIfNotEmpty("familyMembers", commandOptions.familyMembers);
queryParams.putIfNotEmpty("familyMemberSamples", commandOptions.familyMemberSamples);
queryParams.putIfNotEmpty("panels", commandOptions.panels);
queryParams.putIfNotNull("locked", commandOptions.locked);
queryParams.putIfNotEmpty("analystId", commandOptions.analystId);
queryParams.putIfNotEmpty("priority", commandOptions.priority);
queryParams.putIfNotEmpty("flags", commandOptions.flags);
queryParams.putIfNotEmpty("creationDate", commandOptions.creationDate);
queryParams.putIfNotEmpty("modificationDate", commandOptions.modificationDate);
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);
queryParams.putIfNotNull("deleted", commandOptions.deleted);
queryParams.putIfNotEmpty("field", commandOptions.field);
if (queryParams.get("study") == null && OpencgaMain.isShellMode()) {
queryParams.putIfNotEmpty("study", sessionManager.getSession().getCurrentStudy());
}

return openCGAClient.getClinicalAnalysisClient().aggregationStats(queryParams);
}

private RestResponse<Job> loadAnnotationSets() throws Exception {
logger.debug("Executing loadAnnotationSets in Analysis - Clinical command line");

Expand Down Expand Up @@ -432,6 +480,35 @@ private RestResponse<ObjectMap> distinct() throws Exception {
return openCGAClient.getClinicalAnalysisClient().distinct(commandOptions.field, queryParams);
}

private RestResponse<FacetField> aggregationStatsInterpretation() throws Exception {
logger.debug("Executing aggregationStatsInterpretation in Analysis - Clinical command line");

AnalysisClinicalCommandOptions.AggregationStatsInterpretationCommandOptions commandOptions = analysisClinicalCommandOptions.aggregationStatsInterpretationCommandOptions;

ObjectMap queryParams = new ObjectMap();
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);
queryParams.putIfNotEmpty("panels", commandOptions.panels);
queryParams.putIfNotEmpty("primaryFindings", commandOptions.primaryFindings);
queryParams.putIfNotEmpty("secondaryFindings", commandOptions.secondaryFindings);
queryParams.putIfNotEmpty("creationDate", commandOptions.creationDate);
queryParams.putIfNotEmpty("modificationDate", commandOptions.modificationDate);
queryParams.putIfNotEmpty("status", commandOptions.status);
queryParams.putIfNotEmpty("internalStatus", commandOptions.internalStatus);
queryParams.putIfNotEmpty("release", commandOptions.release);
queryParams.putIfNotEmpty("field", commandOptions.field);
if (queryParams.get("study") == null && OpencgaMain.isShellMode()) {
queryParams.putIfNotEmpty("study", sessionManager.getSession().getCurrentStudy());
}

return openCGAClient.getClinicalAnalysisClient().aggregationStatsInterpretation(queryParams);
}

private RestResponse<ObjectMap> distinctInterpretation() throws Exception {
logger.debug("Executing distinctInterpretation in Analysis - Clinical command line");

Expand Down
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