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server: Remove study/{}/variant and study/{}/alignment webservices. C…
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…loses #672.

- Remove study variants command line.
- Other minor improvements.
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@pfurio
pfurio committed Aug 9, 2017
1 parent 7468a92 commit f61c80b
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Showing 33 changed files with 179 additions and 916 deletions.
8 changes: 4 additions & 4 deletions opencga-analysis/src/test/java/org/opencb/opencga/analysis/JobFactoryTest.java
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Expand Up @@ -24,7 +24,7 @@
import org.opencb.commons.datastore.core.QueryResult;
import org.opencb.commons.utils.StringUtils;
import org.opencb.opencga.catalog.managers.CatalogManager;
import org.opencb.opencga.catalog.CatalogManagerExternalResource;
import org.opencb.opencga.catalog.managers.CatalogManagerExternalResource;
import org.opencb.opencga.catalog.models.*;

import java.io.BufferedReader;
Expand Down Expand Up @@ -61,9 +61,9 @@ public void before() throws Exception {
sessionId = catalogManager.getUserManager().login(userId, "user", "localhost").first().getId();
projectId = catalogManager.getProjectManager().create("p1", "p1", "Project 1", "ACME", "Homo sapiens",
null, null, "GRCh38", new QueryOptions(), sessionId).first().getId();
studyId = catalogManager.getStudyManager().create(projectId, "s1", "s1", Study.Type.CASE_CONTROL, null, "Study 1", null, null,
null, null, Collections.singletonMap(File.Bioformat.VARIANT, new DataStore("mongodb", DB_NAME)), null, null, null,
sessionId).first().getId();
studyId = catalogManager.getStudyManager().create(String.valueOf(projectId), "s1", "s1", Study.Type.CASE_CONTROL, null, "Study " +
"1", null, null, null, null, Collections.singletonMap(File.Bioformat.VARIANT, new DataStore("mongodb", DB_NAME)), null,
null, null, sessionId).first().getId();
output = catalogManager.getFileManager().createFolder(Long.toString(studyId), Paths.get("data", "index").toString(), null, false,
null, QueryOptions.empty(), sessionId).first();

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1 change: 0 additions & 1 deletion opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java
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Expand Up @@ -112,7 +112,6 @@ public OpencgaCliOptionsParser(boolean interactive) {
studySubCommands.addCommand("files", studyCommandOptions.filesCommandOptions);
studySubCommands.addCommand("jobs", studyCommandOptions.jobsCommandOptions);
studySubCommands.addCommand("samples", studyCommandOptions.samplesCommandOptions);
studySubCommands.addCommand("variants", studyCommandOptions.variantsCommandOptions);
studySubCommands.addCommand("help", studyCommandOptions.helpCommandOptions);
studySubCommands.addCommand("groups", studyCommandOptions.groupsCommandOptions);
studySubCommands.addCommand("groups-create", studyCommandOptions.groupsCreateCommandOptions);
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108 changes: 0 additions & 108 deletions ...src/main/java/org/opencb/opencga/app/cli/main/executors/catalog/StudyCommandExecutor.java
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Expand Up @@ -36,8 +36,6 @@
import org.opencb.opencga.catalog.models.Study;
import org.opencb.opencga.catalog.models.acls.permissions.StudyAclEntry;
import org.opencb.opencga.catalog.models.summaries.StudySummary;
import org.opencb.opencga.client.rest.catalog.StudyClient;
import org.opencb.opencga.storage.core.variant.adaptors.VariantQueryParam;

import java.io.IOException;
import java.util.ArrayList;
Expand Down Expand Up @@ -103,9 +101,6 @@ public void execute() throws Exception {
case "jobs":
queryResponse = jobs();
break;
case "variants":
queryResponse = variants();
break;
case "acl":
queryResponse = getAcl();
break;
Expand Down Expand Up @@ -365,109 +360,6 @@ private QueryResponse<Sample> samples() throws CatalogException, IOException {
return openCGAClient.getStudyClient().getSamples(studiesCommandOptions.samplesCommandOptions.study, queryOptions);
}

@Deprecated
private QueryResponse variants() throws CatalogException, IOException {

logger.debug("Listing variants of a study.");

QueryOptions queryOptions = new QueryOptions();
queryOptions.putAll(studiesCommandOptions.commonCommandOptions.params);

queryOptions.putIfNotEmpty(VariantQueryParam.ID.key(), studiesCommandOptions.variantsCommandOptions.ids);
queryOptions.putIfNotEmpty(VariantQueryParam.REGION.key(),
studiesCommandOptions.variantsCommandOptions.region);
queryOptions.putIfNotEmpty(VariantQueryParam.CHROMOSOME.key(),
studiesCommandOptions.variantsCommandOptions.chromosome);
queryOptions.putIfNotEmpty(VariantQueryParam.GENE.key(),
studiesCommandOptions.variantsCommandOptions.gene);
queryOptions.putIfNotNull(VariantQueryParam.TYPE.key(), studiesCommandOptions.variantsCommandOptions.type);
queryOptions.putIfNotEmpty(VariantQueryParam.REFERENCE.key(),
studiesCommandOptions.variantsCommandOptions.reference);
queryOptions.putIfNotEmpty(VariantQueryParam.ALTERNATE.key(),
studiesCommandOptions.variantsCommandOptions.alternate);
queryOptions.putIfNotEmpty(VariantQueryParam.RETURNED_STUDIES.key(),
studiesCommandOptions.variantsCommandOptions.returnedStudies);
queryOptions.putIfNotEmpty(VariantQueryParam.RETURNED_SAMPLES.key(),
studiesCommandOptions.variantsCommandOptions.returnedSamples);
queryOptions.putIfNotEmpty(VariantQueryParam.RETURNED_FILES.key(),
studiesCommandOptions.variantsCommandOptions.returnedFiles);
queryOptions.putIfNotEmpty(VariantQueryParam.FILES.key(),
studiesCommandOptions.variantsCommandOptions.files);
queryOptions.putIfNotEmpty(VariantQueryParam.STATS_MAF.key(),
studiesCommandOptions.variantsCommandOptions.maf);
queryOptions.putIfNotEmpty(VariantQueryParam.STATS_MGF.key(),
studiesCommandOptions.variantsCommandOptions.mgf);
queryOptions.putIfNotEmpty(VariantQueryParam.MISSING_ALLELES.key(),
studiesCommandOptions.variantsCommandOptions.missingAlleles);
queryOptions.putIfNotEmpty(VariantQueryParam.MISSING_GENOTYPES.key(),
studiesCommandOptions.variantsCommandOptions.missingGenotypes);
// queryOptions.put(CatalogVariantDBAdaptor.VariantQueryParams.ANNOTATION_EXISTS.key(),
// studiesCommandOptions.variantsCommandOptions.annotationExists);
queryOptions.putIfNotEmpty(VariantQueryParam.GENOTYPE.key(),
studiesCommandOptions.variantsCommandOptions.genotype);
queryOptions.putIfNotEmpty(VariantQueryParam.ANNOT_CONSEQUENCE_TYPE.key(),
studiesCommandOptions.variantsCommandOptions.annot_ct);
queryOptions.putIfNotEmpty(VariantQueryParam.ANNOT_XREF.key(),
studiesCommandOptions.variantsCommandOptions.annot_xref);
queryOptions.putIfNotEmpty(VariantQueryParam.ANNOT_BIOTYPE.key(),
studiesCommandOptions.variantsCommandOptions.annot_biotype);
queryOptions.putIfNotEmpty(VariantQueryParam.ANNOT_POLYPHEN.key(),
studiesCommandOptions.variantsCommandOptions.polyphen);
queryOptions.putIfNotEmpty(VariantQueryParam.ANNOT_SIFT.key(),
studiesCommandOptions.variantsCommandOptions.sift);
queryOptions.putIfNotEmpty(VariantQueryParam.ANNOT_CONSERVATION.key(),
studiesCommandOptions.variantsCommandOptions.conservation);
queryOptions.putIfNotEmpty(VariantQueryParam.ANNOT_POPULATION_MINOR_ALLELE_FREQUENCY.key(),
studiesCommandOptions.variantsCommandOptions.annotPopulationMaf);
queryOptions.putIfNotEmpty(VariantQueryParam.ANNOT_POPULATION_ALTERNATE_FREQUENCY.key(),
studiesCommandOptions.variantsCommandOptions.alternate_frequency);
queryOptions.putIfNotEmpty(VariantQueryParam.ANNOT_POPULATION_REFERENCE_FREQUENCY.key(),
studiesCommandOptions.variantsCommandOptions.reference_frequency);
queryOptions.putIfNotEmpty(VariantQueryParam.ANNOT_TRANSCRIPTION_FLAGS.key(),
studiesCommandOptions.variantsCommandOptions.transcriptionFlags);
queryOptions.putIfNotEmpty(VariantQueryParam.ANNOT_GENE_TRAITS_ID.key(),
studiesCommandOptions.variantsCommandOptions.geneTraitId);
queryOptions.putIfNotEmpty(VariantQueryParam.ANNOT_GENE_TRAITS_NAME.key(),
studiesCommandOptions.variantsCommandOptions.geneTraitName);
queryOptions.putIfNotEmpty(VariantQueryParam.ANNOT_HPO.key(),
studiesCommandOptions.variantsCommandOptions.hpo);
queryOptions.putIfNotEmpty(VariantQueryParam.ANNOT_GO.key(),
studiesCommandOptions.variantsCommandOptions.go);
queryOptions.putIfNotEmpty(VariantQueryParam.ANNOT_EXPRESSION.key(),
studiesCommandOptions.variantsCommandOptions.expression);
queryOptions.putIfNotEmpty(VariantQueryParam.ANNOT_PROTEIN_KEYWORDS.key(),
studiesCommandOptions.variantsCommandOptions.proteinKeyword);
queryOptions.putIfNotEmpty(VariantQueryParam.ANNOT_DRUG.key(),
studiesCommandOptions.variantsCommandOptions.drug);
queryOptions.putIfNotEmpty(VariantQueryParam.ANNOT_FUNCTIONAL_SCORE.key(),
studiesCommandOptions.variantsCommandOptions.functionalScore);
queryOptions.putIfNotEmpty(VariantQueryParam.UNKNOWN_GENOTYPE.key(),
studiesCommandOptions.variantsCommandOptions.unknownGenotype);
queryOptions.put(QueryOptions.SORT, studiesCommandOptions.variantsCommandOptions.sort);
// queryOptions.putIfNotEmpty("merge", studiesCommandOptions.variantsCommandOptions.merge);

queryOptions.putIfNotEmpty(QueryOptions.INCLUDE, studiesCommandOptions.variantsCommandOptions.include);
queryOptions.putIfNotEmpty(QueryOptions.EXCLUDE, studiesCommandOptions.variantsCommandOptions.exclude);
queryOptions.putIfNotEmpty(QueryOptions.LIMIT, studiesCommandOptions.variantsCommandOptions.limit);
queryOptions.putIfNotEmpty(QueryOptions.SKIP, studiesCommandOptions.variantsCommandOptions.skip);

queryOptions.put("samplesMetadata", studiesCommandOptions.variantsCommandOptions.samplesMetadata);
queryOptions.putIfNotEmpty("groupBy", studiesCommandOptions.variantsCommandOptions.groupBy);
queryOptions.put("histogram", studiesCommandOptions.variantsCommandOptions.histogram);
queryOptions.putIfNotEmpty("interval", studiesCommandOptions.variantsCommandOptions.interval);
queryOptions.put("count", studiesCommandOptions.variantsCommandOptions.count);

if (studiesCommandOptions.variantsCommandOptions.count) {
return openCGAClient.getStudyClient().countVariants(studiesCommandOptions.variantsCommandOptions.study, queryOptions);
} else if (studiesCommandOptions.variantsCommandOptions.samplesMetadata
|| StringUtils.isNoneEmpty(studiesCommandOptions.variantsCommandOptions.groupBy)
|| studiesCommandOptions.variantsCommandOptions.histogram) {
return openCGAClient.getStudyClient().getVariantsGeneric(studiesCommandOptions.variantsCommandOptions.study, queryOptions);
} else {
return openCGAClient.getStudyClient().getVariants(studiesCommandOptions.variantsCommandOptions.study, queryOptions);
}
}

/************************************************* Groups commands *********************************************************/
private QueryResponse<ObjectMap> groups() throws CatalogException,IOException {
logger.debug("Groups");
Expand Down

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