Merge branch 'TASK-6766' of github.com:opencb/opencga into TASK-6766

opencga-analysis/src/main/java/org/opencb/opencga/analysis/models/IndividualPrivateUpdateParams.java

@@ -6,6 +6,7 @@
 import org.opencb.biodata.models.core.SexOntologyTermAnnotation;
 import org.opencb.biodata.models.pedigree.IndividualProperty;
 import org.opencb.opencga.core.models.common.AnnotationSet;
+import org.opencb.opencga.core.models.common.QualityControlStatus;
 import org.opencb.opencga.core.models.common.StatusParams;
 import org.opencb.opencga.core.models.individual.*;
 import org.opencb.opencga.core.models.sample.SampleReferenceParam;
@@ -27,7 +28,7 @@ public IndividualPrivateUpdateParams(String id, String name, IndividualReference
                                          IndividualProperty.LifeStatus lifeStatus, List<SampleReferenceParam> samples,
                                          List<AnnotationSet> annotationSets, List<Phenotype> phenotypes, List<Disorder> disorders,
                                          StatusParams status, IndividualQualityControl qualityControl,
-                                         IndividualQualityControlStatus qualityControlStatus, Map<String, Object> attributes,
+                                         QualityControlStatus qualityControlStatus, Map<String, Object> attributes,
                                          IndividualInternal internal) {
         super(id, name, father, mother, creationDate, modificationDate, parentalConsanguinity, location, sex, ethnicity, population,
                 dateOfBirth, karyotypicSex, lifeStatus, samples, annotationSets, phenotypes, disorders, status, qualityControl,

opencga-analysis/src/main/java/org/opencb/opencga/analysis/models/SamplePrivateUpdateParams.java

@@ -3,6 +3,7 @@
 import org.opencb.biodata.models.clinical.Phenotype;
 import org.opencb.opencga.core.models.common.AnnotationSet;
 import org.opencb.opencga.core.models.common.ExternalSource;
+import org.opencb.opencga.core.models.common.QualityControlStatus;
 import org.opencb.opencga.core.models.common.StatusParams;
 import org.opencb.opencga.core.models.sample.*;
 
@@ -18,7 +19,7 @@ public SamplePrivateUpdateParams() {
 
     public SamplePrivateUpdateParams(String id, String description, String creationDate, String modificationDate, String individualId,
                                      ExternalSource source, SampleProcessing processing, SampleCollection collection,
-                                     SampleQualityControl qualityControl, SampleQualityControlStatus qualityControlStatus, Boolean somatic,
+                                     SampleQualityControl qualityControl, QualityControlStatus qualityControlStatus, Boolean somatic,
                                      List<Phenotype> phenotypes, List<AnnotationSet> annotationSets, Map<String, Object> attributes,
                                      StatusParams status, SampleInternal internal) {
         super(id, description, creationDate, modificationDate, individualId, source, processing, collection, qualityControl,

opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/VariantAnalysisTest.java

@@ -71,6 +71,7 @@
 import org.opencb.opencga.core.models.cohort.CohortCreateParams;
 import org.opencb.opencga.core.models.cohort.CohortUpdateParams;
 import org.opencb.opencga.core.models.common.AnnotationSet;
+import org.opencb.opencga.core.models.common.QualityControlStatus;
 import org.opencb.opencga.core.models.family.Family;
 import org.opencb.opencga.core.models.family.FamilyQualityControl;
 import org.opencb.opencga.core.models.family.FamilyUpdateParams;
@@ -83,7 +84,10 @@
 import org.opencb.opencga.core.models.organizations.OrganizationUpdateParams;
 import org.opencb.opencga.core.models.project.ProjectCreateParams;
 import org.opencb.opencga.core.models.project.ProjectOrganism;
-import org.opencb.opencga.core.models.sample.*;
+import org.opencb.opencga.core.models.sample.Sample;
+import org.opencb.opencga.core.models.sample.SampleQualityControl;
+import org.opencb.opencga.core.models.sample.SampleReferenceParam;
+import org.opencb.opencga.core.models.sample.SampleUpdateParams;
 import org.opencb.opencga.core.models.variant.*;
 import org.opencb.opencga.core.response.OpenCGAResult;
 import org.opencb.opencga.core.testclassification.duration.LongTests;
@@ -775,15 +779,15 @@ public void testSampleQcStats() throws Exception {
         System.out.println("outDir = " + outDir);
 
         SampleQualityControl qc = new SampleQualityControl();
-        SampleUpdateParams updateParams = new SampleUpdateParams().setQualityControl(qc).setQualityControlStatus(new SampleQualityControlStatus());
+        SampleUpdateParams updateParams = new SampleUpdateParams().setQualityControl(qc).setQualityControlStatus(new QualityControlStatus());
         catalogManager.getSampleManager().update(CANCER_STUDY, cancer_sample, updateParams, null, token);
 
         SampleQcAnalysisParams params = new SampleQcAnalysisParams();
         params.setSamples(Collections.singletonList(cancer_sample));
         params.setVsId("test");
         params.setVsDescription("Description test");
         params.setVsQuery(new AnnotationVariantQueryParams());
-        params.setSkip(Arrays.asList(SIGNATURE_ANALYSIS_ID, GENOME_PLOT_ANALYSIS_ID));
+        params.setSkipAnalysis(Arrays.asList(SIGNATURE_ANALYSIS_ID, GENOME_PLOT_ANALYSIS_ID));
 
         toolRunner.execute(SampleVariantQcAnalysis.class, params, new ObjectMap(ParamConstants.STUDY_PARAM, CANCER_STUDY),
                 outDir, null, false, token);

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisVariantCommandExecutor.java

@@ -941,7 +941,7 @@ private RestResponse<Job> runIndividualQc() throws Exception {
             putNestedIfNotEmpty(beanParams, "sample",commandOptions.sample, true);
             putNestedIfNotEmpty(beanParams, "inferredSexMethod",commandOptions.inferredSexMethod, true);
             putNestedIfNotEmpty(beanParams, "resourcesDir",commandOptions.resourcesDir, true);
-            putNestedIfNotNull(beanParams, "skip",commandOptions.skip, true);
+            putNestedIfNotNull(beanParams, "skipAnalysis",commandOptions.skipAnalysis, true);
             putNestedIfNotNull(beanParams, "skipIndex",commandOptions.skipIndex, true);
             putNestedIfNotNull(beanParams, "overwrite",commandOptions.overwrite, true);
             putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
@@ -1529,7 +1529,7 @@ private RestResponse<Job> runSampleQc() throws Exception {
             putNestedIfNotEmpty(beanParams, "gpId",commandOptions.gpId, true);
             putNestedIfNotEmpty(beanParams, "gpDescription",commandOptions.gpDescription, true);
             putNestedIfNotEmpty(beanParams, "gpConfigFile",commandOptions.gpConfigFile, true);
-            putNestedIfNotNull(beanParams, "skip",commandOptions.skip, true);
+            putNestedIfNotNull(beanParams, "skipAnalysis",commandOptions.skipAnalysis, true);
             putNestedIfNotNull(beanParams, "skipIndex",commandOptions.skipIndex, true);
             putNestedIfNotNull(beanParams, "overwrite",commandOptions.overwrite, true);
             putNestedIfNotEmpty(beanParams, "resourcesDir",commandOptions.resourcesDir, true);

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/IndividualsCommandExecutor.java

@@ -19,6 +19,7 @@
 import org.opencb.opencga.catalog.utils.ParamUtils.CompleteUpdateAction;
 import org.opencb.opencga.client.exceptions.ClientException;
 import org.opencb.opencga.core.common.JacksonUtils;
+import org.opencb.opencga.core.models.common.QualityControlStatus;
 import org.opencb.opencga.core.models.common.StatusParams;
 import org.opencb.opencga.core.models.common.TsvAnnotationParams;
 import org.opencb.opencga.core.models.individual.Individual;
@@ -27,7 +28,6 @@
 import org.opencb.opencga.core.models.individual.IndividualCreateParams;
 import org.opencb.opencga.core.models.individual.IndividualPopulation;
 import org.opencb.opencga.core.models.individual.IndividualQualityControl;
-import org.opencb.opencga.core.models.individual.IndividualQualityControlStatus;
 import org.opencb.opencga.core.models.individual.IndividualReferenceParam;
 import org.opencb.opencga.core.models.individual.IndividualUpdateParams;
 import org.opencb.opencga.core.models.individual.Location;
@@ -453,7 +453,6 @@ private RestResponse<Individual> update() throws Exception {
             putNestedIfNotEmpty(beanParams, "qualityControlStatus.date",commandOptions.qualityControlStatusDate, true);
             putNestedIfNotEmpty(beanParams, "qualityControlStatus.version",commandOptions.qualityControlStatusVersion, true);
             putNestedIfNotEmpty(beanParams, "qualityControlStatus.commit",commandOptions.qualityControlStatusCommit, true);
-            putNestedIfNotNull(beanParams, "qualityControlStatus.code",commandOptions.qualityControlStatusCode, true);
             putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true);
 
             individualUpdateParams = JacksonUtils.getDefaultObjectMapper().copy()

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/SamplesCommandExecutor.java

@@ -18,6 +18,7 @@
 import org.opencb.opencga.client.exceptions.ClientException;
 import org.opencb.opencga.core.common.JacksonUtils;
 import org.opencb.opencga.core.models.common.ExternalSource;
+import org.opencb.opencga.core.models.common.QualityControlStatus;
 import org.opencb.opencga.core.models.common.RgaIndex.Status;
 import org.opencb.opencga.core.models.common.StatusParams;
 import org.opencb.opencga.core.models.common.TsvAnnotationParams;
@@ -29,7 +30,6 @@
 import org.opencb.opencga.core.models.sample.SampleCreateParams;
 import org.opencb.opencga.core.models.sample.SampleProcessing;
 import org.opencb.opencga.core.models.sample.SampleQualityControl;
-import org.opencb.opencga.core.models.sample.SampleQualityControlStatus;
 import org.opencb.opencga.core.models.sample.SampleUpdateParams;
 import org.opencb.opencga.core.models.sample.SampleVariantQualityControlMetrics;
 import org.opencb.opencga.core.response.QueryType;
@@ -473,7 +473,6 @@ private RestResponse<Sample> update() throws Exception {
             putNestedIfNotEmpty(beanParams, "qualityControlStatus.date",commandOptions.qualityControlStatusDate, true);
             putNestedIfNotEmpty(beanParams, "qualityControlStatus.version",commandOptions.qualityControlStatusVersion, true);
             putNestedIfNotEmpty(beanParams, "qualityControlStatus.commit",commandOptions.qualityControlStatusCommit, true);
-            putNestedIfNotNull(beanParams, "qualityControlStatus.code",commandOptions.qualityControlStatusCode, true);
             putNestedIfNotNull(beanParams, "somatic",commandOptions.somatic, true);
             putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true);
             putNestedIfNotEmpty(beanParams, "status.id",commandOptions.statusId, true);

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisVariantCommandOptions.java

@@ -1301,8 +1301,8 @@ public class RunIndividualQcCommandOptions {
         @Parameter(names = {"--resources-dir"}, description = "Directory where the QC resource files are located", required = false, arity = 1)
         public String resourcesDir;
 
-        @Parameter(names = {"--skip"}, description = "Individual QC analysis to skip. Valid values are: inferred-sex, mendelian-errors", required = false, arity = 1)
-        public String skip;
+        @Parameter(names = {"--skip-analysis"}, description = "List of individual QC analysis to skip. Valid values are: inferred-sex, mendelian-errors and relatedness (if parents are present)", required = false, arity = 1)
+        public String skipAnalysis;
 
         @Parameter(names = {"--skip-index"}, description = "Do not save the computed quality control in catalog", required = false, arity = 1)
         public Boolean skipIndex;
@@ -2307,8 +2307,8 @@ public class RunSampleQcCommandOptions {
         @Parameter(names = {"--gp-config-file"}, description = "Genome plot configuration file.", required = false, arity = 1)
         public String gpConfigFile;
 
-        @Parameter(names = {"--skip"}, description = "Quality control metrics to skip. Valid values are: variant-stats, signature, signature-catalogue, signature-fitting, genome-plot", required = false, arity = 1)
-        public String skip;
+        @Parameter(names = {"--skip-analysis"}, description = "Quality control metrics to skip. Valid values are: variant-stats, signature, signature-catalogue, signature-fitting, genome-plot", required = false, arity = 1)
+        public String skipAnalysis;
 
         @Parameter(names = {"--skip-index"}, description = "Do not save the computed quality control in catalog", required = false, arity = 1)
         public Boolean skipIndex;

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/IndividualsCommandOptions.java

@@ -680,9 +680,6 @@ public class UpdateCommandOptions {
         @Parameter(names = {"--quality-control-status-commit"}, description = "The body web service commit parameter", required = false, arity = 1)
         public String qualityControlStatusCommit;
 
-        @Parameter(names = {"--quality-control-status-code"}, description = "The body web service code parameter", required = false, arity = 1)
-        public Integer qualityControlStatusCode;
-
         @DynamicParameter(names = {"--attributes"}, description = "The body web service attributes parameter. Use: --attributes key=value", required = false)
         public java.util.Map<java.lang.String,java.lang.Object> attributes = new HashMap<>(); //Dynamic parameters must be initialized;
 

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/SamplesCommandOptions.java

@@ -712,9 +712,6 @@ public class UpdateCommandOptions {
         @Parameter(names = {"--quality-control-status-commit"}, description = "The body web service commit parameter", required = false, arity = 1)
         public String qualityControlStatusCommit;
 
-        @Parameter(names = {"--quality-control-status-code"}, description = "The body web service code parameter", required = false, arity = 1)
-        public Integer qualityControlStatusCode;
-
         @Parameter(names = {"--somatic"}, description = "The body web service somatic parameter", required = false, arity = 1)
         public Boolean somatic;
 

opencga-core/src/main/java/org/opencb/opencga/core/api/FieldConstants.java

@@ -204,8 +204,8 @@ public class FieldConstants {
     public static final String INDIVIDUAL_QC_SAMPLE_ID_DESCRIPTION = "Sample ID (required when the individual has multiple samples)";
     @Deprecated
     public static final String INFERRED_SEX_METHOD_DESCRIPTION = "Inferred sex method.";
-    public static final String INDIVIDUAL_QC_SKIP_DESCRIPTION = "Individual QC analysis to skip. Valid values are: " + INFERRED_SEX_ID
-            + ", " + MENDELIAN_ERRORS_ID;
+    public static final String INDIVIDUAL_QC_SKIP_ANALYSIS_DESCRIPTION = "List of individual QC analysis to skip. Valid values are: "
+            + INFERRED_SEX_ID + ", " + MENDELIAN_ERRORS_ID + " and " + RELATEDNESS_ID + " (if parents are present)";
     public static final String INDIVIDUAL_QC_INFERRED_SEX_DESCRIPTION = "Inferred sex results for the individual";
     public static final String INDIVIDUAL_QC_RELATEDNESS_DESCRIPTION = "Relatedness results for the individual";
     public static final String INDIVIDUAL_QC_MENDELIAN_ERROR_DESCRIPTION = "Mendelian error results for the individual";

opencga-core/src/main/java/org/opencb/opencga/core/models/common/QualityControlStatus.java

@@ -24,14 +24,13 @@ public class QualityControlStatus extends InternalStatus {
     /*
      * States
      *
-     * NONE --> COMPUTING --> READY
-     *                    --> INCOMPLETE
+     * NONE --> READY
+     *          ERROR
      */
     public static final String NONE = "NONE";
-    public static final String COMPUTING = "COMPUTING";
-    public static final String INCOMPLETE = "INCOMPLETE";
+    public static final String ERROR = "ERROR";
 
-    protected static final List<String> STATUS_LIST = Arrays.asList(READY, DELETED, NONE, COMPUTING, INCOMPLETE);
+    protected static final List<String> STATUS_LIST = Arrays.asList(READY, DELETED, NONE, ERROR);
 
     public QualityControlStatus(String status, String message) {
         if (isValid(status)) {
@@ -57,8 +56,7 @@ public static boolean isValid(String status) {
         return status != null
                 && (status.equals(READY)
                 || status.equals(DELETED)
-                || status.equals(INCOMPLETE)
                 || status.equals(NONE)
-                || status.equals(COMPUTING));
+                || status.equals(ERROR));
     }
 }

opencga-core/src/main/java/org/opencb/opencga/core/models/individual/IndividualInternal.java

@@ -23,20 +23,20 @@
 
 public class IndividualInternal extends Internal {
 
-    private IndividualQualityControlStatus qualityControlStatus;
+    private QualityControlStatus qualityControlStatus;
 
     public IndividualInternal() {
     }
 
     public IndividualInternal(InternalStatus status, String registrationDate, String modificationDate,
-                              IndividualQualityControlStatus qualityControlStatus) {
+                              QualityControlStatus qualityControlStatus) {
         super(status, registrationDate, modificationDate);
         this.qualityControlStatus = qualityControlStatus;
     }
 
     public static IndividualInternal init() {
         String time = TimeUtils.getTime();
-        return new IndividualInternal(new InternalStatus(InternalStatus.READY), time, time, new IndividualQualityControlStatus());
+        return new IndividualInternal(new InternalStatus(InternalStatus.READY), time, time, new QualityControlStatus());
     }
 
     @Override
@@ -77,11 +77,11 @@ public IndividualInternal setLastModified(String lastModified) {
         return this;
     }
 
-    public IndividualQualityControlStatus getQualityControlStatus() {
+    public QualityControlStatus getQualityControlStatus() {
         return qualityControlStatus;
     }
 
-    public IndividualInternal setQualityControlStatus(IndividualQualityControlStatus qualityControlStatus) {
+    public IndividualInternal setQualityControlStatus(QualityControlStatus qualityControlStatus) {
         this.qualityControlStatus = qualityControlStatus;
         return this;
     }