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

.gitignore

@@ -100,3 +100,6 @@ venv
 
 # Java annotation processor (APT)
 .factorypath
+
+#app
+opencga-app/app/analysis/qc/resources

opencga-analysis/src/main/java/org/opencb/opencga/analysis/family/qc/FamilyVariantQcAnalysis.java

@@ -39,7 +39,7 @@
 import org.opencb.opencga.core.models.family.FamilyInternal;
 import org.opencb.opencga.core.models.family.FamilyQualityControl;
 import org.opencb.opencga.core.models.family.FamilyUpdateParams;
-import org.opencb.opencga.core.models.variant.FamilyQcAnalysisParams;
+import org.opencb.opencga.core.models.variant.qc.FamilyQcAnalysisParams;
 import org.opencb.opencga.core.response.OpenCGAResult;
 import org.opencb.opencga.core.tools.annotations.Tool;
 import org.opencb.opencga.core.tools.annotations.ToolParams;

opencga-analysis/src/main/java/org/opencb/opencga/analysis/family/qc/FamilyVariantQcLocalAnalysisExecutor.java

@@ -21,7 +21,7 @@
 import org.opencb.opencga.analysis.utils.VariantQcAnalysisExecutorUtils;
 import org.opencb.opencga.core.common.JacksonUtils;
 import org.opencb.opencga.core.exceptions.ToolExecutorException;
-import org.opencb.opencga.core.models.variant.FamilyQcAnalysisParams;
+import org.opencb.opencga.core.models.variant.qc.FamilyQcAnalysisParams;
 import org.opencb.opencga.core.tools.annotations.ToolExecutor;
 import org.opencb.opencga.core.tools.variant.FamilyVariantQcAnalysisExecutor;
 

opencga-analysis/src/main/java/org/opencb/opencga/analysis/individual/qc/IndividualVariantQcAnalysis.java

@@ -41,7 +41,7 @@
 import org.opencb.opencga.core.models.individual.IndividualInternal;
 import org.opencb.opencga.core.models.individual.IndividualQualityControl;
 import org.opencb.opencga.core.models.individual.IndividualUpdateParams;
-import org.opencb.opencga.core.models.variant.IndividualQcAnalysisParams;
+import org.opencb.opencga.core.models.variant.qc.IndividualQcAnalysisParams;
 import org.opencb.opencga.core.response.OpenCGAResult;
 import org.opencb.opencga.core.tools.annotations.Tool;
 import org.opencb.opencga.core.tools.annotations.ToolParams;

opencga-analysis/src/main/java/org/opencb/opencga/analysis/individual/qc/IndividualVariantQcLocalAnalysisExecutor.java

@@ -21,7 +21,7 @@
 import org.opencb.opencga.analysis.utils.VariantQcAnalysisExecutorUtils;
 import org.opencb.opencga.core.common.JacksonUtils;
 import org.opencb.opencga.core.exceptions.ToolExecutorException;
-import org.opencb.opencga.core.models.variant.IndividualQcAnalysisParams;
+import org.opencb.opencga.core.models.variant.qc.IndividualQcAnalysisParams;
 import org.opencb.opencga.core.tools.annotations.ToolExecutor;
 import org.opencb.opencga.core.tools.variant.IndividualVariantQcAnalysisExecutor;
 

opencga-analysis/src/main/java/org/opencb/opencga/analysis/sample/qc/SampleVariantQcAnalysis.java

@@ -41,7 +41,7 @@
 import org.opencb.opencga.core.models.sample.Sample;
 import org.opencb.opencga.core.models.sample.SampleQualityControl;
 import org.opencb.opencga.core.models.sample.SampleUpdateParams;
-import org.opencb.opencga.core.models.variant.SampleQcAnalysisParams;
+import org.opencb.opencga.core.models.variant.qc.SampleQcAnalysisParams;
 import org.opencb.opencga.core.models.variant.SampleVariantStatsAnalysisParams;
 import org.opencb.opencga.core.response.OpenCGAResult;
 import org.opencb.opencga.core.tools.annotations.Tool;

opencga-analysis/src/main/java/org/opencb/opencga/analysis/sample/qc/SampleVariantQcLocalAnalysisExecutor.java

@@ -22,7 +22,7 @@
 import org.opencb.opencga.analysis.utils.VariantQcAnalysisExecutorUtils;
 import org.opencb.opencga.core.common.JacksonUtils;
 import org.opencb.opencga.core.exceptions.ToolExecutorException;
-import org.opencb.opencga.core.models.variant.SampleQcAnalysisParams;
+import org.opencb.opencga.core.models.variant.qc.SampleQcAnalysisParams;
 import org.opencb.opencga.core.tools.annotations.ToolExecutor;
 import org.opencb.opencga.core.tools.variant.SampleVariantQcAnalysisExecutor;
 

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

@@ -89,6 +89,8 @@
 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.models.variant.qc.FamilyQcAnalysisParams;
+import org.opencb.opencga.core.models.variant.qc.SampleQcAnalysisParams;
 import org.opencb.opencga.core.response.OpenCGAResult;
 import org.opencb.opencga.core.testclassification.duration.LongTests;
 import org.opencb.opencga.core.tools.result.ExecutionResult;

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

@@ -63,6 +63,9 @@
 import org.opencb.opencga.core.models.common.mixins.GenericRecordAvroJsonMixin;
 import org.opencb.opencga.core.models.operations.variant.*;
 import org.opencb.opencga.core.models.variant.*;
+import org.opencb.opencga.core.models.variant.qc.FamilyQcAnalysisParams;
+import org.opencb.opencga.core.models.variant.qc.IndividualQcAnalysisParams;
+import org.opencb.opencga.core.models.variant.qc.SampleQcAnalysisParams;
 import org.opencb.opencga.core.tools.ToolParams;
 import org.opencb.opencga.storage.core.exceptions.StorageEngineException;
 import org.opencb.opencga.storage.core.exceptions.VariantSearchException;

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

@@ -1615,7 +1615,7 @@ public class SampleVariantQcCommandOptions {
         public String genomePlotConfigFile;
 
         // Other
-        @Parameter(names = {"--skip"}, description = FieldConstants.SAMPLE_QUALITY_CONTROL_SKIP_DESCRIPTION)
+        @Parameter(names = {"--skip"}, description = FieldConstants.SAMPLE_QC_SKIP_ANALYSIS_DESCRIPTION)
         public List<String> skip;
 
         @Parameter(names = {"-o", "--outdir"}, description = FieldConstants.JOB_OUT_DIR_DESCRIPTION)

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

@@ -33,22 +33,26 @@
 import org.opencb.opencga.core.models.variant.AnnotationVariantQueryParams;
 import org.opencb.opencga.core.models.variant.CircosAnalysisParams;
 import org.opencb.opencga.core.models.variant.CohortVariantStatsAnalysisParams;
-import org.opencb.opencga.core.models.variant.FamilyQcAnalysisParams;
 import org.opencb.opencga.core.models.variant.GatkWrapperParams;
 import org.opencb.opencga.core.models.variant.GenomePlotAnalysisParams;
 import org.opencb.opencga.core.models.variant.GwasAnalysisParams;
 import org.opencb.opencga.core.models.variant.HRDetectAnalysisParams;
-import org.opencb.opencga.core.models.variant.IndividualQcAnalysisParams;
 import org.opencb.opencga.core.models.variant.KnockoutAnalysisParams;
 import org.opencb.opencga.core.models.variant.MutationalSignatureAnalysisParams;
 import org.opencb.opencga.core.models.variant.PlinkWrapperParams;
 import org.opencb.opencga.core.models.variant.RvtestsWrapperParams;
 import org.opencb.opencga.core.models.variant.SampleEligibilityAnalysisParams;
-import org.opencb.opencga.core.models.variant.SampleQcAnalysisParams;
 import org.opencb.opencga.core.models.variant.SampleVariantFilterParams;
 import org.opencb.opencga.core.models.variant.SampleVariantStatsAnalysisParams;
 import org.opencb.opencga.core.models.variant.VariantExportParams;
 import org.opencb.opencga.core.models.variant.VariantStatsAnalysisParams;
+import org.opencb.opencga.core.models.variant.qc.FamilyQcAnalysisParams;
+import org.opencb.opencga.core.models.variant.qc.IndividualQcAnalysisParams;
+import org.opencb.opencga.core.models.variant.qc.SampleQcAnalysisParams;
+import org.opencb.opencga.core.models.variant.qc.SampleQcGenomePlotAnalysisParams;
+import org.opencb.opencga.core.models.variant.qc.SampleQcSignatureAnalysisParams;
+import org.opencb.opencga.core.models.variant.qc.SampleQcSignatureFittingAnalysisParams;
+import org.opencb.opencga.core.models.variant.qc.SampleQcVariantStatsAnalysisParams;
 import org.opencb.opencga.core.response.QueryType;
 import org.opencb.opencga.core.response.RestResponse;
 import org.opencb.opencga.core.tools.annotations.ToolParams;
@@ -1485,6 +1489,8 @@ private RestResponse<Job> runSampleQc() throws Exception {
             ObjectMap beanParams = new ObjectMap();
             putNestedIfNotEmpty(beanParams, "sample",commandOptions.sample, true);
             putNestedIfNotNull(beanParams, "samples",commandOptions.samples, true);
+            putNestedIfNotEmpty(beanParams, "statsParams.id",commandOptions.statsParamsId, true);
+            putNestedIfNotEmpty(beanParams, "statsParams.description",commandOptions.statsParamsDescription, true);
             putNestedIfNotEmpty(beanParams, "vsId",commandOptions.vsId, true);
             putNestedIfNotEmpty(beanParams, "vsDescription",commandOptions.vsDescription, true);
             putNestedIfNotEmpty(beanParams, "vsQuery.id",commandOptions.vsQueryId, true);
@@ -1513,6 +1519,8 @@ private RestResponse<Job> runSampleQc() throws Exception {
             putNestedIfNotEmpty(beanParams, "vsQuery.clinical",commandOptions.vsQueryClinical, true);
             putNestedIfNotEmpty(beanParams, "vsQuery.clinicalSignificance",commandOptions.vsQueryClinicalSignificance, true);
             putNestedIfNotNull(beanParams, "vsQuery.clinicalConfirmedStatus",commandOptions.vsQueryClinicalConfirmedStatus, true);
+            putNestedIfNotEmpty(beanParams, "signatureParams.id",commandOptions.signatureParamsId, true);
+            putNestedIfNotEmpty(beanParams, "signatureParams.description",commandOptions.signatureParamsDescription, true);
             putNestedIfNotEmpty(beanParams, "msId",commandOptions.msId, true);
             putNestedIfNotEmpty(beanParams, "msDescription",commandOptions.msDescription, true);
             putNestedIfNotEmpty(beanParams, "msQuery",commandOptions.msQuery, true);
@@ -1526,9 +1534,13 @@ private RestResponse<Job> runSampleQc() throws Exception {
             putNestedIfNotNull(beanParams, "msFitMaxRareSigs",commandOptions.msFitMaxRareSigs, true);
             putNestedIfNotEmpty(beanParams, "msFitSignaturesFile",commandOptions.msFitSignaturesFile, true);
             putNestedIfNotEmpty(beanParams, "msFitRareSignaturesFile",commandOptions.msFitRareSignaturesFile, true);
+            putNestedIfNotEmpty(beanParams, "genomePlotParams.id",commandOptions.genomePlotParamsId, true);
+            putNestedIfNotEmpty(beanParams, "genomePlotParams.description",commandOptions.genomePlotParamsDescription, true);
+            putNestedIfNotEmpty(beanParams, "genomePlotParams.configFile",commandOptions.genomePlotParamsConfigFile, true);
             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);

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

@@ -2175,6 +2175,12 @@ public class RunSampleQcCommandOptions {
         @Parameter(names = {"--samples"}, description = "List of sample IDs", required = false, arity = 1)
         public String samples;
 
+        @Parameter(names = {"--stats-params-id"}, description = "Sample variant stats ID", required = false, arity = 1)
+        public String statsParamsId;
+
+        @Parameter(names = {"--stats-params-description"}, description = "Sample variant stats description", required = false, arity = 1)
+        public String statsParamsDescription;
+
         @Parameter(names = {"--vs-id"}, description = "Variant stats ID.", required = false, arity = 1)
         public String vsId;
 
@@ -2259,6 +2265,12 @@ public class RunSampleQcCommandOptions {
         @Parameter(names = {"--vs-query-clinical-confirmed-status"}, description = "The body web service clinicalConfirmedStatus parameter", required = false, help = true, arity = 0)
         public boolean vsQueryClinicalConfirmedStatus = false;
 
+        @Parameter(names = {"--signature-params-id"}, description = "Signature ID", required = false, arity = 1)
+        public String signatureParamsId;
+
+        @Parameter(names = {"--signature-params-description"}, description = "Signature description", required = false, arity = 1)
+        public String signatureParamsDescription;
+
         @Parameter(names = {"--ms-id"}, description = "Signature ID.", required = false, arity = 1)
         public String msId;
 
@@ -2298,6 +2310,15 @@ public class RunSampleQcCommandOptions {
         @Parameter(names = {"--ms-fit-rare-signatures-file"}, description = "The file name containing mutational signatures. Each signature is in a column, with signature names as column hearders and channel names as row names in the first column with no header. Each column must sum to 1. Use only to provide your own signatures. When fitmethod=FitMS, these signatures are considered rare signatures.", required = false, arity = 1)
         public String msFitRareSignaturesFile;
 
+        @Parameter(names = {"--genome-plot-params-id"}, description = "Genome plot ID", required = false, arity = 1)
+        public String genomePlotParamsId;
+
+        @Parameter(names = {"--genome-plot-params-description"}, description = "Genome plot description", required = false, arity = 1)
+        public String genomePlotParamsDescription;
+
+        @Parameter(names = {"--genome-plot-params-config-file"}, description = "Genome plot configuration file", required = false, arity = 1)
+        public String genomePlotParamsConfigFile;
+
         @Parameter(names = {"--gp-id"}, description = "Genome plot ID.", required = false, arity = 1)
         public String gpId;
 
@@ -2307,7 +2328,10 @@ public class RunSampleQcCommandOptions {
         @Parameter(names = {"--gp-config-file"}, description = "Genome plot configuration file.", required = false, arity = 1)
         public String gpConfigFile;
 
-        @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)
+        @Parameter(names = {"--skip"}, description = "Quality control analysis to skip", required = false, arity = 1)
+        public String skip;
+
+        @Parameter(names = {"--skip-analysis"}, description = "Quality control analysis to skip", 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)

opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java

@@ -36,22 +36,22 @@
 import org.opencb.opencga.core.models.operations.variant.VariantStatsExportParams;
 import org.opencb.opencga.core.models.variant.CircosAnalysisParams;
 import org.opencb.opencga.core.models.variant.CohortVariantStatsAnalysisParams;
-import org.opencb.opencga.core.models.variant.FamilyQcAnalysisParams;
 import org.opencb.opencga.core.models.variant.GatkWrapperParams;
 import org.opencb.opencga.core.models.variant.GenomePlotAnalysisParams;
 import org.opencb.opencga.core.models.variant.GwasAnalysisParams;
 import org.opencb.opencga.core.models.variant.HRDetectAnalysisParams;
-import org.opencb.opencga.core.models.variant.IndividualQcAnalysisParams;
 import org.opencb.opencga.core.models.variant.KnockoutAnalysisParams;
 import org.opencb.opencga.core.models.variant.MutationalSignatureAnalysisParams;
 import org.opencb.opencga.core.models.variant.PlinkWrapperParams;
 import org.opencb.opencga.core.models.variant.RvtestsWrapperParams;
 import org.opencb.opencga.core.models.variant.SampleEligibilityAnalysisParams;
-import org.opencb.opencga.core.models.variant.SampleQcAnalysisParams;
 import org.opencb.opencga.core.models.variant.SampleVariantFilterParams;
 import org.opencb.opencga.core.models.variant.SampleVariantStatsAnalysisParams;
 import org.opencb.opencga.core.models.variant.VariantExportParams;
 import org.opencb.opencga.core.models.variant.VariantStatsAnalysisParams;
+import org.opencb.opencga.core.models.variant.qc.FamilyQcAnalysisParams;
+import org.opencb.opencga.core.models.variant.qc.IndividualQcAnalysisParams;
+import org.opencb.opencga.core.models.variant.qc.SampleQcAnalysisParams;
 import org.opencb.opencga.core.response.RestResponse;
 import org.opencb.opencga.core.tools.annotations.ToolParams;