core: update family and individual QC parameters, then clients are up…

…dated automatically, #TASK-6772, #TASK-6766

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

@@ -622,6 +622,8 @@ private RestResponse<Job> runFamilyQc() throws Exception {
             putNestedIfNotEmpty(beanParams, "family",commandOptions.family, true);
             putNestedIfNotEmpty(beanParams, "relatednessMethod",commandOptions.relatednessMethod, true);
             putNestedIfNotEmpty(beanParams, "relatednessMaf",commandOptions.relatednessMaf, true);
+            putNestedIfNotNull(beanParams, "skipIndex",commandOptions.skipIndex, true);
+            putNestedIfNotNull(beanParams, "overwrite",commandOptions.overwrite, true);
             putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true);
 
             familyQcAnalysisParams = JacksonUtils.getDefaultObjectMapper().copy()

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

@@ -809,16 +809,22 @@ public class RunFamilyQcCommandOptions {
         @Parameter(names = {"--job-dry-run"}, description = "Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will validate that all parameters and prerequisites are correctly set for successful execution, but the job will not actually run.", required = false, arity = 1)
         public Boolean jobDryRun; 
 
-        @Parameter(names = {"--family"}, description = "The body web service family parameter", required = false, arity = 1)
+        @Parameter(names = {"--family"}, description = "Family ID", required = false, arity = 1)
         public String family;
 
         @Parameter(names = {"--relatedness-method"}, description = "The body web service relatednessMethod parameter", required = false, arity = 1)
         public String relatednessMethod;
 
-        @Parameter(names = {"--relatedness-maf"}, description = "The body web service relatednessMaf parameter", required = false, arity = 1)
+        @Parameter(names = {"--relatedness-maf"}, description = "Minor allele frequence (MAF) is used to filter variants before computing relatedness, e.g.: 1000G:CEU>0.35 or cohort:ALL>0.05", required = false, arity = 1)
         public String relatednessMaf;
 
-        @Parameter(names = {"--outdir"}, description = "The body web service outdir parameter", required = false, arity = 1)
+        @Parameter(names = {"--skip-index"}, description = "Do not save the computed quality control in catalog", required = false, arity = 1)
+        public Boolean skipIndex;
+
+        @Parameter(names = {"--overwrite"}, description = "Overwrite quality control in catalog", required = false, arity = 1)
+        public Boolean overwrite;
+
+        @Parameter(names = {"--outdir"}, description = "Output dir for the job.", required = false, arity = 1)
         public String outdir;
 
     }

opencga-client/src/main/R/R/Variant-methods.R

@@ -223,7 +223,7 @@ setMethod("variantClient", "OpencgaR", function(OpencgaR, endpointName, params=N
         #' @param jobScheduledStartTime Time when the job is scheduled to start.
         #' @param jobPriority Priority of the job.
         #' @param jobDryRun Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will validate that all parameters and prerequisites are correctly set for successful execution, but the job will not actually run.
-        #' @param data Family QC analysis params. Family ID. Relatedness method, by default 'PLINK/IBD'. Minor  allele frequence (MAF) is used to filter variants before computing relatedness, e.g.: 1000G:CEU>0.35 or cohort:ALL>0.05.
+        #' @param data Family QC analysis params.
         runFamilyQc=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL,
                 subcategory="variant/family/qc", subcategoryId=NULL, action="run", params=params, httpMethod="POST",
                 as.queryParam=NULL, ...),

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

@@ -298,8 +298,7 @@ public RestResponse<ObjectMap> genotypesFamily(String modeOfInheritance, ObjectM
 
     /**
      * Run quality control (QC) for a given family. It computes the relatedness scores among the family members.
-     * @param data Family QC analysis params. Family ID. Relatedness method, by default 'PLINK/IBD'. Minor  allele frequence (MAF) is used
-     *     to filter variants before computing relatedness, e.g.: 1000G:CEU>0.35 or cohort:ALL>0.05.
+     * @param data Family QC analysis params.
      * @param params Map containing any of the following optional parameters.
      *       study: Study [[organization@]project:]study where study and project can be either the ID or UUID.
      *       jobId: Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided.

opencga-client/src/main/javascript/Variant.js

@@ -227,8 +227,7 @@ export default class Variant extends OpenCGAParentClass {
     }
 
     /** Run quality control (QC) for a given family. It computes the relatedness scores among the family members
-    * @param {Object} data - Family QC analysis params. Family ID. Relatedness method, by default 'PLINK/IBD'. Minor  allele frequence (MAF)
-    *     is used to filter variants before computing relatedness, e.g.: 1000G:CEU>0.35 or cohort:ALL>0.05.
+    * @param {Object} data - Family QC analysis params.
     * @param {Object} [params] - The Object containing the following optional parameters:
     * @param {String} [params.study] - Study [[organization@]project:]study where study and project can be either the ID or UUID.
     * @param {String} [params.jobId] - Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not

opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py

@@ -288,10 +288,7 @@ def run_family_qc(self, data=None, **options):
             relatedness scores among the family members.
         PATH: /{apiVersion}/analysis/variant/family/qc/run
 
-        :param dict data: Family QC analysis params. Family ID. Relatedness
-            method, by default 'PLINK/IBD'. Minor  allele frequence (MAF) is
-            used to filter variants before computing relatedness, e.g.:
-            1000G:CEU>0.35 or cohort:ALL>0.05. (REQUIRED)
+        :param dict data: Family QC analysis params. (REQUIRED)
         :param str study: Study [[organization@]project:]study where study and
             project can be either the ID or UUID.
         :param str job_id: Job ID. It must be a unique string within the

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

@@ -4,6 +4,7 @@
 import org.opencb.opencga.core.models.variant.MutationalSignatureAnalysisParams;
 import org.opencb.opencga.core.models.variant.SampleQcAnalysisParams;
 import org.opencb.opencga.core.tools.variant.IndividualQcAnalysisExecutor;
+import org.opencb.opencga.core.tools.variant.InferredSexAnalysisExecutor;
 
 public class FieldConstants {
 
@@ -45,7 +46,7 @@ public class FieldConstants {
     public static final String ORGANIZATION_ADMINS_DESCRIPTION = "Administrative users of the organization.";
     public static final String ORGANIZATION_PROJECTS_DESCRIPTION = "Projects the organization holds.";
     public static final String ORGANIZATION_NOTES_DESCRIPTION = "Notes of organization scope.";
-//    public static final String ORGANIZATION_AUTHENTICATION_ORIGINS_DESCRIPTION = "Authentication origins used by the organization. This "
+    //    public static final String ORGANIZATION_AUTHENTICATION_ORIGINS_DESCRIPTION = "Authentication origins used by the organization. This "
 //            + "contains all the configuration necessary to be able to communicate with the external authentication origins.";
     public static final String ORGANIZATION_CONFIGURATION_DESCRIPTION = "Organization configuration information.";
     public static final String ORGANIZATION_INTERNAL_DESCRIPTION = "Organization internal information.";
@@ -98,6 +99,7 @@ public class FieldConstants {
     public static final String SAMPLE_COLLECTION_METHOD_DESCRIPTION = "Describes which method was used to collect the sample.";
     public static final String SAMPLE_COLLECTION_FROM_DESCRIPTION = "OntologyTermAnnotation list.";
     public static final String SAMPLE_COLLECTION_TYPE_DESCRIPTION = "Type of the sample collection.";
+
     //SampleQualityControl
     public static final String SAMPLE_QUALITY_CONTROL_FILES_DESCRIPTION = "Files used for the quality control of the sample.";
     public static final String SAMPLE_QUALITY_CONTROL_COMMENTS_DESCRIPTION = "Comments for the quality control of the sample.";
@@ -180,23 +182,32 @@ public class FieldConstants {
 
     public static final String DISORDER_ID = "Disorder ID.";
 
-    //FamilyQualityControl
-    public static final String FAMILY_QUALITY_CONTROL_RELATEDNESS_DESCRIPTION = "Reports of family relationship.";
+    // Quality control
+    public static final String QC_SKIP_INDEX_DESCRIPTION = "Do not save the computed quality control in catalog";
+    public static final String QC_OVERWRITE_DESCRIPTION = "Overwrite quality control in catalog";
 
+    // Family quality control
+    public static final String FAMILY_QC_FAMILY_ID_DESCRIPTION = "Family ID";
+    public static final String FAMILY_QC_RELATEDNESS_MAF_DESCRIPTION = "Minor allele frequence (MAF) is used to filter variants before"
+            + " computing relatedness, e.g.: " + ParamConstants.POP_FREQ_1000G + ":CEU>0.35 or cohort:ALL>0.05";
+    public static final String FAMILY_QUALITY_CONTROL_RELATEDNESS_DESCRIPTION = "Reports of family relationship.";
 
     // Individual quality control
+    public static final String INFERRED_SEX_ID = "inferred-sex";
+    public static final String MENDELIAN_ERRORS_ID = "mendelian-errors";
     public static final String INDIVIDUAL_QC_INDIVIDUAL_ID_DESCRIPTION = "Individual ID";
     public static final String INDIVIDUAL_QC_SAMPLE_ID_DESCRIPTION = "Sample ID (required when the individual has multiple samples)";
     public static final String INFERRED_SEX_METHOD_DESCRIPTION = "Inferred sex method. Valid values: "
             + IndividualQcAnalysisExecutor.COVERAGE_RATIO_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_QUALITY_CONTROL_INFERRED_SEX_REPORT_DESCRIPTION = "List of inferred sex reports, it depends on"
             + " the method (currently by coverage ratio).";
     public static final String INDIVIDUAL_QUALITY_CONTROL_SAMPLE_RELATEDNESS_REPORT_DESCRIPTION = "Reports of samples relatedness.";
     public static final String INDIVIDUAL_QUALITY_CONTROL_MENDELIAN_ERRORS_DESCRIPTION = "Mendelian errors.";
 
-
     //Status
-    public static final String STATUS_DATE_DESCRIPTION = "Date has setted the status.";
+    public static final String STATUS_DATE_DESCRIPTION = "Date has set the status.";
     public static final String STATUS_MESSAGE_DESCRIPTION = "Deprecated: Message describing the status.";
 
 
@@ -504,7 +515,7 @@ public class FieldConstants {
     public static final String HRDETECT_CNV_QUERY_DESCRIPTION = "CNV query";
     public static final String HRDETECT_INDEL_QUERY_DESCRIPTION = "INDEL query";
     public static final String HRDETECT_SNV3_CUSTOM_NAME_DESCRIPTION = "Custom signature name that will be considered as SNV3 input for"
-        + " HRDetect.";
+            + " HRDetect.";
     public static final String HRDETECT_SNV8_CUSTOM_NAME_DESCRIPTION = "Custom signature name that will be considered as SNV8 input for"
             + " HRDetect.";
     public static final String HRDETECT_SV3_CUSTOM_NAME_DESCRIPTION = "Custom signature name that will be considered as SV3 input for"
@@ -531,7 +542,7 @@ public class FieldConstants {
     public static final String COVERAGE_INDEX_BAM_FILE_ID_DESCRIPTION = "BAM file ID.";
     public static final String COVERAGE_INDEX_BAI_FILE_ID_DESCRIPTION = "BAI file ID.";
     public static final String COVERAGE_INDEX_OVERWRITE_DESCRIPTION = "Window size (i.e., the size of the bins, in bases, for the output"
-        + " of the BIGWIG file).";
+            + " of the BIGWIG file).";
 
     // Alignment QC analysis (asample-qc-run)
     public static final String ALIGNMENT_QC_BAM_FILE_DESCRIPTION = "ID for the BAM file to process.";

opencga-core/src/main/java/org/opencb/opencga/core/models/variant/FamilyQcAnalysisParams.java

@@ -16,35 +16,61 @@
 
 package org.opencb.opencga.core.models.variant;
 
+import org.opencb.commons.annotations.DataField;
+import org.opencb.opencga.core.api.FieldConstants;
 import org.opencb.opencga.core.api.ParamConstants;
 import org.opencb.opencga.core.tools.ToolParams;
 
+import java.util.List;
+
 public class FamilyQcAnalysisParams extends ToolParams {
-    public static final String DESCRIPTION = "Family QC analysis params. Family ID. Relatedness method, by default 'PLINK/IBD'. Minor "
-            + " allele frequence (MAF) is used to filter variants before computing relatedness, e.g.: " + ParamConstants.POP_FREQ_1000G
-            + ":CEU>0.35 or cohort:ALL>0.05";
+    public static final String DESCRIPTION = "Family QC analysis params.";
+
+    @DataField(id = "family", description = FieldConstants.FAMILY_QC_FAMILY_ID_DESCRIPTION)
     private String family;
+
+    @Deprecated
     private String relatednessMethod;
+
+    @DataField(id = "relatednessMaf", description = FieldConstants.FAMILY_QC_RELATEDNESS_MAF_DESCRIPTION)
     private String relatednessMaf;
 
+    @DataField(id = "skipIndex", description = FieldConstants.QC_SKIP_INDEX_DESCRIPTION)
+    private Boolean skipIndex;
+
+    @DataField(id = "overwrite", description = FieldConstants.QC_OVERWRITE_DESCRIPTION)
+    private Boolean overwrite;
+
+    @DataField(id = "outdir", description = FieldConstants.JOB_OUT_DIR_DESCRIPTION)
     private String outdir;
 
     public FamilyQcAnalysisParams() {
     }
 
+    @Deprecated
     public FamilyQcAnalysisParams(String family, String relatednessMethod, String relatednessMaf, String outdir) {
         this.family = family;
         this.relatednessMethod = relatednessMethod;
         this.relatednessMaf = relatednessMaf;
         this.outdir = outdir;
     }
 
+    public FamilyQcAnalysisParams(String family, String relatednessMaf, Boolean skipIndex, Boolean overwrite, String outdir) {
+        this.family = family;
+        this.relatednessMaf = relatednessMaf;
+        this.skipIndex = skipIndex;
+        this.overwrite = overwrite;
+        this.outdir = outdir;
+    }
+
     @Override
     public String toString() {
         final StringBuilder sb = new StringBuilder("FamilyQcAnalysisParams{");
         sb.append("family='").append(family).append('\'');
         sb.append(", relatednessMethod='").append(relatednessMethod).append('\'');
         sb.append(", relatednessMaf='").append(relatednessMaf).append('\'');
+        sb.append(", skipIndex=").append(skipIndex);
+        sb.append(", overwrite=").append(overwrite);
         sb.append(", outdir='").append(outdir).append('\'');
         sb.append('}');
         return sb.toString();
@@ -59,10 +85,12 @@ public FamilyQcAnalysisParams setFamily(String family) {
         return this;
     }
 
+    @Deprecated
     public String getRelatednessMethod() {
         return relatednessMethod;
     }
 
+    @Deprecated
     public FamilyQcAnalysisParams setRelatednessMethod(String relatednessMethod) {
         this.relatednessMethod = relatednessMethod;
         return this;
@@ -77,6 +105,24 @@ public FamilyQcAnalysisParams setRelatednessMaf(String relatednessMaf) {
         return this;
     }
 
+    public Boolean getSkipIndex() {
+        return skipIndex;
+    }
+
+    public FamilyQcAnalysisParams setSkipIndex(Boolean skipIndex) {
+        this.skipIndex = skipIndex;
+        return this;
+    }
+
+    public Boolean getOverwrite() {
+        return overwrite;
+    }
+
+    public FamilyQcAnalysisParams setOverwrite(Boolean overwrite) {
+        this.overwrite = overwrite;
+        return this;
+    }
+
     public String getOutdir() {
         return outdir;
     }

opencga-core/src/main/java/org/opencb/opencga/core/models/variant/IndividualQcAnalysisParams.java

@@ -21,6 +21,8 @@
 import org.opencb.opencga.core.tools.ToolParams;
 import org.opencb.opencga.core.tools.variant.IndividualQcAnalysisExecutor;
 
+import java.util.List;
+
 public class IndividualQcAnalysisParams extends ToolParams {
     public static final String DESCRIPTION = "Individual QC analysis params";
 
@@ -30,29 +32,53 @@ public class IndividualQcAnalysisParams extends ToolParams {
     @DataField(id = "sample", description = FieldConstants.INDIVIDUAL_QC_SAMPLE_ID_DESCRIPTION)
     private String sample;
 
+    @Deprecated
     @DataField(id = "inferredSexMethod", description = FieldConstants.INFERRED_SEX_METHOD_DESCRIPTION,
-            defaultValue = IndividualQcAnalysisExecutor.COVERAGE_RATIO_INFERRED_SEX_METHOD)
+            defaultValue = IndividualQcAnalysisExecutor.COVERAGE_RATIO_INFERRED_SEX_METHOD, deprecated = true)
     private String inferredSexMethod;
 
+    @DataField(id = "skip", description = FieldConstants.INDIVIDUAL_QC_SKIP_DESCRIPTION)
+    private List<String> skip;
+
+    @DataField(id = "skipIndex", description = FieldConstants.QC_SKIP_INDEX_DESCRIPTION)
+    private Boolean skipIndex;
+
+    @DataField(id = "overwrite", description = FieldConstants.QC_OVERWRITE_DESCRIPTION)
+    private Boolean overwrite;
+
     @DataField(id = "outdir", description = FieldConstants.JOB_OUT_DIR_DESCRIPTION)
     private String outdir;
 
     public IndividualQcAnalysisParams() {
     }
 
+    @Deprecated
     public IndividualQcAnalysisParams(String individual, String sample, String inferredSexMethod, String outdir) {
         this.individual = individual;
         this.sample = sample;
         this.inferredSexMethod = inferredSexMethod;
         this.outdir = outdir;
     }
 
+    public IndividualQcAnalysisParams(String individual, String sample, List<String> skip, Boolean skipIndex, Boolean overwrite,
+                                      String outdir) {
+        this.individual = individual;
+        this.sample = sample;
+        this.skip = skip;
+        this.skipIndex = skipIndex;
+        this.overwrite = overwrite;
+        this.outdir = outdir;
+    }
+
     @Override
     public String toString() {
         final StringBuilder sb = new StringBuilder("IndividualQcAnalysisParams{");
         sb.append("individual='").append(individual).append('\'');
         sb.append(", sample='").append(sample).append('\'');
         sb.append(", inferredSexMethod='").append(inferredSexMethod).append('\'');
+        sb.append(", skip=").append(skip);
+        sb.append(", skipIndex=").append(skipIndex);
+        sb.append(", overwrite=").append(overwrite);
         sb.append(", outdir='").append(outdir).append('\'');
         sb.append('}');
         return sb.toString();
@@ -76,10 +102,12 @@ public IndividualQcAnalysisParams setSample(String sample) {
         return this;
     }
 
+    @Deprecated
     public String getInferredSexMethod() {
         return inferredSexMethod;
     }
 
+    @Deprecated
     public IndividualQcAnalysisParams setInferredSexMethod(String inferredSexMethod) {
         this.inferredSexMethod = inferredSexMethod;
         return this;