Resolve conflicts by generating the OpenCGA clientes code automatical…

…ly, #TASK-4641

.github/workflows/test-analysis.yml

@@ -8,6 +8,7 @@ on:
         required: true
       mvn_opts:
         type: string
+
         required: false
         default: ""
     secrets:
@@ -82,3 +83,4 @@ jobs:
           report_paths: './**/surefire-reports/TEST-*.xml'
           commit: '${{ github.sha }}'
           fail_on_test_failures: true
+

opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/exomiser/ExomiserWrapperAnalysisExecutor.java

@@ -7,7 +7,6 @@
 import org.opencb.biodata.models.clinical.Phenotype;
 import org.opencb.biodata.models.clinical.pedigree.Member;
 import org.opencb.biodata.models.clinical.pedigree.Pedigree;
-import org.opencb.biodata.models.core.SexOntologyTermAnnotation;
 import org.opencb.biodata.models.pedigree.IndividualProperty;
 import org.opencb.commons.datastore.core.QueryOptions;
 import org.opencb.commons.exec.Command;
@@ -21,12 +20,9 @@
 import org.opencb.opencga.core.exceptions.ToolExecutorException;
 import org.opencb.opencga.core.models.family.Family;
 import org.opencb.opencga.core.models.individual.Individual;
-import org.opencb.opencga.core.models.sample.Sample;
 import org.opencb.opencga.core.tools.annotations.ToolExecutor;
 import org.opencb.opencga.storage.core.exceptions.StorageEngineException;
-import org.opencb.opencga.storage.core.variant.adaptors.VariantField;
 import org.opencb.opencga.storage.core.variant.adaptors.VariantQuery;
-import org.opencb.opencga.storage.core.variant.adaptors.VariantQueryParam;
 import org.opencb.opencga.storage.core.variant.io.VariantWriterFactory;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -36,7 +32,6 @@
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.*;
-import java.util.stream.Collectors;
 
 @ToolExecutor(id = ExomiserWrapperAnalysisExecutor.ID,
         tool = ExomiserWrapperAnalysis.ID,
@@ -133,7 +128,8 @@ public void run() throws ToolException {
                 .sample(sampleId)
                 .includeSample(samples)
                 .includeSampleData("GT")
-                .unknownGenotype("./.");
+                .unknownGenotype("./.")
+                .append("includeAllFromSampleIndex", true);
 
         QueryOptions queryOptions = new QueryOptions(QueryOptions.INCLUDE, "id,studies.samples");
 

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java

@@ -1,5 +1,5 @@
 /*
-* Copyright 2015-2023-08-31 OpenCB
+* Copyright 2015-2023-09-08 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java

@@ -1,5 +1,5 @@
 /*
-* Copyright 2015-2023-08-31 OpenCB
+* Copyright 2015-2023-09-08 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.

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

@@ -275,7 +275,7 @@ public class DistinctCommandOptions {
         @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1)
         public String study; 
 
-        @Parameter(names = {"--id"}, description = "Comma separated list of Clinical Analysis IDs up to a maximum of 100", required = false, arity = 1)
+        @Parameter(names = {"--id"}, description = "Comma separated list of Clinical Analysis IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
         public String id; 
 
         @Parameter(names = {"--uuid"}, description = "Comma separated list of Clinical Analysis UUIDs up to a maximum of 100", required = false, arity = 1)
@@ -284,7 +284,7 @@ public class DistinctCommandOptions {
         @Parameter(names = {"--type"}, description = "Clinical Analysis type", required = false, arity = 1)
         public String type; 
 
-        @Parameter(names = {"--disorder"}, description = "Clinical Analysis disorder", required = false, arity = 1)
+        @Parameter(names = {"--disorder"}, description = "Clinical Analysis disorder. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
         public String disorder; 
 
         @Parameter(names = {"--files"}, description = "Clinical Analysis files", required = false, arity = 1)
@@ -364,7 +364,7 @@ public class DistinctInterpretationCommandOptions {
         @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1)
         public String study; 
 
-        @Parameter(names = {"--id"}, description = "Comma separated list of Interpretation IDs up to a maximum of 100", required = false, arity = 1)
+        @Parameter(names = {"--id"}, description = "Comma separated list of Interpretation IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
         public String id; 
 
         @Parameter(names = {"--uuid"}, description = "Comma separated list of Interpretation UUIDs up to a maximum of 100", required = false, arity = 1)
@@ -376,7 +376,7 @@ public class DistinctInterpretationCommandOptions {
         @Parameter(names = {"--analyst-id"}, description = "Analyst ID", required = false, arity = 1)
         public String analystId; 
 
-        @Parameter(names = {"--method-name"}, description = "Interpretation method name", required = false, arity = 1)
+        @Parameter(names = {"--method-name"}, description = "Interpretation method name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
         public String methodName; 
 
         @Parameter(names = {"--panels"}, description = "Interpretation panels", required = false, arity = 1)
@@ -432,7 +432,7 @@ public class SearchInterpretationCommandOptions {
         @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1)
         public String study; 
 
-        @Parameter(names = {"--id"}, description = "Comma separated list of Interpretation IDs up to a maximum of 100", required = false, arity = 1)
+        @Parameter(names = {"--id"}, description = "Comma separated list of Interpretation IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
         public String id; 
 
         @Parameter(names = {"--uuid"}, description = "Comma separated list of Interpretation UUIDs up to a maximum of 100", required = false, arity = 1)
@@ -444,7 +444,7 @@ public class SearchInterpretationCommandOptions {
         @Parameter(names = {"--analyst-id"}, description = "Analyst ID", required = false, arity = 1)
         public String analystId; 
 
-        @Parameter(names = {"--method-name"}, description = "Interpretation method name", required = false, arity = 1)
+        @Parameter(names = {"--method-name"}, description = "Interpretation method name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
         public String methodName; 
 
         @Parameter(names = {"--panels"}, description = "Interpretation panels", required = false, arity = 1)
@@ -1488,7 +1488,7 @@ public class SearchCommandOptions {
         @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1)
         public String study; 
 
-        @Parameter(names = {"--id"}, description = "Comma separated list of Clinical Analysis IDs up to a maximum of 100", required = false, arity = 1)
+        @Parameter(names = {"--id"}, description = "Comma separated list of Clinical Analysis IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
         public String id; 
 
         @Parameter(names = {"--uuid"}, description = "Comma separated list of Clinical Analysis UUIDs up to a maximum of 100", required = false, arity = 1)
@@ -1497,7 +1497,7 @@ public class SearchCommandOptions {
         @Parameter(names = {"--type"}, description = "Clinical Analysis type", required = false, arity = 1)
         public String type; 
 
-        @Parameter(names = {"--disorder"}, description = "Clinical Analysis disorder", required = false, arity = 1)
+        @Parameter(names = {"--disorder"}, description = "Clinical Analysis disorder. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
         public String disorder; 
 
         @Parameter(names = {"--files"}, description = "Clinical Analysis files", required = false, arity = 1)

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

@@ -242,10 +242,10 @@ public class DistinctCommandOptions {
         @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1)
         public String study; 
 
-        @Parameter(names = {"--id"}, description = "Comma separated list of cohort IDs up to a maximum of 100", required = false, arity = 1)
+        @Parameter(names = {"--id"}, description = "Comma separated list of cohort IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
         public String id; 
 
-        @Parameter(names = {"--name", "-n"}, description = "Comma separated list of cohort names up to a maximum of 100", required = false, arity = 1)
+        @Parameter(names = {"--name", "-n"}, description = "Comma separated list of cohort names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
         public String name; 
 
         @Parameter(names = {"--uuid"}, description = "Comma separated list of cohort IDs up to a maximum of 100", required = false, arity = 1)
@@ -334,7 +334,7 @@ public class GenerateCommandOptions {
         @Parameter(names = {"--status"}, description = "Filter by status", required = false, arity = 1)
         public String status; 
 
-        @Parameter(names = {"--phenotypes"}, description = "Comma separated list of phenotype ids or names", required = false, arity = 1)
+        @Parameter(names = {"--phenotypes"}, description = "Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
         public String phenotypes; 
 
         @Parameter(names = {"--annotation"}, description = "Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0", required = false, arity = 1)
@@ -411,10 +411,10 @@ public class SearchCommandOptions {
         @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1)
         public String study; 
 
-        @Parameter(names = {"--id"}, description = "Comma separated list of cohort IDs up to a maximum of 100", required = false, arity = 1)
+        @Parameter(names = {"--id"}, description = "Comma separated list of cohort IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
         public String id; 
 
-        @Parameter(names = {"--name", "-n"}, description = "Comma separated list of cohort names up to a maximum of 100", required = false, arity = 1)
+        @Parameter(names = {"--name", "-n"}, description = "Comma separated list of cohort names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1)
         public String name; 
 
         @Parameter(names = {"--uuid"}, description = "Comma separated list of cohort IDs up to a maximum of 100", required = false, arity = 1)