Merge pull request #2359 from opencb/TASK-5006

TASK-5006 - Exomiser fails in the opencga

opencga-app/app/cloud/docker/opencga-base/Dockerfile

@@ -7,7 +7,7 @@ ARG BUILD_PATH="."
 ENV OPENCGA_HOME=/opt/opencga
 ENV OPENCGA_CONFIG_DIR=${OPENCGA_HOME}/conf
 
-RUN apt-get update && apt-get -y upgrade && apt-get install -y lsb-release sshpass ca-certificates curl gnupg jq ncurses-bin && \
+RUN apt-get update && apt-get -y upgrade && apt-get install -y lsb-release sshpass ca-certificates curl gnupg jq ncurses-bin unzip vim && \
     ## Install Docker repository
     install -m 0755 -d /etc/apt/keyrings && \
     curl -fsSL https://download.docker.com/linux/ubuntu/gpg | gpg --dearmor -o /etc/apt/keyrings/docker.gpg && \

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

@@ -1,5 +1,5 @@
 /*
-* Copyright 2015-2023-11-28 OpenCB
+* Copyright 2015-2023-12-04 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
@@ -60,7 +60,7 @@ public abstract class OpenCgaCompleter implements Completer {
             .map(Candidate::new)
             .collect(toList());
 
-    private List<Candidate> clinicalList = asList( "acl-update","clinical-configuration-update","create","distinct","interpretation-distinct","interpretation-search","interpretation-info","interpreter-cancer-tiering-run","interpreter-exomiser-run","interpreter-team-run","interpreter-tiering-run","interpreter-zetta-run","rga-aggregation-stats","rga-gene-query","rga-gene-summary","rga-index-run","rga-individual-query","rga-individual-summary","rga-variant-query","rga-variant-summary","search","variant-query","acl","delete","update","info","interpretation-create","interpretation-clear","interpretation-delete","interpretation-revert","interpretation-update")
+    private List<Candidate> clinicalList = asList( "acl-update","annotation-sets-load","clinical-configuration-update","create","distinct","interpretation-distinct","interpretation-search","interpretation-info","interpreter-cancer-tiering-run","interpreter-exomiser-run","interpreter-team-run","interpreter-tiering-run","interpreter-zetta-run","rga-aggregation-stats","rga-gene-query","rga-gene-summary","rga-index-run","rga-individual-query","rga-individual-summary","rga-variant-query","rga-variant-summary","search","variant-query","acl","delete","update","annotation-sets-annotations-update","info","interpretation-create","interpretation-clear","interpretation-delete","interpretation-revert","interpretation-update")
             .stream()
             .map(Candidate::new)
             .collect(toList());

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

@@ -1,5 +1,5 @@
 /*
-* Copyright 2015-2023-11-28 OpenCB
+* Copyright 2015-2023-12-04 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
@@ -128,6 +128,7 @@ public OpencgaCliOptionsParser() {
         jCommander.addCommand("clinical", analysisClinicalCommandOptions);
         JCommander analysisClinicalSubCommands = jCommander.getCommands().get("clinical");
         analysisClinicalSubCommands.addCommand("acl-update", analysisClinicalCommandOptions.updateAclCommandOptions);
+        analysisClinicalSubCommands.addCommand("annotation-sets-load", analysisClinicalCommandOptions.loadAnnotationSetsCommandOptions);
         analysisClinicalSubCommands.addCommand("clinical-configuration-update", analysisClinicalCommandOptions.updateClinicalConfigurationCommandOptions);
         analysisClinicalSubCommands.addCommand("create", analysisClinicalCommandOptions.createCommandOptions);
         analysisClinicalSubCommands.addCommand("distinct", analysisClinicalCommandOptions.distinctCommandOptions);
@@ -152,6 +153,7 @@ public OpencgaCliOptionsParser() {
         analysisClinicalSubCommands.addCommand("acl", analysisClinicalCommandOptions.aclCommandOptions);
         analysisClinicalSubCommands.addCommand("delete", analysisClinicalCommandOptions.deleteCommandOptions);
         analysisClinicalSubCommands.addCommand("update", analysisClinicalCommandOptions.updateCommandOptions);
+        analysisClinicalSubCommands.addCommand("annotation-sets-annotations-update", analysisClinicalCommandOptions.updateAnnotationSetsAnnotationsCommandOptions);
         analysisClinicalSubCommands.addCommand("info", analysisClinicalCommandOptions.infoCommandOptions);
         analysisClinicalSubCommands.addCommand("interpretation-create", analysisClinicalCommandOptions.createInterpretationCommandOptions);
         analysisClinicalSubCommands.addCommand("interpretation-clear", analysisClinicalCommandOptions.clearInterpretationCommandOptions);

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

@@ -265,7 +265,7 @@ public class CreateCommandOptions {
         @Parameter(names = {"--type"}, description = "Enum param allowed values: FILE, VIRTUAL, DIRECTORY", required = false, arity = 1)
         public String type;
 
-        @Parameter(names = {"--format"}, description = "Enum param allowed values: VCF, BCF, GVCF, TBI, BIGWIG, SAM, BAM, BAI, CRAM, CRAI, FASTQ, FASTA, PED, TAB_SEPARATED_VALUES, COMMA_SEPARATED_VALUES, XML, PROTOCOL_BUFFER, JSON, AVRO, PARQUET, IMAGE, PLAIN, BINARY, NONE, UNKNOWN", required = false, arity = 1)
+        @Parameter(names = {"--format"}, description = "Enum param allowed values: VCF, BCF, GVCF, TBI, BIGWIG, SAM, BAM, BAI, CRAM, CRAI, FASTQ, FASTA, PED, TAB_SEPARATED_VALUES, COMMA_SEPARATED_VALUES, XML, PROTOCOL_BUFFER, JSON, AVRO, PARQUET, PDF, IMAGE, PLAIN, BINARY, NONE, UNKNOWN", required = false, arity = 1)
         public String format;
 
         @Parameter(names = {"--bioformat"}, description = "Enum param allowed values: MICROARRAY_EXPRESSION_ONECHANNEL_AGILENT, MICROARRAY_EXPRESSION_ONECHANNEL_AFFYMETRIX, MICROARRAY_EXPRESSION_ONECHANNEL_GENEPIX, MICROARRAY_EXPRESSION_TWOCHANNELS_AGILENT, MICROARRAY_EXPRESSION_TWOCHANNELS_GENEPIX, DATAMATRIX_EXPRESSION, IDLIST, IDLIST_RANKED, ANNOTATION_GENEVSANNOTATION, OTHER_NEWICK, OTHER_BLAST, OTHER_INTERACTION, OTHER_GENOTYPE, OTHER_PLINK, OTHER_VCF, OTHER_PED, VCF4, VARIANT, ALIGNMENT, COVERAGE, SEQUENCE, PEDIGREE, REFERENCE_GENOME, NONE, UNKNOWN", required = false, arity = 1)
@@ -808,7 +808,7 @@ public class UpdateCommandOptions {
         @Parameter(names = {"--checksum"}, description = "The body web service checksum parameter", required = false, arity = 1)
         public String checksum;
 
-        @Parameter(names = {"--format"}, description = "Enum param allowed values: VCF, BCF, GVCF, TBI, BIGWIG, SAM, BAM, BAI, CRAM, CRAI, FASTQ, FASTA, PED, TAB_SEPARATED_VALUES, COMMA_SEPARATED_VALUES, XML, PROTOCOL_BUFFER, JSON, AVRO, PARQUET, IMAGE, PLAIN, BINARY, NONE, UNKNOWN", required = false, arity = 1)
+        @Parameter(names = {"--format"}, description = "Enum param allowed values: VCF, BCF, GVCF, TBI, BIGWIG, SAM, BAM, BAI, CRAM, CRAI, FASTQ, FASTA, PED, TAB_SEPARATED_VALUES, COMMA_SEPARATED_VALUES, XML, PROTOCOL_BUFFER, JSON, AVRO, PARQUET, PDF, IMAGE, PLAIN, BINARY, NONE, UNKNOWN", required = false, arity = 1)
         public String format;
 
         @Parameter(names = {"--bioformat"}, description = "Enum param allowed values: MICROARRAY_EXPRESSION_ONECHANNEL_AGILENT, MICROARRAY_EXPRESSION_ONECHANNEL_AFFYMETRIX, MICROARRAY_EXPRESSION_ONECHANNEL_GENEPIX, MICROARRAY_EXPRESSION_TWOCHANNELS_AGILENT, MICROARRAY_EXPRESSION_TWOCHANNELS_GENEPIX, DATAMATRIX_EXPRESSION, IDLIST, IDLIST_RANKED, ANNOTATION_GENEVSANNOTATION, OTHER_NEWICK, OTHER_BLAST, OTHER_INTERACTION, OTHER_GENOTYPE, OTHER_PLINK, OTHER_VCF, OTHER_PED, VCF4, VARIANT, ALIGNMENT, COVERAGE, SEQUENCE, PEDIGREE, REFERENCE_GENOME, NONE, UNKNOWN", required = false, arity = 1)

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

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-11-28
+#    Autogenerated on: 2023-12-04
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.

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

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-11-28
+#    Autogenerated on: 2023-12-04
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.

opencga-client/src/main/R/R/AllGenerics.R

@@ -1,46 +1,46 @@
 # ##############################################################################
 ## UserClient
-setGeneric("userClient", function(OpencgaR, users, user, filterId, endpointName, params=NULL, ...)
+setGeneric("userClient", function(OpencgaR, user, users, filterId, endpointName, params=NULL, ...)
     standardGeneric("userClient"))
 
 # ##############################################################################
 ## ProjectClient
-setGeneric("projectClient", function(OpencgaR, projects, project, endpointName, params=NULL, ...)
+setGeneric("projectClient", function(OpencgaR, project, projects, endpointName, params=NULL, ...)
     standardGeneric("projectClient"))
 
 # ##############################################################################
 ## StudyClient
-setGeneric("studyClient", function(OpencgaR, study, members, templateId, variableSet, group, studies, endpointName, params=NULL, ...)
+setGeneric("studyClient", function(OpencgaR, study, templateId, variableSet, members, studies, group, endpointName, params=NULL, ...)
     standardGeneric("studyClient"))
 
 # ##############################################################################
 ## FileClient
-setGeneric("fileClient", function(OpencgaR, file, annotationSet, members, folder, files, endpointName, params=NULL, ...)
+setGeneric("fileClient", function(OpencgaR, file, folder, annotationSet, members, files, endpointName, params=NULL, ...)
     standardGeneric("fileClient"))
 
 # ##############################################################################
 ## JobClient
-setGeneric("jobClient", function(OpencgaR, job, members, jobs, endpointName, params=NULL, ...)
+setGeneric("jobClient", function(OpencgaR, members, job, jobs, endpointName, params=NULL, ...)
     standardGeneric("jobClient"))
 
 # ##############################################################################
 ## SampleClient
-setGeneric("sampleClient", function(OpencgaR, samples, members, sample, annotationSet, endpointName, params=NULL, ...)
+setGeneric("sampleClient", function(OpencgaR, members, samples, sample, annotationSet, endpointName, params=NULL, ...)
     standardGeneric("sampleClient"))
 
 # ##############################################################################
 ## IndividualClient
-setGeneric("individualClient", function(OpencgaR, individuals, members, individual, annotationSet, endpointName, params=NULL, ...)
+setGeneric("individualClient", function(OpencgaR, members, individual, individuals, annotationSet, endpointName, params=NULL, ...)
     standardGeneric("individualClient"))
 
 # ##############################################################################
 ## FamilyClient
-setGeneric("familyClient", function(OpencgaR, members, families, annotationSet, family, endpointName, params=NULL, ...)
+setGeneric("familyClient", function(OpencgaR, family, members, annotationSet, families, endpointName, params=NULL, ...)
     standardGeneric("familyClient"))
 
 # ##############################################################################
 ## CohortClient
-setGeneric("cohortClient", function(OpencgaR, annotationSet, members, cohorts, cohort, endpointName, params=NULL, ...)
+setGeneric("cohortClient", function(OpencgaR, cohort, members, cohorts, annotationSet, endpointName, params=NULL, ...)
     standardGeneric("cohortClient"))
 
 # ##############################################################################
@@ -60,7 +60,7 @@ setGeneric("variantClient", function(OpencgaR, endpointName, params=NULL, ...)
 
 # ##############################################################################
 ## ClinicalClient
-setGeneric("clinicalClient", function(OpencgaR, members, clinicalAnalysis, interpretation, clinicalAnalyses, interpretations, endpointName, params=NULL, ...)
+setGeneric("clinicalClient", function(OpencgaR, annotationSet, clinicalAnalysis, interpretation, clinicalAnalyses, interpretations, members, endpointName, params=NULL, ...)
     standardGeneric("clinicalClient"))
 
 # ##############################################################################