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TASK-6255 - Update Exomiser Docker image to v14.0.0 #2462

Merged
merged 21 commits into from
Aug 20, 2024
Merged

TASK-6255 - Update Exomiser Docker image to v14.0.0 #2462

merged 21 commits into from
Aug 20, 2024

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jtarraga
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@jtarraga jtarraga commented Jun 7, 2024

Task 6255
Update Exomier Docker image to v14.0.0; and support multiple Exomiser versions, currently 13.1.0 and 14.0.0

@jtarraga
analysis: update Exomiser analysis in order to use the Docker version…
f35865a 
… 14.0.0 by taking it from the configuration file, #TASK-6297, #TASK-6255
@jtarraga
app: add Exomiser version as paremeter for the Exomiser interpretatio…
4867904 
…n analysis, #TASK-6297, #TASK-6255
@jtarraga
app: add parameter descriptions, #TASK-6297, #TASK-6255
ad7bd6a
@jtarraga
client: generate clients, #TASK-6297, #TASK-6255
28e32c5
@jtarraga
core: fix configuration file, #TASK-6297, #TASK-6255
d1efc04
@jtarraga
analysis: use the FileUtils.copyFile and rename Tool to AnalysisTool,…
f0e47fa 
… #TASK-6297, #TASK-6255

On branch TASK-6255
Changes to be committed:
	modified:   opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/executors/DockerWrapperAnalysisExecutor.java
	modified:   opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/exomiser/ExomiserWrapperAnalysisExecutor.java
	modified:   opencga-core/src/main/java/org/opencb/opencga/core/config/Analysis.java
	renamed:    opencga-core/src/main/java/org/opencb/opencga/core/config/Tool.java -> opencga-core/src/main/java/org/opencb/opencga/core/config/AnalysisTool.java
@jtarraga
analysis: use a list of tools instead of a map in the configuration f…
e2b001c 
…ile and update code according to that, #TASK-6297, #TASK-6255

On branch TASK-6255
Changes to be committed:
	modified:   opencga-analysis/src/main/java/org/opencb/opencga/analysis/ConfigurationUtils.java
	modified:   opencga-analysis/src/main/java/org/opencb/opencga/analysis/clinical/exomiser/ExomiserInterpretationAnalysis.java
	modified:   opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/executors/DockerWrapperAnalysisExecutor.java
	modified:   opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/exomiser/ExomiserWrapperAnalysis.java
	modified:   opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/exomiser/ExomiserWrapperAnalysisExecutor.java
	modified:   opencga-analysis/src/test/java/org/opencb/opencga/analysis/clinical/exomiser/ExomiserInterpretationAnalysisTest.java
	modified:   opencga-app/src/main/java/org/opencb/opencga/app/cli/internal/options/ClinicalCommandOptions.java
	modified:   opencga-app/src/main/java/org/opencb/opencga/app/cli/internal/options/VariantCommandOptions.java
	modified:   opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisClinicalCommandOptions.java
	modified:   opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisVariantCommandOptions.java
	modified:   opencga-catalog/src/test/resources/configuration-test.yml
	modified:   opencga-core/src/main/java/org/opencb/opencga/core/api/FieldConstants.java
	modified:   opencga-core/src/main/java/org/opencb/opencga/core/config/Analysis.java
	modified:   opencga-core/src/main/java/org/opencb/opencga/core/config/AnalysisTool.java
	modified:   opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/ExomiserInterpretationAnalysisParams.java
	modified:   opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/ExomiserWrapperParams.java
	modified:   opencga-core/src/main/resources/configuration.yml
@jtarraga
analysis: use the resource version instead of the exomiser version to…
0c2fe66 
… identify the Exomiser files to download, #TASK-6297, #TASK-6255

On branch TASK-6255
Changes to be committed:
	modified:   opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/exomiser/ExomiserWrapperAnalysisExecutor.java
	modified:   opencga-analysis/src/test/java/org/opencb/opencga/analysis/clinical/exomiser/ExomiserInterpretationAnalysisTest.java
@jtarraga
analysis: set dinamically the ClinVar white list depending on the fil…
dc29730 
…e exists in the Exomiser data, #TASK-6297, TASK-6255

In addition:
 - the user is set in the docker command line according to the user/group of the job dir.
 - the assembly is checked (a little step to support GRCh37)

On branch TASK-6255
Changes to be committed:
	modified:   opencga-analysis/src/main/java/org/opencb/opencga/analysis/clinical/exomiser/ExomiserInterpretationAnalysis.java
	modified:   opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/executors/DockerWrapperAnalysisExecutor.java
	modified:   opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/exomiser/ExomiserWrapperAnalysis.java
	modified:   opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/exomiser/ExomiserWrapperAnalysisExecutor.java
	modified:   opencga-analysis/src/test/java/org/opencb/opencga/analysis/clinical/exomiser/ExomiserInterpretationAnalysisTest.java
	modified:   opencga-analysis/src/test/resources/exomiser/application.properties
	modified:   opencga-app/app/analysis/exomiser/application.properties
	modified:   opencga-core/src/main/resources/configuration.yml
@jtarraga
analysis: improve log messages, #TASK-6297, #TASK-6255
2077cc5 
On branch TASK-6255
Changes to be committed:
	modified:   opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/exomiser/ExomiserWrapperAnalysisExecutor.java
@jtarraga
core: improve description of the Exomiser version parameter, #TASK-62…
53c4c27 
…97, #TASK-6255

On branch TASK-6255
Changes to be committed:
	modified:   opencga-core/src/main/java/org/opencb/opencga/core/api/FieldConstants.java
@jtarraga
client: generate clients, #TASK-6297, #TASK-6255
a770236 
On branch TASK-6255
Changes to be committed:
	modified:   opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java
	modified:   opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java
	modified:   opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisClinicalCommandOptions.java
	modified:   opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisVariantCommandOptions.java
	modified:   opencga-client/src/main/R/R/Admin-methods.R
	modified:   opencga-client/src/main/R/R/Alignment-methods.R
	modified:   opencga-client/src/main/R/R/AllGenerics.R
	modified:   opencga-client/src/main/R/R/Clinical-methods.R
	modified:   opencga-client/src/main/R/R/Cohort-methods.R
	modified:   opencga-client/src/main/R/R/Family-methods.R
	modified:   opencga-client/src/main/R/R/File-methods.R
	modified:   opencga-client/src/main/R/R/GA4GH-methods.R
	modified:   opencga-client/src/main/R/R/Individual-methods.R
	modified:   opencga-client/src/main/R/R/Job-methods.R
	modified:   opencga-client/src/main/R/R/Meta-methods.R
	modified:   opencga-client/src/main/R/R/Operation-methods.R
	modified:   opencga-client/src/main/R/R/Organization-methods.R
	modified:   opencga-client/src/main/R/R/Panel-methods.R
	modified:   opencga-client/src/main/R/R/Project-methods.R
	modified:   opencga-client/src/main/R/R/Sample-methods.R
	modified:   opencga-client/src/main/R/R/Study-methods.R
	modified:   opencga-client/src/main/R/R/User-methods.R
	modified:   opencga-client/src/main/R/R/Variant-methods.R
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/OrganizationClient.java
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java
	modified:   opencga-client/src/main/javascript/Admin.js
	modified:   opencga-client/src/main/javascript/Alignment.js
	modified:   opencga-client/src/main/javascript/ClinicalAnalysis.js
	modified:   opencga-client/src/main/javascript/Cohort.js
	modified:   opencga-client/src/main/javascript/DiseasePanel.js
	modified:   opencga-client/src/main/javascript/Family.js
	modified:   opencga-client/src/main/javascript/File.js
	modified:   opencga-client/src/main/javascript/GA4GH.js
	modified:   opencga-client/src/main/javascript/Individual.js
	modified:   opencga-client/src/main/javascript/Job.js
	modified:   opencga-client/src/main/javascript/Meta.js
	modified:   opencga-client/src/main/javascript/Organization.js
	modified:   opencga-client/src/main/javascript/Project.js
	modified:   opencga-client/src/main/javascript/Sample.js
	modified:   opencga-client/src/main/javascript/Study.js
	modified:   opencga-client/src/main/javascript/User.js
	modified:   opencga-client/src/main/javascript/Variant.js
	modified:   opencga-client/src/main/javascript/VariantOperation.js
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/family_client.py
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/file_client.py
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/job_client.py
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/organization_client.py
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/project_client.py
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/study_client.py
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/user_client.py
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py
@halender
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halender commented Jun 7, 2024

Task linked: TASK-6255 Update Exomiser Docker image to v14.0.0

@jtarraga
Merge branch 'develop' into TASK-6255
1c1862e 
Resolve conflicts by generating clients:
	opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java
	opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java
	opencga-client/src/main/R/R/Admin-methods.R
	opencga-client/src/main/R/R/Alignment-methods.R
	opencga-client/src/main/R/R/AllGenerics.R
	opencga-client/src/main/R/R/Clinical-methods.R
	opencga-client/src/main/R/R/Cohort-methods.R
	opencga-client/src/main/R/R/Family-methods.R
	opencga-client/src/main/R/R/File-methods.R
	opencga-client/src/main/R/R/GA4GH-methods.R
	opencga-client/src/main/R/R/Individual-methods.R
	opencga-client/src/main/R/R/Job-methods.R
	opencga-client/src/main/R/R/Meta-methods.R
	opencga-client/src/main/R/R/Operation-methods.R
	opencga-client/src/main/R/R/Organization-methods.R
	opencga-client/src/main/R/R/Panel-methods.R
	opencga-client/src/main/R/R/Project-methods.R
	opencga-client/src/main/R/R/Sample-methods.R
	opencga-client/src/main/R/R/Study-methods.R
	opencga-client/src/main/R/R/User-methods.R
	opencga-client/src/main/R/R/Variant-methods.R
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/OrganizationClient.java
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java
	opencga-client/src/main/javascript/Admin.js
	opencga-client/src/main/javascript/Alignment.js
	opencga-client/src/main/javascript/ClinicalAnalysis.js
	opencga-client/src/main/javascript/Cohort.js
	opencga-client/src/main/javascript/DiseasePanel.js
	opencga-client/src/main/javascript/Family.js
	opencga-client/src/main/javascript/File.js
	opencga-client/src/main/javascript/GA4GH.js
	opencga-client/src/main/javascript/Individual.js
	opencga-client/src/main/javascript/Job.js
	opencga-client/src/main/javascript/Meta.js
	opencga-client/src/main/javascript/Organization.js
	opencga-client/src/main/javascript/Project.js
	opencga-client/src/main/javascript/Sample.js
	opencga-client/src/main/javascript/Study.js
	opencga-client/src/main/javascript/User.js
	opencga-client/src/main/javascript/Variant.js
	opencga-client/src/main/javascript/VariantOperation.js
	opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py
	opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py
	opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py
	opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py
	opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py
	opencga-client/src/main/python/pyopencga/rest_clients/family_client.py
	opencga-client/src/main/python/pyopencga/rest_clients/file_client.py
	opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py
	opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py
	opencga-client/src/main/python/pyopencga/rest_clients/job_client.py
	opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py
	opencga-client/src/main/python/pyopencga/rest_clients/organization_client.py
	opencga-client/src/main/python/pyopencga/rest_clients/project_client.py
	opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py
	opencga-client/src/main/python/pyopencga/rest_clients/study_client.py
	opencga-client/src/main/python/pyopencga/rest_clients/user_client.py
	opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py
	opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py
juanfeSanahuja
juanfeSanahuja previously approved these changes Jun 11, 2024
View reviewed changes
@jtarraga
analysis: add config files for Exomiser versions 13.1 and 14.0 using …
b4319d0 
…different default values, #TASK-6297, #TASK-6255

On branch TASK-6255
Changes to be committed:
	modified:   opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/exomiser/ExomiserWrapperAnalysisExecutor.java
	modified:   opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/OpenCGATestExternalResource.java
	renamed:    opencga-app/app/analysis/exomiser/application.properties -> opencga-app/app/analysis/exomiser/13.1/application.properties
	renamed:    opencga-app/app/analysis/exomiser/exomiser-analysis.yml -> opencga-app/app/analysis/exomiser/13.1/exomiser-analysis.yml
	renamed:    opencga-app/app/analysis/exomiser/output.yml -> opencga-app/app/analysis/exomiser/13.1/output.yml
	new file:   opencga-app/app/analysis/exomiser/14.0/application.properties
	new file:   opencga-app/app/analysis/exomiser/14.0/exomiser-analysis.yml
	new file:   opencga-app/app/analysis/exomiser/14.0/output.yml
@jtarraga
Merge branch 'develop' into TASK-6255
fbecf0a 
  - Update JUnit tests related to Exomiser, and
  - Resolve conflicts:
	opencga-analysis/src/main/java/org/opencb/opencga/analysis/clinical/exomiser/ExomiserInterpretationAnalysis.java
	opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/executors/DockerWrapperAnalysisExecutor.java
	opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/exomiser/ExomiserWrapperAnalysis.java
	opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/exomiser/ExomiserWrapperAnalysisExecutor.java
	opencga-analysis/src/test/java/org/opencb/opencga/analysis/clinical/exomiser/ExomiserInterpretationAnalysisTest.java
	opencga-app/src/main/java/org/opencb/opencga/app/cli/internal/executors/VariantInternalCommandExecutor.java
	opencga-app/src/main/java/org/opencb/opencga/app/cli/internal/options/VariantCommandOptions.java
	opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisVariantCommandExecutor.java
	opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisVariantCommandOptions.java
	opencga-core/src/main/java/org/opencb/opencga/core/api/FieldConstants.java
	opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/ExomiserWrapperParams.java
juanfeSanahuja
juanfeSanahuja previously approved these changes Jul 4, 2024
View reviewed changes
@jtarraga
Merge branch 'develop' into TASK-6255
88faaac
@jtarraga
Merge branch 'develop' into TASK-6255
e190dd8 
Resolve conflicts by generating clients:
	opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisClinicalCommandOptions.java
	opencga-client/src/main/R/R/Clinical-methods.R
pfurio
pfurio previously approved these changes Jul 11, 2024
View reviewed changes
juanfeSanahuja
juanfeSanahuja previously approved these changes Jul 17, 2024
View reviewed changes
@jtarraga jtarraga changed the base branch from develop to release-3.2.x July 22, 2024 10:39
@jtarraga jtarraga dismissed stale reviews from juanfeSanahuja and pfurio July 22, 2024 10:39

The base branch was changed.

halender
halender previously approved these changes Jul 25, 2024
View reviewed changes
pfurio
pfurio previously approved these changes Jul 25, 2024
View reviewed changes
@jtarraga jtarraga dismissed stale reviews from pfurio and halender via f031313 August 13, 2024 14:06
@pfurio pfurio merged commit c636e41 into release-3.2.x Aug 20, 2024
5 of 6 checks passed
@pfurio pfurio deleted the TASK-6255 branch August 20, 2024 14:13
@j-coll j-coll changed the title Task 6255 Update Exomiser Docker image to v14.0.0 TASK-6255 - Update Exomiser Docker image to v14.0.0 Oct 29, 2024
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@juanfeSanahuja juanfeSanahuja juanfeSanahuja approved these changes

@halender halender halender left review comments

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4 participants
@jtarraga @halender @pfurio @juanfeSanahuja