Move scripts to resources

Move scripts to resources Update to 1.0.1
cBioPortal · Nov 3, 2023 · 92e6fb0 · 92e6fb0
1 parent 3104fc3
commit 92e6fb0
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diff --git a/pom.xml b/pom.xml
@@ -9,7 +9,7 @@
 
 	<groupId>org.mskcc.cbio</groupId>
 	<artifactId>core</artifactId>
-	<version>1.0.0</version>
+	<version>1.0.1</version>
 
 	<name>Portal Core</name>
 	<description>Core libraries shared among other modules</description>

diff --git a/src/main/scripts/addCaseList.pl → src/main/resources/scripts/addCaseList.pl b/src/main/scripts/addCaseList.pl → src/main/resources/scripts/addCaseList.pl
diff --git a/src/main/scripts/all-breast-su2c.sh → ...main/resources/scripts/all-breast-su2c.sh b/src/main/scripts/all-breast-su2c.sh → ...main/resources/scripts/all-breast-su2c.sh
diff --git a/src/main/scripts/all-coadread-public.sh → .../resources/scripts/all-coadread-public.sh b/src/main/scripts/all-coadread-public.sh → .../resources/scripts/all-coadread-public.sh
diff --git a/src/main/scripts/all-gbm-public.sh → src/main/resources/scripts/all-gbm-public.sh b/src/main/scripts/all-gbm-public.sh → src/main/resources/scripts/all-gbm-public.sh
diff --git a/src/main/scripts/all-lusc-public.sh → ...main/resources/scripts/all-lusc-public.sh b/src/main/scripts/all-lusc-public.sh → ...main/resources/scripts/all-lusc-public.sh
diff --git a/src/main/scripts/all-ovarian-public.sh → ...n/resources/scripts/all-ovarian-public.sh b/src/main/scripts/all-ovarian-public.sh → ...n/resources/scripts/all-ovarian-public.sh
diff --git a/src/main/scripts/all-ovarian-su2c.sh → ...ain/resources/scripts/all-ovarian-su2c.sh b/src/main/scripts/all-ovarian-su2c.sh → ...ain/resources/scripts/all-ovarian-su2c.sh
diff --git a/src/main/scripts/all-prostate-broad.sh → ...n/resources/scripts/all-prostate-broad.sh b/src/main/scripts/all-prostate-broad.sh → ...n/resources/scripts/all-prostate-broad.sh
diff --git a/src/main/scripts/all-prostate-mich.sh → ...in/resources/scripts/all-prostate-mich.sh b/src/main/scripts/all-prostate-mich.sh → ...in/resources/scripts/all-prostate-mich.sh
diff --git a/src/main/scripts/all-prostate-mskcc.sh → ...n/resources/scripts/all-prostate-mskcc.sh b/src/main/scripts/all-prostate-mskcc.sh → ...n/resources/scripts/all-prostate-mskcc.sh
diff --git a/src/main/scripts/all-prostate-su2c.sh → ...in/resources/scripts/all-prostate-su2c.sh b/src/main/scripts/all-prostate-su2c.sh → ...in/resources/scripts/all-prostate-su2c.sh
diff --git a/src/main/scripts/all-prostate-tcga.sh → ...in/resources/scripts/all-prostate-tcga.sh b/src/main/scripts/all-prostate-tcga.sh → ...in/resources/scripts/all-prostate-tcga.sh
diff --git a/src/main/scripts/all-su2c.sh → src/main/resources/scripts/all-su2c.sh b/src/main/scripts/all-su2c.sh → src/main/resources/scripts/all-su2c.sh
diff --git a/src/main/scripts/all-ucec-su2c.sh → src/main/resources/scripts/all-ucec-su2c.sh b/src/main/scripts/all-ucec-su2c.sh → src/main/resources/scripts/all-ucec-su2c.sh
diff --git a/src/main/scripts/calculateCoExpression.pl → ...esources/scripts/calculateCoExpression.pl b/src/main/scripts/calculateCoExpression.pl → ...esources/scripts/calculateCoExpression.pl
diff --git a/...n/scripts/calculateMutationFrequencies.py → ...s/scripts/calculateMutationFrequencies.py b/...n/scripts/calculateMutationFrequencies.py → ...s/scripts/calculateMutationFrequencies.py
diff --git a/...n/scripts/compareDirectAndBulkDBMSload.pl → ...s/scripts/compareDirectAndBulkDBMSload.pl b/...n/scripts/compareDirectAndBulkDBMSload.pl → ...s/scripts/compareDirectAndBulkDBMSload.pl
diff --git a/src/main/scripts/convertCosmicVcfToMaf.pl → ...esources/scripts/convertCosmicVcfToMaf.pl b/src/main/scripts/convertCosmicVcfToMaf.pl → ...esources/scripts/convertCosmicVcfToMaf.pl
diff --git a/src/main/scripts/convertExpressionZscores.pl → ...urces/scripts/convertExpressionZscores.pl b/src/main/scripts/convertExpressionZscores.pl → ...urces/scripts/convertExpressionZscores.pl
diff --git a/src/main/scripts/convertGeneIds.pl → src/main/resources/scripts/convertGeneIds.pl b/src/main/scripts/convertGeneIds.pl → src/main/resources/scripts/convertGeneIds.pl
diff --git a/src/main/scripts/convertGeneSymbols.pl → ...n/resources/scripts/convertGeneSymbols.pl b/src/main/scripts/convertGeneSymbols.pl → ...n/resources/scripts/convertGeneSymbols.pl
diff --git a/src/main/scripts/convertSvsImages.pl → ...ain/resources/scripts/convertSvsImages.pl b/src/main/scripts/convertSvsImages.pl → ...ain/resources/scripts/convertSvsImages.pl
diff --git a/src/main/scripts/cutInvalidCases.pl → ...main/resources/scripts/cutInvalidCases.pl b/src/main/scripts/cutInvalidCases.pl → ...main/resources/scripts/cutInvalidCases.pl
diff --git a/src/main/scripts/deleteAllCaseLists.pl → ...n/resources/scripts/deleteAllCaseLists.pl b/src/main/scripts/deleteAllCaseLists.pl → ...n/resources/scripts/deleteAllCaseLists.pl
diff --git a/src/main/scripts/downloadChromosomeSizes.py → ...ources/scripts/downloadChromosomeSizes.py b/src/main/scripts/downloadChromosomeSizes.py → ...ources/scripts/downloadChromosomeSizes.py
diff --git a/src/main/scripts/dumpPortalInfo.pl → src/main/resources/scripts/dumpPortalInfo.pl b/src/main/scripts/dumpPortalInfo.pl → src/main/resources/scripts/dumpPortalInfo.pl
diff --git a/src/main/scripts/env.pl → src/main/resources/scripts/env.pl b/src/main/scripts/env.pl → src/main/resources/scripts/env.pl
diff --git a/src/main/scripts/env.sh → src/main/resources/scripts/env.sh b/src/main/scripts/env.sh → src/main/resources/scripts/env.sh
diff --git a/src/main/scripts/envSimple.pl → src/main/resources/scripts/envSimple.pl b/src/main/scripts/envSimple.pl → src/main/resources/scripts/envSimple.pl
diff --git a/src/main/scripts/exportProfile.pl → src/main/resources/scripts/exportProfile.pl b/src/main/scripts/exportProfile.pl → src/main/resources/scripts/exportProfile.pl
diff --git a/src/main/scripts/fetchBCRDataDict.sh → ...ain/resources/scripts/fetchBCRDataDict.sh b/src/main/scripts/fetchBCRDataDict.sh → ...ain/resources/scripts/fetchBCRDataDict.sh
diff --git a/src/main/scripts/filterCases.pl → src/main/resources/scripts/filterCases.pl b/src/main/scripts/filterCases.pl → src/main/resources/scripts/filterCases.pl
diff --git a/src/main/scripts/filterCases.sh → src/main/resources/scripts/filterCases.sh b/src/main/scripts/filterCases.sh → src/main/resources/scripts/filterCases.sh
diff --git a/...flagStudyForProductionPortalDeployment.py → ...flagStudyForProductionPortalDeployment.py b/...flagStudyForProductionPortalDeployment.py → ...flagStudyForProductionPortalDeployment.py
diff --git a/src/main/scripts/generateMutationData.pl → ...resources/scripts/generateMutationData.pl b/src/main/scripts/generateMutationData.pl → ...resources/scripts/generateMutationData.pl
diff --git a/src/main/scripts/hot-deploy.sh → src/main/resources/scripts/hot-deploy.sh b/src/main/scripts/hot-deploy.sh → src/main/resources/scripts/hot-deploy.sh
diff --git a/src/main/scripts/hotDeploy.py → src/main/resources/scripts/hotDeploy.py b/src/main/scripts/hotDeploy.py → src/main/resources/scripts/hotDeploy.py
diff --git a/src/main/scripts/import-portal-users.sh → .../resources/scripts/import-portal-users.sh b/src/main/scripts/import-portal-users.sh → .../resources/scripts/import-portal-users.sh
diff --git a/...in/scripts/import-prad-su2c-caises-xml.sh → ...es/scripts/import-prad-su2c-caises-xml.sh b/...in/scripts/import-prad-su2c-caises-xml.sh → ...es/scripts/import-prad-su2c-caises-xml.sh
diff --git a/src/main/scripts/importAccessRights.pl → ...n/resources/scripts/importAccessRights.pl b/src/main/scripts/importAccessRights.pl → ...n/resources/scripts/importAccessRights.pl
diff --git a/src/main/scripts/importCancerStudy.pl → ...in/resources/scripts/importCancerStudy.pl b/src/main/scripts/importCancerStudy.pl → ...in/resources/scripts/importCancerStudy.pl
diff --git a/src/main/scripts/importCaseList.pl → src/main/resources/scripts/importCaseList.pl b/src/main/scripts/importCaseList.pl → src/main/resources/scripts/importCaseList.pl
diff --git a/src/main/scripts/importCaseListData.pl → ...n/resources/scripts/importCaseListData.pl b/src/main/scripts/importCaseListData.pl → ...n/resources/scripts/importCaseListData.pl
diff --git a/src/main/scripts/importClinicalData.pl → ...n/resources/scripts/importClinicalData.pl b/src/main/scripts/importClinicalData.pl → ...n/resources/scripts/importClinicalData.pl
diff --git a/...in/scripts/importCopyNumberSegmentData.pl → ...es/scripts/importCopyNumberSegmentData.pl b/...in/scripts/importCopyNumberSegmentData.pl → ...es/scripts/importCopyNumberSegmentData.pl
diff --git a/src/main/scripts/importCosmicData.pl → ...ain/resources/scripts/importCosmicData.pl b/src/main/scripts/importCosmicData.pl → ...ain/resources/scripts/importCosmicData.pl
diff --git a/src/main/scripts/importDrugData.pl → src/main/resources/scripts/importDrugData.pl b/src/main/scripts/importDrugData.pl → src/main/resources/scripts/importDrugData.pl
diff --git a/src/main/scripts/importGenePanel.pl → ...main/resources/scripts/importGenePanel.pl b/src/main/scripts/importGenePanel.pl → ...main/resources/scripts/importGenePanel.pl
diff --git a/src/main/scripts/importGenes.pl → src/main/resources/scripts/importGenes.pl b/src/main/scripts/importGenes.pl → src/main/resources/scripts/importGenes.pl
diff --git a/src/main/scripts/importGenesetData.pl → ...in/resources/scripts/importGenesetData.pl b/src/main/scripts/importGenesetData.pl → ...in/resources/scripts/importGenesetData.pl
diff --git a/src/main/scripts/importGenesetHierarchy.pl → ...sources/scripts/importGenesetHierarchy.pl b/src/main/scripts/importGenesetHierarchy.pl → ...sources/scripts/importGenesetHierarchy.pl
diff --git a/src/main/scripts/importGistic.pl → src/main/resources/scripts/importGistic.pl b/src/main/scripts/importGistic.pl → src/main/resources/scripts/importGistic.pl
diff --git a/src/main/scripts/importHprd.pl → src/main/resources/scripts/importHprd.pl b/src/main/scripts/importHprd.pl → src/main/resources/scripts/importHprd.pl
diff --git a/src/main/scripts/importMicroRNAIDs.pl → ...in/resources/scripts/importMicroRNAIDs.pl b/src/main/scripts/importMicroRNAIDs.pl → ...in/resources/scripts/importMicroRNAIDs.pl
diff --git a/src/main/scripts/importMicroRna.pl → src/main/resources/scripts/importMicroRna.pl b/src/main/scripts/importMicroRna.pl → src/main/resources/scripts/importMicroRna.pl
diff --git a/src/main/scripts/importMutSig.pl → src/main/resources/scripts/importMutSig.pl b/src/main/scripts/importMutSig.pl → src/main/resources/scripts/importMutSig.pl
diff --git a/src/main/scripts/importPiHelperData.pl → ...n/resources/scripts/importPiHelperData.pl b/src/main/scripts/importPiHelperData.pl → ...n/resources/scripts/importPiHelperData.pl
diff --git a/src/main/scripts/importProfileData.pl → ...in/resources/scripts/importProfileData.pl b/src/main/scripts/importProfileData.pl → ...in/resources/scripts/importProfileData.pl
diff --git a/src/main/scripts/importReferenceGenome.pl → ...esources/scripts/importReferenceGenome.pl b/src/main/scripts/importReferenceGenome.pl → ...esources/scripts/importReferenceGenome.pl
diff --git a/src/main/scripts/importSif.pl → src/main/resources/scripts/importSif.pl b/src/main/scripts/importSif.pl → src/main/resources/scripts/importSif.pl
diff --git a/src/main/scripts/importTimelineData.pl → ...n/resources/scripts/importTimelineData.pl b/src/main/scripts/importTimelineData.pl → ...n/resources/scripts/importTimelineData.pl
diff --git a/src/main/scripts/importTypesOfCancer.pl → .../resources/scripts/importTypesOfCancer.pl b/src/main/scripts/importTypesOfCancer.pl → .../resources/scripts/importTypesOfCancer.pl
diff --git a/src/main/scripts/importUsers.py → src/main/resources/scripts/importUsers.py b/src/main/scripts/importUsers.py → src/main/resources/scripts/importUsers.py
diff --git a/src/main/scripts/importer/__init__.py → ...in/resources/scripts/importer/__init__.py b/src/main/scripts/importer/__init__.py → ...in/resources/scripts/importer/__init__.py
diff --git a/...n/scripts/importer/allowed_data_types.txt → ...s/scripts/importer/allowed_data_types.txt b/...n/scripts/importer/allowed_data_types.txt → ...s/scripts/importer/allowed_data_types.txt
diff --git a/...in/scripts/importer/cbioportalImporter.py → ...es/scripts/importer/cbioportalImporter.py b/...in/scripts/importer/cbioportalImporter.py → ...es/scripts/importer/cbioportalImporter.py
diff --git a/...ain/scripts/importer/cbioportal_common.py → ...ces/scripts/importer/cbioportal_common.py b/...ain/scripts/importer/cbioportal_common.py → ...ces/scripts/importer/cbioportal_common.py
diff --git a/...in/scripts/importer/chromosome_sizes.json → ...es/scripts/importer/chromosome_sizes.json b/...in/scripts/importer/chromosome_sizes.json → ...es/scripts/importer/chromosome_sizes.json
diff --git a/...ipts/importer/data_cna_pd_annotations.txt → ...ipts/importer/data_cna_pd_annotations.txt b/...ipts/importer/data_cna_pd_annotations.txt → ...ipts/importer/data_cna_pd_annotations.txt
diff --git a/...ripts/importer/importOncokbDiscreteCNA.py → ...ripts/importer/importOncokbDiscreteCNA.py b/...ripts/importer/importOncokbDiscreteCNA.py → ...ripts/importer/importOncokbDiscreteCNA.py
diff --git a/.../scripts/importer/importOncokbMutation.py → .../scripts/importer/importOncokbMutation.py b/.../scripts/importer/importOncokbMutation.py → .../scripts/importer/importOncokbMutation.py
diff --git a/src/main/scripts/importer/libImportOncokb.py → ...urces/scripts/importer/libImportOncokb.py b/src/main/scripts/importer/libImportOncokb.py → ...urces/scripts/importer/libImportOncokb.py
diff --git a/src/main/scripts/importer/metaImport.py → .../resources/scripts/importer/metaImport.py b/src/main/scripts/importer/metaImport.py → .../resources/scripts/importer/metaImport.py
diff --git a/...ripts/importer/updateOncokbAnnotations.py → ...ripts/importer/updateOncokbAnnotations.py b/...ripts/importer/updateOncokbAnnotations.py → ...ripts/importer/updateOncokbAnnotations.py
diff --git a/src/main/scripts/importer/validateData.py → ...esources/scripts/importer/validateData.py b/src/main/scripts/importer/validateData.py → ...esources/scripts/importer/validateData.py
diff --git a/src/main/scripts/importer/validateStudies.py → ...urces/scripts/importer/validateStudies.py b/src/main/scripts/importer/validateStudies.py → ...urces/scripts/importer/validateStudies.py
diff --git a/...ter/validation_report_template.html.jinja → ...ter/validation_report_template.html.jinja b/...ter/validation_report_template.html.jinja → ...ter/validation_report_template.html.jinja
diff --git a/src/main/scripts/init.sh → src/main/resources/scripts/init.sh b/src/main/scripts/init.sh → src/main/resources/scripts/init.sh
diff --git a/src/main/scripts/loadNetwork.sh → src/main/resources/scripts/loadNetwork.sh b/src/main/scripts/loadNetwork.sh → src/main/resources/scripts/loadNetwork.sh
diff --git a/src/main/scripts/loadSampleData.sh → src/main/resources/scripts/loadSampleData.sh b/src/main/scripts/loadSampleData.sh → src/main/resources/scripts/loadSampleData.sh
diff --git a/...ipts/massagePortalDataForCancerStudies.pl → ...ipts/massagePortalDataForCancerStudies.pl b/...ipts/massagePortalDataForCancerStudies.pl → ...ipts/massagePortalDataForCancerStudies.pl
diff --git a/src/main/scripts/migrate_db.py → src/main/resources/scripts/migrate_db.py b/src/main/scripts/migrate_db.py → src/main/resources/scripts/migrate_db.py
diff --git a/src/main/scripts/mini_load_ova.sh → src/main/resources/scripts/mini_load_ova.sh b/src/main/scripts/mini_load_ova.sh → src/main/resources/scripts/mini_load_ova.sh
diff --git a/src/main/scripts/ovarian/preprocess-all.py → ...sources/scripts/ovarian/preprocess-all.py b/src/main/scripts/ovarian/preprocess-all.py → ...sources/scripts/ovarian/preprocess-all.py
diff --git a/src/main/scripts/ovarian/preprocess-mrna.py → ...ources/scripts/ovarian/preprocess-mrna.py b/src/main/scripts/ovarian/preprocess-mrna.py → ...ources/scripts/ovarian/preprocess-mrna.py
diff --git a/src/main/scripts/ovarian/preprocess-rae.py → ...sources/scripts/ovarian/preprocess-rae.py b/src/main/scripts/ovarian/preprocess-rae.py → ...sources/scripts/ovarian/preprocess-rae.py
diff --git a/...in/scripts/ovarian/removeNullMutations.py → ...es/scripts/ovarian/removeNullMutations.py b/...in/scripts/ovarian/removeNullMutations.py → ...es/scripts/ovarian/removeNullMutations.py
diff --git a/src/main/scripts/portal-client.py → src/main/resources/scripts/portal-client.py b/src/main/scripts/portal-client.py → src/main/resources/scripts/portal-client.py
diff --git a/src/main/scripts/prepareBasicPiHelperData.sh → ...urces/scripts/prepareBasicPiHelperData.sh b/src/main/scripts/prepareBasicPiHelperData.sh → ...urces/scripts/prepareBasicPiHelperData.sh
diff --git a/src/main/scripts/prepareCosmicData.sh → ...in/resources/scripts/prepareCosmicData.sh b/src/main/scripts/prepareCosmicData.sh → ...in/resources/scripts/prepareCosmicData.sh
diff --git a/src/main/scripts/prepareGeneData.sh → ...main/resources/scripts/prepareGeneData.sh b/src/main/scripts/prepareGeneData.sh → ...main/resources/scripts/prepareGeneData.sh
diff --git a/...main/scripts/preparePathwayCommonsData.sh → ...rces/scripts/preparePathwayCommonsData.sh b/...main/scripts/preparePathwayCommonsData.sh → ...rces/scripts/preparePathwayCommonsData.sh
diff --git a/src/main/scripts/prepareSangerCGC.sh → ...ain/resources/scripts/prepareSangerCGC.sh b/src/main/scripts/prepareSangerCGC.sh → ...ain/resources/scripts/prepareSangerCGC.sh
diff --git a/...ipts/processPathwayCommonsInteractions.py → ...ipts/processPathwayCommonsInteractions.py b/...ipts/processPathwayCommonsInteractions.py → ...ipts/processPathwayCommonsInteractions.py
diff --git a/src/main/scripts/reload.sh → src/main/resources/scripts/reload.sh b/src/main/scripts/reload.sh → src/main/resources/scripts/reload.sh
diff --git a/src/main/scripts/resetDb.pl → src/main/resources/scripts/resetDb.pl b/src/main/scripts/resetDb.pl → src/main/resources/scripts/resetDb.pl
diff --git a/src/main/scripts/showAllCaseLists.pl → ...ain/resources/scripts/showAllCaseLists.pl b/src/main/scripts/showAllCaseLists.pl → ...ain/resources/scripts/showAllCaseLists.pl
diff --git a/src/main/scripts/statDb.pl → src/main/resources/scripts/statDb.pl b/src/main/scripts/statDb.pl → src/main/resources/scripts/statDb.pl
diff --git a/src/main/scripts/updateGenePanel.pl → ...main/resources/scripts/updateGenePanel.pl b/src/main/scripts/updateGenePanel.pl → ...main/resources/scripts/updateGenePanel.pl
diff --git a/src/main/scripts/updateMetaData.pl → src/main/resources/scripts/updateMetaData.pl b/src/main/scripts/updateMetaData.pl → src/main/resources/scripts/updateMetaData.pl
diff --git a/src/main/scripts/verifyGeneSets.pl → src/main/resources/scripts/verifyGeneSets.pl b/src/main/scripts/verifyGeneSets.pl → src/main/resources/scripts/verifyGeneSets.pl