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Merge branch 'hotfix-1.31.10'
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@arteymix
arteymix committed Aug 7, 2024
2 parents 44dfb2c + 00d7725 commit ef09084
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Showing 334 changed files with 11,273 additions and 2,324 deletions.
2 changes: 1 addition & 1 deletion gemma-cli/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
<parent>
<artifactId>gemma</artifactId>
<groupId>gemma</groupId>
<version>1.31.9</version>
<version>1.31.10</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>gemma-cli</artifactId>
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16 changes: 13 additions & 3 deletions gemma-cli/src/main/config/bash_completion.d/gemma-cli
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Original file line number Diff line number Diff line change
Expand Up @@ -2,11 +2,11 @@ function __gemma_cli_complete() {
COMPREPLY=()
words="${COMP_WORDS[*]}"
current_option="${COMP_WORDS[$COMP_CWORD-1]}"
if ! [[ " $words " =~ ' '(adATcleanup|addExternalDatabase|addGEOData|addPlatformSequences|addTSVData|affyAltsUpdate|affyCollapse|affyFromCel|blackList|blatPlatform|coexpAnalyze|corrMat|ctdDownload|deleteDiffEx|deleteExperiments|deletePhenotypes|deletePlatformElements|detachSequences|dgaDownload|diffExAnalyze|dumpForNIF|evidenceImport|fetchMeshTerms|fillBatchInfo|findDatasetPubs|findObsoleteTerms|geneUpdate|generateDataFile|genericPlatform|getDataMatrix|gwasDownload|importDesign|listExternalDatabases|listGEOData|loadEvidenceForClassifier|loadGenesFromFile|loadTaxa|makePlatformAnnotFiles|makePrivate|makeProcessedData|makePublic|mapPlatformToGenes|mergePlatforms|migrateFactorValues|omimDownload|orderVectorsByDesign|pca|platformMapSummary|platformRepeatScan|platformSubsumptionTest|printExperimentalDesign|probeRename|pubmedAssociateToExperiments|pubmedLoad|pubmedSearchAndSave|refreshExperiment|replaceData|rgdDownload|rnaseqBatchInfo|rnaseqDataAdd|runGeeq|searchIndex|seqCleanup|sfariDownload|splitExperiment|switchExperimentPlatform|updateEe2c|updateExternalDatabase|updateGOAnnots|updateMultifunc|updatePubMeds|vectorMerge|viewExpDesigns)' ' ]]; then
if ! [[ " $words " =~ ' '(adATcleanup|addExternalDatabase|addGEOData|addPlatformSequences|addTSVData|affyAltsUpdate|affyCollapse|affyFromCel|blackList|blatPlatform|coexpAnalyze|corrMat|ctdDownload|deleteDiffEx|deleteExperiments|deletePhenotypes|deletePlatformElements|detachSequences|dgaDownload|diffExAnalyze|dumpForNIF|evidenceImport|fetchMeshTerms|fillBatchInfo|findDatasetPubs|findObsoleteTerms|geneUpdate|generateDataFile|genericPlatform|getDataMatrix|gwasDownload|importDesign|listExternalDatabases|listGEOData|loadEvidenceForClassifier|loadGenesFromFile|loadTaxa|makePlatformAnnotFiles|makePrivate|makeProcessedData|makePublic|mapPlatformToGenes|mergePlatforms|migrateFactorValues|omimDownload|orderVectorsByDesign|pca|platformMapSummary|platformRepeatScan|platformSubsumptionTest|printExperimentalDesign|probeRename|pubmedAssociateToExperiments|pubmedLoad|pubmedSearchAndSave|refreshExperiment|replaceData|rgdDownload|rnaseqBatchInfo|rnaseqDataAdd|runGeeq|searchIndex|seqCleanup|sfariDownload|splitExperiment|switchExperimentPlatform|updateEe2Ad|updateEe2c|updateExternalDatabase|updateGOAnnots|updateGene2Cs|updateMultifunc|updatePubMeds|vectorMerge|viewExpDesigns)' ' ]]; then
if ! [[ "$current_option" =~ (--completion-executable|--completion-shell|--logger|--verbosity|-ce|-cs|-logger|-v) ]]; then
mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "'--completion' '--completion-executable' '--completion-shell' '--help' '--help-all' '--logger' '--profiling' '--testdb' '--verbosity' '--version' '-c' '-ce' '-cs' '-h' '-ha' '-logger' '-profiling' '-testdb' '-v' '-version'" -- "$2")
fi
mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "'adATcleanup' 'addExternalDatabase' 'addGEOData' 'addPlatformSequences' 'addTSVData' 'affyAltsUpdate' 'affyCollapse' 'affyFromCel' 'blackList' 'blatPlatform' 'coexpAnalyze' 'corrMat' 'ctdDownload' 'deleteDiffEx' 'deleteExperiments' 'deletePhenotypes' 'deletePlatformElements' 'detachSequences' 'dgaDownload' 'diffExAnalyze' 'dumpForNIF' 'evidenceImport' 'fetchMeshTerms' 'fillBatchInfo' 'findDatasetPubs' 'findObsoleteTerms' 'geneUpdate' 'generateDataFile' 'genericPlatform' 'getDataMatrix' 'gwasDownload' 'importDesign' 'listExternalDatabases' 'listGEOData' 'loadEvidenceForClassifier' 'loadGenesFromFile' 'loadTaxa' 'makePlatformAnnotFiles' 'makePrivate' 'makeProcessedData' 'makePublic' 'mapPlatformToGenes' 'mergePlatforms' 'migrateFactorValues' 'omimDownload' 'orderVectorsByDesign' 'pca' 'platformMapSummary' 'platformRepeatScan' 'platformSubsumptionTest' 'printExperimentalDesign' 'probeRename' 'pubmedAssociateToExperiments' 'pubmedLoad' 'pubmedSearchAndSave' 'refreshExperiment' 'replaceData' 'rgdDownload' 'rnaseqBatchInfo' 'rnaseqDataAdd' 'runGeeq' 'searchIndex' 'seqCleanup' 'sfariDownload' 'splitExperiment' 'switchExperimentPlatform' 'updateEe2c' 'updateExternalDatabase' 'updateGOAnnots' 'updateMultifunc' 'updatePubMeds' 'vectorMerge' 'viewExpDesigns'" -- "$2")
mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "'adATcleanup' 'addExternalDatabase' 'addGEOData' 'addPlatformSequences' 'addTSVData' 'affyAltsUpdate' 'affyCollapse' 'affyFromCel' 'blackList' 'blatPlatform' 'coexpAnalyze' 'corrMat' 'ctdDownload' 'deleteDiffEx' 'deleteExperiments' 'deletePhenotypes' 'deletePlatformElements' 'detachSequences' 'dgaDownload' 'diffExAnalyze' 'dumpForNIF' 'evidenceImport' 'fetchMeshTerms' 'fillBatchInfo' 'findDatasetPubs' 'findObsoleteTerms' 'geneUpdate' 'generateDataFile' 'genericPlatform' 'getDataMatrix' 'gwasDownload' 'importDesign' 'listExternalDatabases' 'listGEOData' 'loadEvidenceForClassifier' 'loadGenesFromFile' 'loadTaxa' 'makePlatformAnnotFiles' 'makePrivate' 'makeProcessedData' 'makePublic' 'mapPlatformToGenes' 'mergePlatforms' 'migrateFactorValues' 'omimDownload' 'orderVectorsByDesign' 'pca' 'platformMapSummary' 'platformRepeatScan' 'platformSubsumptionTest' 'printExperimentalDesign' 'probeRename' 'pubmedAssociateToExperiments' 'pubmedLoad' 'pubmedSearchAndSave' 'refreshExperiment' 'replaceData' 'rgdDownload' 'rnaseqBatchInfo' 'rnaseqDataAdd' 'runGeeq' 'searchIndex' 'seqCleanup' 'sfariDownload' 'splitExperiment' 'switchExperimentPlatform' 'updateEe2Ad' 'updateEe2c' 'updateExternalDatabase' 'updateGOAnnots' 'updateGene2Cs' 'updateMultifunc' 'updatePubMeds' 'vectorMerge' 'viewExpDesigns'" -- "$2")
fi
if [[ " $words " =~ ' addGEOData ' ]]; then
if ! [[ "$current_option" =~ (--acc|--file|-batchFormat|-batchOutputFile|-e|-f|-softfile) ]]; then
Expand Down Expand Up @@ -216,8 +216,15 @@ function __gemma_cli_complete() {
mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -f -- "$2")
fi
fi
if [[ " $words " =~ ' updateEe2Ad ' ]]; then
if ! [[ "$current_option" =~ (-mdate) ]]; then
mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "'--help' '-h' '-mdate'" -- "$2")
fi
fi
if [[ " $words " =~ ' updateEe2c ' ]]; then
mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "'--help' '--truncate' '-h' '-truncate'" -- "$2")
if ! [[ "$current_option" =~ (-mdate) ]]; then
mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "'--help' '--truncate' '-h' '-mdate' '-truncate'" -- "$2")
fi
fi
if [[ " $words " =~ ' vectorMerge ' ]]; then
if ! [[ "$current_option" =~ (--eeListfile|--excludeEEFile|--experiment|--expressionQuery|--taxon|-batchFormat|-batchOutputFile|-e|-eeset|-f|-q|-t|-x) ]]; then
Expand Down Expand Up @@ -494,5 +501,8 @@ function __gemma_cli_complete() {
if [[ " $words " =~ ' pubmedSearchAndSave ' ]]; then
mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "'--help' '--persist' '-d' '-h'" -- "$2")
fi
if [[ " $words " =~ ' updateGene2Cs ' ]]; then
mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "'--help' '-h'" -- "$2")
fi
}
complete -o filenames -o bashdefault -F __gemma_cli_complete 'gemma-cli'
16 changes: 13 additions & 3 deletions gemma-cli/src/main/config/bash_completion.d/gemma-cli-staging
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,11 +2,11 @@ function __gemma_cli_complete() {
COMPREPLY=()
words="${COMP_WORDS[*]}"
current_option="${COMP_WORDS[$COMP_CWORD-1]}"
if ! [[ " $words " =~ ' '(adATcleanup|addExternalDatabase|addGEOData|addPlatformSequences|addTSVData|affyAltsUpdate|affyCollapse|affyFromCel|blackList|blatPlatform|coexpAnalyze|corrMat|ctdDownload|deleteDiffEx|deleteExperiments|deletePhenotypes|deletePlatformElements|detachSequences|dgaDownload|diffExAnalyze|dumpForNIF|evidenceImport|fetchMeshTerms|fillBatchInfo|findDatasetPubs|findObsoleteTerms|geneUpdate|generateDataFile|genericPlatform|getDataMatrix|gwasDownload|importDesign|listExternalDatabases|listGEOData|loadEvidenceForClassifier|loadGenesFromFile|loadTaxa|makePlatformAnnotFiles|makePrivate|makeProcessedData|makePublic|mapPlatformToGenes|mergePlatforms|migrateFactorValues|omimDownload|orderVectorsByDesign|pca|platformMapSummary|platformRepeatScan|platformSubsumptionTest|printExperimentalDesign|probeRename|pubmedAssociateToExperiments|pubmedLoad|pubmedSearchAndSave|refreshExperiment|replaceData|rgdDownload|rnaseqBatchInfo|rnaseqDataAdd|runGeeq|searchIndex|seqCleanup|sfariDownload|splitExperiment|switchExperimentPlatform|updateEe2c|updateExternalDatabase|updateGOAnnots|updateMultifunc|updatePubMeds|vectorMerge|viewExpDesigns)' ' ]]; then
if ! [[ " $words " =~ ' '(adATcleanup|addExternalDatabase|addGEOData|addPlatformSequences|addTSVData|affyAltsUpdate|affyCollapse|affyFromCel|blackList|blatPlatform|coexpAnalyze|corrMat|ctdDownload|deleteDiffEx|deleteExperiments|deletePhenotypes|deletePlatformElements|detachSequences|dgaDownload|diffExAnalyze|dumpForNIF|evidenceImport|fetchMeshTerms|fillBatchInfo|findDatasetPubs|findObsoleteTerms|geneUpdate|generateDataFile|genericPlatform|getDataMatrix|gwasDownload|importDesign|listExternalDatabases|listGEOData|loadEvidenceForClassifier|loadGenesFromFile|loadTaxa|makePlatformAnnotFiles|makePrivate|makeProcessedData|makePublic|mapPlatformToGenes|mergePlatforms|migrateFactorValues|omimDownload|orderVectorsByDesign|pca|platformMapSummary|platformRepeatScan|platformSubsumptionTest|printExperimentalDesign|probeRename|pubmedAssociateToExperiments|pubmedLoad|pubmedSearchAndSave|refreshExperiment|replaceData|rgdDownload|rnaseqBatchInfo|rnaseqDataAdd|runGeeq|searchIndex|seqCleanup|sfariDownload|splitExperiment|switchExperimentPlatform|updateEe2Ad|updateEe2c|updateExternalDatabase|updateGOAnnots|updateGene2Cs|updateMultifunc|updatePubMeds|vectorMerge|viewExpDesigns)' ' ]]; then
if ! [[ "$current_option" =~ (--completion-executable|--completion-shell|--logger|--verbosity|-ce|-cs|-logger|-v) ]]; then
mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "'--completion' '--completion-executable' '--completion-shell' '--help' '--help-all' '--logger' '--profiling' '--testdb' '--verbosity' '--version' '-c' '-ce' '-cs' '-h' '-ha' '-logger' '-profiling' '-testdb' '-v' '-version'" -- "$2")
fi
mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "'adATcleanup' 'addExternalDatabase' 'addGEOData' 'addPlatformSequences' 'addTSVData' 'affyAltsUpdate' 'affyCollapse' 'affyFromCel' 'blackList' 'blatPlatform' 'coexpAnalyze' 'corrMat' 'ctdDownload' 'deleteDiffEx' 'deleteExperiments' 'deletePhenotypes' 'deletePlatformElements' 'detachSequences' 'dgaDownload' 'diffExAnalyze' 'dumpForNIF' 'evidenceImport' 'fetchMeshTerms' 'fillBatchInfo' 'findDatasetPubs' 'findObsoleteTerms' 'geneUpdate' 'generateDataFile' 'genericPlatform' 'getDataMatrix' 'gwasDownload' 'importDesign' 'listExternalDatabases' 'listGEOData' 'loadEvidenceForClassifier' 'loadGenesFromFile' 'loadTaxa' 'makePlatformAnnotFiles' 'makePrivate' 'makeProcessedData' 'makePublic' 'mapPlatformToGenes' 'mergePlatforms' 'migrateFactorValues' 'omimDownload' 'orderVectorsByDesign' 'pca' 'platformMapSummary' 'platformRepeatScan' 'platformSubsumptionTest' 'printExperimentalDesign' 'probeRename' 'pubmedAssociateToExperiments' 'pubmedLoad' 'pubmedSearchAndSave' 'refreshExperiment' 'replaceData' 'rgdDownload' 'rnaseqBatchInfo' 'rnaseqDataAdd' 'runGeeq' 'searchIndex' 'seqCleanup' 'sfariDownload' 'splitExperiment' 'switchExperimentPlatform' 'updateEe2c' 'updateExternalDatabase' 'updateGOAnnots' 'updateMultifunc' 'updatePubMeds' 'vectorMerge' 'viewExpDesigns'" -- "$2")
mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "'adATcleanup' 'addExternalDatabase' 'addGEOData' 'addPlatformSequences' 'addTSVData' 'affyAltsUpdate' 'affyCollapse' 'affyFromCel' 'blackList' 'blatPlatform' 'coexpAnalyze' 'corrMat' 'ctdDownload' 'deleteDiffEx' 'deleteExperiments' 'deletePhenotypes' 'deletePlatformElements' 'detachSequences' 'dgaDownload' 'diffExAnalyze' 'dumpForNIF' 'evidenceImport' 'fetchMeshTerms' 'fillBatchInfo' 'findDatasetPubs' 'findObsoleteTerms' 'geneUpdate' 'generateDataFile' 'genericPlatform' 'getDataMatrix' 'gwasDownload' 'importDesign' 'listExternalDatabases' 'listGEOData' 'loadEvidenceForClassifier' 'loadGenesFromFile' 'loadTaxa' 'makePlatformAnnotFiles' 'makePrivate' 'makeProcessedData' 'makePublic' 'mapPlatformToGenes' 'mergePlatforms' 'migrateFactorValues' 'omimDownload' 'orderVectorsByDesign' 'pca' 'platformMapSummary' 'platformRepeatScan' 'platformSubsumptionTest' 'printExperimentalDesign' 'probeRename' 'pubmedAssociateToExperiments' 'pubmedLoad' 'pubmedSearchAndSave' 'refreshExperiment' 'replaceData' 'rgdDownload' 'rnaseqBatchInfo' 'rnaseqDataAdd' 'runGeeq' 'searchIndex' 'seqCleanup' 'sfariDownload' 'splitExperiment' 'switchExperimentPlatform' 'updateEe2Ad' 'updateEe2c' 'updateExternalDatabase' 'updateGOAnnots' 'updateGene2Cs' 'updateMultifunc' 'updatePubMeds' 'vectorMerge' 'viewExpDesigns'" -- "$2")
fi
if [[ " $words " =~ ' addGEOData ' ]]; then
if ! [[ "$current_option" =~ (--acc|--file|-batchFormat|-batchOutputFile|-e|-f|-softfile) ]]; then
Expand Down Expand Up @@ -216,8 +216,15 @@ function __gemma_cli_complete() {
mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -f -- "$2")
fi
fi
if [[ " $words " =~ ' updateEe2Ad ' ]]; then
if ! [[ "$current_option" =~ (-mdate) ]]; then
mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "'--help' '-h' '-mdate'" -- "$2")
fi
fi
if [[ " $words " =~ ' updateEe2c ' ]]; then
mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "'--help' '--truncate' '-h' '-truncate'" -- "$2")
if ! [[ "$current_option" =~ (-mdate) ]]; then
mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "'--help' '--truncate' '-h' '-mdate' '-truncate'" -- "$2")
fi
fi
if [[ " $words " =~ ' vectorMerge ' ]]; then
if ! [[ "$current_option" =~ (--eeListfile|--excludeEEFile|--experiment|--expressionQuery|--taxon|-batchFormat|-batchOutputFile|-e|-eeset|-f|-q|-t|-x) ]]; then
Expand Down Expand Up @@ -494,5 +501,8 @@ function __gemma_cli_complete() {
if [[ " $words " =~ ' pubmedSearchAndSave ' ]]; then
mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "'--help' '--persist' '-d' '-h'" -- "$2")
fi
if [[ " $words " =~ ' updateGene2Cs ' ]]; then
mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "'--help' '-h'" -- "$2")
fi
}
complete -o filenames -o bashdefault -F __gemma_cli_complete 'gemma-cli-staging'
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