Add a --file-type option to addMetadataFile to add MultiQC reports & al.

Author: arteymix

gemma-cli/src/main/config/bash_completion.d/gemma-cli

@@ -35,13 +35,19 @@ function __gemma_cli_complete() {
         fi
     fi
     if [[ " $words " =~ ' ubic.gemma.apps.ExpressionExperimentMetadataFileAdderCli ' ]]; then
-        if ! [[ "$current_option" =~ (--changelog-entry|--experiment|-ce|-e) ]]; then
-            mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "--changelog-entry --experiment --force --help -ce -e -force -h" -- "$2")
+        if ! [[ "$current_option" =~ (--changelog-entry|--experiment|--file-type|-ce|-e|-fileType) ]]; then
+            mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "--changelog-entry --experiment --file-type --force --help -ce -e -fileType -force -h" -- "$2")
+        fi
+        if [[ "$current_option" =~ (--file-type|-fileType) ]]; then
+            mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -f -- "$2")
         fi
     fi
     if [[ " $words " =~ ' addMetadataFile ' ]]; then
-        if ! [[ "$current_option" =~ (--changelog-entry|--experiment|-ce|-e) ]]; then
-            mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "--changelog-entry --experiment --force --help -ce -e -force -h" -- "$2")
+        if ! [[ "$current_option" =~ (--changelog-entry|--experiment|--file-type|-ce|-e|-fileType) ]]; then
+            mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "--changelog-entry --experiment --file-type --force --help -ce -e -fileType -force -h" -- "$2")
+        fi
+        if [[ "$current_option" =~ (--file-type|-fileType) ]]; then
+            mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -f -- "$2")
         fi
     fi
     if [[ " $words " =~ ' ubic.gemma.apps.LoadSimpleExpressionDataCli ' ]]; then

gemma-cli/src/main/config/bash_completion.d/gemma-cli-sc

@@ -35,13 +35,19 @@ function __gemma_cli_sc_complete() {
         fi
     fi
     if [[ " $words " =~ ' ubic.gemma.apps.ExpressionExperimentMetadataFileAdderCli ' ]]; then
-        if ! [[ "$current_option" =~ (--changelog-entry|--experiment|-ce|-e) ]]; then
-            mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "--changelog-entry --experiment --force --help -ce -e -force -h" -- "$2")
+        if ! [[ "$current_option" =~ (--changelog-entry|--experiment|--file-type|-ce|-e|-fileType) ]]; then
+            mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "--changelog-entry --experiment --file-type --force --help -ce -e -fileType -force -h" -- "$2")
+        fi
+        if [[ "$current_option" =~ (--file-type|-fileType) ]]; then
+            mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -f -- "$2")
         fi
     fi
     if [[ " $words " =~ ' addMetadataFile ' ]]; then
-        if ! [[ "$current_option" =~ (--changelog-entry|--experiment|-ce|-e) ]]; then
-            mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "--changelog-entry --experiment --force --help -ce -e -force -h" -- "$2")
+        if ! [[ "$current_option" =~ (--changelog-entry|--experiment|--file-type|-ce|-e|-fileType) ]]; then
+            mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "--changelog-entry --experiment --file-type --force --help -ce -e -fileType -force -h" -- "$2")
+        fi
+        if [[ "$current_option" =~ (--file-type|-fileType) ]]; then
+            mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -f -- "$2")
         fi
     fi
     if [[ " $words " =~ ' ubic.gemma.apps.LoadSimpleExpressionDataCli ' ]]; then

gemma-cli/src/main/config/bash_completion.d/gemma-cli-staging

@@ -35,13 +35,19 @@ function __gemma_cli_staging_complete() {
         fi
     fi
     if [[ " $words " =~ ' ubic.gemma.apps.ExpressionExperimentMetadataFileAdderCli ' ]]; then
-        if ! [[ "$current_option" =~ (--changelog-entry|--experiment|-ce|-e) ]]; then
-            mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "--changelog-entry --experiment --force --help -ce -e -force -h" -- "$2")
+        if ! [[ "$current_option" =~ (--changelog-entry|--experiment|--file-type|-ce|-e|-fileType) ]]; then
+            mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "--changelog-entry --experiment --file-type --force --help -ce -e -fileType -force -h" -- "$2")
+        fi
+        if [[ "$current_option" =~ (--file-type|-fileType) ]]; then
+            mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -f -- "$2")
         fi
     fi
     if [[ " $words " =~ ' addMetadataFile ' ]]; then
-        if ! [[ "$current_option" =~ (--changelog-entry|--experiment|-ce|-e) ]]; then
-            mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "--changelog-entry --experiment --force --help -ce -e -force -h" -- "$2")
+        if ! [[ "$current_option" =~ (--changelog-entry|--experiment|--file-type|-ce|-e|-fileType) ]]; then
+            mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "--changelog-entry --experiment --file-type --force --help -ce -e -fileType -force -h" -- "$2")
+        fi
+        if [[ "$current_option" =~ (--file-type|-fileType) ]]; then
+            mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -f -- "$2")
         fi
     fi
     if [[ " $words " =~ ' ubic.gemma.apps.LoadSimpleExpressionDataCli ' ]]; then

gemma-cli/src/main/config/fish/completions/gemma-cli-sc.fish

@@ -57,11 +57,13 @@ complete -c gemma-cli-sc -n '__fish_seen_subcommand_from addGEOData' -o batchRep
 complete -c gemma-cli-sc -n "not __fish_seen_subcommand_from $gemma_all_subcommands" -f -a ubic.gemma.apps.ExpressionExperimentMetadataFileAdderCli --description 'Add a metadata file to the given experiment and record an entry in the changelog file.'
 complete -c gemma-cli-sc -n '__fish_seen_subcommand_from ubic.gemma.apps.ExpressionExperimentMetadataFileAdderCli' -s h -l help -f --description 'Print this message'
 complete -c gemma-cli-sc -n '__fish_seen_subcommand_from ubic.gemma.apps.ExpressionExperimentMetadataFileAdderCli' -s e -l experiment -r -a '(gemma-cli-sc complete dataset 2>/dev/null)' -f --description 'Dataset identifier. Most tools recognize comma-delimited values given on the command line, and if this option is omitted (and none other provided), the tool will be applied to all expression experiments.'
+complete -c gemma-cli-sc -n '__fish_seen_subcommand_from ubic.gemma.apps.ExpressionExperimentMetadataFileAdderCli' -o fileType -l file-type -r -a '(echo -e "BASE_METADATA\t\nALIGNMENT_METADATA\t\nMUTLQC_REPORT\t\nADDITIONAL_PIPELINE_CONFIGURATIONS\t" 2>/dev/null)' -F --description 'Type of metadata file to be added. Possible values are: BASE_METADATA, ALIGNMENT_METADATA, MUTLQC_REPORT, ADDITIONAL_PIPELINE_CONFIGURATIONS.'
 complete -c gemma-cli-sc -n '__fish_seen_subcommand_from ubic.gemma.apps.ExpressionExperimentMetadataFileAdderCli' -o ce -l changelog-entry -r -f --description 'Changelog entry to be add. If not supplied, a text editor will be prompted.'
 complete -c gemma-cli-sc -n '__fish_seen_subcommand_from ubic.gemma.apps.ExpressionExperimentMetadataFileAdderCli' -o force -l force -f --description 'Ignore other reasons for skipping entities (e.g., troubled experiments) and overwrite existing data (see documentation for this tool to see exact behavior if not clear)'
 complete -c gemma-cli-sc -n "not __fish_seen_subcommand_from $gemma_all_subcommands" -f -a addMetadataFile --description 'Add a metadata file to the given experiment and record an entry in the changelog file.'
 complete -c gemma-cli-sc -n '__fish_seen_subcommand_from addMetadataFile' -s h -l help -f --description 'Print this message'
 complete -c gemma-cli-sc -n '__fish_seen_subcommand_from addMetadataFile' -s e -l experiment -r -a '(gemma-cli-sc complete dataset 2>/dev/null)' -f --description 'Dataset identifier. Most tools recognize comma-delimited values given on the command line, and if this option is omitted (and none other provided), the tool will be applied to all expression experiments.'
+complete -c gemma-cli-sc -n '__fish_seen_subcommand_from addMetadataFile' -o fileType -l file-type -r -a '(echo -e "BASE_METADATA\t\nALIGNMENT_METADATA\t\nMUTLQC_REPORT\t\nADDITIONAL_PIPELINE_CONFIGURATIONS\t" 2>/dev/null)' -F --description 'Type of metadata file to be added. Possible values are: BASE_METADATA, ALIGNMENT_METADATA, MUTLQC_REPORT, ADDITIONAL_PIPELINE_CONFIGURATIONS.'
 complete -c gemma-cli-sc -n '__fish_seen_subcommand_from addMetadataFile' -o ce -l changelog-entry -r -f --description 'Changelog entry to be add. If not supplied, a text editor will be prompted.'
 complete -c gemma-cli-sc -n '__fish_seen_subcommand_from addMetadataFile' -o force -l force -f --description 'Ignore other reasons for skipping entities (e.g., troubled experiments) and overwrite existing data (see documentation for this tool to see exact behavior if not clear)'
 complete -c gemma-cli-sc -n "not __fish_seen_subcommand_from $gemma_all_subcommands" -f -a ubic.gemma.apps.LoadSimpleExpressionDataCli --description 'Load an experiment from a tab-delimited file instead of GEO'

gemma-cli/src/main/config/fish/completions/gemma-cli-staging.fish

@@ -57,11 +57,13 @@ complete -c gemma-cli-staging -n '__fish_seen_subcommand_from addGEOData' -o bat
 complete -c gemma-cli-staging -n "not __fish_seen_subcommand_from $gemma_all_subcommands" -f -a ubic.gemma.apps.ExpressionExperimentMetadataFileAdderCli --description 'Add a metadata file to the given experiment and record an entry in the changelog file.'
 complete -c gemma-cli-staging -n '__fish_seen_subcommand_from ubic.gemma.apps.ExpressionExperimentMetadataFileAdderCli' -s h -l help -f --description 'Print this message'
 complete -c gemma-cli-staging -n '__fish_seen_subcommand_from ubic.gemma.apps.ExpressionExperimentMetadataFileAdderCli' -s e -l experiment -r -a '(gemma-cli-staging complete dataset 2>/dev/null)' -f --description 'Dataset identifier. Most tools recognize comma-delimited values given on the command line, and if this option is omitted (and none other provided), the tool will be applied to all expression experiments.'
+complete -c gemma-cli-staging -n '__fish_seen_subcommand_from ubic.gemma.apps.ExpressionExperimentMetadataFileAdderCli' -o fileType -l file-type -r -a '(echo -e "BASE_METADATA\t\nALIGNMENT_METADATA\t\nMUTLQC_REPORT\t\nADDITIONAL_PIPELINE_CONFIGURATIONS\t" 2>/dev/null)' -F --description 'Type of metadata file to be added. Possible values are: BASE_METADATA, ALIGNMENT_METADATA, MUTLQC_REPORT, ADDITIONAL_PIPELINE_CONFIGURATIONS.'
 complete -c gemma-cli-staging -n '__fish_seen_subcommand_from ubic.gemma.apps.ExpressionExperimentMetadataFileAdderCli' -o ce -l changelog-entry -r -f --description 'Changelog entry to be add. If not supplied, a text editor will be prompted.'
 complete -c gemma-cli-staging -n '__fish_seen_subcommand_from ubic.gemma.apps.ExpressionExperimentMetadataFileAdderCli' -o force -l force -f --description 'Ignore other reasons for skipping entities (e.g., troubled experiments) and overwrite existing data (see documentation for this tool to see exact behavior if not clear)'
 complete -c gemma-cli-staging -n "not __fish_seen_subcommand_from $gemma_all_subcommands" -f -a addMetadataFile --description 'Add a metadata file to the given experiment and record an entry in the changelog file.'
 complete -c gemma-cli-staging -n '__fish_seen_subcommand_from addMetadataFile' -s h -l help -f --description 'Print this message'
 complete -c gemma-cli-staging -n '__fish_seen_subcommand_from addMetadataFile' -s e -l experiment -r -a '(gemma-cli-staging complete dataset 2>/dev/null)' -f --description 'Dataset identifier. Most tools recognize comma-delimited values given on the command line, and if this option is omitted (and none other provided), the tool will be applied to all expression experiments.'
+complete -c gemma-cli-staging -n '__fish_seen_subcommand_from addMetadataFile' -o fileType -l file-type -r -a '(echo -e "BASE_METADATA\t\nALIGNMENT_METADATA\t\nMUTLQC_REPORT\t\nADDITIONAL_PIPELINE_CONFIGURATIONS\t" 2>/dev/null)' -F --description 'Type of metadata file to be added. Possible values are: BASE_METADATA, ALIGNMENT_METADATA, MUTLQC_REPORT, ADDITIONAL_PIPELINE_CONFIGURATIONS.'
 complete -c gemma-cli-staging -n '__fish_seen_subcommand_from addMetadataFile' -o ce -l changelog-entry -r -f --description 'Changelog entry to be add. If not supplied, a text editor will be prompted.'
 complete -c gemma-cli-staging -n '__fish_seen_subcommand_from addMetadataFile' -o force -l force -f --description 'Ignore other reasons for skipping entities (e.g., troubled experiments) and overwrite existing data (see documentation for this tool to see exact behavior if not clear)'
 complete -c gemma-cli-staging -n "not __fish_seen_subcommand_from $gemma_all_subcommands" -f -a ubic.gemma.apps.LoadSimpleExpressionDataCli --description 'Load an experiment from a tab-delimited file instead of GEO'

gemma-cli/src/main/config/fish/completions/gemma-cli.fish

@@ -57,11 +57,13 @@ complete -c gemma-cli -n '__fish_seen_subcommand_from addGEOData' -o batchReport
 complete -c gemma-cli -n "not __fish_seen_subcommand_from $gemma_all_subcommands" -f -a ubic.gemma.apps.ExpressionExperimentMetadataFileAdderCli --description 'Add a metadata file to the given experiment and record an entry in the changelog file.'
 complete -c gemma-cli -n '__fish_seen_subcommand_from ubic.gemma.apps.ExpressionExperimentMetadataFileAdderCli' -s h -l help -f --description 'Print this message'
 complete -c gemma-cli -n '__fish_seen_subcommand_from ubic.gemma.apps.ExpressionExperimentMetadataFileAdderCli' -s e -l experiment -r -a '(gemma-cli complete dataset 2>/dev/null)' -f --description 'Dataset identifier. Most tools recognize comma-delimited values given on the command line, and if this option is omitted (and none other provided), the tool will be applied to all expression experiments.'
+complete -c gemma-cli -n '__fish_seen_subcommand_from ubic.gemma.apps.ExpressionExperimentMetadataFileAdderCli' -o fileType -l file-type -r -a '(echo -e "BASE_METADATA\t\nALIGNMENT_METADATA\t\nMUTLQC_REPORT\t\nADDITIONAL_PIPELINE_CONFIGURATIONS\t" 2>/dev/null)' -F --description 'Type of metadata file to be added. Possible values are: BASE_METADATA, ALIGNMENT_METADATA, MUTLQC_REPORT, ADDITIONAL_PIPELINE_CONFIGURATIONS.'
 complete -c gemma-cli -n '__fish_seen_subcommand_from ubic.gemma.apps.ExpressionExperimentMetadataFileAdderCli' -o ce -l changelog-entry -r -f --description 'Changelog entry to be add. If not supplied, a text editor will be prompted.'
 complete -c gemma-cli -n '__fish_seen_subcommand_from ubic.gemma.apps.ExpressionExperimentMetadataFileAdderCli' -o force -l force -f --description 'Ignore other reasons for skipping entities (e.g., troubled experiments) and overwrite existing data (see documentation for this tool to see exact behavior if not clear)'
 complete -c gemma-cli -n "not __fish_seen_subcommand_from $gemma_all_subcommands" -f -a addMetadataFile --description 'Add a metadata file to the given experiment and record an entry in the changelog file.'
 complete -c gemma-cli -n '__fish_seen_subcommand_from addMetadataFile' -s h -l help -f --description 'Print this message'
 complete -c gemma-cli -n '__fish_seen_subcommand_from addMetadataFile' -s e -l experiment -r -a '(gemma-cli complete dataset 2>/dev/null)' -f --description 'Dataset identifier. Most tools recognize comma-delimited values given on the command line, and if this option is omitted (and none other provided), the tool will be applied to all expression experiments.'
+complete -c gemma-cli -n '__fish_seen_subcommand_from addMetadataFile' -o fileType -l file-type -r -a '(echo -e "BASE_METADATA\t\nALIGNMENT_METADATA\t\nMUTLQC_REPORT\t\nADDITIONAL_PIPELINE_CONFIGURATIONS\t" 2>/dev/null)' -F --description 'Type of metadata file to be added. Possible values are: BASE_METADATA, ALIGNMENT_METADATA, MUTLQC_REPORT, ADDITIONAL_PIPELINE_CONFIGURATIONS.'
 complete -c gemma-cli -n '__fish_seen_subcommand_from addMetadataFile' -o ce -l changelog-entry -r -f --description 'Changelog entry to be add. If not supplied, a text editor will be prompted.'
 complete -c gemma-cli -n '__fish_seen_subcommand_from addMetadataFile' -o force -l force -f --description 'Ignore other reasons for skipping entities (e.g., troubled experiments) and overwrite existing data (see documentation for this tool to see exact behavior if not clear)'
 complete -c gemma-cli -n "not __fish_seen_subcommand_from $gemma_all_subcommands" -f -a ubic.gemma.apps.LoadSimpleExpressionDataCli --description 'Load an experiment from a tab-delimited file instead of GEO'