diff --git a/Dockerfile b/Dockerfile index 7622250..54a69f2 100644 --- a/Dockerfile +++ b/Dockerfile @@ -12,4 +12,4 @@ COPY run.py ./ ENTRYPOINT [ "python", "./run.py" ] CMD ["--help"] -LABEL org.nrg.commands="[{\"name\": \"pixi-bli-image-splitter\", \"label\": \"pixi-bli-image-splitter\", \"description\": \"Split multi-subject BLI image sessions into single subject image sessions\", \"version\": \"0.1.0-SNAPSHOT\", \"schema-version\": \"1.0\", \"info-url\": \"https://github.com/preclinical-imaging/pixi-bli-split\", \"type\": \"docker\", \"working-directory\": \"/usr/src/app\", \"command-line\": \"python run.py /input/SCANS /output #LOG_LEVEL# -x \$XNAT_HOST -u \$XNAT_USER -p \$XNAT_PASS #PROJECT# #EXPERIMENT#\", \"override-entrypoint\": true, \"mounts\": [{\"name\": \"input-mount\", \"writable\": false, \"path\": \"/input\"}, {\"name\": \"output-mount\", \"writable\": true, \"path\": \"/output\"}], \"inputs\": [{\"name\": \"project\", \"description\": \"XNAT Project ID\", \"type\": \"string\", \"required\": true, \"replacement-key\": \"#PROJECT#\", \"command-line-flag\": \"--project\"}, {\"name\": \"experiment\", \"description\": \"XNAT Experiment Label\", \"type\": \"string\", \"required\": true, \"replacement-key\": \"#EXPERIMENT#\", \"command-line-flag\": \"--experiment\"}, {\"name\": \"log-level\", \"description\": \"Log Level\", \"type\": \"select\", \"required\": false, \"default-value\": \"DEBUG\", \"replacement-key\": \"#LOG_LEVEL#\", \"command-line-flag\": \"--log-level\", \"user-settable\": true, \"select-values\": [\"INFO\", \"DEBUG\"]}], \"outputs\": [], \"xnat\": [{\"name\": \"bli-hotel-session-splitter\", \"label\": \"BLI Hotel Session Splitter\", \"description\": \"Split BLI hotel image sessions into single subject image sessions\", \"contexts\": [\"pixi:bliSessionData\"], \"external-inputs\": [{\"name\": \"image-session\", \"description\": \"BLI hotel session input\", \"type\": \"Session\", \"required\": true, \"provides-files-for-command-mount\": \"input-mount\", \"load-children\": true}], \"derived-inputs\": [{\"name\": \"project-id\", \"description\": \"XNAT Project ID\", \"type\": \"string\", \"required\": true, \"provides-value-for-command-input\": \"project\", \"load-children\": false, \"derived-from-wrapper-input\": \"image-session\", \"derived-from-xnat-object-property\": \"project-id\", \"multiple\": false}, {\"name\": \"session-label\", \"description\": \"XNAT Image Session Label\", \"type\": \"string\", \"required\": true, \"provides-value-for-command-input\": \"experiment\", \"user-settable\": true, \"load-children\": false, \"derived-from-wrapper-input\": \"image-session\", \"derived-from-xnat-object-property\": \"label\", \"multiple\": false}], \"output-handlers\": []}, {\"name\": \"bli-scan-record-splitter\", \"label\": \"BLI Scan Record Splitter\", \"description\": \"Split BLI hotel image sessions into single subject image sessions based on scan record inputs\", \"contexts\": [\"pixi:hotelScanRecord\"], \"external-inputs\": [{\"name\": \"scan-record\", \"description\": \"Hotel scan record input\", \"type\": \"ProjectAsset\", \"required\": true, \"load-children\": true}], \"derived-inputs\": [{\"name\": \"session-label\", \"description\": \"XNAT Image Session Label\", \"type\": \"string\", \"required\": true, \"provides-value-for-command-input\": \"experiment\", \"load-children\": true, \"derived-from-wrapper-input\": \"scan-record\", \"derived-from-xnat-object-property\": \"datatype-string\", \"parser\": \"/XFTItem/session_label[1]\"}, {\"name\": \"project\", \"description\": \"XNAT Project\", \"type\": \"Project\", \"required\": true, \"load-children\": true, \"derived-from-wrapper-input\": \"scan-record\"}, {\"name\": \"project-id\", \"description\": \"XNAT Project ID\", \"type\": \"string\", \"required\": true, \"provides-value-for-command-input\": \"project\", \"load-children\": true, \"derived-from-wrapper-input\": \"project\", \"derived-from-xnat-object-property\": \"id\"}, {\"name\": \"subject\", \"label\": null, \"description\": \"Subject\", \"type\": \"Subject\", \"matcher\": \"'#EXPERIMENT#' in @.sessions[*].label\", \"required\": true, \"load-children\": true, \"derived-from-wrapper-input\": \"project\"}, {\"name\": \"session\", \"description\": \"Session\", \"type\": \"Session\", \"matcher\": \"@.label == '#EXPERIMENT#'\", \"required\": true, \"provides-files-for-command-mount\": \"input-mount\", \"derived-from-wrapper-input\": \"subject\"}], \"output-handlers\": []}]}]" +LABEL org.nrg.commands="[{\"name\": \"pixi-bli-image-splitter\", \"label\": \"pixi-bli-image-splitter\", \"description\": \"Split multi-subject BLI image sessions into single subject image sessions\", \"version\": \"0.1.0-SNAPSHOT\", \"schema-version\": \"1.0\", \"info-url\": \"https://github.com/preclinical-imaging/pixi-bli-split\", \"type\": \"docker\", \"working-directory\": \"/usr/src/app\", \"command-line\": \"python run.py /input/SCANS /output #LOG_LEVEL# -x \$XNAT_HOST -u \$XNAT_USER -p \$XNAT_PASS #PROJECT# #EXPERIMENT#\", \"override-entrypoint\": true, \"mounts\": [{\"name\": \"input-mount\", \"writable\": false, \"path\": \"/input\"}, {\"name\": \"output-mount\", \"writable\": true, \"path\": \"/output\"}], \"inputs\": [{\"name\": \"project\", \"description\": \"XNAT Project ID\", \"type\": \"string\", \"required\": true, \"replacement-key\": \"#PROJECT#\", \"command-line-flag\": \"--project\"}, {\"name\": \"experiment\", \"description\": \"XNAT Experiment Label\", \"type\": \"string\", \"required\": true, \"replacement-key\": \"#EXPERIMENT#\", \"command-line-flag\": \"--experiment\"}, {\"name\": \"log-level\", \"description\": \"Log Level\", \"type\": \"select-one\", \"required\": false, \"default-value\": \"DEBUG\", \"replacement-key\": \"#LOG_LEVEL#\", \"command-line-flag\": \"--log-level\", \"user-settable\": true, \"select-values\": [\"INFO\", \"DEBUG\"]}], \"outputs\": [], \"xnat\": [{\"name\": \"bli-hotel-session-splitter\", \"label\": \"BLI Hotel Session Splitter\", \"description\": \"Split BLI hotel image sessions into single subject image sessions\", \"contexts\": [\"pixi:bliSessionData\"], \"external-inputs\": [{\"name\": \"image-session\", \"description\": \"BLI hotel session input\", \"type\": \"Session\", \"required\": true, \"provides-files-for-command-mount\": \"input-mount\", \"load-children\": true}], \"derived-inputs\": [{\"name\": \"project-id\", \"description\": \"XNAT Project ID\", \"type\": \"string\", \"required\": true, \"provides-value-for-command-input\": \"project\", \"load-children\": false, \"derived-from-wrapper-input\": \"image-session\", \"derived-from-xnat-object-property\": \"project-id\", \"multiple\": false}, {\"name\": \"session-label\", \"description\": \"XNAT Image Session Label\", \"type\": \"string\", \"required\": true, \"provides-value-for-command-input\": \"experiment\", \"user-settable\": true, \"load-children\": false, \"derived-from-wrapper-input\": \"image-session\", \"derived-from-xnat-object-property\": \"label\", \"multiple\": false}], \"output-handlers\": []}, {\"name\": \"bli-scan-record-splitter\", \"label\": \"BLI Scan Record Splitter\", \"description\": \"Split BLI hotel image sessions into single subject image sessions based on scan record inputs\", \"contexts\": [\"pixi:hotelScanRecord\"], \"external-inputs\": [{\"name\": \"scan-record\", \"description\": \"Hotel scan record input\", \"type\": \"ProjectAsset\", \"required\": true, \"load-children\": true}], \"derived-inputs\": [{\"name\": \"session-label\", \"description\": \"XNAT Image Session Label\", \"type\": \"string\", \"required\": true, \"provides-value-for-command-input\": \"experiment\", \"load-children\": true, \"derived-from-wrapper-input\": \"scan-record\", \"derived-from-xnat-object-property\": \"datatype-string\", \"parser\": \"/XFTItem/session_label[1]\"}, {\"name\": \"project\", \"description\": \"XNAT Project\", \"type\": \"Project\", \"required\": true, \"load-children\": true, \"derived-from-wrapper-input\": \"scan-record\"}, {\"name\": \"project-id\", \"description\": \"XNAT Project ID\", \"type\": \"string\", \"required\": true, \"provides-value-for-command-input\": \"project\", \"load-children\": true, \"derived-from-wrapper-input\": \"project\", \"derived-from-xnat-object-property\": \"id\"}, {\"name\": \"subject\", \"label\": null, \"description\": \"Subject\", \"type\": \"Subject\", \"matcher\": \"'#EXPERIMENT#' in @.sessions[*].label\", \"required\": true, \"load-children\": true, \"derived-from-wrapper-input\": \"project\"}, {\"name\": \"session\", \"description\": \"Session\", \"type\": \"Session\", \"matcher\": \"@.label == '#EXPERIMENT#'\", \"required\": true, \"provides-files-for-command-mount\": \"input-mount\", \"derived-from-wrapper-input\": \"subject\"}], \"output-handlers\": []}]}]" diff --git a/command.json b/command.json index aef092e..a0b8627 100644 --- a/command.json +++ b/command.json @@ -41,7 +41,7 @@ { "name": "log-level", "description": "Log Level", - "type": "select", + "type": "select-one", "required": false, "default-value": "DEBUG", "replacement-key": "#LOG_LEVEL#",