From 5539eb35446252f514998f7b6be84dfbd599daa3 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Wed, 7 Aug 2024 06:40:39 +1000 Subject: [PATCH] cleared output --- tutorial/ais-pipelines-tutorial.ipynb | 639 ++------------------------ 1 file changed, 36 insertions(+), 603 deletions(-) diff --git a/tutorial/ais-pipelines-tutorial.ipynb b/tutorial/ais-pipelines-tutorial.ipynb index 834af7f..5ea1c20 100644 --- a/tutorial/ais-pipelines-tutorial.ipynb +++ b/tutorial/ais-pipelines-tutorial.ipynb @@ -66,59 +66,10 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "id": "7de3909f", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\u001b[01;34m.\u001b[0m\n", - "├── \u001b[00mLICENSE\u001b[0m\n", - "├── \u001b[00mREADME.md\u001b[0m\n", - "├── \u001b[00mcodecov.yml\u001b[0m\n", - "├── \u001b[01;34mdocs\u001b[0m\n", - "├── \u001b[00mrequirements.txt\u001b[0m\n", - "├── \u001b[01;34mspecs\u001b[0m\n", - "│   └── \u001b[01;34maustralian-imaging-service-community\u001b[0m\n", - "│   ├── \u001b[01;34mau\u001b[0m\n", - "│   │   └── \u001b[01;34medu\u001b[0m\n", - "│   │   └── \u001b[01;34msydney\u001b[0m\n", - "│   │   └── \u001b[01;34msydneyimaging\u001b[0m\n", - "│   │   └── \u001b[00mt1_preproc.yaml\u001b[0m\n", - "│   └── \u001b[01;34mexamples\u001b[0m\n", - "│   ├── \u001b[00mbet.yaml\u001b[0m\n", - "│   └── \u001b[00mzip.yaml\u001b[0m\n", - "├── \u001b[01;34msrc\u001b[0m\n", - "│   └── \u001b[01;34mau.edu.sydney.sydneyimaging\u001b[0m\n", - "│   ├── \u001b[00mREADME.md\u001b[0m\n", - "│   ├── \u001b[01;34maustralianimagingservice\u001b[0m\n", - "│   │   └── \u001b[01;34mcommunity\u001b[0m\n", - "│   │   └── \u001b[01;34mau\u001b[0m\n", - "│   │   └── \u001b[01;34medu\u001b[0m\n", - "│   │   └── \u001b[01;34msydney\u001b[0m\n", - "│   │   └── \u001b[01;34msydneyimaging\u001b[0m\n", - "│   │   ├── \u001b[00m__init__.py\u001b[0m\n", - "│   │   ├── \u001b[00mt1_preproc.py\u001b[0m\n", - "│   │   └── \u001b[01;34mtests\u001b[0m\n", - "│   │   └── \u001b[00mtest_t1_preproc.py\u001b[0m\n", - "│   └── \u001b[00mpyproject.toml\u001b[0m\n", - "├── \u001b[01;34mtests\u001b[0m\n", - "│   ├── \u001b[00mtest_bet.py\u001b[0m\n", - "│   ├── \u001b[00mtest_build.py\u001b[0m\n", - "│   ├── \u001b[00mtest_docs.py\u001b[0m\n", - "│   └── \u001b[00mtest_zip.py\u001b[0m\n", - "└── \u001b[01;34mtutorial\u001b[0m\n", - " ├── \u001b[00mais-pipelines-tutorial.ipynb\u001b[0m\n", - " ├── \u001b[00mrequirements.txt\u001b[0m\n", - " ├── \u001b[00mstart-up-script.sh\u001b[0m\n", - " └── \u001b[00mxnat4tests-config.yaml\u001b[0m\n", - "\n", - "20 directories, 20 files\n" - ] - } - ], + "outputs": [], "source": [ "cd ~/git/pipelines-community\n", "tree . --gitignore" @@ -134,92 +85,10 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": null, "id": "7fafd93b", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "# The version of the specification format used for this file\n", - "spec_version: 1.0\n", - "# Short name for the pipeline referenced in the UI\n", - "title: \"Zips up a file or directory\"\n", - "version:\n", - " # The version of Ubuntu's zip we are using\n", - " package: \"3.0\"\n", - "base_image:\n", - " # Pick a generic base image, in this case Ubuntu - Jammy (22.04LTS)\n", - " name: ubuntu\n", - " tag: jammy\n", - "authors:\n", - " # Authors of the pipeline. The first email will be considered to be the maintainer of\n", - " # the generated container images\n", - " - name: Thomas G. Close\n", - " email: thomas.close@sydney.edu.au\n", - "docs:\n", - " # Link to the external documentation for the tool\n", - " info_url: https://manpages.ubuntu.com/manpages/focal/man1/zip.1.html\n", - " # Description for auto-generated docss\n", - " description: |\n", - " This is a simple pipeline that zips up the given directory\n", - "packages:\n", - " # Install the zip command in the Ubuntu image\n", - " system:\n", - " - zip\n", - "command:\n", - " # Use the generic \"shell-command\" task\n", - " task: pydra2app.common:shell\n", - " # the pipeline is desgined to run on imaging \"sessions\" as opposed to \"subjects\" or \"projects\"\n", - " row_frequency: session\n", - " # List the inputs that are presented to end-user in UI\n", - " inputs:\n", - " to_zip:\n", - " # MIME-type or \"MIME-like\" format, generic/fs-object corresponds a file or directory\n", - " datatype: generic/fs-object\n", - " # description of field presented in UI\n", - " help: \"Input file-system object to zip\"\n", - " # Additional config args that are passed to the shell task as part of the \"inputs\" dict\n", - " configuration:\n", - " # Position of field on command line call. Negative numbers are indexed backwards from the end\n", - " argstr: \"\"\n", - " # prefix for field when printed to command line\n", - " position: -1\n", - " # List the outputs generated by the pipeline\n", - " outputs:\n", - " zipped:\n", - " # MIME-type or \"MIME-like\" format\n", - " datatype: application/zip\n", - " # description of field presented in UI\n", - " help: Zipped file-system Object\n", - " # Additional config args that are passed to the shell task as part of the \"outputs\" dict\n", - " configuration:\n", - " # Position of field on command line call. Negative numbers are indexed backwards from the end\n", - " argstr: \"\"\n", - " # prefix for field when printed to command line\n", - " position: -2\n", - " # Parameters exposed to user to UI\n", - " parameters:\n", - " compression:\n", - " # Format of the field\n", - " datatype: field/integer\n", - " # description of field presented in UI\n", - " help: the level of compression applied\n", - " # Default value, filled in on the UI\n", - " default: 5\n", - " # Additional config args that are passed to the shell task in the \"parameters\" dict\n", - " configuration:\n", - " # string template for field when printed to command line. \"{field-name}\" are\n", - " # replaced by the value provided to the field name\n", - " argstr: -{compression}\n", - " # Additional args passed to shell\n", - " configuration:\n", - " # the command to run\n", - " executable: zip\n" - ] - } - ], + "outputs": [], "source": [ "cat specs/australian-imaging-service-community/examples/zip.yaml" ] @@ -260,27 +129,10 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "id": "fefe84fb", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "2024-08-06 18:12:25,419 - xnat4tests - INFO - Building xnat4tests in '/Users/tclose/.xnat4tests/build' directory\n", - "2024-08-06 18:14:05,134 - xnat4tests - INFO - Built xnat4tests successfully\n", - "2024-08-06 18:14:05,141 - xnat4tests - INFO - Did not find xnat4tests container, relaunching\n", - "2024-08-06 18:14:05,629 - xnat4tests - INFO - xnat4tests launched successfully\n", - "2024-08-06 18:14:05,629 - xnat4tests - INFO - Attempting to connect to http://localhost:8080\n", - "2024-08-06 18:14:05,629 - xnat4tests - INFO - Connecting to http://localhost:8080 as 'admin'\n", - "2024-08-06 18:14:10,638 - xnat4tests - INFO - Connecting to http://localhost:8080 as 'admin'\n", - "2024-08-06 18:14:15,647 - xnat4tests - INFO - Connecting to http://localhost:8080 as 'admin'\n", - "2024-08-06 18:15:45,805 - xnat4tests - INFO - Connected to http://localhost:8080 successfully\n", - "2024-08-06 18:15:45,878 - xnat4tests - INFO - Configuing docker server for container service\n" - ] - } - ], + "outputs": [], "source": [ "xnat4tests -c ~/git/pipelines-community/tutorial/xnat4tests-config.yaml start" ] @@ -297,23 +149,10 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "id": "56a8b6fb", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "2024-08-06 18:18:26,382 - xnat4tests - INFO - Connecting to http://localhost:8080 as 'admin'\n", - "2024-08-06 18:18:27,331 - xnat4tests - INFO - Connecting to http://localhost:8080 as 'admin'\n", - "2024-08-06 18:18:33,253 - xnat4tests - INFO - Connecting to http://localhost:8080 as 'admin'\n", - "2024-08-06 18:18:37,026 - xnat4tests - INFO - Connecting to http://localhost:8080 as 'admin'\n", - "2024-08-06 18:18:37,778 - xnat4tests - INFO - Connecting to http://localhost:8080 as 'admin'\n", - "2024-08-06 18:18:40,868 - xnat4tests - INFO - Connecting to http://localhost:8080 as 'admin'\n" - ] - } - ], + "outputs": [], "source": [ "xnat4tests -c ~/git/pipelines-community/tutorial/xnat4tests-config.yaml add-data simple-dir\n", "xnat4tests -c ~/git/pipelines-community/tutorial/xnat4tests-config.yaml add-data openneuro-t1w" @@ -350,7 +189,7 @@ }, { "cell_type": "code", - "execution_count": 43, + "execution_count": null, "id": "2f910886-c303-4bb8-8efb-55c8d39ea126", "metadata": {}, "outputs": [], @@ -422,91 +261,10 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": null, "id": "3a6a38f7", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Usage: pydra2app make [OPTIONS] TARGET SPEC_PATH\n", - "\n", - " Construct and build a docker image containing a pipeline to be run on data\n", - " stored in a data repository or structure (e.g. XNAT Container Service\n", - " Pipeline or BIDS App)\n", - "\n", - " TARGET is the type of image to build. For standard images just the pydra2app\n", - " sub-package is required (e.g. 'xnat' or 'common'). However, specific App\n", - " subclasses can be specified using : format,\n", - " e.g. pydra2app.xnat:XnatApp\n", - "\n", - " SPEC_PATH is the file system path to the specification to build, or\n", - " directory containing multiple specifications\n", - "\n", - "Options:\n", - " --registry TEXT The Docker registry to deploy the pipeline\n", - " to\n", - " --build-dir PATH Specify the directory to build the Docker\n", - " image in. Defaults to `.build` in the\n", - " directory containing the YAML specification\n", - " --release \n", - " Name of the release for the package as a\n", - " whole (i.e. for all pipelines)\n", - " --tag-latest / --dont-tag-latest\n", - " whether to tag the release as the \"latest\"\n", - " or not\n", - " --save-manifest PATH File path at which to save the build\n", - " manifest\n", - " --logfile PATH Log output to file instead of stdout\n", - " --loglevel TEXT The level to display logs at\n", - " --use-local-packages / --dont-use-local-packages\n", - " Use locally installed Python packages,\n", - " instead of pulling them down from PyPI\n", - " --install-extras TEXT Install extras to use when installing\n", - " Pydra2App inside the container image.\n", - " Typically only used in tests to provide\n", - " 'test' extra\n", - " --use-test-config / --dont-use-test-config\n", - " Build the image so that it can be run in\n", - " Pydra2App's test configuration (only for\n", - " internal use)\n", - " --raise-errors / --log-errors Raise exceptions instead of logging failures\n", - " --generate-only / --build Just create the build directory and\n", - " dockerfile\n", - " --license \n", - " Licenses provided at build time to be stored\n", - " in the image (instead of downloaded at\n", - " runtime)\n", - " --license-to-download TEXT Specify licenses that are not provided at\n", - " runtime and instead downloaded from the data\n", - " store at runtime in order to satisfy their\n", - " conditions\n", - " --check-registry / --dont-check-registry\n", - " Check the registry to see if an existing\n", - " image with the same tag is present, and if\n", - " so whether the specification matches (and\n", - " can be skipped) or not (raise an error)\n", - " --push / --dont-push push built images to registry\n", - " --clean-up / --dont-clean-up Remove built images after they are pushed to\n", - " the registry\n", - " --spec-root PATH The root path to consider the specs to be\n", - " relative to, defaults to CWD\n", - " -s, --source-package PATH Path to a local Python package to be\n", - " included in the image. Needs to have a\n", - " package definition that can be built into a\n", - " source distribution and the name of the\n", - " directory needs to match that of the package\n", - " to be installed. Multiple packages can be\n", - " specified by repeating the option.\n", - " -e, --export-file \n", - " Path to be exported from the Docker build\n", - " directory for convenience. Multiple files\n", - " can be specified by repeating the option.\n", - " --help Show this message and exit.\n" - ] - } - ], + "outputs": [], "source": [ "pydra2app make --help" ] @@ -527,23 +285,10 @@ }, { "cell_type": "code", - "execution_count": 18, + "execution_count": null, "id": "1d824073", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "INFO - Building sdist...\n", - "INFO - Building sdist...\n", - "INFO - Dockerfile for 'australian-imaging-service-community/examples.zip:3.0' generated at specs/australian-imaging-service-community/examples/.build-zip/Dockerfile\n", - "INFO - Successfully built docker image australian-imaging-service-community/examples.zip:3.0\n", - "australian-imaging-service-community/examples.zip:3.0\n", - "INFO - Successfully built australian-imaging-service-community/examples.zip:3.0 pipeline\n" - ] - } - ], + "outputs": [], "source": [ "pydra2app make xnat \\\n", "./specs/australian-imaging-service-community/examples/zip.yaml \\\n", @@ -568,172 +313,10 @@ }, { "cell_type": "code", - "execution_count": 19, + "execution_count": null, "id": "fa298a80", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "{\n", - " \"name\": \"examples.zip\",\n", - " \"description\": \"examples.zip 3.0: Zips up a file or directory\",\n", - " \"label\": \"examples.zip\",\n", - " \"schema-version\": \"1.0\",\n", - " \"image\": \"australian-imaging-service-community/examples.zip:3.0\",\n", - " \"index\": \"docker.io\",\n", - " \"datatype\": \"docker\",\n", - " \"override-entrypoint\": true,\n", - " \"mounts\": [\n", - " {\n", - " \"name\": \"in\",\n", - " \"writable\": false,\n", - " \"path\": \"/input\"\n", - " },\n", - " {\n", - " \"name\": \"out\",\n", - " \"writable\": true,\n", - " \"path\": \"/output\"\n", - " },\n", - " {\n", - " \"name\": \"work\",\n", - " \"writable\": true,\n", - " \"path\": \"/work\"\n", - " }\n", - " ],\n", - " \"ports\": {},\n", - " \"inputs\": [\n", - " {\n", - " \"name\": \"to_zip\",\n", - " \"description\": \"Match resource (application/x-fs-object) [SCAN-TYPE]: Input file-system object to zip \",\n", - " \"type\": \"string\",\n", - " \"default-value\": \"\",\n", - " \"required\": false,\n", - " \"user-settable\": true,\n", - " \"replacement-key\": \"[TO_ZIP_INPUT]\"\n", - " },\n", - " {\n", - " \"name\": \"compression\",\n", - " \"description\": \"Parameter (): the level of compression applied\",\n", - " \"type\": \"number\",\n", - " \"default-value\": 5,\n", - " \"required\": false,\n", - " \"user-settable\": true,\n", - " \"replacement-key\": \"[COMPRESSION_PARAM]\"\n", - " },\n", - " {\n", - " \"name\": \"Pydra2App_flags\",\n", - " \"description\": \"Flags passed to `run-pydra2app-pipeline` command\",\n", - " \"type\": \"string\",\n", - " \"default-value\": \"--plugin serial --work /wl --dataset-name default --loglevel info --export-work /work\",\n", - " \"required\": false,\n", - " \"user-settable\": true,\n", - " \"replacement-key\": \"#PYDRA2APP_FLAGS#\"\n", - " },\n", - " {\n", - " \"name\": \"PROJECT_ID\",\n", - " \"description\": \"Project ID\",\n", - " \"type\": \"string\",\n", - " \"required\": true,\n", - " \"user-settable\": false,\n", - " \"replacement-key\": \"[PROJECT_ID]\"\n", - " },\n", - " {\n", - " \"name\": \"SESSION_LABEL\",\n", - " \"description\": \"Imaging session label\",\n", - " \"type\": \"string\",\n", - " \"required\": true,\n", - " \"user-settable\": false,\n", - " \"replacement-key\": \"[SESSION_LABEL]\"\n", - " },\n", - " {\n", - " \"name\": \"SUBJECT_LABEL\",\n", - " \"description\": \"Subject label\",\n", - " \"type\": \"string\",\n", - " \"required\": true,\n", - " \"user-settable\": false,\n", - " \"replacement-key\": \"[SUBJECT_LABEL]\"\n", - " }\n", - " ],\n", - " \"outputs\": [\n", - " {\n", - " \"name\": \"zipped\",\n", - " \"description\": \"zipped (application/zip)\",\n", - " \"required\": true,\n", - " \"mount\": \"out\",\n", - " \"path\": \"zipped.zip\",\n", - " \"glob\": null\n", - " }\n", - " ],\n", - " \"xnat\": [\n", - " {\n", - " \"name\": \"examples.zip\",\n", - " \"description\": \"Zips up a file or directory\",\n", - " \"contexts\": [\n", - " \"xnat:imageSessionData\"\n", - " ],\n", - " \"external-inputs\": [\n", - " {\n", - " \"name\": \"SESSION\",\n", - " \"description\": \"Imaging session\",\n", - " \"type\": \"Session\",\n", - " \"source\": null,\n", - " \"default-value\": null,\n", - " \"required\": true,\n", - " \"replacement-key\": null,\n", - " \"sensitive\": null,\n", - " \"provides-value-for-command-input\": null,\n", - " \"provides-files-for-command-mount\": \"in\",\n", - " \"via-setup-command\": null,\n", - " \"user-settable\": false,\n", - " \"load-children\": true\n", - " }\n", - " ],\n", - " \"derived-inputs\": [\n", - " {\n", - " \"name\": \"__SESSION_LABEL__\",\n", - " \"type\": \"string\",\n", - " \"derived-from-wrapper-input\": \"SESSION\",\n", - " \"derived-from-xnat-object-property\": \"label\",\n", - " \"provides-value-for-command-input\": \"SESSION_LABEL\",\n", - " \"user-settable\": false\n", - " },\n", - " {\n", - " \"name\": \"__SUBJECT_ID__\",\n", - " \"type\": \"string\",\n", - " \"derived-from-wrapper-input\": \"SESSION\",\n", - " \"derived-from-xnat-object-property\": \"subject-id\",\n", - " \"provides-value-for-command-input\": \"SUBJECT_LABEL\",\n", - " \"user-settable\": false\n", - " },\n", - " {\n", - " \"name\": \"__PROJECT_ID__\",\n", - " \"type\": \"string\",\n", - " \"derived-from-wrapper-input\": \"SESSION\",\n", - " \"derived-from-xnat-object-property\": \"project-id\",\n", - " \"provides-value-for-command-input\": \"PROJECT_ID\",\n", - " \"user-settable\": false\n", - " }\n", - " ],\n", - " \"output-handlers\": [\n", - " {\n", - " \"name\": \"zipped-resource\",\n", - " \"accepts-command-output\": \"zipped\",\n", - " \"via-wrapup-command\": null,\n", - " \"as-a-child-of\": \"SESSION\",\n", - " \"type\": \"Resource\",\n", - " \"label\": \"zipped\",\n", - " \"format\": \"application/zip\"\n", - " }\n", - " ]\n", - " }\n", - " ],\n", - " \"command-line\": \"conda run --no-capture-output -n pydra2app pydra2app ext xnat cs-entrypoint xnat-cs//[PROJECT_ID] --input to_zip '[TO_ZIP_INPUT]' --output zipped 'zipped' --parameter compression '[COMPRESSION_PARAM]' --dataset-hierarchy subject,session --ids [SESSION_LABEL] #PYDRA2APP_FLAGS#\"\n", - "}\n" - ] - } - ], + "outputs": [], "source": [ "cat ~/zip-xnat-command.json" ] @@ -814,23 +397,10 @@ }, { "cell_type": "code", - "execution_count": 32, + "execution_count": null, "id": "03db8871", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "INFO - Building sdist...\n", - "INFO - Building sdist...\n", - "INFO - Dockerfile for 'australian-imaging-service-community/examples.bet:6.0.6.4-1' generated at specs/australian-imaging-service-community/examples/.build-bet/Dockerfile\n", - "INFO - Successfully built docker image australian-imaging-service-community/examples.bet:6.0.6.4-1\n", - "australian-imaging-service-community/examples.bet:6.0.6.4-1\n", - "INFO - Successfully built australian-imaging-service-community/examples.bet:6.0.6.4-1 pipeline\n" - ] - } - ], + "outputs": [], "source": [ "pydra2app make xnat \\\n", "./specs/australian-imaging-service-community/examples/bet.yaml \\\n", @@ -856,18 +426,10 @@ }, { "cell_type": "code", - "execution_count": 27, + "execution_count": null, "id": "7cc01126", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Saved alias/token for 'http://localhost:8080' XNAT in '/Users/tclose/.pydra2app_xnat_user_token.json' file, please ensure the file is secure\n" - ] - } - ], + "outputs": [], "source": [ "pydra2app ext xnat save-token \\\n", "--server http://localhost:8080 \\\n", @@ -877,20 +439,10 @@ }, { "cell_type": "code", - "execution_count": 37, + "execution_count": null, "id": "3c57c1fb", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Reading existing alias/token pair from '/Users/tclose/.pydra2app_xnat_user_token.json\n", - "INFO - Deleted existing command 'examples.bet'\n", - "Successfully installed the 'australian-imaging-service-community/examples.bet:6.0.6.4-1' pipeline on 'http://localhost:8080'\n" - ] - } - ], + "outputs": [], "source": [ "pydra2app ext xnat install-command \\\n", "australian-imaging-service-community/examples.bet:6.0.6.4-1 \\\n", @@ -901,19 +453,10 @@ }, { "cell_type": "code", - "execution_count": 42, + "execution_count": null, "id": "cf75564c", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Reading existing alias/token pair from '/Users/tclose/.pydra2app_xnat_user_token.json\n", - "Successfully launched the 'examples.bet' pipeline on 'subject01_MR01' session in 'OPENNEURO_T1W' project on 'http://localhost:8080'\n" - ] - } - ], + "outputs": [], "source": [ "pydra2app ext xnat launch-command \\\n", "examples.bet \\\n", @@ -968,28 +511,10 @@ }, { "cell_type": "code", - "execution_count": 28, + "execution_count": null, "id": "17b98c06", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Usage: pydra2app [OPTIONS] COMMAND [ARGS]...\n", - "Try 'pydra2app --help' for help.\n", - "\n", - "Error: No such command 'bootstrap'.\n", - "bash: --base-image-name: command not found\n" - ] - }, - { - "ename": "", - "evalue": "127", - "output_type": "error", - "traceback": [] - } - ], + "outputs": [], "source": [ "export INSTITUTION_NAME=\"name-of-your-institution-goes-here\" # e.g. \"sydney\" for The University of Sydney\n", "export GROUP_NAME=\"name-of-your-group-goes-here\" # e.g. \"sydneyimaging\" for Sydney Imaging\n", @@ -1023,24 +548,10 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": null, "id": "e0451e1a", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "bash: name-of-your-institution-goes-here: No such file or directory\n" - ] - }, - { - "ename": "", - "evalue": "1", - "output_type": "error", - "traceback": [] - } - ], + "outputs": [], "source": [ "cat ./specs/australian-image-service-community/au/edu/${INSITUTION_NAME}/${GROUP_NAME}/mri_convert.yaml" ] @@ -1063,24 +574,10 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": null, "id": "d6d655fd", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "bash: name-of-your-institution-goes-here: No such file or directory\n" - ] - }, - { - "ename": "", - "evalue": "1", - "output_type": "error", - "traceback": [] - } - ], + "outputs": [], "source": [ "pydra2app make xnat \\\n", "./specs/australian-image-service-community/au/edu/${INSITUTION_NAME}/${GROUP_NAME}/mri_convert.yaml \\\n", @@ -1102,54 +599,10 @@ }, { "cell_type": "code", - "execution_count": 22, + "execution_count": null, "id": "1af18b4b", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Traceback (most recent call last):\n", - " File \"/Users/tclose/.pyenv/versions/frametree-test/bin/frametree\", line 8, in \n", - " sys.exit(cli())\n", - " ^^^^^\n", - " File \"/Users/tclose/.pyenv/versions/3.11.8/envs/frametree-test/lib/python3.11/site-packages/click/core.py\", line 1157, in __call__\n", - " return self.main(*args, **kwargs)\n", - " ^^^^^^^^^^^^^^^^^^^^^^^^^^\n", - " File \"/Users/tclose/.pyenv/versions/3.11.8/envs/frametree-test/lib/python3.11/site-packages/click/core.py\", line 1078, in main\n", - " rv = self.invoke(ctx)\n", - " ^^^^^^^^^^^^^^^^\n", - " File \"/Users/tclose/.pyenv/versions/3.11.8/envs/frametree-test/lib/python3.11/site-packages/click/core.py\", line 1688, in invoke\n", - " return _process_result(sub_ctx.command.invoke(sub_ctx))\n", - " ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n", - " File \"/Users/tclose/.pyenv/versions/3.11.8/envs/frametree-test/lib/python3.11/site-packages/click/core.py\", line 1688, in invoke\n", - " return _process_result(sub_ctx.command.invoke(sub_ctx))\n", - " ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n", - " File \"/Users/tclose/.pyenv/versions/3.11.8/envs/frametree-test/lib/python3.11/site-packages/click/core.py\", line 1434, in invoke\n", - " return ctx.invoke(self.callback, **ctx.params)\n", - " ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n", - " File \"/Users/tclose/.pyenv/versions/3.11.8/envs/frametree-test/lib/python3.11/site-packages/click/core.py\", line 783, in invoke\n", - " return __callback(*args, **kwargs)\n", - " ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n", - " File \"/Users/tclose/git/workflows/frametree/frametree/core/cli/store.py\", line 84, in add\n", - " store_cls = ClassResolver(DataStore)(type)\n", - " ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n", - " File \"/Users/tclose/git/workflows/frametree/frametree/core/serialize.py\", line 86, in __call__\n", - " klass = self.fromstr(class_str, subpkg=True, pkg=self.package)\n", - " ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n", - " File \"/Users/tclose/git/workflows/frametree/frametree/core/serialize.py\", line 135, in fromstr\n", - " raise ValueError(\n", - "ValueError: Class location 'test-xnat' should contain a ':' unless it is in the builtins module\n" - ] - }, - { - "ename": "", - "evalue": "1", - "output_type": "error", - "traceback": [] - } - ], + "outputs": [], "source": [ "frametree store add xnat test-xnat --server http://localhost:8080 --user admin --password admin" ] @@ -1164,7 +617,7 @@ }, { "cell_type": "code", - "execution_count": 23, + "execution_count": null, "id": "93fcea4c", "metadata": {}, "outputs": [], @@ -1182,21 +635,10 @@ }, { "cell_type": "code", - "execution_count": 25, + "execution_count": null, "id": "50108c2d", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\u001b[38;2;0;255;0m100%\u001b[39m of 1.8 KiB |################################| 3.2 MiB/s Time: 0:00:00\n", - "/var/folders/mz/yn83q2fd3s758w1j75d2nnw80000gn/T/tmpfsd1l7oi/OPENNEURO_T1W/resources/__frametree__/files/_.json\n", - "INFO:frametree:Put freesurfer_LICENSE@ into dataset:None row via API access\n", - "INFO:frametree.core.cli.dataset:Successfully installed 'freesurfer' license for '' dataset on test-xnat store\n" - ] - } - ], + "outputs": [], "source": [ "frametree dataset install-license freesurfer ~/freesurfer-license.txt test-xnat//OPENNEURO_T1W" ] @@ -1257,19 +699,10 @@ }, { "cell_type": "code", - "execution_count": 44, + "execution_count": null, "id": "686d7741-a77e-43da-b175-237f3ba9bef5", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[detached HEAD e6aff42] added specification for Freesurfer's mri_convert\n", - " 1 file changed, 32 insertions(+), 7 deletions(-)\n" - ] - } - ], + "outputs": [], "source": [ "git commit -am\"added specification for Freesurfer's mri_convert\"\n", "git push"