first commit

.dockerignore

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+.git/
+.github/
+.dockerignore
+Dockerfile
+
+*~
+*.DS_Store
+*.egg-info
+__pycache__
+docs/build
+.coverage
+htmlcov
+venv
+.docker
+
+.idea/
+.vscode/

.github/workflows/ci.yml

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+# Automatically build multi-architectural tagged container images and push them to DockerHub
+# https://github.com/FNNDSC/cookiecutter-chrisapp/wiki/Automatic-Builds
+#
+# - targeted platforms: x86_64, PowerPC64, ARM64
+# - master is built as fnndsc/pl-markimg:latest
+# - tagged commits are built as fnndsc/pl-markimg:<tag>
+# - tagged commits are also uploaded to chrisstore.co
+#
+# In order to use this workflow, see
+# https://github.com/FNNDSC/cookiecutter-chrisapp/wiki/Automatic-Builds#steps-to-enable
+
+name: ci
+
+on:
+  push:
+    # we have to guess what the name of the default branch is
+    branches: [ master, main, trunk ]
+    tags: [ '**' ]
+  pull_request:
+    branches: [ master, main, trunk ]
+
+jobs:
+  test: 
+    if: false 
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v2
+      - name: build
+        run: docker build -t "${GITHUB_REPOSITORY,,}" .
+      - name: nose tests
+        run: docker run "${GITHUB_REPOSITORY,,}" nosetests
+
+  publish: 
+    if: github.event_name == 'push' || github.event_name == 'release' # 1. delete this line
+    runs-on: ubuntu-24.04
+
+    # we want to both push the build to DockerHub, but also
+    # keep a local copy so that we can run
+    #
+    #     docker run fnndsc/pl-app app --json > App.json
+    #
+    # buildx currently does not support multiple output locations,
+    # neither can multi-architectural builds be loaded into docker.
+    # Here we use a local registry to cache the build.
+    services:
+      registry:
+        image: registry:2
+        ports:
+          - 5000:5000
+
+    steps:
+      - name: Get git tag
+        id: git_info
+        if: startsWith(github.ref, 'refs/tags/')
+        run: echo "::set-output name=tag::${GITHUB_REF##*/}"
+      - name: Decide image tag name
+        id: determine
+        env:
+          git_tag: ${{ steps.git_info.outputs.tag }}
+        run: |
+          repo="${GITHUB_REPOSITORY,,}"  # to lower case
+          # if build triggered by tag, use tag name
+          tag="${git_tag:-latest}"
+          dock_image=$repo:$tag
+          echo $dock_image
+          echo "::set-output name=dock_image::$dock_image"
+          echo "::set-output name=repo::$repo"
+
+      - uses: actions/checkout@v2
+
+      # QEMU is for emulating non-x86_64 platforms
+      - uses: docker/setup-qemu-action@v1
+      # buildx is the next-generation docker image builder
+      - uses: docker/setup-buildx-action@v1
+        with:
+          driver-opts: network=host
+      # save some time during rebuilds
+      - name: Cache Docker layers
+        uses: actions/cache@v2
+        with:
+          path: /tmp/.buildx-cache
+          key: ${{ runner.os }}-buildx-${{ github.sha }}
+          restore-keys: |
+            ${{ runner.os }}-buildx-
+
+      - name: Login to DockerHub
+        id: dockerhub_login
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PASSWORD }}
+
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v1
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build and push
+        uses: docker/build-push-action@v2
+        id: docker_build
+        with:
+          context: .
+          file: ./Dockerfile
+          tags: |
+            ${{ steps.determine.outputs.dock_image }}
+            localhost:5000/${{ steps.determine.outputs.dock_image }}
+            ghcr.io/${{ steps.determine.outputs.dock_image }}
+          platforms: linux/amd64,linux/ppc64le,linux/arm64
+          push: true
+          cache-from: type=local,src=/tmp/.buildx-cache
+          cache-to: type=local,dest=/tmp/.buildx-cache
+
+      - name: Get plugin meta
+        id: pluginmeta
+        run: |
+          repo=${{ steps.determine.outputs.repo }}
+          dock_image=${{ steps.determine.outputs.dock_image }}
+          plname="$(sed 's/^.*\///' <<< $GITHUB_REPOSITORY)" && echo "name=$plname"
+          docker pull localhost:5000/$dock_image
+          docker tag localhost:5000/$dock_image $dock_image
+          script=$(docker inspect --format '{{ (index .Config.Cmd 0) }}' $dock_image)
+          docker run --rm $dock_image $script --json \
+            | jq '. += {"name":"'$plname'", "dock_image": "'$dock_image'", "public_repo": "'${{ github.server_url }}/${{ github.repository }}'" }' \
+            > /tmp/description.json
+          json="$(docker run --rm $dock_image $script --json)"
+          # Escape single quotes
+          json_escaped=$(echo "$json" | sed "s/'/\\'/g")
+
+          jq <<< "$json"  # pretty print in log
+          echo "json=$json_escaped" >> $GITHUB_OUTPUT
+          echo "title=$(jq -r '.title' <<< "$json")" >> $GITHUB_OUTPUT
+
+      - name: Update DockerHub description
+        uses: peter-evans/dockerhub-description@v2
+        continue-on-error: true  # it is not crucial that this works
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PASSWORD }}
+          short-description: ${{ steps.pluginmeta.outputs.title }}
+          readme-filepath: ./README.rst
+          repository: ${{ steps.determine.outputs.repo }}
+
+      - name: Upload ChRIS Plugin
+        id: upload
+        if: github.ref_type == 'tag'
+        uses: FNNDSC/upload-chris-plugin@main
+        with:
+          description_file: /tmp/description.json
+          username: ${{ secrets.CHRISPROJECT_USERNAME }}
+          password: ${{ secrets.CHRISPROJECT_PASSWORD }}
+          chris_url: https://cube.chrisproject.org/api/v1/
+          compute_names: NERC

.gitignore

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+*~
+*.DS_Store
+*.egg-info
+__pycache__
+docs/build
+.coverage
+htmlcov
+.docker
+.idea/
+.vscode/

Dockerfile

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+# Docker file for cookie_taste ChRIS plugin app
+#
+# Build with
+#
+#   docker build -t <name> .
+#
+# For example if building a local version, you could do:
+#
+#   docker build -t local/pl-cookie_taste .
+#
+# In the case of a proxy (located at 192.168.13.14:3128), do:
+#
+#    docker build --build-arg http_proxy=http://192.168.13.14:3128 --build-arg UID=$UID -t local/pl-cookie_taste .
+#
+# To run an interactive shell inside this container, do:
+#
+#   docker run -ti --entrypoint /bin/bash local/pl-cookie_taste
+#
+# To pass an env var HOST_IP to container, do:
+#
+#   docker run -ti -e HOST_IP=$(ip route | grep -v docker | awk '{if(NF==11) print $9}') --entrypoint /bin/bash local/pl-cookie_taste
+#
+
+FROM python:3.9.1-slim-buster
+LABEL maintainer="FNNDSC <[email protected]>"
+
+WORKDIR /usr/local/src
+
+COPY requirements.txt .
+RUN pip install -r requirements.txt
+
+COPY . .
+RUN pip install .
+
+CMD ["cookie_taste", "--help"]

LICENSE

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+MIT License
+
+Copyright (c) 2024 FNNDSC / BCH
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.rst

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+pl-cookie_taste
+================================
+
+.. image:: https://img.shields.io/docker/v/fnndsc/pl-cookie_taste?sort=semver
+    :target: https://hub.docker.com/r/fnndsc/pl-cookie_taste
+
+.. image:: https://img.shields.io/github/license/fnndsc/pl-cookie_taste
+    :target: https://github.com/FNNDSC/pl-cookie_taste/blob/master/LICENSE
+
+.. image:: https://github.com/FNNDSC/pl-cookie_taste/workflows/ci/badge.svg
+    :target: https://github.com/FNNDSC/pl-cookie_taste/actions
+
+
+.. contents:: Table of Contents
+
+
+Abstract
+--------
+
+A simple plugin to demonstrate a working plugin from cookiecutter-chrisapp
+
+
+Description
+-----------
+
+
+``cookie_taste`` is a *ChRIS fs-type* application that produces ... by ...
+
+
+Usage
+-----
+
+.. code::
+
+    docker run --rm fnndsc/pl-cookie_taste cookie_taste
+        [-h|--help]
+        [--json] [--man] [--meta]
+        [--savejson <DIR>]
+        [-v|--verbosity <level>]
+        [--version]
+        <inputDir> <outputDir>
+
+
+Arguments
+~~~~~~~~~
+
+.. code::
+
+    [-h] [--help]
+    If specified, show help message and exit.
+    
+    [--json]
+    If specified, show json representation of app and exit.
+    
+    [--man]
+    If specified, print (this) man page and exit.
+
+    [--meta]
+    If specified, print plugin meta data and exit.
+    
+    [--savejson <DIR>] 
+    If specified, save json representation file to DIR and exit. 
+    
+    [-v <level>] [--verbosity <level>]
+    Verbosity level for app. Not used currently.
+    
+    [--version]
+    If specified, print version number and exit. 
+
+
+Getting inline help is:
+
+.. code:: bash
+
+    docker run --rm fnndsc/pl-cookie_taste cookie_taste --man
+
+Run
+~~~
+
+You need to specify input and output directories using the `-v` flag to `docker run`.
+
+
+.. code:: bash
+
+    docker run --rm -u $(id -u)                             \
+        -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing      \
+        fnndsc/pl-cookie_taste cookie_taste                        \
+        /incoming /outgoing
+
+
+Development
+-----------
+
+Build the Docker container:
+
+.. code:: bash
+
+    docker build -t local/pl-cookie_taste .
+
+Run unit tests:
+
+.. code:: bash
+
+    docker run --rm local/pl-cookie_taste nosetests
+
+Examples
+--------
+
+Put some examples here!
+
+
+.. image:: https://raw.githubusercontent.com/FNNDSC/cookiecutter-chrisapp/master/doc/assets/badge/light.png
+    :target: https://chrisstore.co

cookie_taste/__main__.py

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+from cookie_taste.cookie_taste import Cookie_taste
+
+
+def main():
+    chris_app = Cookie_taste()
+    chris_app.launch()
+
+
+if __name__ == "__main__":
+    main()