🌂

.dockerignore

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

.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-office-convert:latest
+# - tagged commits are built as fnndsc/pl-office-convert:<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:
+    branches: [ master ]
+    tags: [ '**' ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  test:
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v2
+      - name: Build
+        run: docker build -t pl-office-convert .
+      - name: Run example
+        id: run_example
+        run: |
+          test_output=$(mktemp -d)
+          docker run --rm \
+            -v $GITHUB_WORKSPACE/examples/incoming:/incoming:ro \
+            -v $test_output:/outgoing:rw \
+            pl-office-convert /incoming /outgoing
+          echo "::set-output name=output_dir::test_output"
+      - name: Assert outputs
+        run: diff -rq '${{ github.workspace }}/examples/incoming' '${{ steps.run_example.outputs.output_dir }}'
+
+  publish:
+    if: github.event_name == 'push' || github.event_name == 'release'
+    runs-on: ubuntu-20.04
+
+    # we want to both push the build to DockerHub, but also
+    # keep a local copy so that we can run
+    #
+    #     docker run fnndsc/pl-office-convert office_convert --json > OfficeConvert.json
+    #
+    # buildx currently does not support multiple output locations,
+    # neither can multi-architectural builds be loaded into docker.
+    # Here we use a local registry to cache the build.
+    services:
+      registry:
+        image: registry:2
+        ports:
+          - 5000:5000
+
+    steps:
+      - name: Get git tag
+        id: git_info
+        if: startsWith(github.ref, 'refs/tags/')
+        run: echo "::set-output name=tag::${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: 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 }}
+          platforms: linux/amd64
+          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 }}
+          docker pull localhost:5000/$dock_image
+          docker tag localhost:5000/$dock_image $dock_image
+          script=$(docker inspect --format '{{ (index .Config.Cmd 0) }}' $dock_image)
+          json="$(docker run --rm $dock_image $script --json)"
+          jq <<< "$json"  # pretty print in log
+
+          echo "::set-output name=json::$json"
+          echo "::set-output name=title::$(jq -r '.title' <<< "$json")"
+
+      - 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: ${{ steps.determine.outputs.repo }}
+
+      - name: Upload to ChRIS Store
+        if: "!endsWith(steps.determine.outputs.dock_image, ':latest')"
+        run: |
+          dock_image=${{ steps.determine.outputs.dock_image }}
+          plname="$(sed 's/^.*\///' <<< $GITHUB_REPOSITORY)" && echo "name=$plname"
+          descriptor_file=$(mktemp --suffix .json)
+          cat > $descriptor_file << ENDOFPLUGINJSONDESCRIPTION
+          ${{ steps.pluginmeta.outputs.json }}
+          ENDOFPLUGINJSONDESCRIPTION
+          res=$(
+            curl -s -u "${{ secrets.CHRIS_STORE_USER }}" "https://chrisstore.co/api/v1/plugins/" \
+              -H 'Accept:application/vnd.collection+json' \
+              -F "name=$plname" \
+              -F "dock_image=$dock_image"  \
+              -F "descriptor_file=@$descriptor_file" \
+              -F "public_repo=https://github.com/${{ github.repository }}"
+          )
+          success=$?
+          echo "::debug::$res"
+          if [ "$success" = "0" ]; then
+            href="$(jq -r '.collection.items[0].href' <<< "$res")"
+            echo $href
+            echo "::set-output name=pluginurl::$href"
+          else
+            echo "::error ::Failed upload to ChRIS Store"
+            echo "$res"
+            exit $success
+          fi

.gitignore

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

Dockerfile

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+FROM docker.io/python:3.9.1-slim-buster
+
+LABEL org.opencontainers.image.authors="FNNDSC <[email protected]>" \
+      org.opencontainers.image.title="Office File Converter" \
+      org.opencontainers.image.description="Convert Excel and ODS spreadsheets to plaintext CSV files."
+
+WORKDIR /usr/local/src
+
+COPY requirements.txt .
+RUN pip install -r requirements.txt
+
+COPY . .
+RUN pip install .
+
+CMD ["office_convert", "--help"]

LICENSE

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+MIT License
+
+Copyright (c) 2021 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.md

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+# Excel and ODS Spreadsheet to CSV Converter
+
+[![Version](https://img.shields.io/docker/v/fnndsc/pl-office-convert?sort=semver)](https://hub.docker.com/r/fnndsc/pl-office-convert)
+[![MIT License](https://img.shields.io/github/license/fnndsc/pl-office-convert)](https://github.com/FNNDSC/pl-office-convert/blob/master/LICENSE)
+[![Build](https://github.com/FNNDSC/pl-office-convert/actions/workflows/ci.yml/badge.svg)](https://github.com/FNNDSC/pl-office-convert/actions)
+
+`pl-office-convert` is a _ChRIS ds_ plugin which converts Excel and OpenOffice spreadsheet file
+formats (`*.{xls,xlsx,ods}`) to the plaintext comma-separated values (`*.csv`) format.
+
+## Usage
+
+In `pl-office-convert` version 0.0.1 there are no options.
+Every file in `inputdir/` ending with `.ods`, `.xlsx`, or `.xls` gets processed and written to
+`outputdir/` by the same filename but with its file extension replaced with `.csv`.
+Every other file in `inputdir/` is simply duplicated to `outputdir/`.
+
+WARNING: only the first sheet of every file is converted!
+
+```shell
+singularity exec docker://docker.io/fnndsc/pl-office-convert:0.0.1 office_convert incoming/ outgoing/
+```
+
+## Planned Features
+
+This plugin will eventually be a generic office format converter, being able to convert both ways from
+office file format to plaintext and vice versa. But for now it is a simple single-purpose program.

examples/outgoing/menu.csv

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+food,price
+pizza,3.0
+fries,2.5

examples/outgoing/nonsense.csv

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+hello,how,are,you?
+5,blue,arch,grape
+6,red,fedora,cherry
+7,green,debian,kiwi
+8,purple,solus,tomato

examples/wack/menu.csv

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+mmmfood,price
+pizza,3.0
+fries,2.5

examples/wack/nonsense.csv

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+hello,how,are,you?
+5,blue,arch,grape
+6,red,fedora,cherry
+7,green,debian,kiwi
+8,purple,solus,tomato

office_convert/__main__.py

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+from office_convert.app import OfficeFileConverter
+import logging
+
+
+def main():
+    logging.basicConfig()
+    chris_app = OfficeFileConverter()
+    chris_app.launch()
+
+
+if __name__ == "__main__":
+    main()