version 0.1

.dockerignore

@@ -0,0 +1,17 @@
+.git/
+.github/
+.dockerignore
+Dockerfile
+
+*~
+*.DS_Store
+*.egg-info
+__pycache__
+docs/build
+.coverage
+htmlcov
+venv
+.docker
+
+.idea/
+.vscode/

.github/workflows/ci.yml

@@ -0,0 +1,160 @@
+# 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-sys_info:latest
+# - tagged commits are built as fnndsc/pl-sys_info:<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:
+    # delete the line below to enable automatic testing
+    if: false
+    runs-on: ubuntu-20.04
+    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'
+    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-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: 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,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 }}
+          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

@@ -0,0 +1,10 @@
+*~
+*.DS_Store
+*.egg-info
+__pycache__
+docs/build
+.coverage
+htmlcov
+.docker
+.idea/
+.vscode/

Dockerfile

@@ -0,0 +1,35 @@
+# Docker file for sys_info ChRIS plugin app
+#
+# Build with
+#
+#   docker build -t <name> .
+#
+# For example if building a local version, you could do:
+#
+#   docker build -t local/pl-sys_info .
+#
+# 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=$UID -t local/pl-sys_info .
+#
+# To run an interactive shell inside this container, do:
+#
+#   docker run -ti --entrypoint /bin/bash local/pl-sys_info
+#
+# To pass an env var HOST_IP to container, do:
+#
+#   docker run -ti -e HOST_IP=$(ip route | grep -v docker | awk '{if(NF==11) print $9}') --entrypoint /bin/bash local/pl-sys_info
+#
+
+FROM python:3.9.1-slim-buster
+LABEL maintainer="Sandip Samal <[email protected]>"
+
+WORKDIR /usr/local/src
+
+COPY requirements.txt .
+RUN pip install -r requirements.txt
+
+COPY . .
+RUN pip install .
+
+CMD ["sys_info", "--help"]

LICENSE

@@ -0,0 +1,21 @@
+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.rst

@@ -0,0 +1,114 @@
+pl-sys_info
+================================
+
+.. image:: https://img.shields.io/docker/v/fnndsc/pl-sys_info?sort=semver
+    :target: https://hub.docker.com/r/fnndsc/pl-sys_info
+
+.. image:: https://img.shields.io/github/license/fnndsc/pl-sys_info
+    :target: https://github.com/FNNDSC/pl-sys_info/blob/master/LICENSE
+
+.. image:: https://github.com/FNNDSC/pl-sys_info/workflows/ci/badge.svg
+    :target: https://github.com/FNNDSC/pl-sys_info/actions
+
+
+.. contents:: Table of Contents
+
+
+Abstract
+--------
+
+An app to display systen information
+
+
+Description
+-----------
+
+
+``sys_info`` is a *ChRIS ds-type* application that takes in ... as ... files
+and produces ...
+
+
+Usage
+-----
+
+.. code::
+
+    docker run --rm fnndsc/pl-sys_info sys_info
+        [-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-sys_info sys_info --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-sys_info sys_info                        \
+        /incoming /outgoing
+
+
+Development
+-----------
+
+Build the Docker container:
+
+.. code:: bash
+
+    docker build -t local/pl-sys_info .
+
+Run unit tests:
+
+.. code:: bash
+
+    docker run --rm local/pl-sys_info nosetests
+
+Examples
+--------
+
+Put some examples here!
+
+
+.. image:: https://raw.githubusercontent.com/FNNDSC/cookiecutter-chrisapp/master/doc/assets/badge/light.png
+    :target: https://chrisstore.co

requirements.txt

@@ -0,0 +1,2 @@
+chrisapp~=2.4.0
+nose~=1.3.7

setup.py

@@ -0,0 +1,27 @@
+from os import path
+from setuptools import setup
+
+with open(path.join(path.dirname(path.abspath(__file__)), 'README.rst')) as f:
+    readme = f.read()
+
+setup(
+    name             = 'sys_info',
+    version          = '0.1',
+    description      = 'An app to display systen information',
+    long_description = readme,
+    author           = 'Sandip Samal',
+    author_email     = '[email protected]',
+    url              = 'http://wiki',
+    packages         = ['sys_info'],
+    install_requires = ['chrisapp'],
+    test_suite       = 'nose.collector',
+    tests_require    = ['nose'],
+    license          = 'MIT',
+    zip_safe         = False,
+    python_requires  = '>=3.6',
+    entry_points     = {
+        'console_scripts': [
+            'sys_info = sys_info.__main__:main'
+            ]
+        }
+)