initial commit

.cookiecutterrc

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+# This file exists so you can easily regenerate your project.
+#
+# `cookiepatcher` is a convenient shim around `cookiecutter`
+# for regenerating projects (it will generate a .cookiecutterrc
+# automatically for any template). To use it:
+#
+#    pip install cookiepatcher
+#    cookiepatcher gh:itisfoundation/cookiecutter-osparc-service project-path
+#
+# See:
+#    https://pypi.python.org/pypi/cookiepatcher
+#
+# Alternatively, you can run:
+#
+#    cookiecutter --overwrite-if-exists --config-file=project-path/.cookiecutterrc gh:itisfoundation/cookiecutter-osparc-service
+#
+
+default_context:
+
+    _checkout:                 None
+    _output_dir:               '/home/ordonez/osparc_projects/cookiecutter-osparc-service'
+    _repo_dir:                 '.'
+    _template:                 '.'
+    author_affiliation:        'ZMT ZurichMedTech AG'
+    author_email:              '[email protected]'
+    author_name:               'Javier Garcia Ordonez'
+    contact_email:             '[email protected]'
+    default_docker_registry:   'itisfoundation'
+    docker_base:               'alpine:3.8'
+    git_repo:                  'github'
+    git_username:              'JavierGOrdonnez'
+    number_of_inputs:          '4'
+    number_of_outputs:         '4'
+    project_name:              'Medical Image Processing - Computational Service'
+    project_package_name:      'comp-medimproc'
+    project_short_description: 'Medical Image Processing - Computational Service'
+    project_slug:              'comp-medimproc'
+    project_type:              'computational'
+    release_date:              '2024'
+    version:                   '0.1.0'
+    version_display:           '0.1.0'

.dockerignore

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+## Common.dockerignore
+
+*
+!src/
+!service.cli/
+!docker/
+!.osparc/
+
+# Common
+README.md
+CHANGELOG.md
+docker-compose.yml
+Dockerfile
+
+# git
+.git
+.gitattributes
+.gitignore
+.git*
+
+## Common.gitignore
+
+# output folders
+build/
+output/
+out/
+
+# temporary folders
+tmp/
+
+# explicit mark
+*ignore*
+.tmp*
+
+# vscode configuration
+.vscode
+
+# make outputs
+pytest_*.xml
+.compose*
+
+# validation folder
+!validation/**/*
+# docker ignore
+!.dockerignore
+# git ignore
+!.gitignore

.github/dockerhub_login.bash

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+#!/bin/bash
+# http://redsymbol.net/articles/unofficial-bash-strict-mode/
+set -euo pipefail
+IFS=$'\n\t'
+
+# check needed variables are defined
+if [ ! -v DOCKER_USERNAME ] ||\
+    [ ! -v DOCKER_PASSWORD ] ||\
+    [ ! -v DOCKER_REGISTRY ]; then
+    echo "## ERROR: Please define the environs (DOCKER_USERNAME, DOCKER_PASSWORD, DOCKER_REGISTRY) in your CI settings!"
+    exit 1
+fi
+
+# check script needed variables
+if [ ! -v OWNER ]; then
+    echo "## ERROR: incorrect usage of CI. OWNER (e.g. dockerhub organization like itisfoundation or user private name) not defined!"
+    exit 1
+fi
+
+# only upstream is allowed to push to itisfoundation repo
+if [ "${OWNER,,}" != "itisfoundation" ] &&\
+    { [ ! -v DOCKER_REGISTRY ] || [ -z "${DOCKER_REGISTRY}" ] || [ "$DOCKER_REGISTRY" = "itisfoundation" ]; }; then
+    echo "## ERROR: it is not allowed to push to the main dockerhub repository from a fork!"
+    echo "## Please adapt your CI-defined environs (DOCKER_USERNAME, DOCKER_PASSWORD, DOCKER_REGISTRY)"
+    exit 1
+fi
+
+# these variable must be available securely from the CI
+echo "$DOCKER_PASSWORD" | docker login -u "$DOCKER_USERNAME" --password-stdin
+
+echo "logged into dockerhub successfully, ready to push"
+exit 0

.github/show_system_versions.bash

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+#!/bin/bash
+# http://redsymbol.net/articles/unofficial-bash-strict-mode/
+set -euo pipefail
+IFS=$'\n\t'
+
+echo "------------------------------ environs -----------------------------------"
+env
+
+echo "------------------------------ uname -----------------------------------"
+uname -a
+lsb_release -a
+
+echo "------------------------------ python -----------------------------------"
+if command -v python; then
+    python --version
+fi
+
+echo "------------------------------ python3 -----------------------------------"
+if command -v python3; then
+    python3 --version
+fi
+
+echo "------------------------------ docker -----------------------------------"
+if command -v docker; then
+    docker version
+fi
+
+echo "------------------------------ docker-compose -----------------------------------"
+if command -v docker-compose; then
+    docker-compose version
+fi

.github/workflows/build-test-publish.yml

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+name: Github-CI Push/PR comp-medimproc
+
+on:
+  push:
+  pull_request:
+
+env:
+  # secrets can be set in settings/secrets on github
+  DOCKER_REGISTRY: ${{ secrets.DOCKER_REGISTRY }}
+  DOCKER_USERNAME: ${{ secrets.DOCKER_USERNAME }}
+  DOCKER_PASSWORD: ${{ secrets.DOCKER_PASSWORD }}
+
+jobs:
+  build:
+    name: building comp-medimproc
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python: [3.9]
+        os: [ubuntu-22.04]
+      fail-fast: false
+    steps:
+      - uses: actions/checkout@v3
+      - name: setup python environment
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python }}
+      - name: show versions
+        run: ./.github/show_system_versions.bash
+      - name: set owner variable
+        run: echo "OWNER=${GITHUB_REPOSITORY%/*}" >> $GITHUB_ENV
+      - name: set docker image tag
+        if: github.ref != 'refs/heads/master'
+        run: echo "DOCKER_IMAGE_TAG=${GITHUB_REF##*/}" >> $GITHUB_ENV
+      - name: get current image if available
+        run: make pull-latest || true
+      - name: build
+        run: |
+          make VERSION
+          make build
+          make info-build
+      - name: test
+        run: make tests
+      # - if: github.event_name == 'push' && github.ref == 'refs/heads/master'
+      #   name: push
+      #   run: |
+      #     ./.github/dockerhub_login.bash
+      #     make push
+      # - if: github.event_name == 'push' && github.ref != 'refs/heads/master'
+      #   name: push
+      #   run: |
+      #     ./.github/dockerhub_login.bash
+      #     make push-version

.github/workflows/check-image.yml

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+name: Build and check image
+
+on: [push, pull_request]
+
+jobs:
+  verify-image-build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo content
+        uses: actions/checkout@v2
+      - name: ooil version
+        uses: docker://itisfoundation/ci-service-integration-library:v1.0.4
+        with:
+          args: ooil --version
+      - name: Assemble docker compose spec
+        uses: docker://itisfoundation/ci-service-integration-library:v1.0.4
+        with:
+          args: ooil compose
+      - name: Build all images if multiple
+        uses: docker://itisfoundation/ci-service-integration-library:v1.0.4
+        with:
+          args: docker compose build
+      - name: test
+        run: make tests

.gitignore

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+## Common.gitignore
+
+# output folders
+build/
+output/
+out/
+
+# temporary folders
+tmp/
+
+# explicit mark
+*ignore*
+.tmp*
+
+# vscode configuration
+.vscode
+
+# make outputs
+pytest_*.xml
+.compose*
+
+# validation folder
+!validation/**/*
+# docker ignore
+!.dockerignore
+# git ignore
+!.gitignore

.osparc/docker-compose.overwrite.yml

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+version: "3.7"
+services:
+  comp-medimproc:
+    build:
+      dockerfile: docker/alpine/Dockerfile
+      target: production

.osparc/metadata.yml

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+name: Medical Image Processing - Computational Service
+key: simcore/services/comp/comp-medimproc
+type: computational
+integration-version: 2.0.0
+version: 0.1.0
+description: Medical Image Processing - Computational Service
+contact: [email protected]
+thumbnail: https://github.com/ITISFoundation/osparc-assets/blob/cb43207b6be2f4311c93cd963538d5718b41a023/assets/default-thumbnail-cookiecutter-osparc-service.png?raw=true
+authors:
+  - name: Javier Garcia Ordonez
+    email: [email protected]
+    affiliation: ZMT ZurichMedTech AG
+inputs:
+  input_1:
+    displayOrder: 1
+    label: input_1_label
+    description: The input 1 description
+    type: string
+    defaultValue: some_value(optional)
+    fileToKeyMap:
+      somefilename.ext: input_1
+  input_2:
+    displayOrder: 2
+    label: input_2_label
+    description: The input 2 description
+    type: string
+    defaultValue: some_value(optional)
+    fileToKeyMap:
+      somefilename.ext: input_2
+  input_3:
+    displayOrder: 3
+    label: input_3_label
+    description: The input 3 description
+    type: string
+    defaultValue: some_value(optional)
+    fileToKeyMap:
+      somefilename.ext: input_3
+  input_4:
+    displayOrder: 4
+    label: input_4_label
+    description: The input 4 description
+    type: string
+    defaultValue: some_value(optional)
+    fileToKeyMap:
+      somefilename.ext: input_4
+
+outputs:
+  output_1:
+    displayOrder: 1
+    label: output_1_label
+    description: The input 1 description
+    type: string
+    fileToKeyMap:
+      somefilename.ext: output_1
+  output_2:
+    displayOrder: 2
+    label: output_2_label
+    description: The input 2 description
+    type: string
+    fileToKeyMap:
+      somefilename.ext: output_2
+  output_3:
+    displayOrder: 3
+    label: output_3_label
+    description: The input 3 description
+    type: string
+    fileToKeyMap:
+      somefilename.ext: output_3
+  output_4:
+    displayOrder: 4
+    label: output_4_label
+    description: The input 4 description
+    type: string
+    fileToKeyMap:
+      somefilename.ext: output_4
+

.osparc/runtime.yml

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+restart-policy: no-restart
+settings:
+  - name: Resources
+    type: Resources
+    value:
+      Limits:
+        NanoCPUs: 1000000000 # 100% of CPU cycles on 1 CPU 
+        MemoryBytes: 2147483648 # 2 Gigabytes
+