Initial commit

.dockerignore

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+renv/library/
+renv/local/
+renv/lock/
+renv/python/
+renv/staging/
+
+test
+tests
+workflow_tests

.github/workflows/ci.yaml

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+name: CI Workflow
+
+on:
+  push:
+    branches: ['main']
+
+# Defines two custom environment variables for the workflow. These are used for the Container registry domain, and a name for the Docker image that this workflow builds.
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+# There is a single job in this workflow. It's configured to run on the latest available version of Ubuntu.
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    # Sets the permissions granted to the `GITHUB_TOKEN` for the actions in this job.
+    permissions:
+      contents: read
+      packages: write
+      attestations: write
+      id-token: write
+      #
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      # Uses the `docker/login-action` action to log in to the Container registry registry using the account and password that will publish the packages. Once published, the packages are scoped to the account defined here.
+      - name: Log in to the Container registry
+        uses: docker/[email protected]
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      # This step uses [docker/metadata-action](https://github.com/docker/metadata-action#about) to extract tags and labels that will be applied to the specified image. The `id` "meta" allows the output of this step to be referenced in a subsequent step. The `images` value provides the base name for the tags and labels.
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/[email protected]
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+      # This step uses the `docker/build-push-action` action to build the image, based on your repository's `Dockerfile`. If the build succeeds, it pushes the image to GitHub Packages.
+      # It uses the `context` parameter to define the build's context as the set of files located in the specified path. For more information, see "[Usage](https://github.com/docker/build-push-action#usage)" in the README of the `docker/build-push-action` repository.
+      # It uses the `tags` and `labels` parameters to tag and label the image with the output from the "meta" step.
+      - name: Build and push Docker image
+        id: push
+        uses: docker/[email protected]
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          # A PAT is needed for this action, GITHUB_TOKEN cannot get relevant permission 
+          # secrets: |
+            # github_pat=${{ secrets.GH_PAT }}

.github/workflows/release.yaml

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+name:  Release Workflow
+
+on:
+  push:
+    tags:
+      - '[0-9]+.[0-9]+.[0-9]+' # Push events to any matching semantic tag. For example, 1.10.1 or 2.0.0.
+
+# Defines two custom environment variables for the workflow. These are used for the Container registry domain, and a name for the Docker image that this workflow builds.
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+# There is a single job in this workflow. It's configured to run on the latest available version of Ubuntu.
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    # Sets the permissions granted to the `GITHUB_TOKEN` for the actions in this job.
+    permissions:
+      contents: write
+      packages: write
+      attestations: write
+      id-token: write
+      #
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Update container in operator JSON
+        run: |
+          jq --arg variable "${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${GITHUB_REF##*/}" '.container = $variable' operator.json
+      # Uses the `docker/login-action` action to log in to the Container registry registry using the account and password that will publish the packages. Once published, the packages are scoped to the account defined here.
+      - name: Log in to the Container registry
+        uses: docker/[email protected]
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      # This step uses [docker/metadata-action](https://github.com/docker/metadata-action#about) to extract tags and labels that will be applied to the specified image. The `id` "meta" allows the output of this step to be referenced in a subsequent step. The `images` value provides the base name for the tags and labels.
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/[email protected]
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          tags: |
+            # minimal
+            type=pep440,pattern={{version}}
+      # This step uses the `docker/build-push-action` action to build the image, based on your repository's `Dockerfile`. If the build succeeds, it pushes the image to GitHub Packages.
+      # It uses the `context` parameter to define the build's context as the set of files located in the specified path. For more information, see "[Usage](https://github.com/docker/build-push-action#usage)" in the README of the `docker/build-push-action` repository.
+      # It uses the `tags` and `labels` parameters to tag and label the image with the output from the "meta" step.
+      - name: Build and push Docker image
+        id: push
+        uses: docker/[email protected]
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          # A PAT is needed for this action, GITHUB_TOKEN cannot get relevant permission 
+          # secrets: |
+            # github_pat=${{ secrets.GH_PAT }}
+      - name: Create required package.json
+        run: echo '{}' > package.json
+      - name: Build changelog
+        id: Changelog
+        uses: tercen/generate-changelog-action@master
+      - name: Create release
+        id: create_release
+        uses: actions/create-release@latest
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # This token is provided by Actions, you do not need to create your own token
+        with:
+          tag_name: ${{ github.ref }}
+          release_name: Release ${{ github.ref }}
+          body: ${{steps.Changelog.outputs.changelog}}
+          draft: false
+          prerelease: false

.gitignore

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+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+.idea
+venv/*

.vscode/extensions.json

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+{
+    "recommendations": ["ms-python.python", "ms-toolsai.jupyter"]
+}

.vscode/launch.json

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+{
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python: Current File",
+            "type": "python",
+            "python": "/config/.pyenv/versions/3.9.0/bin/python",
+            "request": "launch",
+            "program": "${file}",
+            "console": "integratedTerminal",
+            "justMyCode": true,
+            "env": { "PYTHONPATH": "${workspaceRoot}"}
+
+        }
+    ]
+}

Dockerfile

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+FROM tercen/runtime-python39:0.1.0
+
+COPY . /operator
+WORKDIR /operator
+
+ENV PYTHONPATH "${PYTHONPATH}:~/.pyenv/versions/3.9.0/bin/python3"
+RUN python3 -m pip install -r ./requirements.txt
+
+ENV TERCEN_SERVICE_URI https://tercen.com
+
+ENTRYPOINT ["python3", "main.py"]
+CMD ["--taskId", "someid", "--serviceUri", "https://tercen.com", "--token", "sometoken"]

README.md

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+
+# Template Python Operator
+
+Cell-wise mean calculated implemented in Python.
+
+## Python operator - Development workflow
+
+* Set up [the Tercen Studio development environment](https://github.com/tercen/tercen_studio)
+* Create a new git repository based on the [template Python operator](https://github.com/tercen/template-python-operator)
+* Open VS Code Server by going to: http://127.0.0.1:8443
+* Clone this repository into VS Code (using the 'Clone from GitHub' command from the Command Palette for example)
+* Load the environment and install core requirements by running the following commands in the terminal:
+
+```bash
+source /config/.pyenv/versions/3.9.0/bin/activate
+pip install -r requirements.txt
+```
+
+* Develop your operator. Note that you can interact with an existing data step by specifying arguments to the `TercenContext` function:
+
+```python
+tercenCtx = ctx.TercenContext()
+```
+
+```python
+tercenCtx = ctx.TercenContext(
+    workflowId="YOUR_WORKFLOW_ID",
+    stepId="YOUR_STEP_ID",
+    username="admin", # if using the local Tercen instance
+    password="admin", # if using the local Tercen instance
+    serviceUri = "http://tercen:5400/" # if using the local Tercen instance 
+)
+```
+
+* Generate requirements
+
+```bash
+python3 -m tercen.util.requirements . > requirements.txt
+```
+
+* Push your changes to GitHub: triggers CI GH workflow
+* Tag the repository: triggers Release GH workflow
+* Go to tercen and install your operator
+
+
+## Helpful Commands
+
+### Install Tercen Python Client
+
+```bash
+python3 -m pip install --force git+https://github.com/tercen/[email protected]
+```
+
+### Wheel
+
+Though not strictly mandatory, many packages require it.
+
+```bash
+python3 -m pip install wheel
+```
+

main.py

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+from tercen.client import context as ctx
+import numpy as np
+
+tercenCtx = ctx.TercenContext()
+
+df = (
+    tercenCtx
+    .select(['.y', '.ci', '.ri'], df_lib="pandas")
+    .groupby(['.ci','.ri'], as_index=False)
+    .mean()
+    .rename(columns={".y":"mean"})
+    .astype({".ci": np.int32, ".ri": np.int32})
+)
+
+df = tercenCtx.add_namespace(df) 
+tercenCtx.save(df)

operator.json

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+{
+    "name": "Template Python operator",
+    "description": "Mean operator implemented in Python",
+    "tags": ["template"],
+    "authors": ["tercen"],
+    "urls": ["https://github.com/tercen/template-python-operator"],
+    "container":"ghcr.io/tercen/template-python-operator:latest",
+    "properties": [
+        {
+            "kind": "DoubleProperty",
+            "name": "Property1",
+            "defaultValue": 42.0,
+            "description": "Example Double Property"
+        },
+        {
+            "kind": "StringProperty",
+            "name": "Property2",
+            "defaultValue": "42",
+            "description": "Example String Property"
+        },
+        {
+            "kind": "BooleanProperty",
+            "name": "Property3",
+            "defaultValue": true,
+            "description": "Example Boolean Property"
+        },
+        {
+            "kind": "EnumeratedProperty",
+            "isSingleSelection":true,
+            "name": "Property4",
+            "defaultValue": "element2",
+            "values": ["element1", "element2", "element3"],
+            "description": "Example Enumerated Property"
+        }
+    ]
+}

requirements.txt

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+git+https://github.com/tercen/[email protected]

tests/Table_1.csv

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+".ci",".ri","ds0.mean"
+0,0,20728.444444444445
+0,1,21271.853658536584
+0,3,20552.3153638814
+1,0,20162.29411764706
+1,1,16876.354166666668
+1,2,7086.0
+1,3,19007.806094182826
+2,0,18338.166666666668
+2,1,5464.103896103896
+2,2,2256.0841121495328
+2,3,5343.584082156611
+3,0,21081.26595744681
+3,1,14656.041958041958
+3,2,6559.210526315789
+3,3,16740.50725416443

tests/Table_2.csv

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+"Rating.Imaging"
+"Above"
+"Below"
+"None"
+"Same"

tests/Table_3.csv

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+"Rating.Effectiveness"
+"Above"
+"Below"
+"None"
+"Same"