Merge pull request #206 from uc-cdis/feat/stata-base-update

HP-1776 Feat/stata base update
uc-cdis · Jan 6, 2025 · 016ffbb · 016ffbb
2 parents 441ddf1 + f53a1b7
commit 016ffbb
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Showing 17 changed files with 125 additions and 136 deletions.
diff --git a/.github/workflows/build_push_stata_gen3_licensed.yml b/.github/workflows/build_push_stata_gen3_licensed.yml
@@ -11,59 +11,41 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - name: Maximize build space
-        uses: easimon/maximize-build-space@master
+      - uses: actions/checkout@v4
+      - uses: prewk/s3-cp-action@v2
         with:
-          root-reserve-mb: 30000
-          swap-size-mb: 1024
-          remove-dotnet: 'true'
-          remove-android: 'true'
-          remove-haskell: 'true'
-      - uses: actions/checkout@v2
-      - uses: prewk/[email protected]
-        env:
-          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
-          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
-          SOURCE: 's3://ctds-stata/Stata17Linux64.tar.gz'
-          DEST: './jupyter-pystata-gen3-licensed/resources/'
+          aws_access_key_id: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          aws_secret_access_key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          source: 's3://ctds-stata/StataNow18Linux64.tar.gz'
+          dest: './jupyter-pystata-gen3-licensed/resources/'
 
       - name: Extract branch name
-        shell: bash
-        run: echo "branch=$(echo $(echo ${GITHUB_REF#refs/*/} | tr / _))" >> $GITHUB_OUTPUT
         id: extract_branch
-
-      - name: Determine image to build
-        id: parse_image
-        shell: python
         run: |
-          import os
-
-          build_target = "jupyter-pystata-licensed"
-          print(f"Will trigger build for: {build_target}")
-          with open(os.environ['GITHUB_OUTPUT'], 'a') as fh:
-            print(f'build_target={build_target}', file=fh)
+          echo "IMAGE_TAG=$(echo ${GITHUB_REF#refs/*/} | tr / _)"
+          echo "IMAGE_TAG=$(echo ${GITHUB_REF#refs/*/} | tr / _)" >> $GITHUB_ENV
 
-      - if: ${{ steps.parse_image.outputs.build_target }}
-        name: Sanitize image name
-        id: sanitize_name
-        run: |
-          IMAGE_NAME=$( sed 's/[^[:alnum:]]/_/g' <<< ${{ steps.parse_image.outputs.build_target }} );
-          echo "image_name=$IMAGE_NAME" >> $GITHUB_OUTPUT
+      - name: Login to Quay.io
+        id: login
+        uses: docker/login-action@v3
+        with:
+          registry: quay.io
+          username: ${{ secrets.QUAY_USERNAME }}
+          password: ${{ secrets.QUAY_ROBOT_TOKEN }}
 
-      - name: Build Image
-        id: build-image
-        uses: redhat-actions/buildah-build@v2
+      - name: Extract metadata
+        id: meta
+        uses: docker/metadata-action@v5
         with:
-          image: jupyter-pystata-gen3-licensed
-          tags: ${{ steps.extract_branch.outputs.branch }}
-          dockerfiles: ./jupyter-pystata-gen3-licensed/Dockerfile
+          images: |
+            quay.io/cdis/jupyter-pystata-gen3-licensed:${{ env.IMAGE_TAG }}
 
-      - name: Push To quay.io
-        id: push-to-quay
-        uses: redhat-actions/push-to-registry@v2
+      - name: Build and Push Image
+        uses: docker/build-push-action@v6
         with:
-          image: ${{ steps.build-image.outputs.image }}
-          tags: ${{ steps.build-image.outputs.tags }}
-          registry: quay.io/cdis
-          username: ${{ secrets.QUAY_SERVICE_ACCOUNT_USER }}
-          password: ${{ secrets.QUAY_SERVICE_ACCOUNT_PASSWORD }}
+          context: ./jupyter-pystata-gen3-licensed
+          file: "./jupyter-pystata-gen3-licensed/Dockerfile"
+          push: true
+          tags: |
+            quay.io/cdis/jupyter-pystata-gen3-licensed:${{ env.IMAGE_TAG }}
+          labels: ${{ steps.meta.outputs.labels }}
diff --git a/.github/workflows/build_push_stata_user_licensed.yml b/.github/workflows/build_push_stata_user_licensed.yml
@@ -11,41 +11,41 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - name: Maximize build space
-        uses: easimon/maximize-build-space@master
+      - uses: actions/checkout@v4
+      - uses: prewk/s3-cp-action@v2
         with:
-          root-reserve-mb: 30000
-          swap-size-mb: 1024
-          remove-dotnet: 'true'
-          remove-android: 'true'
-          remove-haskell: 'true'
-      - uses: actions/checkout@v2
-      - uses: prewk/[email protected]
-        env:
-          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
-          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
-          SOURCE: 's3://ctds-stata/Stata17Linux64.tar.gz'
-          DEST: './jupyter-pystata-user-licensed/resources/'
+          aws_access_key_id: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          aws_secret_access_key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          source: 's3://ctds-stata/StataNow18Linux64.tar.gz'
+          dest: './jupyter-pystata-user-licensed/resources/'
 
       - name: Extract branch name
-        shell: bash
-        run: echo "::set-output name=branch::$(echo $(echo ${GITHUB_REF#refs/*/} | tr / _))"
         id: extract_branch
+        run: |
+          echo "IMAGE_TAG=$(echo ${GITHUB_REF#refs/*/} | tr / _)"
+          echo "IMAGE_TAG=$(echo ${GITHUB_REF#refs/*/} | tr / _)" >> $GITHUB_ENV
 
-      - name: Build Image
-        id: build-image
-        uses: redhat-actions/buildah-build@v2
+      - name: Login to Quay.io
+        id: login
+        uses: docker/login-action@v3
         with:
-          image: jupyter-pystata-user-licensed
-          tags: ${{ steps.extract_branch.outputs.branch }}
-          dockerfiles: ./jupyter-pystata-user-licensed/Dockerfile
+          registry: quay.io
+          username: ${{ secrets.QUAY_USERNAME }}
+          password: ${{ secrets.QUAY_ROBOT_TOKEN }}
 
-      - name: Push To quay.io
-        id: push-to-quay
-        uses: redhat-actions/push-to-registry@v2
+      - name: Extract metadata
+        id: meta
+        uses: docker/metadata-action@v5
         with:
-          image: ${{ steps.build-image.outputs.image }}
-          tags: ${{ steps.build-image.outputs.tags }}
-          registry: quay.io/cdis
-          username: ${{ secrets.QUAY_SERVICE_ACCOUNT_USER }}
-          password: ${{ secrets.QUAY_SERVICE_ACCOUNT_PASSWORD }}
+          images: |
+            quay.io/cdis/jupyter-pystata-user-licensed:${{ env.IMAGE_TAG }}
+
+      - name: Build and Push Image
+        uses: docker/build-push-action@v6
+        with:
+          context: ./jupyter-pystata-user-licensed
+          file: "./jupyter-pystata-user-licensed/Dockerfile"
+          push: true
+          tags: |
+            quay.io/cdis/jupyter-pystata-user-licensed:${{ env.IMAGE_TAG }}
+          labels: ${{ steps.meta.outputs.labels }}
diff --git a/.gitignore b/.gitignore
@@ -1 +1,2 @@
 .vscode/*
+.DS_store
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,12 +1,12 @@
 repos:
 -   repo: [email protected]:Yelp/detect-secrets
-    rev: v1.4.0
+    rev: v1.5.0
     hooks:
     -   id: detect-secrets
         args: ['--baseline', '.secrets.baseline']
         exclude: .lock
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.5.0
+    rev: v4.6.0
     hooks:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer

diff --git a/.secrets.baseline b/.secrets.baseline
@@ -1,5 +1,5 @@
 {
-  "version": "1.4.0",
+  "version": "1.5.0",
   "plugins_used": [
     {
       "name": "ArtifactoryDetector"

diff --git a/jupyter-pystata-gen3-licensed/.gitignore b/jupyter-pystata-gen3-licensed/.gitignore
@@ -1 +1,3 @@
 Stata17Linux64.tar.gz
+StataNow18Linux64.tar.gz
+stata.lic
diff --git a/jupyter-pystata-gen3-licensed/Dockerfile b/jupyter-pystata-gen3-licensed/Dockerfile
@@ -1,23 +1,25 @@
-FROM quay.io/cdis/jupyter-pystata-user-licensed:1.2.1
+FROM quay.io/cdis/jupyter-pystata-user-licensed:feat_stata-base-update
 
 USER root
 RUN apt-get update
 RUN apt-get install -y firefox
-RUN wget https://github.com/mozilla/geckodriver/releases/download/v0.34.0/geckodriver-v0.34.0-linux64.tar.gz
+RUN wget https://github.com/mozilla/geckodriver/releases/download/v0.35.0/geckodriver-v0.35.0-linux64.tar.gz
 RUN tar -xvzf geckodriver*
 RUN mv geckodriver /bin/
 
-COPY jupyter-pystata-gen3-licensed/resources/wait_for_license.sh /tmp/
-COPY jupyter-pystata-gen3-licensed/resources/setup_licensed_notebook.py /tmp/
+COPY ./resources/wait_for_license.sh /tmp/
+COPY ./resources/setup_licensed_notebook.py /tmp/
 RUN chmod 777 /tmp/wait_for_license.sh /tmp/setup_licensed_notebook.py
 
+COPY ./resources/licensed_stata_session.ipynb $HOME
+RUN chown $NB_USER $HOME/licensed_stata_session.ipynb
+
 USER $NB_USER
 RUN pip3 install selenium
 
-# Pin stata_setup to avoid error on splash parameter
 RUN pip3 uninstall --yes stata-setup
-RUN pip3 install stata-setup==0.1.2
+RUN pip3 install stata-setup
+
 
 # Remove the notebook created in jupyter-pystata-user-licensed
 RUN rm $HOME/Stata.ipynb
-COPY jupyter-pystata-gen3-licensed/resources/licensed_stata_session.ipynb $HOME
diff --git a/jupyter-pystata-gen3-licensed/README.md b/jupyter-pystata-gen3-licensed/README.md
@@ -56,15 +56,15 @@ kubectl get secret stata-workspace-gen3-license-g3auto
 
 To build, enter the root directory of this repo and run:
 ```
-docker build -t stata-licensed -f jupyter-pystata-gen3-licensed/Dockerfile .
+docker build -t stata-licensed -f jupyter-pystata-gen3-licensed/Dockerfile ./jupyter-pystata-gen3-licensed
 
-docker run --name stata-licensed -p 8888:8888 stata-licensed /tmp/wait_for_license.sh --NotebookApp.base_url=/lw-workspace/proxy/ --NotebookApp.password='' --NotebookApp.token=''
+docker run --name stata-licensed -p 8888:8888 stata-licensed /tmp/wait_for_license.sh --JupyterNotebookApp.base_url=/lw-workspace/proxy/ --JupyterNotebookApp.password='' --JupyterNotebookApp.token=''
 ```
 
-(You will need a local copy of `Stata17Linux64.tar.gz`.)
+(You will need a local copy of `StataNow18Linux64.tar.gz`.)
 
 Then, with your license `stata.lic`,
 
 ```
-docker cp stata.lic stata-licensed:/usr/local/stata17/stata.lic
+docker cp stata.lic stata-licensed:/usr/local/stata18/stata.lic
 ```
diff --git a/jupyter-pystata-gen3-licensed/resources/licensed_stata_session.ipynb b/jupyter-pystata-gen3-licensed/resources/licensed_stata_session.ipynb
@@ -2,6 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
+   "metadata": {},
    "source": [
     "## Licensed STATA Notebook Workspace\n",
     "This notebook runs a licensed STATA MP session, managed by the Gen3 platform.\n",
@@ -11,38 +12,37 @@
     "Because licenses are protected and limited, this workspace is limited to a single running STATA session, which has already been initialized via the cell below.\n",
     "\n",
     "Users who have an existing STATA license are encouraged to bring it to a self-supplied STATA workspace."
-   ],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "import stata_setup\n",
-    "stata_setup.config(\"/usr/local/stata17\", \"mp\")"
-   ],
-   "outputs": [],
-   "metadata": {}
+    "stata_setup.config(\"/usr/local/stata18\", \"mp\")"
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "%%stata\n",
     ". describe"
-   ],
-   "outputs": [],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "%%mata\n",
     "sqrt(4)"
-   ],
-   "outputs": [],
-   "metadata": {}
+   ]
   }
  ],
  "metadata": {

diff --git a/jupyter-pystata-gen3-licensed/resources/setup_licensed_notebook.py b/jupyter-pystata-gen3-licensed/resources/setup_licensed_notebook.py
@@ -11,15 +11,16 @@
 browser = webdriver.Firefox(options=opts)
 
 print("Checking for .lic file")
-with open("/usr/local/stata17/stata.lic", "r") as lic_file:
+with open("/usr/local/stata18/stata.lic", "r", encoding="utf-8") as lic_file:
     print("Found stata.lic file")
 
 print("Ready to open notebook")
 browser.get("http://127.0.0.1:8888/lw-workspace/proxy/notebooks/licensed_stata_session.ipynb")
 print("Notebook is opened")
 
 actions = ActionChains(browser)
-actions.pause(5)
+actions.pause(10)
+actions.perform()
 
 # Down-arrow to get to the second cell in the notebook
 actions.send_keys(Keys.DOWN)
@@ -31,14 +32,15 @@
 actions.key_down(Keys.SHIFT)
 actions.send_keys(Keys.ENTER)
 actions.key_up(Keys.SHIFT)
-actions.perform()
 actions.pause(5)
+actions.perform()
 
 # Save notebook with output
 print("Ready to save notebook")
 actions.key_down(Keys.CONTROL)
 actions.send_keys("S")
 actions.key_up(Keys.CONTROL)
-actions.pause(1)
+actions.pause(5)
+actions.perform()
 actions.send_keys(Keys.ENTER)
 actions.perform()
diff --git a/jupyter-pystata-gen3-licensed/resources/wait_for_license.sh b/jupyter-pystata-gen3-licensed/resources/wait_for_license.sh
@@ -2,13 +2,13 @@
 
 echo "Checking for license copied by sidecar"
 
-while [ ! -f /usr/local/stata17/stata.lic ];
+while [ ! -f /usr/local/stata18/stata.lic ];
 do
     sleep 5
     echo "Checking for license"
     if [ -f /data/stata.lic ]; then
         echo "Found license"
-        mv /data/stata.lic /usr/local/stata17/stata.lic
+        mv /data/stata.lic /usr/local/stata18/stata.lic
         echo "Copied license"
     fi
 done
@@ -25,6 +25,6 @@ python3 /tmp/setup_licensed_notebook.py
 rm geckodriver*
 
 echo "Init script done."
-rm /usr/local/stata17/stata.lic
+rm /usr/local/stata18/stata.lic
 
 while true; do sleep 1; done
diff --git a/jupyter-pystata-user-licensed/.gitignore b/jupyter-pystata-user-licensed/.gitignore
@@ -1 +1,3 @@
 Stata17Linux64.tar.gz
+StataNow18Linux64.tar.gz
+stata.lic