Experimenting with ODK in github action

.github/workflows/buid_and_release.yml

@@ -13,19 +13,23 @@ on:
 jobs:
   build_and_release:
     runs-on: ubuntu-latest
+#    container: obolibrary/odkfull:v1.4.1
+#    container: obolibrary/odkfull:dev
+    container: obolibrary/odkfull:latest
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v2
-      with:
-        python-version: '3.10'
+#    - name: Set up Python 3.10
+#      uses: actions/setup-python@v2
+#      with:
+#        python-version: '3.10'
     - name: Install
+#        python -m pip install --upgrade pip
       run: |
-        python -m pip install --upgrade pip
         make install
     - name: Create .env file
+#      echo -en "API_KEY=${{ secrets.API_KEY }}" > .env
       run: |
-        echo -en "API_KEY=${{ secrets.API_KEY }}" > .env
+        echo "API_KEY=${{ secrets.API_KEY }}" > .env
     - name: Get current time
       uses: josStorer/[email protected]
       id: current-time
@@ -34,20 +38,30 @@ jobs:
   #      utcOffset: "+08:00"
         format: YYYY-MM-DD
     - name: build
-      run: make automated-release-artefacts -B
+#        echo pwd
+#        pwd
+#        echo -- ls before 2nd env create
+#        ls -a
+#        echo -en "API_KEY=${{ secrets.API_KEY }}" > .env
+#        echo -- ls after  2nd env create
+#        ls -a
+#        echo API KEY: ${{ secrets.API_KEY }}
+      run: |
+        make all
+
+
     - name: Release
       run: echo Uploading files as new release.
 # This one wouldn't work unless it was a tag and on-push.
 #      uses: softprops/action-gh-release@v1
-#    - name: Release
     - uses: "marvinpinto/action-automatic-releases@latest"
       with:
 # Apparently, GITHUB_TOKEN is auto-created: https://dev.to/github/the-githubtoken-in-github-actions-how-it-works-change-permissions-customizations-3cgp
 # ...even though I don't see it here: https://github.com/monarch-initiative/omim/settings/secrets/actions
         repo_token: "${{ secrets.GITHUB_TOKEN }}"
         automatic_release_tag: "${{ steps.current-time.outputs.formattedTime }}"
-#        title: "My Title"
+        title: "${{ steps.current-time.outputs.formattedTime }}"
         prerelease: false
         files: |
           omim.ttl
-#          omim.sssom.tsv
+          omim.sssom.tsv

makefile

@@ -1,4 +1,4 @@
-.PHONY: all help install test scrape get-pmids automated-release cleanup
+.PHONY: all help install test scrape get-pmids automated-release-artefacts cleanup
 
 
 # MAIN COMMANDS / GOALS ------------------------------------------------------------------------------------------------

omim2obo/config.py

@@ -1,14 +1,37 @@
+import os
 from pathlib import Path
 import yaml
 from dotenv import dotenv_values
 
 ROOT_DIR = Path(__file__).resolve().parent.parent
 DATA_DIR = ROOT_DIR / 'data'
+ENV_PATH = ROOT_DIR / '.env'
 
 with open(DATA_DIR / 'dipper/GLOBAL_TERMS.yaml') as file:
     GLOBAL_TERMS = yaml.safe_load(file)
 
 with open(DATA_DIR / 'dipper/curie_map.yaml') as file:
     CURIE_MAP = yaml.safe_load(file)
 
-config = dotenv_values(ROOT_DIR / '.env')
+config = dotenv_values(ENV_PATH)
+print('CONFIG')
+print(config)
+print('env path')
+print(ENV_PATH)
+print('ls root')
+print(os.listdir(ROOT_DIR))
+
+print('env contents')
+with open(ENV_PATH, 'r') as file:
+    lines = file.readlines()
+    for line in lines:
+        var, val = line.split('=')
+        config[var] = val
+    print(lines)
+print('CONFIG')
+print(config)
+
+# TODO: get this to work:
+print(str(config['API_KEY']))
+raise Exception('stop here')
+