update publish wf

bioimage-io · May 23, 2024 · 437691c · 437691c
1 parent 93130d6
commit 437691c
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Showing 3 changed files with 18 additions and 39 deletions.
diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
@@ -51,22 +51,18 @@ jobs:
     needs: generate-initial-collection-json
     uses: bioimage-io/collection/.github/workflows/stage_call.yaml@main
     with:
-      resource_id: 'frank-water-buffalo'
+      concept_id: 'frank-water-buffalo'
       package_url: 'https://uk1s3.embassy.ebi.ac.uk/public-datasets/examples.bioimage.io/frank-water-buffalo_v1.zip'
       environment_name: testing
-    secrets: inherit
+      secrets: inherit
 
   test-publish:
     needs: test-stage
     uses: bioimage-io/collection/.github/workflows/publish_call.yaml@main
     with:
-      resource_id: ${{vars.TEST_PACKAGE_ID}} # testing!
-      stage_number: 1
+      concept_id: 'frank-water-buffalo'
       reviewer: 'github|${{github.actor_id}}'
-      S3_HOST: ${{vars.S3_HOST}}
-      S3_BUCKET: ${{vars.S3_TEST_BUCKET}} # testing!
-      S3_FOLDER: ${{vars.S3_TEST_FOLDER}}/ci # testing!
-      REVIEWERS: ${{vars.REVIEWERS}}
+      environment_name: testing
     secrets: inherit
 
   test-generate-collection-json:

diff --git a/.github/workflows/publish.yaml b/.github/workflows/publish.yaml
@@ -31,12 +31,7 @@
 #   call:
 #     uses: bioimage-io/collection/.github/workflows/publish_call.yaml@main
 #     with:
-#       resource_id: ${{inputs.resource_id}}
-#       stage_number: ${{fromJson(inputs.stage_number)}}  # wo 'fromJson' the number is given as string, see https://github.com/orgs/community/discussions/67182
+#       concept_id: ${{inputs.resource_id}}
 #       reviewer: ${{inputs.reviewer == 'auto detect' && format('github|{0}', github.actor_id) || inputs.reviewer}}
-#       S3_HOST: ${{vars.S3_HOST}}
-#       S3_BUCKET: ${{vars.S3_BUCKET}}
-#       S3_FOLDER: ${{inputs.sandbox && vars.S3_SANDBOX_FOLDER || vars.S3_FOLDER}}
-#       REVIEWERS: ${{vars.REVIEWERS}}
-
+#       environment_name: ${{inputs.sandbox && vars.S3_SANDBOX_FOLDER || vars.S3_FOLDER}}
 #     secrets: inherit
diff --git a/.github/workflows/publish_call.yaml b/.github/workflows/publish_call.yaml
@@ -3,46 +3,30 @@ name: publish call
 on:
   workflow_call:
     inputs:
-      resource_id:
-        description: "Bioimageio ID of the resource - to be used to access the resource on S3"
+      concept_id:
+        description: "Bioimageio resource concept"
         required: true
         type: string
-      stage_number:
-        description: stage number to publish
-        required: true
-        type: number
       reviewer:
         description: GitHub user id (prefixed with 'github|') of the bioimage.io maintainer accepting this resource version
         required: false
         default: 'github|${{github.actor_id}}'
         type: string
-      S3_HOST:
-        required: true
-        type: string
-      S3_BUCKET:
+      environment_name:
         required: true
         type: string
-      S3_FOLDER:
-        required: true
-        type: string
-      REVIEWERS:
-        required: true
-        type: string
-
 
-concurrency: ${{inputs.resource_id}}-call
+concurrency: ${{inputs.environment_name}}-${{inputs.concept_id}}-call
 
 env:
-  S3_HOST: ${{inputs.S3_HOST}}
-  S3_BUCKET: ${{inputs.S3_BUCKET}}
-  S3_FOLDER: ${{inputs.S3_FOLDER}}
-  S3_ACCESS_KEY_ID: ${{secrets.S3_ACCESS_KEY_ID}}
+  S3_HOST: ${{vars.S3_HOST}}
+  S3_BUCKET: ${{vars.S3_BUCKET}}
   S3_SECRET_ACCESS_KEY: ${{secrets.S3_SECRET_ACCESS_KEY}}
-  ZENODO_API_ACCESS_TOKEN: ${{secrets.ZENODO_API_ACCESS_TOKEN}}
-  REVIEWERS: ${{inputs.REVIEWERS}}
+  S3_ACCESS_KEY_ID: ${{secrets.S3_ACCESS_KEY_ID}}
   RUN_URL: ${{github.server_url}}/${{github.repository}}/actions/runs/${{github.run_id}}
   MAIL_PASSWORD: ${{secrets.MAIL_PASSWORD}}
 
+
 jobs:
   run:
     runs-on: ubuntu-latest
@@ -57,3 +41,7 @@ jobs:
           cache: "pip" # caching pip dependencies
       - run: pip install .
       - run: backoffice publish "${{inputs.resource_id}}" "staged/${{inputs.stage_number}}" "${{inputs.reviewer}}"
+        env:
+          S3_FOLDER: ${{vars.S3_FOLDER}}
+          ZENODO_URL: ${{vars.ZENODO_URL}}
+          ZENODO_API_ACCESS_TOKEN: ${{secrets.ZENODO_API_ACCESS_TOKEN}}