Merge pull request #28 from bioimage-io/sandbox

add sandbox flag
bioimage-io · Apr 10, 2024 · 5b41d99 · 5b41d99
2 parents 44699bb + 1ef44ee
commit 5b41d99
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Showing 6 changed files with 40 additions and 13 deletions.
diff --git a/.github/workflows/emails_to_chat.yaml b/.github/workflows/emails_to_chat.yaml
@@ -3,6 +3,12 @@ name: forward emails to chat
 
 on:
   workflow_call:
+    inputs:
+      sandbox:
+        description: Flag to use sandbox instead
+        required: false
+        default: true
+        type: boolean
   # schedule:
   #   - cron: "0 * * * *" # every hour at minute 0
 
@@ -11,7 +17,7 @@ concurrency: forward-emails-to-chat
 env:
   S3_HOST: ${{vars.S3_HOST}}
   S3_BUCKET: ${{vars.S3_BUCKET}}
-  S3_FOLDER: ${{vars.S3_FOLDER}}
+  S3_FOLDER: ${{inputs.sandbox && vars.S3_SANDBOX_FOLDER || vars.S3_FOLDER}}
   S3_ACCESS_KEY_ID: ${{secrets.S3_ACCESS_KEY_ID}}
   S3_SECRET_ACCESS_KEY: ${{secrets.S3_SECRET_ACCESS_KEY}}
   MAIL_PASSWORD: ${{secrets.MAIL_PASSWORD}}

diff --git a/.github/workflows/publish.yaml b/.github/workflows/publish.yaml
@@ -16,7 +16,11 @@ on:
         description: Name of bioimage.io maintainer accepting this resource version
         required: true
         type: string
-
+      sandbox:
+        description: Flag to publish within sandbox instead
+        required: false
+        default: false
+        type: boolean
 
 concurrency: ${{inputs.resource_id}}
 
@@ -29,5 +33,5 @@ jobs:
       reviewer: ${{inputs.reviewer}}
       S3_HOST: ${{vars.S3_HOST}}
       S3_BUCKET: ${{vars.S3_BUCKET}}
-      S3_FOLDER: ${{vars.S3_FOLDER}}
+      S3_FOLDER: ${{inputs.sandbox && vars.S3_SANDBOX_FOLDER || vars.S3_FOLDER}}
     secrets: inherit
diff --git a/.github/workflows/retest_all.yaml b/.github/workflows/retest_all.yaml
@@ -1,6 +1,14 @@
 name: retest all bioimageio resources adding to their logs
 
-on: workflow_dispatch
+on:
+  workflow_dispatch:
+    inputs:
+      sandbox:
+        description: Flag to use sandbox instead
+        required: false
+        default: true
+        type: boolean
+
 concurrency: retest
 
 jobs:
@@ -10,7 +18,7 @@ jobs:
       matrix: ${{steps.get_matrix.outputs.matrix}}
 
     steps:
-      - run: wget ${{vars.S3_HOST}}/${{vars.S3_BUCKET}}/${{vars.S3_FOLDER}}/collection.json
+      - run: wget ${{vars.S3_HOST}}/${{vars.S3_BUCKET}}/${{inputs.sandbox && vars.S3_SANDBOX_FOLDER || vars.S3_FOLDER}}/collection.json
       - shell: python
         id: get_matrix
         run: |
@@ -35,7 +43,7 @@ jobs:
       conclude: 'no'
       S3_HOST: ${{vars.S3_HOST}}
       S3_BUCKET: ${{vars.S3_BUCKET}}
-      S3_FOLDER: ${{vars.S3_FOLDER}}
+      S3_FOLDER: ${{inputs.sandbox && vars.S3_SANDBOX_FOLDER || vars.S3_FOLDER}}
     secrets: inherit
 
 # TODO: call emailer
diff --git a/.github/workflows/stage.yaml b/.github/workflows/stage.yaml
@@ -12,6 +12,11 @@ on:
         description: "Download URL of the resource package zip-file"
         required: true
         type: string
+      sandbox:
+        description: Flag to stage to sandbox instead
+        required: false
+        default: false
+        type: boolean
 
 concurrency: ${{inputs.resource_id}}
 
@@ -23,7 +28,7 @@ jobs:
       package_url: ${{inputs.package_url}}
       S3_HOST: ${{vars.S3_HOST}}
       S3_BUCKET: ${{vars.S3_BUCKET}}
-      S3_FOLDER: ${{vars.S3_FOLDER}}
+      S3_FOLDER: ${{inputs.sandbox && vars.S3_SANDBOX_FOLDER || vars.S3_FOLDER}}
     secrets: inherit
 
   test:
@@ -34,5 +39,5 @@ jobs:
       version: ${{needs.stage.outputs.version}}
       S3_HOST: ${{vars.S3_HOST}}
       S3_BUCKET: ${{vars.S3_BUCKET}}
-      S3_FOLDER: ${{vars.S3_FOLDER}}
+      S3_FOLDER: ${{inputs.sandbox && vars.S3_SANDBOX_FOLDER || vars.S3_FOLDER}}
     secrets: inherit
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
@@ -12,6 +12,11 @@ on:
         description: stage number to test
         required: true
         type: number
+      sandbox:
+        description: Flag to test resource in sandbox instead
+        required: false
+        default: false
+        type: boolean
 
 concurrency: ${{inputs.resource_id}}
 
@@ -23,7 +28,7 @@ jobs:
       version: staged/${{inputs.stage_number}}
       S3_HOST: ${{vars.S3_HOST}}
       S3_BUCKET: ${{vars.S3_BUCKET}}
-      S3_FOLDER: ${{vars.S3_FOLDER}}
+      S3_FOLDER: ${{inputs.sandbox && vars.S3_SANDBOX_FOLDER || vars.S3_FOLDER}}
     secrets: inherit
 
 # TODO: call emailer
diff --git a/bioimageio_collection_backoffice/s3_client.py b/bioimageio_collection_backoffice/s3_client.py
@@ -41,6 +41,9 @@ class Client:
 
     def __post_init__(self):
         self.prefix = self.prefix.strip("/")
+        if not self.prefix:
+            raise ValueError("empty prefix not allowed")
+
         self._client = Minio(
             self.host,
             access_key=self.access_key,
@@ -178,10 +181,6 @@ def _cp_dir(self, src: str, tgt: str):
 
         return objects
 
-    def rm_obj(self, name: str) -> None:
-        """remove single object"""
-        self._client.remove_object(self.bucket, name)
-
     def _rm_objs(
         self, objects: Sequence[Object], *, bypass_governance_mode: bool
     ) -> None: