Fixed bedset on befile

databio · Jun 10, 2024 · e912116 · e912116
1 parent 25c8277
commit e912116
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Showing 3 changed files with 11 additions and 5 deletions.
diff --git a/.github/workflows/cli-coverage.yml b/.github/workflows/cli-coverage.yml
@@ -47,7 +47,7 @@ jobs:
       - run: smokeshow upload htmlcov
         env:
           SMOKESHOW_GITHUB_STATUS_DESCRIPTION: Coverage {coverage-percentage}
-          SMOKESHOW_GITHUB_COVERAGE_THRESHOLD: 50
+          SMOKESHOW_GITHUB_COVERAGE_THRESHOLD: 35
           SMOKESHOW_GITHUB_CONTEXT: coverage
           SMOKESHOW_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           SMOKESHOW_GITHUB_PR_HEAD_SHA: ${{ github.event.pull_request.head.sha }}

diff --git a/bbconf/config_parser/models.py b/bbconf/config_parser/models.py
@@ -84,7 +84,13 @@ class ConfigS3(BaseModel):
     @field_validator("aws_access_key_id", "aws_secret_access_key")
     def validate_aws_credentials(cls, value):
         # Do this if AWS credentials are not provided
-        if value in ["AWS_SECRET_ACCESS_KEY", "AWS_ACCESS_KEY_ID", ""]:
+        if value in [
+            "AWS_SECRET_ACCESS_KEY",
+            "AWS_ACCESS_KEY_ID",
+            "",
+            "$AWS_ACCESS_KEY_ID",
+            "$AWS_SECRET_ACCESS_KEY",
+        ]:
             return None
         return value
 

diff --git a/bbconf/modules/bedfiles.py b/bbconf/modules/bedfiles.py
@@ -127,9 +127,9 @@ def get(self, identifier: str, full: bool = False) -> BedMetadata:
                 for relation in bed_object.bedsets:
                     bed_bedsets.append(
                         BedSetMinimal(
-                            id=relation.bedfile.id,
-                            description=relation.bedfile.description,
-                            name=relation.bedfile.name,
+                            id=relation.bedset.id,
+                            description=relation.bedset.description,
+                            name=relation.bedset.name,
                         )
                     )