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Pin rocrate<0.15.0 until roc-validator supports RO-Crate Metadata Specification 1.2
rocrate 0.15.0 produces crates conforming to 1.2 spec by default, which causes roc-validator validation errors like: ``` The RO-Crate metadata file descriptor MUST have a `conformsTo` property with the RO-Crate specification version ``` xref https://github.com/crs4/rocrate-validator/issues/107 Also: - Remove unused `BaseWorkflowPopulator.validate_invocation_crate_directory()` method.
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@@ -2551,13 +2551,6 @@ class BaseWorkflowPopulator(BasePopulator):
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)
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return ROCrate(crate_response)
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def validate_invocation_crate_directory(self, crate_directory):
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# TODO: where can a ro_crate be extracted
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metadata_json_path = crate_directory / "ro-crate-metadata.json"
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with metadata_json_path.open() as f:
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metadata_json = json.load(f)
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assert metadata_json["@context"] == "https://w3id.org/ro/crate/1.1/context"
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def invoke_workflow_raw(self, workflow_id: str, request: dict, assert_ok: bool = False) -> Response:
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url = f"workflows/{workflow_id}/invocations"
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invocation_response = self._post(url, data=request, json=True)
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@@ -59,7 +59,7 @@ install_requires =
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pypng
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python-magic
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pysam>=0.21
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rocrate
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rocrate<0.15.0
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social-auth-core>=4.5.0
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SQLAlchemy>=2.0.37,<2.1,!=2.0.41
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tifffile
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+1
-1
@@ -91,7 +91,7 @@ dependencies = [
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"refgenconf>=0.13.0", # https://github.com/refgenie/refgenconf/pull/149
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"regex",
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"requests",
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"rocrate",
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"rocrate<0.15.0", # https://github.com/crs4/rocrate-validator/issues/107
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"Routes",
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"s3fs>=2023.1.0",
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"schema-salad>=8.7.20240905150001", # Python 3.13 support
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