optional order fasta file

fgcz · Feb 4, 2025 · 2935e04 · 2935e04
1 parent ec5e861
commit 2935e04
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Showing 3 changed files with 13 additions and 3 deletions.
diff --git a/bfabric_app_runner/docs/changelog.md b/bfabric_app_runner/docs/changelog.md
@@ -8,6 +8,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
 
 - New input type `file` which replaces `file_scp` and preserves timestamps whenever possible and allows to create
     symlinks instead of copying the file, as needed.
+- `BfabricOrderFastaSpec.required` which allows specifying whether the order fasta is required or not
 
 ## \[0.0.14\] - 2025-01-30
 

diff --git a/bfabric_app_runner/src/bfabric_app_runner/input_preparation/prepare.py b/bfabric_app_runner/src/bfabric_app_runner/input_preparation/prepare.py
@@ -109,21 +109,29 @@ def prepare_dataset(self, spec: BfabricDatasetSpec) -> None:
         dataset.write_csv(path=target_path, separator=spec.separator)
 
     def prepare_order_fasta(self, spec: BfabricOrderFastaSpec) -> None:
+        # Determine the result file.
+        result_name = self._working_dir / spec.filename
+        result_name.parent.mkdir(exist_ok=True, parents=True)
+
         # Find the order.
         match spec.entity:
             case "workunit":
                 workunit = Workunit.find(id=spec.id, client=self._client)
                 if not isinstance(workunit.container, Order):
-                    raise ValueError(f"Workunit {workunit.id} is not associated with an order")
+                    msg = f"Workunit {workunit.id} is not associated with an order"
+                    if spec.required:
+                        raise ValueError(msg)
+                    else:
+                        logger.warning(msg)
+                        result_name.write_text("")
+                        return
                 order = workunit.container
             case "order":
                 order = Order.find(id=spec.id, client=self._client)
             case _:
                 assert_never(spec.entity)
 
         # Write the result into the file
-        result_name = self._working_dir / spec.filename
-        result_name.parent.mkdir(exist_ok=True, parents=True)
         fasta_content = order.data_dict.get("fastasequence", "")
         if fasta_content and fasta_content[-1] != "\n":
             fasta_content += "\n"

diff --git a/bfabric_app_runner/src/bfabric_app_runner/specs/inputs/bfabric_order_fasta_spec.py b/bfabric_app_runner/src/bfabric_app_runner/specs/inputs/bfabric_order_fasta_spec.py
@@ -16,6 +16,7 @@ class BfabricOrderFastaSpec(BaseModel):
     id: int
     entity: Literal["workunit", "order"]
     filename: RelativeFilePath
+    required: bool = False
 
     def resolve_filename(self, client: Bfabric) -> str:
         return self.filename