delete the default resource

src/depiction_targeted_preprocbatch/executor.py

@@ -54,6 +54,7 @@ def __init__(
 
     def run(self, n_jobs: int) -> None:
         """Runs all jobs, executing up to `n_jobs` in parallel."""
+        self._set_workunit_processing()
         self._work_dir.mkdir(exist_ok=True, parents=True)
         batch_dataset = BatchDataset(dataset_id=self._workunit_config.input_dataset_id, client=self._client)
         pipeline_parameters = self._prepare_pipeline_parameters()
@@ -114,6 +115,17 @@ def _prepare_pipeline_parameters(self) -> Path:
             yaml.dump(self._workunit_config.pipeline_parameters.model_dump(mode="json"), file)
         return result_file
 
+    def _set_workunit_processing(self) -> None:
+        """Sets the workunit to processing and deletes the default resource if it is available."""
+        self._client.save(
+            "workunit",
+            {
+                "id": self._workunit_config.workunit_id,
+                "status": "processing",
+            },
+        )
+        JobExportResults.delete_default_resource(workunit_id=self._workunit_config.workunit_id, client=self._client)
+
 
 app = cyclopts.App()
 

src/depiction_targeted_preprocbatch/job_export_results.py

@@ -4,7 +4,8 @@
 from pathlib import Path
 
 from bfabric import Bfabric
-from bfabric.entities import Storage
+from bfabric.entities import Storage, Resource
+from loguru import logger
 
 from depiction.persistence.file_checksums import FileChecksums
 from depiction_targeted_preproc.app.workunit_config import WorkunitConfig
@@ -28,6 +29,10 @@ def __init__(
         self._output_storage = output_storage
         self._force_ssh_user = force_ssh_user
 
+    @property
+    def _workunit_id(self) -> int:
+        return self._workunit_config.workunit_id
+
     @classmethod
     def export(
         cls,
@@ -55,6 +60,10 @@ def export_results(self, sample_name: str, result_files: list[Path]) -> None:
         output_path_relative = self._copy_zip_to_storage(zip_file_path)
         self._register_zip_in_workunit(output_path_relative, zip_file_path)
 
+    def delete_local(self):
+        # TODO this functionality will be needed when processing large jobs
+        raise NotImplementedError
+
     def _create_zip_file(self, result_files: list[Path], sample_name: str) -> Path:
         """Creates a ZIP file containing the results for one sample, and returns the zip file's path."""
         self.output_dir.mkdir(exist_ok=True, parents=True)
@@ -70,7 +79,7 @@ def _register_zip_in_workunit(self, output_path_relative: Path, zip_file_path: P
             "resource",
             {
                 "name": zip_file_path.name,
-                "workunitid": self._workunit_config.workunit_id,
+                "workunitid": self._workunit_id,
                 "storageid": self._output_storage.id,
                 "relativepath": output_path_relative,
                 "filechecksum": checksum,
@@ -85,3 +94,21 @@ def _copy_zip_to_storage(self, zip_file_path: Path) -> Path:
         output_uri = f"{self._output_storage.scp_prefix}{output_path_relative}"
         scp(zip_file_path, output_uri, username=self._force_ssh_user)
         return output_path_relative
+
+    @staticmethod
+    def delete_default_resource(workunit_id: int, client: Bfabric) -> bool:
+        """Deletes the default resource created by the wrapper creator if it exists. Returns true if the resource was
+        successfully deleted.
+        """
+        resources = Resource.find_by(
+            {"name": "MSI_Targeted_PreprocBatch 0 - resource", "workunitid": workunit_id}, client=client
+        )
+        if len(resources) == 1:
+            resource_id = list(resources.values())[0].id
+            logger.info(f"Deleting default resource with ID {resource_id}")
+            result = client.delete("resource", resource_id, check=False)
+            return result.is_success
+        elif len(resources) > 1:
+            raise ValueError("There should never be more than one default resource.")
+        else:
+            return False