pass correct url

catalystneuro · Aug 16, 2023 · 11b0918 · 11b0918
1 parent 4031fec
commit 11b0918
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Showing 4 changed files with 8 additions and 3 deletions.
diff --git a/containers/run_script.py b/containers/run_script.py
@@ -205,6 +205,9 @@ def main(
     - AWS_DEFAULT_REGION
     - AWS_ACCESS_KEY_ID
     - AWS_SECRET_ACCESS_KEY
+
+    If saving results to DANDI archive, the following ENV variables should be present:
+    - DANDI_API_TOKEN
     """
 
     # Order of priority for definition of running arguments:
@@ -317,7 +320,7 @@ def main(
 
     elif source == "dandi":
         dandiset_s3_file_url = source_data_paths["file"]
-        if not dandiset_s3_file_url.startswith("https://dandiarchive.s3.amazonaws.com"):
+        if not dandiset_s3_file_url.startswith("https://dandiarchive"):
             raise Exception(f"DANDISET_S3_FILE_URL should be a valid Dandiset S3 url. Value received was: {dandiset_s3_file_url}")
 
         if not test_with_subrecording:            

diff --git a/rest/clients/dandi.py b/rest/clients/dandi.py
@@ -138,7 +138,9 @@ def get_nwbfile_info_fsspec(self, dandiset_id: str, file_path: str) -> dict:
             with h5py.File(f) as file:
                 with pynwb.NWBHDF5IO(file=file, load_namespaces=True) as io:
                     nwbfile = io.read()
-                    return self.extract_nwbfile_info(nwbfile=nwbfile)
+                    file_info = self.extract_nwbfile_info(nwbfile=nwbfile)
+                    file_info["url"] = file_s3_url
+                    return file_info
 
 
     def get_nwbfile_info_ros3(self, dandiset_id: str, file_path: str) -> dict:

diff --git a/rest/routes/dandi.py b/rest/routes/dandi.py
@@ -45,7 +45,6 @@ async def route_get_nwbfile_info(dandiset_id: str, file_path: str) -> JSONRespon
         dandi_client = DandiClient(token=settings.DANDI_API_TOKEN)
         # file_info = dandi_client.get_nwbfile_info_ros3(dandiset_id, file_path)
         file_info = dandi_client.get_nwbfile_info_fsspec(dandiset_id, file_path)
-        file_info["url"] = dandi_client.get_file_url(dandiset_id, file_path)
     except Exception as e:
         print(e)
         raise HTTPException(status_code=500, detail="Internal server error")

diff --git a/rest/routes/sorting.py b/rest/routes/sorting.py
@@ -25,6 +25,7 @@ def sorting_background_task(payload, run_identifier):
             client_local_worker.run_sorting(**payload)
         elif run_at == "aws":
             job_kwargs = {k.upper(): v for k, v in payload.items()}
+            job_kwargs["DANDI_API_TOKEN"] = settings.DANDI_API_TOKEN
             client_aws = AWSClient()
             client_aws.submit_job(
                 job_name=f"sorting-{run_identifier}",