Make gen3 manager compatible with rest of client

drs_downloader/cli.py

@@ -240,6 +240,7 @@ def gen3(
 ):
     """Copy files from gen3 server."""
     # read from manifest
+    assert api_key_path is not None, "If using gen3 mode an api key path must be provided with --api-key-path"
     ids_from_manifest = _extract_tsv_info(Path(manifest_path), drs_column_name)
 
     _perform_downloads(
@@ -346,8 +347,6 @@ def _perform_downloads(
     drs_objects = drs_manager.get_objects(ids_from_manifest, verbose=verbose)
 
     file_logger.info(f"Drs Objects after get_objects function {drs_objects}")
-    if verbose:
-        logger.info(f"Drs Objects after get_objects function {drs_objects}")
 
     # If every object has an error exit early since these early errors are not recoverable
     if all(len(obj.errors) > 0 for obj in drs_objects):

drs_downloader/clients/gen3.py

@@ -1,6 +1,8 @@
 import json
 import logging
 import os
+import ssl
+import certifi
 from pathlib import Path
 from typing import Optional
 
@@ -98,7 +100,7 @@ async def download_part(
             drs_object.errors.append(str(e))
             return None
 
-    async def sign_url(self, drs_object: DrsObject, verbose: bool) -> DrsObject:
+    async def sign_url(self, drs_object: DrsObject, verbose: bool, user_project=None) -> DrsObject:
         """Call fence's /user/data/download/ endpoint."""
 
         headers = {
@@ -143,10 +145,11 @@ async def get_object(self, object_id: str, verbose: bool) -> DrsObject:
             "authorization": "Bearer " + self.token,
             "content-type": "application/json",
         }
-
+        context = ssl.create_default_context(cafile=certifi.where())
         async with aiohttp.ClientSession(headers=headers) as session:
             async with session.get(
-                url=f"{self.endpoint}{self.drs_api}/{object_id.split(':')[-1]}"
+                url=f"{self.endpoint}{self.drs_api}/{object_id.split(':')[-1]}",
+                ssl=context
             ) as response:
                 try:
                     self.statistics.set_max_files_open()

drs_downloader/manager.py

@@ -172,14 +172,14 @@ async def wait_till_completed(self, tasks, err_function_msg):
                     y = await t
                     completed_tasks.append(y)
 
-                except Exception:
+                except Exception as e:
                     updated_drs_object = DrsObject(
                         self_uri="",
                         id="",
                         checksums=[],
                         size=0,
                         name=None,
-                        errors=[f"Exception in {err_function_msg} function"]
+                        errors=[f"Exception in {err_function_msg} function {str(e)}"]
                     )
 
                     completed_tasks.append(updated_drs_object)

tests/fixtures/gen3-small.tsv

@@ -1,17 +1,2 @@
-ga4gh_drs_uri
-drs://FOOBAR:d62af3ff-756d-4e73-b6c6-e0bbd3bae50d
-drs://FOOBAR:755fb48b-c4c9-41b6-a3fd-2604ebaa21af
-drs://FOOBAR:cdff48c3-69a6-4c24-84d8-82681803003f
-drs://FOOBAR:da8cb14b-8274-4b5a-a5ed-279140c9cf74
-drs://FOOBAR:82808bc8-a21b-43bc-af61-fcbc0437cd13
-drs://FOOBAR:82b3224d-98a5-453c-ab50-edb96e72fda6
-drs://FOOBAR:93f7ca81-93dc-4046-a537-40a36465062c
-drs://FOOBAR:f4b29275-499f-4260-8725-d6c9f5d5bcb8
-drs://FOOBAR:839de941-4317-4508-968e-83883590bec9
-drs://FOOBAR:80164516-695a-473f-9c76-eacb9e191a6a
-drs://FOOBAR:c5196828-493b-4f62-976a-46468088547e
-drs://FOOBAR:6d5df2b1-5811-4206-a53b-7eac9e8f6383
-drs://FOOBAR:f905ecc0-e865-47fc-9d62-9087f5a4150e
-drs://FOOBAR:9ed5fcf8-c461-46ad-84a3-12d709d378d4
-drs://FOOBAR:892f99d6-8cdf-432b-bc8b-7d965d0cad53
-drs://FOOBAR:34819aba-29f7-4a83-b5d4-84b10a3f6b1b
+ga4gh_drs_uri
+drs://PREFIX:c5956122-ee2d-595f-8f60-48c05d781c28