♻️ Don't use retry Sessions

kf_utils/dataservice/delete.py

@@ -2,7 +2,8 @@
 from pprint import pformat
 from urllib.parse import urlparse
 
-from d3b_utils.requests_retry import Session
+# from d3b_utils.requests_retry import Session
+from requests import Session
 from kf_utils.dataservice.meta import get_endpoint
 from kf_utils.dataservice.scrape import yield_kfids
 

kf_utils/dataservice/descendants.py

@@ -325,7 +325,7 @@ def _inner(parent_type, parent_kfids, descendants):
         if parent_type in done:
             return
         done.add(parent_type)
-        for (child_type, link_on_parent, link_on_child) in descendancy.get(
+        for child_type, link_on_parent, link_on_child in descendancy.get(
             parent_type, []
         ):
             if use_api:
@@ -387,7 +387,7 @@ def _inner(parent_type, parent_kfids, descendants):
                     for k, v in descendants["genomic_file"].items()
                     if k not in to_remove
                 }
-        for (child_type, _, _) in descendancy.get(parent_type, []):
+        for child_type, _, _ in descendancy.get(parent_type, []):
             if descendants.get(child_type):
                 _inner(child_type, descendants[child_type].keys(), descendants)
 

kf_utils/dataservice/patch.py

@@ -1,6 +1,8 @@
+from pprint import pformat
 from concurrent.futures import ThreadPoolExecutor, as_completed
 
-from d3b_utils.requests_retry import Session
+# from d3b_utils.requests_retry import Session
+from requests import Session
 from kf_utils.dataservice.meta import get_endpoint
 
 
@@ -15,10 +17,15 @@ def send_patches(host, patches):
     host = host.strip("/")
 
     def do_patch(url, patch):
-        msg = f"Patched {url} with {patch}"
         resp = Session().patch(url, json=patch)
         if not resp.ok:
-            raise Exception(f"{resp.status_code} -- {msg} -- {resp.json()}")
+            msg = f"Patched {url} with {patch}"
+            raise Exception(
+                f"{resp.status_code} -- {msg} -- Response:\n{resp.text}"
+            )
+        else:
+            msg = f"Patched {url} with {patch}. Response:\n{pformat(resp.json())}"
+
         return msg
 
     with ThreadPoolExecutor() as tpex:

kf_utils/dataservice/scrape.py

@@ -1,6 +1,7 @@
 from concurrent.futures import ThreadPoolExecutor, as_completed
 
-from d3b_utils.requests_retry import Session
+# from d3b_utils.requests_retry import Session
+from requests import Session
 from kf_utils.dataservice.meta import get_endpoint
 from tqdm import tqdm
 
@@ -52,7 +53,7 @@ def yield_entities_from_filter(host, endpoint, filters, show_progress=False):
                     pbar.update()
                     yield entity
             try:
-                for (key, i) in [("after", 1), ("after_uuid", 2)]:
+                for key, i in [("after", 1), ("after_uuid", 2)]:
                     which[key] = j["_links"]["next"].split("=")[i].split("&")[0]
             except KeyError:
                 break

kf_utils/dbgap/release.py

@@ -1,5 +1,7 @@
 import xmltodict
-from d3b_utils.requests_retry import Session
+
+# from d3b_utils.requests_retry import Session
+from requests import Session
 from xml.etree import ElementTree
 
 # from defusedxml import ElementTree as DefusedET
@@ -27,7 +29,8 @@ def get_latest_sample_status(phs_id, required_status="released"):
         print(f"Querying dbGaP for study {phs_string}")
         print(f"Manifest URL -> {url}")
 
-        data = Session(status_forcelist=(502, 503, 504)).get(url)
+        # data = Session(status_forcelist=(502, 503, 504)).get(url)
+        data = Session().get(url)
         if data.status_code != 200:
             tried[phs_string] = f"status {data.status_code}"
             raise Exception(