apscale - pypi Package Compare versions

Comparing version 4.1.4 to 4.1.5

apscale.egg-info/PKG-INFO

 Metadata-Version: 2.4
 Name: apscale
-Version: 4.1.4
+Version: 4.1.5
 Summary: Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data
@@ -5,0 +5,0 @@ Home-page: https://github.com/DominikBuchner/apscale

apscale/pages/4_Perform_GBIF_validation.py

@@ -1,2 +0,2 @@
-import duckdb, pyproj, time, requests
+import duckdb, pyproj, time, requests, random
 import pandas as pd
@@ -12,2 +12,3 @@ import pathlib
 from pygbif import occurrences as occ
+from pygbif.gbifutils import NoResultException
 
@@ -154,3 +155,3 @@
     while True:
-        data_chunk = distinct_sequences.fetch_df_chunk(1)
+        data_chunk = distinct_sequences.fetch_df_chunk()
         if data_chunk.empty:
@@ -282,2 +283,4 @@ break
 def validation_api_request(species_name, wkt_string) -> str:
+    # define a backoff factor for each individual request
+    backoff = 1.0
     # perform the api call
@@ -287,5 +290,8 @@ while True:
             validation_result = occ.search(
-                scientificName=species_name, geometry=wkt_string, timeout=60
+                scientificName=species_name, geometry=wkt_string, limit=1, timeout=60
             )
-            break
+            print(validation_result)
+            return (
+                "plausible" if validation_result.get("count", 0) > 0 else "implausible"
+            )
         except (
@@ -296,9 +302,10 @@ requests.exceptions.HTTPError,
             if e.response.status_code == 429:
-                time.sleep(1)
-                continue
+                wait = backoff + random.uniform(0, 1)
+                time.sleep(wait)
+                backoff *= 2
 
-    if validation_result["count"] > 0:
-        return "plausible"
-    else:
-        return "implausible"
+        except NoResultException:
+            wait = backoff + random.uniform(0, 1)
+            time.sleep(wait)
+            backoff *= 2
 
@@ -337,3 +344,3 @@
             )
-            validation_status = Parallel(n_jobs=-2)(
+            validation_status = Parallel(n_jobs=1)(
                 delayed(validation_api_request)(species_name, wkt_string)
@@ -340,0 +347,0 @@ for species_name, wkt_string in chunk_args

PKG-INFO

 Metadata-Version: 2.4
 Name: apscale
-Version: 4.1.4
+Version: 4.1.5
 Summary: Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data
@@ -5,0 +5,0 @@ Home-page: https://github.com/DominikBuchner/apscale

setup.py

@@ -8,3 +8,3 @@ import setuptools
     name="apscale",
-    version="4.1.4",
+    version="4.1.5",
     author="Dominik Buchner",
@@ -11,0 +11,0 @@ author_email="[e-mail]",

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Improved metrics

Total package byte prevSize

259957

0.15%

Lines of code

5606

0.13%