Added retries to textpresso api + new paper evidence

alliance-genome · Jul 17, 2024 · c88888a · c88888a
1 parent ae455fe
commit c88888a
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Showing 2 changed files with 14 additions and 9 deletions.
diff --git a/genedescriptions/api_manager.py b/genedescriptions/api_manager.py
@@ -34,15 +34,18 @@ def get_textpresso_popularity(self, keyword: str):
             data = data.encode('utf-8')
             res = None
             num_tries = 0
-            try:
-                num_tries += 1
-                req = urllib.request.Request(self.tpc_api_endpoint, data, headers={'Content-type': 'application/json',
-                                                                                   'Accept': 'application/json'})
-                res = urllib.request.urlopen(req)
-            except HTTPException:
-                if num_tries > 5:
-                    raise HTTPException
-            logger.debug("Sending request to Textpresso Central API")
+            while num_tries < 5:
+                try:
+                    num_tries += 1
+                    logger.debug("Sending request to Textpresso Central API")
+                    req = urllib.request.Request(self.tpc_api_endpoint, data, headers={'Content-type': 'application/json',
+                                                                                       'Accept': 'application/json'})
+                    res = urllib.request.urlopen(req)
+                    break
+                except Exception:
+                    pass
+            if num_tries >= 5:
+                raise HTTPException
             popularity = int(json.loads(res.read().decode('utf-8')))
             self.tpc_cache[keyword] = popularity
             return popularity

diff --git a/genedescriptions/descriptions_writer.py b/genedescriptions/descriptions_writer.py
@@ -96,6 +96,8 @@ def write_ace(self, file_path: str, curators_list: List[str], release_version: s
                                   release_version + " version of WormBase\"\n")
                     outfile.write("Automated_description\t\"" + genedesc.description +
                                   "\"\tPaper_evidence\t\"WBPaper00065943\"\n\n")
+                    outfile.write("Automated_description\t\"" + genedesc.description +
+                                  "\"\tPaper_evidence\t\"WBPaper00067038\"\n\n")
 
     def write_plain_text(self, file_path):
         """write the descriptions to a plain text file