Update classify_abs.py

classify_abs.py

@@ -288,46 +288,44 @@ def streamlist_getAbs(searchterm_list:Union[List[str],List[int],str], maxResults
             searchterm_list = [searchterm_list]
         else:
             searchterm_list = list(searchterm_list)
+    #maxResults is multiplied by a little bit because sometimes the results returned is more than maxResults
+    percent_by_step = 1/(maxResults*1.25) 
+    PMIDs_bar = st.progress(0):
+    for dz in searchterm_list:
+        term = ''
+        dz_words = dz.split()
+        for word in dz_words:
+            term += word + '%20'
+        query = term[:-3]
+
+        url = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term='+query
+        r = requests.get(url)
+        root = ET.fromstring(r.content)
+
+        for result in root.iter('IdList'):
+            if len(pmids) >= maxResults:
+                break
+            pmidlist = [pmid.text for pmid in result.iter('Id')]
+            pmids.update(pmidlist)
+            PMIDs_bar.progress(round(len(pmids)*percent_by_step,1))
+
+        url = 'https://www.ebi.ac.uk/europepmc/webservices/rest/search?query='+query+'&resulttype=core'
+        r = requests.get(url)
+        root = ET.fromstring(r.content)
+
+        for result in root.iter('result'):
+            if len(pmids) >= maxResults:
+                break
+            pmidlist = [pmid.text for pmid in result.iter('id')]
+            if len(pmidlist) > 0:
+                pmid = pmidlist[0]
+                if pmid[0].isdigit():
+                    pmids.add(pmid)
+                    PMIDs_bar.progress(round(len(pmids)*percent_by_step,1))
+    PMIDs_bar.empty()
     
-    percent_by_step = 1/(maxResults*1.25) #maxResults is multiplied by a little bit because sometimes the results returned is more than maxResults
-    
-    with PMIDs_bar = st.progress(0):
-        
-        
-        for dz in searchterm_list:
-            term = ''
-            dz_words = dz.split()
-            for word in dz_words:
-                term += word + '%20'
-            query = term[:-3]
-
-            url = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term='+query
-            r = requests.get(url)
-            root = ET.fromstring(r.content)
-    
-            for result in root.iter('IdList'):
-                if len(pmids) >= maxResults:
-                    break
-                pmidlist = [pmid.text for pmid in result.iter('Id')]
-                pmids.update(pmidlist)
-                PMIDs_bar.progress(round(len(pmids)*percent_by_step,1))
-    
-            url = 'https://www.ebi.ac.uk/europepmc/webservices/rest/search?query='+query+'&resulttype=core'
-            r = requests.get(url)
-            root = ET.fromstring(r.content)
-    
-            for result in root.iter('result'):
-                if len(pmids) >= maxResults:
-                    break
-                pmidlist = [pmid.text for pmid in result.iter('id')]
-                if len(pmidlist) > 0:
-                    pmid = pmidlist[0]
-                    if pmid[0].isdigit():
-                        pmids.add(pmid)
-                        PMIDs_bar.progress(round(len(pmids)*percent_by_step,1))
-        st.success('Found',len(pmids),'PMIDs. Gathering Abstracts and Filtering...')
-        
-    with abstracts_bar = st.progress(0):
+    with st.success('Found',len(pmids),'PMIDs. Gathering Abstracts and Filtering...'):
+        abstracts_bar = st.progress(0):
         percent_by_step = 1/(maxResults)
         if filtering !='none' or filtering !='strict':
             filter_terms = set(searchterm_list).union(set(str(re.sub(',','',' '.join(searchterm_list))).split()).difference(STOPWORDS))
@@ -353,7 +351,7 @@ def streamlist_getAbs(searchterm_list:Union[List[str],List[int],str], maxResults
                     if set(filter_terms).intersection(set(word_tokenize(abstract))):
                         pmid_abs[pmid] = abstract
                         abstracts_bar.progress(round(len(pmid_abs)*percent_by_step,1))
-
+        abstracts_bar.empty()
     st.success('Found',len(pmids),'PMIDs. Gathered',len(pmid_abs),'Relevant Abstracts.')
     
     return pmid_abs