__other__

furas · furas · commit 89d843e69b9b · 2022-08-01T16:36:04.000+02:00
diff --git a/__other__/pubmed - download and textract/main.py b/__other__/pubmed - download and textract/main.py
@@ -0,0 +1,45 @@
+# author: Bartlomiej "furas" Burek (https://blog.furas.pl)
+# date: 2022.07.19
+# [python - getting weird results from metapub and pubmed - Stack Overflow](https://stackoverflow.com/questions/73043246/getting-weird-results-from-metapub-and-pubmed/)
+
+import os
+from urllib.request import urlretrieve
+import metapub
+import textract
+
+#another_path = '/content/Articles/'
+another_path = './'
+
+pmid_list = ['35566889','33538053', '30848212']
+
+for query in pmid_list:
+
+    print('query:', query)
+
+    url = metapub.FindIt(query).url
+    print('url:', url)
+
+    if url:
+
+        try:
+            out_file = os.path.join(another_path, query)
+            print('out_file:', out_file)
+
+            print('... downloading')
+
+            urlretrieve(url, out_file + '.pdf')
+
+            print('... processing')
+
+            data = textract.process(out_file + '.pdf', extension='pdf', method='pdftotext', encoding="utf_8")
+
+            print('... saving')
+
+            with open(out_file + '.txt', "wb") as textfile:  # save bytes
+                textfile.write(data)
+
+            print('... OK')
+
+        except Exception as ex:
+            print('Exception:', ex)
+
