Merge pull request #1477 from gyorilab/edirect-fix

Edirect esearch fix

Author: bgyori

indra/literature/pubmed_client.py

@@ -370,7 +370,11 @@ def get_full_xml_by_pmids(
                            "for instructions.")
 
     tree = lxml_etree.fromstring(xml_bytes, parser=parser)
-    # Each article is in a <PubmedArticle> tag, encapsulated in a <PubmedArticleSet> tag
+    # Each article is in a <PubmedArticle> tag, encapsulated in a
+    # <PubmedArticleSet> tag.
+    # Note that the <PubmedArticle> tags are sorted by PMID numerically e.g.,
+    # 10, 11, 20, 1000, and not lexicographically e.g., 10, 1000, 11, 20,
+    # regardless of the order in which the pmids are passed
     if fname is not None:
         pretty_save_xml(tree, fname)
     return tree
@@ -1250,9 +1254,10 @@ def get_all_ids(search_term):
                            "for instructions.")
     # Output is divided by new lines
     elements = res.split('\n')
-    # If there are more than 10k IDs, the CLI outputs a . for each
-    # iteration, these have to be filtered out
-    pmids = [e for e in elements if '.' not in e]
+    # The CLI automatically retries on errors, subprocess.getoutput unfortunately
+    # adds the error message associated with the retry to the output, so we need
+    # to filter out non-numeric elements
+    pmids = [e for e in elements if e.isdigit()]
     return pmids
 
 

indra/tests/test_pubmed_client.py

@@ -283,14 +283,16 @@ def test_get_article_from_full_xml2():
 @pytest.mark.nogha
 def test_get_full_xml_by_pmids():
     # Uses edirect CLI
-    pmids = ["35814366", "35814367"]
+    pmids = ["35814367", "35814366"]
+    pmids_int_sort = sorted(pmids, key=int)
     full_xml = pubmed_client.get_full_xml_by_pmids(pmids)
     pubmed_articles = full_xml.findall(".//PubmedArticle")
     assert len(pubmed_articles) == 2, len(pubmed_articles)
-    for pmid, pubmed_article in zip(pmids, pubmed_articles):
+    for pmid_int_sort, pubmed_article in zip(pmids_int_sort, pubmed_articles):
         xml_pmid = pubmed_article.find(".//PMID")
         assert xml_pmid is not None
-        assert xml_pmid.text == pmid, xml_pmid.text
+        # Check that the pubmed articles are sorted numerically by PMID
+        assert xml_pmid.text == pmid_int_sort, xml_pmid.text
 
 
 @pytest.mark.webservice