d827b292f2da39b290412c402752b1bd68b37d2e
lrnassar
  Wed Oct 25 17:00:56 2023 -0700
Adding a new condition to check for another regex expression. I found that two of the broken examples had spaces in the URL, so try to match on that and translate them. I also found one which had three backslashes incorrectly, so try to fix that too. I added it to a new loop so as not to affect the original functionality. This seems to cover all of the broken cases we had noted. Refs #31963

diff --git src/hg/encode/getTrackReferences/getTrackReferences src/hg/encode/getTrackReferences/getTrackReferences
index 234dd03..2b99cb9 100755
--- src/hg/encode/getTrackReferences/getTrackReferences
+++ src/hg/encode/getTrackReferences/getTrackReferences
@@ -108,44 +108,57 @@
     if not re.search("\.$", dateStr):
         dateStr = dateStr + "."
     # construct hyperlinks for PMID and PMCID (if it exists)
     idStr = "PMID: <a href=\"%s\" target=\"_blank\">%s</a>" % (htmlEscape(infoDict['url']), infoDict['pubmed'])
     if 'pmc' in infoDict:
         idStr = idStr + "; PMC: <a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/%s/\" target=\"_blank\">%s</a>" % (infoDict['pmc'], infoDict['pmc'])
     if doi and 'doi' in infoDict:
         idStr = ("DOI: <a href=\"https://doi.org/%s\" target=\"_blank\">%s</a>; " % (htmlEscape(infoDict['doi']), infoDict['doi'] ) ) + idStr
 
     # now that the pubmed link has been constructed, we can overwrite the url in infoDict with the original article URL
 
     # make sure the portlet that generates outlinks for PubMed didn't fail.  If it did, try again until
     # it works or we give up.
     # Note: no longer sure this is necessary - seems like NCBI is doing something different now, but at
     # any rate urllib2 no longer seems to fetch the links list in at least some cases.  Requests works.
+    origUrl = infoDict['url']
     for try_count in range(10):
         origComment = ""
+        infoDict['url'] = origUrl
         fetch = requests.get(infoDict['url'])
+        try:
 	    m = re.search('<div class="full-text-links-list">\s*<a\s+(class="[^"]*"\s+)?href="(\S+)"', fetch.text)
             if m:
                 if m.group(2):
+                    # Rhetorical: how can m match without m.group(1) being defined for this regex? Anyway ....
                     infoDict['url'] = m.group(2).replace("&amp;", "&")
                 break
             else:
-            origComment = "<!-- Can't find original article link for %s -->" % infoDict['url']
                 #n = re.search('<div class="icons"></div>', doc) # another possible detection of failed portlet
                 p = re.search('Default output of portlet NCBIPageSection', doc)
                 if p is None:
                     break
+        except:
+	    try:
+		m = re.search('<div class="full-text-links-list">\s*<a\s+(class="[^"]*"\s+)?href="(.+)"', fetch.text)
+                if m:
+                    if m.group(2):
+                        # Rhetorical: how can m match without m.group(1) being defined for this regex? Anyway ....
+                        infoDict['url'] = m.group(2).replace("&amp;", "&").replace(" ", "%20").replace("///","//")
+                    break
+            except:
+                print "Failed to fetch complete links from NCBI after 10 tries.  Try again later or just use the PubMed paper link."
     else:
         print "Failed to fetch complete links from NCBI after 10 tries.  Try again later or just use the PubMed paper link."
 
     htmlLines = list()
     htmlLines.append("<p>")
     htmlLines.append("%s" % authStr)
     htmlLines.append("<a href=\"%s\" target=\"_blank\">" % htmlEscape(infoDict['url']))
     htmlLines.append("%s</a>." % htmlEscape(title))
     htmlLines.append("<em>%s</em>. %s" % (htmlEscape(journal), dateStr))
     htmlLines.append("%s" % idStr)
     htmlLines.append("</p>")
     if plain:
         htmlLines = list()
         idStr = "PMID: %s" % infoDict['pubmed'];
         if 'pmc' in infoDict: