updates to new script

Author: mtholder

scripts/investigate-amendment-dups.py

@@ -1,11 +1,15 @@
 #!/usr/bin/env python3
 import sys
 import re
-from peyutil import read_as_json
+import os
+from peyutil import read_as_json, write_as_json
 
 no_app_pat = re.compile(r"^amende?ment [#](\d+) not applied:")
 homonym_pat = re.compile(r"^amende?ment [#](\d+) not applied: ([A-Za-z][-A-Za-z0-9 ]+[A-Za-z0-9]) is a homonym of (\d+)")
 
+src_fn_pat = re.compile(r"^(additions\-\d+\-\d+):(\d+)$")
+by_study_id = {}
+
 def check_if_del_works(amend_num, name, ott_id, edott, amendments_repo):
     exp_amend_idx = amend_num - 1
     rel_amends = []
@@ -20,13 +24,28 @@ def check_if_del_works(amend_num, name, ott_id, edott, amendments_repo):
         return (False, "solo")
     if rel_amends[0][0] == exp_amend_idx:
         return False, "first"
-    found = False
+    found = None
     for ra in rel_amends[1:]:
         if ra[0] == exp_amend_idx:
-            found = True
+            found = ra[1]
             break
-    if not found:
+    if found is None:
         return False, "notfound"
+    taxon = found["taxon"]
+    src = taxon["sourceinfo"]
+    m = src_fn_pat.match(src)
+    if not m:
+        raise ValueError(f"'sourceinfo' {src} does not fit pattern.")
+    fn_frag = m.group(1)
+    bogus_id = int(m.group(2))
+    fn = f"{fn_frag}.json"
+    fp = os.path.join(amendments_repo, "amendments", fn)
+    if not os.path.isfile(fp):
+        raise RuntimeError(f"amendments file {fp} does not exist")
+    offending_amend = read_as_json(fp)
+    study_id = offending_amend['study_id']
+    name_set = by_study_id.setdefault(study_id, set())
+    name_set.add(name)
     return True, ""
 
 def main(edott_fp,
@@ -43,22 +62,42 @@ def main(edott_fp,
                     amend_num = int(hm.group(1))
                     name = hm.group(2)
                     ott_id = int(hm.group(3))
-                    print(amend_num, name, ott_id)
                     rc = check_if_del_works(amend_num, name, ott_id, edott, amendments_repo)
                     if rc[0]:
                         to_del.append(amend_num)
                     else:
                         prob = rc[1]
                         if prob == "solo":
-                            print("Atypical homonym. Solo in amendments {amend_num}:", edott[amend_num -1])
+                            sys.stderr.write(f"Atypical homonym. Solo in amendments {amend_num}: {edott[amend_num -1]}\n")
                         elif prob == "notfound":
-                            print("PROBLEM {amend_num} does not match:", edott[amend_num -1])
+                            sys.stderr.write(f"PROBLEM {amend_num} does not match: {edott[amend_num -1]}\n")
                         else:
                             assert(prob == "first")
-                            print("Atypical homonym. First in amendments {amend_num} is bad:", edott[amend_num -1])
+                            sys.stderr.write(f"Atypical homonym. First in amendments {amend_num} is bad: {edott[amend_num -1]}\n")
                 else:
-                    print(m.group(1), "not a homonym")
+                    sys.stderr.write(m.group(1) + " not a homonym")
+    sk = list(by_study_id.keys())
+    sk.sort()
+    for study_id in sk:
+        name_set = by_study_id[study_id]
+        if len(name_set) == 1:
+            name = next(name_set)
+            sys.stderr.write(f"In https://tree.opentreeoflife.org/curator/study/view/{study_id} need to remap 1 taxon: \"{name}\"\n") 
+        else:
+            sys.stderr.write(f"In https://tree.opentreeoflife.org/curator/study/view/{study_id} need to remap {len(name_set)} taxa:\n")
+            nl = list(name_set)
+            nl.sort()
+            for name in nl:
+                sys.stderr.write(f"    \"{name}\"\n")
 
+    if to_del:
+        tds = set([i-1 for i in to_del])
+        new_edott = []
+        for amend_idx, amend in enumerate(edott):
+            if amend_idx not in tds:
+                new_edott.append(amend)
+        write_as_json(new_edott, sys.stdout, indent=2)
+        
 if __name__ == "__main__":
     try:
         _args = list(sys.argv[1:4])