Simplified getting all authors for a list of PMIDs

src/pmidcite/icite/entry.py

@@ -83,6 +83,10 @@ def from_jsondct(cls, icite_dct, nih_group_num):
         cls_dct['num_refs'] = len(icite_dct['references'])
         return cls(icite_dct['pmid'], cls_dct)
 
+    def get_authors(self):
+        """Get the list of authors from NIH's iCite for this paper"""
+        return self.dct.get('authors')
+
     def get_au1_lastname(self):
         """Get the last name of the first author"""
         aus = self.dct['authors']

src/pmidcite/icite/paper.py

@@ -50,18 +50,22 @@ def get_icite(self):
         """Get NIHiCiteEntry for this paper"""
         return self.pmid2icite[self.pmid]
 
+    def get_authors(self):
+        """Get authors for this paper"""
+        return self.pmid2icite[self.pmid].get_authors()
+
     def str_line(self):
         """Return a string summarizing the the paper described herein"""
         txt = str(self.icite)
         if not self.pmid2note:
             return txt
         if self.pmid in self.pmid2note:
-            return '{TXT} {NOTE}'.format(TXT=txt, NOTE=self.pmid2note[self.pmid])
+            return f'{txt} {self.pmid2note[self.pmid]}'
         return txt
 
     def prt_top(self, prt=stdout):
         """Print TOP paper"""
-        prt.write('TOP {iCite}\n'.format(iCite=self.str_line()))
+        prt.write(f'TOP {self.str_line()}\n')
 
     @staticmethod
     def prt_keys(prt=stdout):
@@ -74,23 +78,21 @@ def prt_keys(prt=stdout):
     def prt_summary(self, prt=stdout, sortby_cites='nih_group', sortby_refs='nih_group'):
         """Print summary of paper"""
         if self.hdr:
-            prt.write('NAME: {NAME}\n'.format(NAME=self.hdr))
-        prt.write('TOP {iCite}\n'.format(iCite=self.str_line()))
+            prt.write(f'NAME: {self.hdr}\n')
+        prt.write(f'TOP {self.str_line()}\n')
         # Citations by clinical papers
         if self.cited_by_clin:
-            prt.write('Cited by {N} Clinical papers:\n'.format(N=len(self.cited_by_clin)))
+            prt.write(f'Cited by {len(self.cited_by_clin)} Clinical papers:\n')
         self._prt_list(self.cited_by_clin, 'CLI', prt, sortby_cites)
         # Citations
         if self.cited_by:
-            prt.write('{N} of {M} citations downloaded:\n'.format(
-                N=len(self.cited_by),
-                M=self.icite.dct['citation_count']))
+            prt.write(f'{len(self.cited_by)} of {self.icite.dct["citation_count"]} '
+                       'citations downloaded:\n')
         self._prt_list(self.cited_by, 'CIT', prt, sortby_cites)
         # References
         if self.references:
-            prt.write('{N} of {M} References downloaded:\n'.format(
-                N=len(self.references),
-                M=self.icite.dct['num_refs']))
+            prt.write(f'{len(self.references)} of {self.icite.dct["num_refs"]} '
+                       'References downloaded:\n')
             self._prt_list(self.references, 'REF', prt, sortby_refs)
 
     def get_sorted(self, icites, sortby=None):
@@ -109,13 +111,12 @@ def _prt_list(self, icites, desc, prt, sortby=None):
             s_pmid2note = self.pmid2note
             for icite in icites:
                 if icite.pmid in s_pmid2note:
-                    prt.write('{DESC} {iCite} {note}\n'.format(
-                        DESC=desc, iCite=str(icite), note=s_pmid2note[icite.pmid]))
+                    prt.write(f'{desc} {str(icite)} {s_pmid2note[icite.pmid]}\n')
                 else:
-                    prt.write('{DESC} {iCite}\n'.format(DESC=desc, iCite=str(icite)))
+                    prt.write('{desc} {str(icite.}\n')
             return
         for icite in icites:
-            prt.write('{DESC} {iCite}\n'.format(DESC=desc, iCite=str(icite)))
+            prt.write('{desc} {str(icite)}\n')
 
     def _init_pmids(self, name):
         """Load citation/reference PMIDs, if the 'top' paper has NIH iCite data"""
@@ -128,15 +129,5 @@ def __str__(self):
         """Get the line containing data downloaded from NIH iCite for only the featured paper"""
         return self.str_line()
 
-    ## TBD:
-    ## def __eq__(self, rhs):
-    ##     if self.pmid != rhs.pmid:
-    ##         return False
-    ##     if self.cited_by != rhs.cited_by:
-    ##         print('LHS:', self.cited_by)
-    ##         print('RHS:', rhs.cited_by)
-    ##         return False
-    ##     return True
-
 
 # Copyright (C) 2019-present DV Klopfenstein, PhD. All rights reserved.

src/tests/test_selfcite.py

@@ -1,20 +1,18 @@
 #!/usr/bin/env python3
-"""Test self-citing functions"""
+"""Test getting all authors for a bunch of papers"""
 
 from pmidcite.cfg import Cfg
-from pmidcite.icite.entry import NIHiCiteEntry
-#from pmidcite.cli.entry_keyset import get_details_cites_refs
 from pmidcite.icite.downloader import get_downloader
 
 def test_selfcite():
-    """Test self-citing functions"""
-    authors = [
-        'Nasserdine Papa Mze',
-        'Cécile Fernand-Laurent',
-        'Solen Daugabel',
-        'Olfa Zanzouri',
-        'Stéphanie Marque Juillet',
-    ]
+    """Test getting all authors for a bunch of papers"""
+    #authors = [
+    #    'Nasserdine Papa Mze',
+    #    'Cécile Fernand-Laurent',
+    #    'Solen Daugabel',
+    #    'Olfa Zanzouri',
+    #    'Stéphanie Marque Juillet',
+    #]
     ref_pmids = [
         30753724, # TOP 30753724 H.M.c 40 2 2019    10  1  22 au[41](Lambert Assoumou)
         30517632, # TOP 30517632 H.M.. 21 2 2019     5  0  35 au[17](Paula C Aulicino)
@@ -31,28 +29,20 @@ def test_selfcite():
     ]
 
     cfg = Cfg()
-
-    details_cites_refs = set(NIHiCiteEntry.associated_pmid_keys)
-    print(f'details_cites_refs: {details_cites_refs}')
-
     groupobj = cfg.get_nihgrouper()
-    print(groupobj)
-
     dnldr = get_downloader(groupobj)
-    print(dnldr)
 
-    pmid2icitepaper = dnldr.get_pmid2paper(ref_pmids, None)
     # Get PMID and pmidcite.icite.paper.NIHiCitePaper
-    # TODO: Improve researcher experience here
+    pmid2icitepaper = dnldr.get_pmid2paper(ref_pmids, None)
     for pmid, icitepaper in pmid2icitepaper.items():
-        entry = icitepaper.get_icite()
-        authors = entry.dct['authors']
-        print(entry)
-        for author in authors:
-            print(f'{pmid:8} {author}')
-
-    print()
-    print(entry.dct.keys())
+        for author in icitepaper.get_authors():
+            print(f'PAPER: {pmid:8} {author}')
+
+    # Even simpler:
+    # Get pmidcite.icite.paper.NIHiCiteEntry for each PMID in the references
+    for icitepaper in dnldr.get_icites(ref_pmids):
+        for author in icitepaper.get_authors():
+            print(f'iCite: {icitepaper.pmid:8} {author}')
 
 
 if __name__ == '__main__':