Merge pull request #49 from dvklopfenstein/dvk

Summarize NIH citation data for a set of PMIDs

CHANGELOG.md

@@ -3,6 +3,7 @@
 ## Summary
 
 * [**Unreleased**](#unreleased)
+* [**Release 2022-12-22 v0.0.41**](#release-2022-12-22-v0042) Added summarize_papers script
 * [**Release 2022-12-06 v0.0.41**](#release-2022-12-06-v0041) setup.py updates for make target, install 
 * [**Release 2022-11-26 v0.0.40**](#release-2022-11-28-v0040) Added pmidcite.scripts.icite; pip3, not pip from Python2
 * [**Release 2022-11-26 v0.0.38**](#release-2022-11-26-v0038) Added instructions, and console_script to run script, icite
@@ -42,6 +43,11 @@
 
 ### Unreleased
 
+### release 2022-12-30 v0.0.42
+* ADDED summarize_papers script
+* ADDED requests package as a pre-requisite
+* CHANGED API to NCBI E-utils such that a missing LID (Local ID) is ignored on a PubMed entry
+
 ### release 2022-12-06 v0.0.41
 * CHANGED setup.py PACKAGES variable to run install make target
 

README.md

@@ -1,4 +1,4 @@
-# PubMed ID (PMID) Cite
+# PubMedj ID (PMID) Cite
 
 [![Tweet](https://img.shields.io/twitter/url/http/shields.io.svg?style=social)](https://twitter.com/intent/tweet?text=Python%20library%20to%20download%20pubmed%20citation%20counts%20and%20data,%20given%20a%20PMID&url=https://github.com/dvklopfenstein/pmidcite&via=dvklopfenstein&hashtags=pubmed,pmid,citations,pubmed2cite,writingtips,scientificwriting)
 [![build](https://github.com/dvklopfenstein/pmidcite/actions/workflows/build.yml/badge.svg)](https://github.com/dvklopfenstein/pmidcite/actions/workflows/build.yml)
@@ -20,6 +20,7 @@ Contact: [email protected]
 * [**1) Download citation counts and data for a research paper**](https://github.com/dvklopfenstein/pmidcite#1-download-citation-counts-and-data-for-a-research-paper)
 * [**2) Forward citation search**](https://github.com/dvklopfenstein/pmidcite#2-forward-citation-search): following a paper's *Cited by* links or *Forward snowballing*
 * [**3) Backward citation search**](https://github.com/dvklopfenstein/pmidcite#3-backward-citation-search): following the links to a paper's references or *Backward snowballing*
+* [**4) Summarize a group of citations**](https://github.com/dvklopfenstein/pmidcite#4-summarize-a-group-of-citations)
 
 ## 1) Download citation counts and data for a research paper
 ```$ icite -H 26032263```    
@@ -56,6 +57,57 @@ Also known as following links to a paper's references or *Backward snowballing*
 or    
 ```$ icite -H; icite 26032263 -r | sort -k6 -r```     
 
+## 4) Summarize a group of citations
+* 4a) Examine a paper with PMID `30022098`. Print the column headers(`-H`):   
+`icite -H 30022098`
+* 4b) Download the details about each paper(`-c`) that cites `30022098` into a file(`-o goatools_cites.txt`):    
+`icite 30022098 -c -o goatools_cites.txt`
+* 4c) Summarize the overall performace of the 300+ citing papers contained in `goatools_cites.txt`    
+`summarize_papers goatools_cites.txt -p TOP CIT CLI`
+
+### 4a) Examine a paper with PMID `30022098`. Print the column headers(`-H`):
+```
+$ icite -H 30022098
+COL 2        3  4       5 6 7        8  9  10 au[11](authors)
+TYP PMID     RP HAMCc   % G YEAR   cit cli ref au[00](authors) title
+TOP 30022098 R. .A..c 100 4 2018   318  1  23 au[14](D V Klopfenstein) GOATOOLS: A Python library for Gene Ontology analyses.
+```
+
+Paper with PMID `30022098` is cited by `318`(`cit`) other research papers and `1`(`cli`) clinical study. It has `23` references(`ref`).    
+
+### 4b) Download the details about each paper(`-c`) that cites `30022098` into a file(`-o goatools_cites.txt`):
+```
+$ icite 30022098 -c -o goatools_cites.txt
+```
+
+The requested paper (PMID=`30022098`) is described in one one line in `goatools_cites.txt`:
+```
+$ grep TOP goatools_cites.txt
+TOP 30022098 R. .A..c 100 4 2018   318  1  23 au[14](D V Klopfenstein) GOATOOLS: A Python library for Gene Ontology analyses.
+```
+
+The paper (PMID=`30022098`) is cited by 381(`CIT`) research papers plus 1(`CLI`) clinical study:
+```
+$ grep CIT goatools_cites.txt | wc -l
+318
+
+$ grep CLI goatools_cites.txt | wc -l
+1
+```
+
+### 4c) Summarize all the papers in `goatools_cites.txt`
+**NEW FUNCTIONALITY; INPUT REQUESTED: What would you like to see?** [Open an issue](https://github.com/dvklopfenstein/pmidcite/issues) to comment.   
+```
+$ summarize_papers goatools_cites.txt -p TOP CIT CLI
+i=033.4% 4=003.4% 3=020.9% 2=021.9% 1=015.9% 0=004.4%   4 years:2018-2022   320 papers goatools_cites.txt
+```
+
+* Output is on one line so many files containing sets of PMIDs may be compared. TBD: Add multiline verbose option.
+* The groups are from newest(`i`) to top-performing(`4`), great(`3`), very good(`2`), and overlooked(`1` and `0`)
+* The percentages of papers in `goatools_citations.txt` in each group follow the group name
+
+
+
 # PubMed vs Google Scholar
 <p align="center">
 <img src="https://github.com/dvklopfenstein/pmidcite/raw/main/docs/images/Search_Features_GS_v_PubMed.png" alt="Google Scholar vs PubMed" width="600"/>
@@ -456,4 +508,4 @@ Fiorini N ... Lu Zhiyong
 [email protected]    
 https://orcid.org/0000-0003-0161-7603
 
-Copyright (C) 2019-present [pmidcite](https://dvklopfenstein.github.io/pmidcite/), DV Klopfenstein. All rights reserved.
+Copyright (C) 2019-present [pmidcite](https://dvklopfenstein.github.io/pmidcite/), DV Klopfenstein, PhD. All rights reserved.

makefile

@@ -18,6 +18,9 @@ p:
 d:
 	find src -regextype posix-extended -regex "[a-z./]*" -type d
 
+cli:
+	find src/pmidcite/cli -name \*.py
+
 diff0:
 	git diff --compact-summary
 

setup.py

@@ -10,6 +10,8 @@
 from setuptools import setup
 # import versioneer
 
+__copyright__ = 'Copyright (C) 2019, DV Klopfenstein, PhD. All rights reserved'
+__author__ = 'DV Klopfenstein, PhD'
 
 NAME = 'pmidcite'
 
@@ -42,7 +44,7 @@ def get_long_description():
 setup(
     name=NAME,
     ## version=versioneer.get_version(),
-    version='0.0.41',
+    version='0.0.42',
     author='DV Klopfenstein, PhD',
     author_email='[email protected]',
     ## cmdclass=versioneer.get_cmdclass(),
@@ -55,6 +57,7 @@ def get_long_description():
     entry_points={
         'console_scripts':[
             'icite=pmidcite.scripts.icite:main',
+            'summarize_papers=pmidcite.scripts.icite:summarize_papers',
         ],
     },
     # https://pypi.org/classifiers/
@@ -68,9 +71,11 @@ def get_long_description():
         'Topic :: Scientific/Engineering :: Information Analysis',
     ],
     url='http://github.com/dvklopfenstein/pmidcite',
-    description="Augment's a PubMed literature search with citation data from NIH-OCC's iCite.",
+    description="Turbocharge a PubMed literature search using citation data from the NIH",
     # https://packaging.python.org/guides/making-a-pypi-friendly-readme/
     long_description=get_long_description(),
     long_description_content_type='text/markdown',
-    # install_requires=['docopt'],
+    install_requires=['requests'],
 )
+
+# Copyright (C) 2019, DV Klopfenstein, PhD. All rights reserved

src/bin/icite.py

@@ -1,8 +1,8 @@
 #!/usr/bin/env python3
 """Given a PubMed ID (PMID), return a list of citing publications"""
 
-__copyright__ = "Copyright (C) 2019-present, DV Klopfenstein. All rights reserved."
-__author__ = "DV Klopfenstein"
+__copyright__ = "Copyright (C) 2019-present, DV Klopfenstein, PhD. All rights reserved."
+__author__ = "DV Klopfenstein, PhD"
 
 from pmidcite.cli.icite import NIHiCiteCli  # get_argparser
 from pmidcite.cfg import get_cfgparser
@@ -16,4 +16,4 @@ def main():
 if __name__ == '__main__':
     main()
 
-# Copyright (C) 2019-present, DV Klopfenstein. All rights reserved.
+# Copyright (C) 2019-present, DV Klopfenstein, PhD. All rights reserved.

src/pmidcite/__version__.py

@@ -1,3 +1,3 @@
 """Version of pmidcite project"""
 
-__version__ = '0.0.41'
+__version__ = '0.0.42'

src/pmidcite/cfg.py

@@ -1,7 +1,7 @@
 """Manage pmidcite Configuration"""
 
-__copyright__ = "Copyright (C) 2019-present, DV Klopfenstein. All rights reserved."
-__author__ = "DV Klopfenstein"
+__copyright__ = "Copyright (C) 2019-present, DV Klopfenstein, PhD. All rights reserved."
+__author__ = "DV Klopfenstein, PhD"
 
 from os import environ
 from os import getcwd
@@ -57,7 +57,7 @@ class Cfg(object):
     }
 
     def __init__(self, check=True, prt=stdout, prt_fullname=True):
-        self.cfgfile = self._init_cfgfilename()
+        self.cfgfile = self._init_cfgfilename(prt)
         self.cfgparser = self._get_dflt_cfgparser()
         if check:
             self._run_chk(prt, prt_fullname)
@@ -135,14 +135,14 @@ def _get_dirname_str(dirname):
         """Convert None to the str, "None", as needed by configparser"""
         return 'None' if dirname is None or dirname == 'None' else dirname
 
-    def get_nihgrouper(self):
+    def get_nihgrouper(self, min1=None, min2=None, min3=None, min4=None):
         """Get an NIH Grouper with default values from the cfg file"""
         cfg = self.cfgparser['pmidcite']
         return NihGrouper(
-            float(cfg['group1_min']),
-            float(cfg['group2_min']),
-            float(cfg['group3_min']),
-            float(cfg['group4_min']))
+            float(cfg['group1_min'] if not min1 else min1),
+            float(cfg['group2_min'] if not min2 else min2),
+            float(cfg['group3_min'] if not min3 else min3),
+            float(cfg['group4_min'] if not min4 else min4))
 
     def _run_chk(self, prt, prt_fullname):
         if not self.rd_rc(prt, prt_fullname):
@@ -215,19 +215,18 @@ def prt_rcfile_dflt(self, prt=stdout):
         cfgparser = self._get_dflt_cfgparser()
         cfgparser.write(prt)
 
-    def _init_cfgfilename(self):
+    def _init_cfgfilename(self, prt=None):
         """Get the configuration filename"""
         if self.envvar in environ:
             cfgfile = environ[self.envvar]
             if exists(cfgfile):
                 return cfgfile
-            print('**WARNING: NO pmidcite CONFIG FILE FOUND AT {ENVVAR}={F}'.format(
-                F=cfgfile, ENVVAR=self.envvar))
-        if not exists(self.dfltcfgfile):
-            print('**WARNING: NO pmidcite CONFIG FILE FOUND: {F}'.format(
-                F=self.dfltcfgfile))
+            if prt:
+                prt.write(f'**WARNING: NO pmidcite CONFIG FILE FOUND AT {self.envvar}={cfgfile}\n')
+        if not exists(self.dfltcfgfile) and prt:
+            prt.write(f'**WARNING: NO pmidcite CONFIG FILE FOUND: {self.dfltcfgfile}\n')
         return self.dfltcfgfile
 
 
 
-# Copyright (C) 2019-present DV Klopfenstein. All rights reserved.
+# Copyright (C) 2019-present DV Klopfenstein, PhD. All rights reserved.

src/pmidcite/cli/icite.py

@@ -1,7 +1,7 @@
 """Manage args for NIH iCite run for one PubMed ID (PMID)"""
 
-__copyright__ = "Copyright (C) 2019-present, DV Klopfenstein. All rights reserved."
-__author__ = "DV Klopfenstein"
+__copyright__ = "Copyright (C) 2019-present, DV Klopfenstein, PhD. All rights reserved."
+__author__ = "DV Klopfenstein, PhD"
 
 from sys import stdout
 import argparse
@@ -11,7 +11,7 @@
 from pmidcite.cli.utils import get_outfile
 from pmidcite.cli.utils import get_pmids
 from pmidcite.cli.entry_keyset import get_details_cites_refs
-from pmidcite.icite.nih_grouper import NihGrouper
+from pmidcite.icite.nih_grouper import get_nihgrouper
 from pmidcite.icite.downloader import get_downloader
 from pmidcite.icite.downloader import prt_hdr
 from pmidcite.icite.downloader import prt_keys
@@ -61,10 +61,10 @@ def get_argparser(self):
             help='Load and print a descriptive list of citations and references for each paper.')
         parser.add_argument(
             '-c', '--load_citations', action='store_true', default=False,
-            help='Load and print a descriptive list of citations for each paper.')
+            help='Load and print of papers and clinical studies that cited the requested paper.')
         parser.add_argument(
             '-r', '--load_references', action='store_true', default=False,
-            help='Load and print a descriptive list of references for each paper.')
+            help='Load and print the references for each requested paper.')
         # pylint: disable=line-too-long
         parser.add_argument(
             '-R', '--no_references', action='store_true',
@@ -120,7 +120,7 @@ def cli(self):
         """Run iCite/PubMed using command-line interface"""
         argparser = self.get_argparser()
         args = self._get_args(argparser)
-        ## print('ICITE ARGS ../pmidcite/src/pmidcite/cli/icite.py', args)
+        ##print('ICITE ARGS ../pmidcite/src/pmidcite/cli/icite.py', args)
         self._run(args, argparser)
 
     def _run(self, args, argparser):
@@ -173,7 +173,7 @@ def _get_downloader(args):
             args.load_citations,
             args.load_references,
             args.no_references)
-        groupobj = NihGrouper(args.min1, args.min2, args.min3, args.min4)
+        groupobj = get_nihgrouper(args.min1, args.min2, args.min3, args.min4)
         return get_downloader(
             details_cites_refs,
             groupobj,
@@ -261,4 +261,4 @@ def _prt_no_icite(pmids):
             Ps=' '.join(str(p) for p in pmids)))
 
 
-# Copyright (C) 2019-present DV Klopfenstein. All rights reserved.
+# Copyright (C) 2019-present DV Klopfenstein, PhD. All rights reserved.

src/pmidcite/cli/summarize_papers.py

@@ -5,6 +5,7 @@
 from pmidcite.cli.utils import prt_loc_rcfile
 from pmidcite.cli.utils import get_files_exists
 from pmidcite.summarize_papers import SummarizePapers
+from pmidcite.icite.top_cit_ref import TopCitRef
 
 __copyright__ = "Copyright (C) 2022-present, DV Klopfenstein, PhD. All rights reserved."
 __author__ = "DV Klopfenstein, PhD"
@@ -15,11 +16,12 @@ class SummarizePapersCli:
 
     def __init__(self, cfg):
         self.cfg = cfg
+        self.topcitref = TopCitRef()
 
     def get_argparser(self):
         """Argument parser for summarizing the citations on set(s) of papers"""
         parser = ArgumentParser(
-            description="Summarize NIH's citation on a set(s) of papers",
+            description="Summarize NIH's citation data on a set(s) of papers",
             add_help=False)
         ##cfg = self.cfg
         # https://docs.python.org/3/library/argparse.html
@@ -48,28 +50,34 @@ def get_argparser(self):
         parser.add_argument(
             '--print-rcfile', action='store_true',
             help='Print the location of the pmidcite configuration file (env var: PMIDCITECONF)')
+        self.topcitref.add_arguments(parser)
         return parser
 
-
     def cli(self):
         """Run citation summary on a set(s) of PMIDs"""
         argparser = self.get_argparser()
         args = argparser.parse_args()
-        print('ARGS CITE SUMMARY ../pmidcite/src/pmidcite/cli/summarize_papers.py', args)
+        ##print('ARGS CITE SUMMARY ../pmidcite/src/pmidcite/cli/summarize_papers.py', args)
         if args.print_rcfile:
             prt_loc_rcfile(self.cfg, stdout)
-            return
-        files = get_files_exists(args.files)
+        files = get_files_exists(args.files, stdout)
         if args.help or not files:
             argparser.print_help()
-            print('\nHelp message printed because: -h or --help == True')
-            return
-        ##self._run(args, argparser)
-        nih_grouper = self.cfg.get_nihgrouper()
+            ##print(f'\nHelp message printed because: -h or --help == {args.help} or {args.files}')
+        nih_grouper = self.cfg.get_nihgrouper(args.min1, args.min2, args.min3, args.min4)
+        self._summarize_papers(files, nih_grouper, self.topcitref.adjust_args(args.paper_labels))
+        if args.prt_nihgrpr:
+            print(nih_grouper)
+
+    @staticmethod
+    def _summarize_papers(files, nih_grouper, top_cit_refs):
+        """Summarize papers"""
         for filename in files:
-            sumpap = SummarizePapers.from_file(filename, nih_grouper)
+            sumpap = SummarizePapers.from_file(
+                filename=filename,
+                nih_grouper=nih_grouper,
+                top_cit_ref=top_cit_refs)
             print(sumpap.str_oneline())
-        return
 
 
 # Copyright (C) 2022-present, DV Klopfenstein, PhD. All rights reserved.

src/pmidcite/eutils/pubmed/rdwr.py

@@ -1,7 +1,7 @@
 """Write Python module for downloaded abstracts."""
 
-__copyright__ = "Copyright (C) 2019-present, DV Klopfenstein. All rights reserved."
-__author__ = "DV Klopfenstein"
+__copyright__ = "Copyright (C) 2019-present, DV Klopfenstein, PhD. All rights reserved."
+__author__ = "DV Klopfenstein, PhD"
 
 import sys
 import os
@@ -151,8 +151,9 @@ def _lid_add_to_dict(fld2objs, fld, line, pmid):
         if fld not in fld2objs:
             fld2objs[fld] = {}
         key0 = line.rfind('[')
-        # TBD Change these fatals to messages
-        assert key0 != -1, '**FATAL LID: {} {}'.format(fld, line)
+        if key0 == -1:
+            ##print(f'**WARNING Local ID (LID): {fld} KEY({key0}) {line}')
+            return
         assert line[-1] == ']', '**FATAL LID: {} {}'.format(fld, line)
         key = line[key0 + 1:-1]
         val = line[:key0].strip()
@@ -347,7 +348,7 @@ def _init_date(self, fld2objs, fld, str_date, pmid):
 
                         #### mtch = match(r'(\d{4} \S{3} \d{1,2})\s*-', str_date)
                         #### if mtch:
-                        ####     fld2objs[fld] = datetime.datetime.strptime(mtch.group(1), "%Y %b %d")
+                        ##     fld2objs[fld] = datetime.datetime.strptime(mtch.group(1), "%Y %b %d")
                         #### mtch = match(r'(\d{4} \S{3})\w?\s*-', str_date)
                         #### if mtch:
                         ####     fld2objs[fld] = datetime.datetime.strptime(mtch.group(1), "%Y %b")
@@ -453,4 +454,4 @@ def _extract_fldvals(self, line):
                     self.fldvals[-1][1].append(line_body)
 
 
-  # Copyright (C) 2019-present, DV Klopfenstein. All rights reserved.
+  # Copyright (C) 2019-present, DV Klopfenstein, PhD. All rights reserved.