diff --git a/prepare_input.py b/prepare_input.py
index 19f970df9ee0f62f0b970dd597a4e7ccbaff42cb..334be25f6852191e59dd04dc32a14b427c2fab47 100644
--- a/prepare_input.py
+++ b/prepare_input.py
@@ -77,7 +77,7 @@ def get_volume(name, volume):
def get_journal(name):
if name not in journals.keys():
- return "*** Unknown journal '" + name + "' encountered! Please put it in the list of known journals or remove this article from the input list. ***"
+ return None
return journals[name]
@@ -102,11 +102,13 @@ def prepare_input(list_of_papers, output_file, configuration, exclusion_list):
dois = []
data = []
- error = []
-
- counter = 0
- counter_skip = 0
- counter_error = 0
+ unknownJournals = set()
+ unknown_counter = 0
+ skip_counter = 0
+ excluded = []
+ duplicates = []
+ noAuthor = []
+ invalidPage = []
# Loop over all papers which are stored in bib
for n, p in enumerate(list_of_papers.entries, 1):
@@ -119,12 +121,14 @@ def prepare_input(list_of_papers, output_file, configuration, exclusion_list):
doi_lower = doi.lower()
# Skip excluded DOIs
if doi_lower in exclusion_list:
- counter_skip += 1
+ skip_counter += 1
+ excluded.append(doi)
print('\nINFO: This paper with DOI:{} is excluded and will be skipped.'.format(doi))
continue
# Skip any duplicates
if doi_lower in dois:
- counter_skip += 1
+ skip_counter += 1
+ duplicates.append(doi)
print('\nWARNING: This paper with DOI:{} is a duplicate and will be skipped.'.format(doi))
continue
else:
@@ -132,7 +136,20 @@ def prepare_input(list_of_papers, output_file, configuration, exclusion_list):
# Get the arXiv paper id (if defined)
eprint = (p['eprint'] if 'eprint' in p else '')
-
+
+ # Get fixed journal name (see more detailed description above)
+ journal_name = get_name(p['journal'], p['volume'])
+
+ # Journal (according to CroRIS nomenclature)
+ journal = get_journal(journal_name)
+
+ # Catch articles from unknown journals
+ if journal is None:
+ unknown_counter += 1
+ unknownJournals.add(journal_name)
+ print('\nWARNING: This paper with DOI:{} was published in an unknown journal {}. Skipping.'.format(doi, journal_name))
+ continue
+
# Fetch paper data from Inspire HEP in JSON format
# More info at: https://github.com/inspirehep/rest-api-doc
url = 'https://inspirehep.net/api/doi/{}'.format(doi)
@@ -206,7 +223,8 @@ def prepare_input(list_of_papers, output_file, configuration, exclusion_list):
# Check if any authors are found
if len(authors_pretty)==0:
- counter_skip += 1
+ skip_counter += 1
+ noAuthor.append(doi)
print('\nWARNING: No authors found for this paper with DOI:{}. Skipping.'.format(doi))
continue
@@ -307,15 +325,9 @@ def prepare_input(list_of_papers, output_file, configuration, exclusion_list):
# Year
year = p['year']
- # Get fixed journal name (see more detailed description above)
- journal_name = get_name(p['journal'], p['volume'])
-
# Volume
volume = get_volume(p['journal'], p['volume'])
- # Journal (according to CroRIS nomenclature)
- journal = get_journal(journal_name)
-
# ISSN
issn = get_issn(journal_name)
@@ -398,6 +410,13 @@ def prepare_input(list_of_papers, output_file, configuration, exclusion_list):
_temp['ukupno_stranica'] = page_tot
validity_counter[1] += 1
+ # Check page info status
+ if validity_counter[0] < 2 and validity_counter[1] < 2:
+ skip_counter += 1
+ invalidPage.append(doi)
+ print('\nWARNING: This paper with DOI:{} has invalid page info. Skipping.'.format(doi))
+ continue
+
ml = [
{
"jezik": "en",
@@ -424,13 +443,9 @@ def prepare_input(list_of_papers, output_file, configuration, exclusion_list):
projekti.append(p_dict)
_temp['projekti'] = projekti
- # Catch articles with unknown journal or invalid page info status
- if 'Unknown journal' in journal or (validity_counter[0] < 2 and validity_counter[1] < 2):
- error.append(_temp)
- counter_error += 1
- else:
- data.append(_temp)
- counter += 1
+
+ # Append paper info
+ data.append(_temp)
print('\nDOI:', doi)
print('arXiv:', (eprint if eprint != '' else 'N/A'))
@@ -452,22 +467,38 @@ def prepare_input(list_of_papers, output_file, configuration, exclusion_list):
print('------------------------------------------------')
- print('\n%i paper(s) prepared for upload\n' % counter)
- if counter_skip > 0:
- print('%i paper(s) skipped\n' % counter_skip)
- if counter_error > 0:
- print('%i paper(s) with unknown journal(s)\n' % counter_error)
+ print('\n%i paper(s) prepared for upload' % len(data))
+ if skip_counter > 0:
+ print('\n%i paper(s) skipped:' % skip_counter)
+ if len(excluded) > 0:
+ print('\n %i excluded DOIs:\n' % len(excluded))
+ for doi in excluded:
+ print(' {}'.format(doi))
+ if len(duplicates) > 0:
+ print('\n %i duplicate DOIs:\n' % len(duplicates))
+ for doi in duplicates:
+ print(' {}'.format(doi))
+ if len(noAuthor) > 0:
+ print('\n %i DOIs with missing author info:\n' % len(noAuthor))
+ for doi in noAuthor:
+ print(' {}'.format(doi))
+ if len(invalidPage) > 0:
+ print('\n %i DOIs with invalid page info:\n' % len(invalidPage))
+ for doi in invalidPage:
+ print(' {}'.format(doi))
+ if unknown_counter == 0:
+ print('')
+ if unknown_counter > 0:
+ print('\n%i paper(s) from the following unknown journal(s):\n' % unknown_counter)
+ for j in sorted(unknownJournals):
+ print(j)
+ print('\nPlease add the unknown journal info to configuration.py\n')
# Output file, i.e. input for CroRIS
- if counter > 0:
+ if len(data) > 0:
with open(output_file, 'w', encoding='utf8') as outfile:
json.dump(data, outfile, ensure_ascii=False, indent=2)
- # Output file for papers with unknown journals
- if counter_error > 0:
- with open(output_file.rstrip('.json')+'_error.json', 'w', encoding='utf8') as outfile:
- json.dump(error, outfile, ensure_ascii=False, indent=2)
-
# --------------------------------------------------
if __name__ == '__main__':