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Examples of basic allofplos functions





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import datetime
from allofplos.plos_regex import (validate_doi, show_invalid_dois, find_valid_dois)
from allofplos.samples.corpus_analysis import (get_random_list_of_dois, get_all_local_dois,
                                               get_all_plos_dois)
from allofplos.corpus.plos_corpus import (get_uncorrected_proofs, get_all_solr_dois)
from allofplos import Article

Get example DOIs: get_random_list_of_dois()





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example_dois = get_random_list_of_dois(count=10)
example_doi = example_dois[0]
article = Article(example_doi)
example_file = article.filepath
example_url = article.url
print("Three ways to represent an article\nArticle as DOI: {}\nArticle as local file: {}\nArticle as url: {}" \
       .format(example_doi, example_file, example_url))



    


















    






Three ways to represent an article
Article as DOI: 10.1371/journal.pone.0088313
Article as local file: allofplos_xml/journal.pone.0088313.xml
Article as url: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0088313&type=manuscript

















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example_corrections_dois = ['10.1371/journal.pone.0166537',
                            '10.1371/journal.ppat.1005301',
                            '10.1371/journal.pone.0100397']



    











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example_retractions_dois = ['10.1371/journal.pone.0180272',
                            '10.1371/journal.pone.0155388',
                            '10.1371/journal.pone.0102411']



    











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example_vor_doi = '10.1371/journal.ppat.1006307'
example_uncorrected_proofs = get_uncorrected_proofs()

Validate PLOS DOI format: validate.doi(string), show_invalid_dois(list)





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validate_doi('10.1371/journal.pbio.2000797')



    











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validate_doi('10.1371/journal.pone.12345678')  # too many trailing digits



    











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doi_list = ['10.1371/journal.pbio.2000797', '10.1371/journal.pone.12345678', '10.1371/journal.pmed.1234567']
show_invalid_dois(doi_list)

Check if a DOI resolves correctly: article.check_if_doi_resolves()





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article = Article('10.1371/journal.pbio.2000797')  # working DOI
article.check_if_doi_resolves()



    











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article = Article('10.1371/annotation/b8b66a84-4919-4a3e-ba3e-bb11f3853755')   # working DOI
article.check_if_doi_resolves()



    











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article = Article('10.1371/journal.pone.1111111')  # valid DOI structure, but article doesn't exist
article.check_if_doi_resolves()

Check if uncorrected proof: article.proof





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article = Article(next(iter(example_uncorrected_proofs)))
article.proof



    











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article = Article(example_vor_doi)
article.proof

Find PLOS DOIs in a string: find_valid_dois(string)





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find_valid_dois("ever seen 10.1371/journal.pbio.2000797, it's great! or maybe 10.1371/journal.pone.1234567?")

Get article pubdate: article.pubdate





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# returns a datetime object
article = Article(example_doi)
article.pubdate



    











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# datetime object can be transformed into any string format
article = Article(example_doi)
dates = article.get_dates(string_=True, string_format='%Y-%b-%d')
print(dates['epub'])

Check (JATS) article type of article file: article.type_





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article = Article(example_doi)
article.authors



    


















    
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[{'affiliations': ['Department of Psychology, Elmhurst College, Elmhurst, Illinois, United States of America'],
  'author_roles': {'author_notes': ['Conceived and designed the experiments',
    'Performed the experiments',
    'Analyzed the data',
    'Contributed reagents/materials/analysis tools',
    'Wrote the paper']},
  'author_type': 'corresponding',
  'contrib_initials': 'KSM',
  'contrib_type': 'author',
  'editor_type': None,
  'email': ['katherine.moore@elmhurst.edu'],
  'footnotes': [],
  'given_names': 'Katherine Sledge',
  'group_name': None,
  'ids': [],
  'rid_dict': {'aff': ['aff1'], 'corresp': ['cor1']},
  'surname': 'Moore'},
 {'affiliations': ['Department of Psychology, University of Michigan, Ann Arbor, Michigan, United States of America'],
  'author_roles': {'author_notes': ['Conceived and designed the experiments',
    'Wrote the paper']},
  'author_type': 'contributing',
  'contrib_initials': 'DHW',
  'contrib_type': 'author',
  'editor_type': None,
  'email': None,
  'footnotes': [],
  'given_names': 'Daniel H.',
  'group_name': None,
  'ids': [],
  'rid_dict': {'aff': ['aff2']},
  'surname': 'Weissman'}]

















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article = Article(example_corrections_dois[0])
article.type_



    











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article = Article(example_retractions_dois[0])
article.type_

For corrections and retractions, get the DOI(s) of the PLOS articles being retracted or corrected.





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article = Article(example_corrections_dois[0])
article.related_dois



    











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article = Article(example_retractions_dois[0])
article.related_dois

Working with many articles at once

Get list of every article DOI indexed on the PLOS search API, Solr: get_all_solr_dois()





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solr_dois = get_all_solr_dois()
print(len(solr_dois), "articles indexed on Solr.")

Get list of every PLOS article you have downloaded: get_all_local_dois()





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all_articles = get_all_local_dois()
print(len(all_articles), "articles on local computer.")

Combine local and solr articles: get_all_plos_dois()





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plos_articles = get_all_plos_dois()



    











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download_updated_xml('allofplos_xml/journal.pcbi.0030158.xml')

Content source: PLOS/allofplos

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