Partial DOIs

allofplos/article.py

@@ -9,8 +9,9 @@
 
 from . import get_corpus_dir
 from .transformations import (filename_to_doi, _get_base_page, LANDING_PAGE_SUFFIX,
-                              URL_SUFFIX, plos_page_dict, doi_url, doi_to_url, doi_to_path)
-from .plos_regex import validate_doi
+                              URL_SUFFIX, plos_page_dict, doi_url, doi_to_url, doi_to_path,
+                              partial_to_doi)
+from .plos_regex import validate_doi, find_valid_partial_dois
 from .elements import (parse_article_date, get_contrib_info,
                        Journal, License, match_contribs_to_dicts)
 from .utils import dedent
@@ -124,6 +125,11 @@ def doi(self):
         """
         return self._doi
 
+    @property
+    def partial_doi(self):
+        """Convert a DOI to a partial DOI."""
+        return self.doi.lstrip('10.1371/').replace('journal.', '')
+
     @property
     def text_viewer(self):
         """Command line application for viewing text to be used with
@@ -1336,3 +1342,15 @@ def from_filename(cls, filename):
         else:
             directory = None
         return cls(filename_to_doi(filename), directory=directory)
+
+    @classmethod
+    def from_partial_doi(cls, partial_doi, directory=None):
+        """Initiate an article object using a partial DOI.
+        Uses regex to make sure it's a valid partial DOI.
+        Used for internal PLOS methods.
+        """
+        if directory is None:
+            directory = get_corpus_dir()
+        doi = partial_to_doi(partial_doi)
+
+        return cls(doi, directory=directory)

allofplos/corpus/corpus.py

@@ -5,7 +5,8 @@
 from itertools import islice
 
 from .. import get_corpus_dir, Article
-from ..transformations import filename_to_doi, doi_to_path
+from ..transformations import filename_to_doi, doi_to_path, partial_to_doi
+from ..plos_regex import validate_doi, validate_partial_doi
 
 
 class Corpus:
@@ -36,13 +37,16 @@ def __iter__(self):
         return (article for article in self.random_article_generator)
 
     def __getitem__(self, key):
-
         if isinstance(key, int):
             return Article(self.dois[key], directory=self.directory)
         elif isinstance(key, slice):
             return (Article(doi, directory=self.directory) 
                     for doi in self.dois[key])
         elif key not in self.dois:
+            if partial_to_doi(key) in self.dois:
+                return Article.from_partial_doi(key, directory=self.directory)
+            elif validate_partial_doi(key):
+                key = partial_to_doi(key)
             path= doi_to_path(key, directory=self.directory)
             raise IndexError(("You attempted get {doi} from "
                               "the corpus at \n{directory}. \n"

allofplos/plos_regex.py

@@ -22,6 +22,10 @@
 full_doi_regex_match = re.compile(regex_match_prefix+regex_body_match)
 full_doi_regex_search = re.compile(r"10\.1371/journal\.p[a-zA-Z]{3}\.[\d]{7}"
                                    "|10\.1371/annotation/[a-zA-Z0-9]{8}-[a-zA-Z0-9]{4}-[a-zA-Z0-9]{4}-[a-zA-Z0-9]{4}-[a-zA-Z0-9]{12}")
+partial_doi_regex_search = re.compile(r"p[a-zA-Z]{3}\.[\d]{7}"
+                                      "|annotation/[a-zA-Z0-9]{8}-[a-zA-Z0-9]{4}-[a-zA-Z0-9]{4}-[a-zA-Z0-9]{4}-[a-zA-Z0-9]{12}")
+partial_doi_regex_match = re.compile(r"^p[a-zA-Z]{3}\.[\d]{7}$"
+                                     r"|^annotation/[a-zA-Z0-9]{8}-[a-zA-Z0-9]{4}-[a-zA-Z0-9]{4}-[a-zA-Z0-9]{4}-[a-zA-Z0-9]{12}$")
 currents_doi_regex = re.compile(regex_match_prefix+regex_body_currents)
 file_regex_match = re.compile(regex_file_search+r"\.xml")
 BASE_URL = 'http://journals.plos.org/plosone/article/file?id='
@@ -41,6 +45,14 @@ def validate_doi(doi):
     return bool(full_doi_regex_match.search(doi))
 
 
+def validate_partial_doi(partial_doi):
+    """For an individual string, tests whether the full string is in a valid PLOS partial DOI format.
+    Example: 'pbio.2000777' is True, but '10.1371/journal.pbio.2000777' is False
+    :return: True if string is in valid PLOS partial DOI format; False if not
+    """ 
+    return bool(partial_doi_regex_match.search(partial_doi))
+
+
 def validate_filename(filename):
     """
     For an individual string, tests whether the full string is in a valid article file. This can take two forms.
@@ -75,6 +87,15 @@ def find_valid_dois(doi):
     return full_doi_regex_search.findall(doi)
 
 
+def find_valid_partial_dois(doi):
+    """
+    For an individual string, searches for any valid partial PLOS DOIs within it and returns them
+    Used for finding DOIs in PLOS job tickets
+    :return: list of valid PLOS partial DOIs contained within string
+    """
+    return partial_doi_regex_search.findall(doi)
+
+
 def show_invalid_dois(doi_list):
     """
     Checks to see whether a list of PLOS DOIs follow the correct format. Used mainly to determine

allofplos/tests/test_partial_dois.py

@@ -0,0 +1,52 @@
+from .. import Corpus, Article, starterdir
+from ..plos_regex import validate_partial_doi, validate_doi
+from ..transformations import partial_to_doi, doi_to_partial
+
+import pytest
+
+
+@pytest.fixture
+def corpus():
+    return Corpus(starterdir, seed=1000)
+
+
+@pytest.fixture
+def test_article():
+    return Article('10.1371/journal.pone.0040259', directory=starterdir)
+
+
+@pytest.fixture
+def test_doi():
+    return '10.1371/journal.pone.0040259'
+
+
+@pytest.fixture
+def test_partial_doi():
+    return 'pone.0040259'
+
+
+def test_partial_doi_regex(test_partial_doi):
+    assert validate_partial_doi(test_partial_doi)
+    assert not validate_partial_doi(' pone.0040259')
+    assert not validate_partial_doi('pone.0040259 ')
+
+
+def test_partial_doi_transform(test_doi, test_partial_doi):
+    partial_doi = doi_to_partial(test_doi)
+    assert partial_doi == test_partial_doi
+
+
+def test_doi_transform(test_partial_doi, test_doi):
+    doi = partial_to_doi(test_partial_doi)
+    assert validate_doi(doi)
+    assert doi == test_doi
+
+
+def test_partial_doi_method_article(test_partial_doi, test_article):
+    article = Article.from_partial_doi(test_partial_doi, directory=starterdir)
+    assert article == test_article
+
+
+def test_partial_doi_method_corpus(corpus, test_article, test_partial_doi):
+    article = corpus[test_partial_doi]
+    assert article == test_article

allofplos/transformations.py

@@ -5,7 +5,7 @@
 
 from . import get_corpus_dir
 
-from .plos_regex import validate_filename, validate_doi
+from .plos_regex import validate_filename, validate_doi, validate_partial_doi
 from .elements import Journal
 
 # URL bases for PLOS's Solr instances, that index PLOS articles
@@ -183,6 +183,22 @@ def doi_to_path(doi, directory=None):
         article_file = os.path.join(directory, doi.lstrip(PREFIX) + SUFFIX_LOWER)
     return article_file
 
+def partial_to_doi(partial_doi):
+    """Convert a partial DOI into a DOI."""
+    if validate_partial_doi(partial_doi) is False:
+        raise Exception("Invalid format for PLOS partial DOI: {}".format(partial_doi))
+    if partial_doi.startswith('annotation'):
+        doi = PREFIX + partial_doi
+    else:
+        doi = ''.join([PREFIX, 'journal.', partial_doi])
+    return doi
+
+def doi_to_partial(doi):
+    """Convert a DOI into a partial DOI."""
+    if validate_doi(doi) is False:
+        raise Exception("Invalid format for PLOS DOI: {}".format(doi))
+    return doi.lstrip('10.1371/').replace('journal.', '')
+
 
 def convert_country(country):
     """