def parse(self, pmid, *a, **kw):
"""\
Convert pmid into a citation object.
"""
def to_medline(article):
abbr = article.Journal.ISOAbbreviation
pubdate = u' '.join(list(article.Journal.JournalIssue.PubDate))
volume = article.Journal.JournalIssue.Volume
issue = article.Journal.JournalIssue.Issue
pages = article.Pagination.MedlinePgn
result = u'%s %s;%s(%s):%s.' % (abbr, pubdate, volume, issue, pages)
return result
def to_author_list(article):
author = article.AuthorList.Author
if not isinstance(author, list):
author = [author]
return [u'%s %s' % (a.LastName, a.Initials) for a in author]
def to_ids(id_):
# assume info and miriam are all valid
miriam_base = u'urn:miriam:pubmed:%s'
info_base = u'info:pmid/%s'
return [miriam_base % id_, info_base % id_]
# XXX need to verify that we already have this item.
try:
raw = self.service.run_eFetch(db=self.db, id=pmid)
except SOAPTimeoutError:
# XXX handle timeout
raise
except Error:
# XXX any SOAP error
raise
except:
# Other errors will just be raised.
raise
# using info for now
obj_id = str('pmid-%s' % pmid)
article = raw.PubmedArticle.MedlineCitation.Article
citation = Citation(obj_id)
citation.ids = to_ids(pmid)
citation.title = unicode(article.ArticleTitle)
citation.creator = to_author_list(article)
citation.issued = unicode(article.Journal.JournalIssue.PubDate.Year)
try:
# XXX sometimes this is not available.
citation.abstract = unicode(article.Abstract.AbstractText)
except:
citation.abstract = u''
citation.bibliographicCitation = to_medline(article)
return [citation]
def test_0000_json_import_export_cycle(self):
testid = 'test1'
citation = Citation(testid)
citation.ids = [
u'urn:test1',
]
citation.title = u'Test Title One'
citation.creator = [u'Tester One', u'Tester Two']
citation.issued = u'2001-01-01'
citation.bibliographicCitation = u'Test Journal'
citation.abstract = None
self.container[citation.id] = citation
jsonstr = self.exporter.export(self.container)
jsonstream = StringIO(jsonstr)
new_container = self.folder
self.importer.parseInto(new_container, jsonstream)
self.assertEqual(new_container[testid].id, self.container[testid].id)
self.assertEqual(new_container[testid].ids[0],
self.container[testid].ids[0])
self.assertEqual(new_container[testid].title,
self.container[testid].title)
self.assertEqual(new_container[testid].creator,
self.container[testid].creator)
def test_0000_json_import_export_cycle(self):
testid = 'test1'
citation = Citation(testid)
citation.ids = [u'urn:test1',]
citation.title = u'Test Title One'
citation.creator = [u'Tester One', u'Tester Two']
citation.issued = u'2001-01-01'
citation.bibliographicCitation = u'Test Journal'
citation.abstract = None
self.container[citation.id] = citation
jsonstr = self.exporter.export(self.container)
jsonstream = StringIO(jsonstr)
new_container = self.folder
self.importer.parseInto(new_container, jsonstream)
self.assertEqual(new_container[testid].id,
self.container[testid].id)
self.assertEqual(new_container[testid].ids[0],
self.container[testid].ids[0])
self.assertEqual(new_container[testid].title,
self.container[testid].title)
self.assertEqual(new_container[testid].creator,
self.container[testid].creator)
def parse(self, stream=None, *a, **kw):
if not hasattr(stream, 'read'):
raise TypeError('input must be a stream')
raw_items = json.load(stream)
results = []
for raw_citation in raw_items:
rawid = raw_citation['id']
item = Citation(str(rawid))
item.ids = raw_citation['ids']
item.title = raw_citation['title']
item.creator = raw_citation['creator']
item.issued = raw_citation['issued']
item.bibliographicCitation = raw_citation['bibliographicCitation']
results.append(item)
return results
def parse(self, stream=None, *a, **kw):
if not hasattr(stream, 'read'):
raise TypeError('input must be a stream')
raw_items = json.load(stream)
results = []
for raw_citation in raw_items:
rawid = raw_citation['id']
item = Citation(str(rawid))
item.ids = raw_citation['ids']
item.title = raw_citation['title']
item.creator = raw_citation['creator']
item.issued = raw_citation['issued']
item.bibliographicCitation = raw_citation['bibliographicCitation']
results.append(item)
return results
