Exemplo n.º 1
0
Arquivo: core.py Projeto: stared/spnet
 def _query_external(self, fetchID):
     'obtain doc data from crossref / NCBI'
     import doi
     try:
         DOI = self._DOI # use cached value
     except AttributeError: # retrieve from shortdoi.org
         DOI = doi.map_to_doi(fetchID)
     doiDict = doi.get_doi_dict(DOI)
     doiDict['id'] = fetchID # shortDOI
     doiDict['doi'] = DOI
     if self._getPubmed:
         try:
             pubmedDict = doi.get_pubmed_from_doi(DOI)
             if pubmedDict:
                 self._pubmedDict = pubmedDict # cache for saving to parent
         except errors.TimeoutError:
             pass
     return doiDict
Exemplo n.º 2
0
 def _query_external(self, fetchID):
     'obtain doc data from crossref / NCBI'
     import doi
     try:
         DOI = self._DOI  # use cached value
     except AttributeError:  # retrieve from shortdoi.org
         DOI = doi.map_to_doi(fetchID)
     doiDict = doi.get_doi_dict(DOI)
     doiDict['id'] = fetchID  # shortDOI
     doiDict['doi'] = DOI
     if self._getPubmed:
         try:
             pubmedDict = doi.get_pubmed_from_doi(DOI)
             if pubmedDict:
                 self._pubmedDict = pubmedDict  # cache for saving to parent
         except errors.TimeoutError:
             pass
     return doiDict
Exemplo n.º 3
0
def destroy_db_and_test():
    '''tests progressively building an spnet db starting from a blank
    slate, adding papers, people, posts, topics, etc. and verifying
    the expected results.  NB: this is a destructive test, i.e. 
    it FLUSHES whatever is in the spnet database and fills it with
    its own test data.'''
    dbconn = connect.init_connection()
    dbconn._conn.drop_database('spnet') # start test from a blank slate
    rootColl = apptree.get_collections()

    lorem = '''Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.'''

    jojo = core.Person(docData=dict(name='jojo', age=37))
    assert jojo != None
    assert jojo.force_reload(delay=1) is False # set timer
    assert jojo.force_reload() is False # timer still waiting
    time.sleep(2)
    assert jojo.force_reload() # timer done

    a1 = core.EmailAddress(docData=dict(address='*****@*****.**', current=True),
                           parent=jojo)
    fred = core.Person(docData=dict(name='fred', age=56))
    a2 = core.EmailAddress(docData=dict(address='*****@*****.**',
                                        authenticated=False), parent=fred)
    a3 = core.EmailAddress(docData=dict(address='*****@*****.**',
                                        note='personal account'), parent=fred)

    paper1 = core.ArxivPaperData('1302.4871', insertNew='findOrInsert').parent
    paper1.update(dict(authors=[jojo._id]))
    paper2 = core.ArxivPaperData('1205.6541', insertNew='findOrInsert').parent
    paper2.update(dict(authors=[fred._id, jojo._id]))

    assert paper1.arxiv.id == '1302.4871'
    assert paper2.arxiv.id == '1205.6541'

    jojoGplus = core.GplusPersonData(docData=dict(id=1234, displayName='Joseph Nye', image={'url':'http://www.nobelprize.org/nobel_prizes/physics/laureates/1921/einstein.jpg'}),
                                    parent=jojo)
    jojoGplus.update(dict(etag='oldversion'))

    sig1 = core.SIG.find_or_insert('cosmology')
    sig2 = core.SIG.find_or_insert('lambdaCDMmodel')

    topicWords = incoming.get_topicIDs(['cosmology', 'astrophysics'],
                                       1, datetime.utcnow(), 'test')
    assert topicWords == ['cosmology', 'astrophysics']
    astroSIG = core.SIG('astrophysics')
    assert astroSIG.name == '#astrophysics'
    assert astroSIG.origin == dict(source='test', id=1)


    int1 = core.PaperInterest(docData=dict(author=jojo._id, topics=[sig1._id]),
                              parent=paper1)
    assert core.Paper(paper1._id).interests == [int1]
    assert core.Paper(paper1._id).get_interests() == {sig1._id:[jojo]}
    assert core.Person(jojo._id).interests == [int1]
    assert core.Person(jojo._id).topics == [sig1._id]
    assert core.SIG(sig1._id).interests == [int1]
    assert core.SIG(sig1._id).get_interests() == {paper1:[jojo]}

    intAgain = core.PaperInterest((paper1._id, jojo._id))
    assert intAgain == int1
    try:
        intAgain.remove_topic(sig2._id)
    except KeyError:
        pass
    else:
        raise AssertionError('failed to catch bad remove_topic()')
    assert intAgain.remove_topic(sig1._id) is None
    assert core.Paper(paper1._id).interests == []

    # test creation via POST
    paperLikes = rootColl['papers'].likes
    sessioninfo.get_session.sessionDict = dict(person=fred)
    int2 = paperLikes._POST(fred._id, sig2._id, '1',
                            parents=dict(paper=paper2))
    assert int2.parent == paper2
    assert int2.author == fred
    assert int2.topics == [sig2]
    assert core.Paper(paper2._id).interests == [int2]
    assert core.Person(fred._id).interests == [int2]
    assert core.Person(fred._id).topics == [sig2._id]
    assert core.SIG(sig2._id).interests == [int2]
    try:
        paperLikes._POST(fred._id, 'this is not allowed', '1',
                         parents=dict(paper=paper2))
    except KeyError:
        pass
    else:
        raise AssertionError('failed to trap bad topic string')
    # test removal via POST
    assert paperLikes._POST(fred._id, sig2._id, '0',
                            parents=dict(paper=core.Paper(paper2._id))) == int2
    assert core.Paper(paper2._id).interests == []

    int3 = paperLikes._POST(fred._id, '#silicene', '1',
                            parents=dict(paper=paper2))
    assert core.SIG('silicene').interests == [int3]
    assert set(core.Person(fred._id).topics) == set([sig2._id, 'silicene'])


    gplus2 = core.GplusPersonData(docData=dict(id=1234, displayName='Joseph Nye'),
                                  insertNew='findOrInsert')

    assert gplus2 == jojoGplus

    gplus3 = core.GplusPersonData(docData=dict(id=5678, displayName='Fred Eiserling'),
                                  insertNew='findOrInsert')
    assert gplus3.parent.name == 'Fred Eiserling'

    rec1 = core.Post(docData=dict(author=fred._id, citationType='recommend', id='1',
                                  title='Why You Need to Read This Important Extension of the CDM Model',
                                  text=lorem),
                               parent=paper1)
    rec2 = core.Post(docData=dict(author=jojo._id, text='must read!',
                                  citationType='mustread', id='2',
                                  sigs=[sig1._id, sig2._id]),
                               parent=paper2._id)
    assert set(core.Person(jojo._id).topics) == set([sig1._id, sig2._id])

    post1 = core.Post(docData=dict(author=fred._id, text='interesting paper!',
                                   id=98765, sigs=[sig1._id]), parent=paper1)
    assert set(core.Person(fred._id).topics) == set([sig1._id, sig2._id, 'silicene'])
    reply1 = core.Reply(docData=dict(author=jojo._id, text='I disagree with Fred.',
                                     id=7890, replyTo=98765), parent=paper1)

    issue1 = core.Issue(docData=dict(paper=paper1, title='The claims are garbage',
                                     category='validity', author=jojo._id,
                                     description='there is a major flaw in the first step of your proof'))

    vote1 = core.IssueVote(docData=dict(person=jojo, rating='crucial',
                                        status='open'),
                           parent=issue1)

    assert core.Person(jojo._id).email == [a1]
    assert core.Person(jojo._id).replies == [reply1]
    jgp = core.GplusPersonData(1234)
    assert jgp.parent == jojo
    assert jgp.etag == 'oldversion'
    assert len(rec1.parent.authors) == 1
    assert rec1.parent.authors[0] == jojo
    assert len(rec2.parent.authors) == 2
    assert jojo in rec2.parent.authors
    assert fred in rec2.parent.authors
    assert len(rec2.parent.recommendations) == 1
    assert len(jojo.recommendations) == 1
    assert jojo.recommendations[0] == rec2
    assert len(jojo.papers) == 2
    assert len(fred.papers) == 1
    assert len(paper2.authors[0].email) == 2
    assert issue1.author == jojo
    p = core.Paper(paper1._id)
    assert len(p.issues) == 1
    posts1 = p.get_all_posts()
    assert len(posts1) == 1
    assert posts1 == [post1]
    assert posts1[0].text == 'interesting paper!'
    assert list(posts1[0].get_replies()) == [reply1]
    assert core.Post(98765).author == fred
    assert core.Reply(7890).replyTo == post1
    assert core.Reply(7890).parent == paper1
    assert filter(lambda x:not x.is_rec(), core.Person(fred._id).posts) == [post1]
    assert filter(lambda x:not x.is_rec(), core.SIG(sig1._id).posts) == [post1]
    assert core.Post(98765).sigs == [sig1]

    replyAgain = core.Reply(docData=dict(author=fred._id, text='interesting paper!',
                                     id=7890, replyTo=98765), parent=paper1,
                            insertNew='findOrInsert')
    assert replyAgain == reply1
    assert core.Paper(paper1._id).replies == [reply1]

    reply2 = core.Reply(docData=dict(author=jojo._id, text='This paper really made me think.',
                                     id=7891, replyTo=98765), parent=paper1,
                            insertNew='findOrInsert')

    assert core.Paper(paper1._id).replies == [reply1, reply2]
    assert core.Paper(str(paper1._id)) == paper1, 'auto ID conversion failed'

    assert p.issues[0] == issue1
    assert len(p.issues[0].votes) == 1
    assert len(rec2.sigs) == 2
    assert rec2.sigs[0] == sig1
    assert sig1.recommendations == [rec2]

    rec1.array_append('sigs', sig2)

    assert len(sig2.recommendations) == 2
    assert core.Post(rec1.id).sigs == [sig2]

    rec2.update(dict(text='totally fascinating!', score=27))
    rec3 = core.Post(rec2.id)
    assert rec3.score == 27

    a4 = core.EmailAddress('*****@*****.**')
    assert a4._parent_link == fred._id
    assert a4.parent == fred

    try:
        p = core.Person('abcdefg')
    except KeyError:
        pass
    else:
        raise AssertionError('failed to trap bad personID')

    try:
        a = core.EmailAddress('*****@*****.**')
    except KeyError:
        pass
    else:
        raise AssertionError('failed to trap bad email')

    try:
        jojo = core.Person(docData=dict(name2='jojo', age=37))
    except ValueError:
        pass
    else:
        raise AssertionError('failed to trap Person w/o name')

    fred.array_append('numbers', 17)
    assert core.Person(fred._id).numbers == [17]
    fred.array_append('numbers', 6)
    assert core.Person(fred._id).numbers == [17, 6]
    fred.array_del('numbers', 17)
    assert core.Person(fred._id).numbers == [6]

    a4.array_append('numbers', 17)
    assert core.EmailAddress(a4.address).numbers == [17]
    a4.array_append('numbers', 6)
    assert core.EmailAddress(a4.address).numbers == [17, 6]
    a4.array_del('numbers', 17)
    assert core.EmailAddress(a4.address).numbers == [6]

    rec3 = core.Post(docData=dict(author=fred._id, citationType='recommend',
                                  text='I think this is a major breakthrough.',
                                  sigs=[sig2._id], id=3456),
                               parent=paper2._id)

    assert core.SIG(sig1._id).recommendations == [rec2]
    assert len(core.SIG(sig2._id).recommendations) == 3

    it = gplus.publicAccess.get_person_posts('107295654786633294692')
    testPosts = list(gplus.publicAccess.find_or_insert_posts(it))
    assert len(testPosts) > 0

    nposts = len(core.Paper(paper1._id).posts)
    nreplies = len(core.Paper(paper1._id).replies)
    it = gplus.publicAccess.get_person_posts('107295654786633294692')
    testPosts2 = list(gplus.publicAccess.find_or_insert_posts(it))
    assert testPosts == testPosts2
    assert nposts == len(core.Paper(paper1._id).posts)
    assert nreplies == len(core.Paper(paper1._id).replies)

    gpd = core.GplusPersonData('112634568601116338347',
                               insertNew='findOrInsert')
    assert gpd.displayName == 'Meenakshi Roy'
    gpd.update_subscriptions(dict(etag='foo', totalItems=1),
                             [dict(id='114744049040264263224')])
    gps = gpd.subscriptions
    assert gps.gplusPerson == gpd
    mrID = gpd.parent._id
    subscriptions = core.Person(mrID).subscriptions
    assert len(subscriptions) == 0

    gpd2 = core.GplusPersonData('114744049040264263224',
                                insertNew='findOrInsert')
    time.sleep(2)
    subscriptions = core.Person(mrID).subscriptions
    assert len(subscriptions) == 1
    assert subscriptions[0].author == gpd2.parent

    cjlposts = gpd2.update_posts(999) # retrieve some recs
    assert len(cjlposts) > 0 # got some
    assert len(core.Person(mrID).received) > 0 # and they were delivered
    assert len(core.Person(mrID).get_deliveries()) > 0 # and UI can retrieve them

    recReply = core.Reply(docData=dict(author=jojo._id, id=78901, replyTo=3456,
                          text='Fred, thanks for your comments!  Your insights are really helpful.'),
                          parent=paper2._id)

    # make sure timestamps present on all recs
    l = [r.published for r in core.Post.find_obj()]
    l = [r.published for r in core.Reply.find_obj()]

    assert recReply.replyTo == rec3
    assert list(recReply.replyTo.get_replies()) == [recReply]

    # pubmed eutils network server constantly failing now??
    ## pubmedDict = pubmed.get_pubmed_dict('23482246')
    ## with open('../pubmed/test1.pickle') as ifile:
    ##     correctDict = pickle.load(ifile)
    ## assert pubmedDict == correctDict

    ## paper3 = core.PubmedPaperData('23482246', insertNew='findOrInsert').parent
    ## paper3.update(dict(authors=[fred._id]))

    ## ppd = core.PubmedPaperData('23139441', insertNew='findOrInsert')
    ## assert ppd.doi.upper() == '10.1016/J.MSEC.2012.05.020'

    ## assert paper3.pubmed.id == '23482246'
    ## assert paper3.title[:40] == correctDict['title'][:40]

    s = 'aabbe'
    t = doi.map_to_doi(s)
    assert t == '10.1002/(SICI)1097-0258(19980815/30)17:15/16<1661::AID-SIM968>3.0.CO;2-2'
    assert s == doi.map_to_shortdoi(t)

    paper4 = core.DoiPaperData(DOI=t, insertNew='findOrInsert').parent
    paper4.update(dict(authors=[fred._id]))
    assert paper4.doi.id == s
    assert paper4.doi.doi == t
    assert paper4.doi.DOI == t.upper()
    paper5 = core.DoiPaperData(s, insertNew='findOrInsert').parent
    assert paper4 == paper5
    assert rootColl['shortDOI']._GET(s) == paper4
    txt = 'some text ' + paper4.doi.get_hashtag()
    refs, topics, primary = incoming.get_citations_types_and_topics(txt,spnetworkOnly=False)
    assert incoming.get_paper(primary,refs[primary][1]) == paper4

    spnetPaper = core.DoiPaperData(DOI='10.3389/fncom.2012.00001',
                                   insertNew='findOrInsert').parent
    assert spnetPaper.title.lower() == 'open peer review by a selected-papers network'
    txt = 'a long comment ' + spnetPaper.doi.get_doctag() + ', some more text'
    refs, topics, primary = incoming.get_citations_types_and_topics(txt,spnetworkOnly=False)
    assert incoming.get_paper(primary,refs[primary][1]) == spnetPaper

    topics, subs = bulk.get_people_subs()
    bulk.deliver_recs(topics, subs)
    assert len(core.Person(jojo._id).received) == 4
    assert len(core.Person(fred._id).received) == 2
Exemplo n.º 4
0
## pubmedDict = pubmed.get_pubmed_dict('23482246')
## with open('../pubmed/test1.pickle') as ifile:
##     correctDict = pickle.load(ifile)
## assert pubmedDict == correctDict

## paper3 = core.PubmedPaperData('23482246', insertNew='findOrInsert').parent
## paper3.update(dict(authors=[fred._id]))

## ppd = core.PubmedPaperData('23139441', insertNew='findOrInsert')
## assert ppd.doi.upper() == '10.1016/J.MSEC.2012.05.020'

## assert paper3.pubmed.id == '23482246'
## assert paper3.title[:40] == correctDict['title'][:40]

s = 'aabbe'
t = doi.map_to_doi(s)
assert t == '10.1002/(SICI)1097-0258(19980815/30)17:15/16<1661::AID-SIM968>3.0.CO;2-2'
assert s == doi.map_to_shortdoi(t)

paper4 = core.DoiPaperData(DOI=t, insertNew='findOrInsert').parent
paper4.update(dict(authors=[fred._id]))
assert paper4.doi.id == s
assert paper4.doi.doi == t
assert paper4.doi.DOI == t.upper()
paper5 = core.DoiPaperData(s, insertNew='findOrInsert').parent
assert paper4 == paper5
assert rootColl['shortDOI']._GET(s) == paper4
txt = 'some text ' + paper4.doi.get_hashtag()
assert incoming.get_hashtag_dict(txt)['paper'] == [paper4]

spnetPaper = core.DoiPaperData(DOI='10.3389/fncom.2012.00001',
Exemplo n.º 5
0
Arquivo: test.py Projeto: darius/spnet
## pubmedDict = pubmed.get_pubmed_dict('23482246')
## with open('../pubmed/test1.pickle') as ifile:
##     correctDict = pickle.load(ifile)
## assert pubmedDict == correctDict

## paper3 = core.PubmedPaperData('23482246', insertNew='findOrInsert').parent
## paper3.update(dict(authors=[fred._id]))

## ppd = core.PubmedPaperData('23139441', insertNew='findOrInsert')
## assert ppd.doi.upper() == '10.1016/J.MSEC.2012.05.020'

## assert paper3.pubmed.id == '23482246'
## assert paper3.title[:40] == correctDict['title'][:40]

s = 'aabbe'
t = doi.map_to_doi(s)
assert t == '10.1002/(SICI)1097-0258(19980815/30)17:15/16<1661::AID-SIM968>3.0.CO;2-2'
assert s == doi.map_to_shortdoi(t)

paper4 = core.DoiPaperData(DOI=t, insertNew='findOrInsert').parent
paper4.update(dict(authors=[fred._id]))
assert paper4.doi.id == s
assert paper4.doi.doi == t
assert paper4.doi.DOI == t.upper()
paper5 = core.DoiPaperData(s, insertNew='findOrInsert').parent
assert paper4 == paper5
assert rootColl['shortDOI']._GET(s) == paper4
txt = 'some text ' + paper4.doi.get_hashtag()
assert incoming.get_hashtag_dict(txt)['paper'] == [paper4]

spnetPaper = core.DoiPaperData(DOI='10.3389/fncom.2012.00001',