Ejemplo n.º 1
0
    def setUp(self):
        self.d = None
        
        self.db = setup_postgres_for_unittests(db, app)

        # setup a clean new redis test database.  We're putting unittest redis at DB Number 8.
        self.r = tiredis.from_url("redis://*****:*****@example.com'
        self.test_meta = {    
                    'max_registered_items': 3, 
                    'planned_use': 'individual CV', 
                    'email': self.test_email, 
                    'notes': '', 
                    'api_key_owner': 'Julia Smith', 
                    "example_url":"", 
                    "organization":"NASA"
                }

        test_meta2 = copy.deepcopy(self.test_meta)
        test_meta2["email"] = '*****@*****.**'
        test_meta2["prefix"] = "SFU"
        self.existing_api_user = ApiUser(**test_meta2)

        self.existing_registered_item = RegisteredItem(self.test_alias_registered, self.existing_api_user)

        self.db.session.add(self.existing_api_user)
        self.db.session.add(self.existing_registered_item)
        self.db.session.commit()
Ejemplo n.º 2
0
    def setUp(self):
        self.config = None #placeholder
        self.TEST_PROVIDER_CONFIG = [
            ("wikipedia", {})
        ]
        self.d = None

        # do the same thing for the redis db, set up the test redis database.  We're using DB Number 8
        self.r = tiredis.from_url("redis://localhost:6379", db=8)
        self.r.flushdb()

        provider_queues = {}
        providers = ProviderFactory.get_providers(self.TEST_PROVIDER_CONFIG)
        for provider in providers:
            provider_queues[provider.provider_name] = backend.PythonQueue(provider.provider_name+"_queue")

        self.b = backend.Backend(
            backend.RedisQueue("alias-unittest", self.r), 
            provider_queues, 
            [backend.PythonQueue("couch_queue")], 
            self.r)

        self.fake_item = {
            "_id": "1",
            "type": "item",
            "num_providers_still_updating":1,
            "aliases":{"pmid":["111"]},
            "biblio": {},
            "metrics": {},
            "last_modified": datetime.datetime(2013, 1, 1)
        }
        self.fake_aliases_dict = {"pmid":["222"]}
        self.tiid = "abcd"

        self.db = setup_postgres_for_unittests(db, app)
Ejemplo n.º 3
0
    def setUp(self):
        self.config = None  #placeholder
        self.TEST_PROVIDER_CONFIG = [("wikipedia", {})]
        self.d = None

        # do the same thing for the redis db, set up the test redis database.  We're using DB Number 8
        self.r = tiredis.from_url("redis://localhost:6379",
                                  db=REDIS_UNITTEST_DATABASE_NUMBER)
        self.r.flushdb()

        provider_queues = {}
        providers = ProviderFactory.get_providers(self.TEST_PROVIDER_CONFIG)
        for provider in providers:
            provider_queues[provider.provider_name] = backend.PythonQueue(
                provider.provider_name + "_queue")

        self.b = backend.Backend(backend.RedisQueue("alias-unittest",
                                                    self.r), provider_queues,
                                 [backend.PythonQueue("couch_queue")], self.r)

        self.fake_item = {
            "_id": "1",
            "type": "item",
            "num_providers_still_updating": 1,
            "aliases": {
                "pmid": ["111"]
            },
            "biblio": {},
            "metrics": {},
            "last_modified": datetime.datetime(2013, 1, 1)
        }
        self.fake_aliases_dict = {"pmid": ["222"]}
        self.tiid = "abcd"

        self.db = setup_postgres_for_unittests(db, app)
Ejemplo n.º 4
0
    def setUp(self):
        ProviderTestCase.setUp(self)

        self.db = setup_postgres_for_unittests(db, app)

        sample_data_dump = open(SAMPLE_EXTRACT_METRICS_PAGE, "r").read()
        sample_data_dump_different_month = open(
            SAMPLE_EXTRACT_METRICS_PAGE_DIFFERENT_MONTH, "r").read()

        test_monthly_data = [{
            "_id": "abc",
            "type": "provider_data_dump",
            "provider": "pmc",
            "raw": sample_data_dump,
            "provider_raw_version": 1.0,
            "created": "2012-11-29T07:34:01.126892",
            "aliases": {
                "pmid": ["111", "222"]
            },
            "min_event_date": "2012-10-01T07:34:01.126892",
            "max_event_date": "2012-10-31T07:34:01.126892"
        }, {
            "_id": "def",
            "type": "provider_data_dump",
            "provider": "pmc",
            "raw": sample_data_dump_different_month,
            "provider_raw_version": 1.0,
            "created": "2012-11-29T08:34:01.126892",
            "aliases": {
                "pmid": ["111"]
            },
            "min_event_date": "2012-01-01T07:34:01.126892",
            "max_event_date": "2012-01-31T07:34:01.126892"
        }, {
            "_id": "abc123",
            "raw":
            "<pmc-web-stat><request year=\"2012\" month=\"10\" jrid=\"elife\" eissn=\"2050-084X\"></request><response status=\"0\" collection=\"eLife\"></response><articles><article id=\"PMC3463246\"><meta-data doi=\"10.7554/eLife.00013\" pmcid=\"PMC3463246\" pubmed-id=\"23066504\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00013\"/><usage unique-ip=\"1368\" full-text=\"1464\" pdf=\"722\" abstract=\"119\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"144\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3463247\"><meta-data doi=\"10.7554/eLife.00240\" pmcid=\"PMC3463247\" pubmed-id=\"23066507\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00240\"/><usage unique-ip=\"514\" full-text=\"606\" pdf=\"230\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"9\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3465569\"><meta-data doi=\"10.7554/eLife.00242\" pmcid=\"PMC3465569\" pubmed-id=\"23066508\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00242\"/><usage unique-ip=\"473\" full-text=\"503\" pdf=\"181\" abstract=\"2\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"13\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3465570\"><meta-data doi=\"10.7554/eLife.00243\" pmcid=\"PMC3465570\" pubmed-id=\"23066509\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00243\"/><usage unique-ip=\"547\" full-text=\"636\" pdf=\"227\" abstract=\"1\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"56\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3466591\"><meta-data doi=\"10.7554/eLife.00065\" pmcid=\"PMC3466591\" pubmed-id=\"23066506\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00065\"/><usage unique-ip=\"2516\" full-text=\"2804\" pdf=\"1583\" abstract=\"195\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"405\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3466783\"><meta-data doi=\"10.7554/eLife.00007\" pmcid=\"PMC3466783\" pubmed-id=\"23066503\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00007\"/><usage unique-ip=\"1331\" full-text=\"1412\" pdf=\"898\" abstract=\"224\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"109\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3467772\"><meta-data doi=\"10.7554/eLife.00270\" pmcid=\"PMC3467772\" pubmed-id=\"23066510\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00270\"/><usage unique-ip=\"1396\" full-text=\"1776\" pdf=\"625\" abstract=\"4\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"0\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3470722\"><meta-data doi=\"10.7554/eLife.00286\" pmcid=\"PMC3470722\" pubmed-id=\"23071903\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00286\"/><usage unique-ip=\"909\" full-text=\"1030\" pdf=\"376\" abstract=\"6\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"0\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3479833\"><meta-data doi=\"10.7554/eLife.00031\" pmcid=\"PMC3479833\" pubmed-id=\"23110253\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00031\"/><usage unique-ip=\"154\" full-text=\"126\" pdf=\"87\" abstract=\"26\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"13\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3470409\"><meta-data doi=\"10.7554/eLife.00048\" pmcid=\"PMC3470409\" pubmed-id=\"23066505\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00048\"/><usage unique-ip=\"1250\" full-text=\"1361\" pdf=\"911\" abstract=\"237\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"317\" supp-data=\"4\" cited-by=\"0\"/></article><article id=\"PMC3482692\"><meta-data doi=\"10.7554/eLife.00102\" pmcid=\"PMC3482692\" pubmed-id=\"23110254\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00102\"/><usage unique-ip=\"259\" full-text=\"232\" pdf=\"133\" abstract=\"36\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"8\" supp-data=\"3\" cited-by=\"0\"/></article><article id=\"PMC3482687\"><meta-data doi=\"10.7554/eLife.00281\" pmcid=\"PMC3482687\" pubmed-id=\"23110255\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00281\"/><usage unique-ip=\"75\" full-text=\"53\" pdf=\"47\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"1\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3482686\"><meta-data doi=\"10.7554/eLife.00005\" pmcid=\"PMC3482686\" pubmed-id=\"23110252\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00005\"/><usage unique-ip=\"324\" full-text=\"249\" pdf=\"263\" abstract=\"71\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"93\" supp-data=\"17\" cited-by=\"0\"/></article></articles></pmc-web-stat>",
            "max_event_date": "2012-10-31T07:34:01.126892",
            "provider": "pmc",
            "aliases": {
                "pmid": [
                    "23066504", "23066507", "23066508", "23066509", "23066506",
                    "23066503", "23066510", "23071903", "23110253", "23066505",
                    "23110254", "23110255", "23110252"
                ]
            },
            "provider_raw_version": 1,
            "type": "provider_data_dump",
            "min_event_date": "2012-10-02T07:34:01.126892",
            "created": "2012-11-29T09:34:01.126892"
        }]
        #print test_monthly_data
        for doc in test_monthly_data:
            new_object = provider_batch_data.create_objects_from_doc(doc)
            print new_object

        self.provider = pmc.Pmc()
        print "after pmc"
Ejemplo n.º 5
0
    def setUp(self):
        self.d = None

        # do the same thing for the redis db, set up the test redis database.  We're using DB Number 8
        self.r = tiredis.from_url("redis://localhost:6379",
                                  db=REDIS_UNITTEST_DATABASE_NUMBER)
        self.r.flushdb()

        self.db = setup_postgres_for_unittests(db, app)

        self.aliases = [["doi", "10.123"], ["doi", "10.124"],
                        ["doi", "10.125"]]
    def setUp(self):
        self.db = setup_postgres_for_unittests(db, app)

        self.test_data = {
               "raw": "<pmc-web-stat><request year=\"2012\" month=\"10\" jrid=\"elife\" eissn=\"2050-084X\"></request><response status=\"0\" collection=\"eLife\"></response><articles><article id=\"PMC3463246\"><meta-data doi=\"10.7554/eLife.00013\" pmcid=\"PMC3463246\" pubmed-id=\"23066504\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00013\"/><usage unique-ip=\"1368\" full-text=\"1464\" pdf=\"722\" abstract=\"119\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"144\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3463247\"><meta-data doi=\"10.7554/eLife.00240\" pmcid=\"PMC3463247\" pubmed-id=\"23066507\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00240\"/><usage unique-ip=\"514\" full-text=\"606\" pdf=\"230\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"9\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3465569\"><meta-data doi=\"10.7554/eLife.00242\" pmcid=\"PMC3465569\" pubmed-id=\"23066508\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00242\"/><usage unique-ip=\"473\" full-text=\"503\" pdf=\"181\" abstract=\"2\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"13\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3465570\"><meta-data doi=\"10.7554/eLife.00243\" pmcid=\"PMC3465570\" pubmed-id=\"23066509\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00243\"/><usage unique-ip=\"547\" full-text=\"636\" pdf=\"227\" abstract=\"1\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"56\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3466591\"><meta-data doi=\"10.7554/eLife.00065\" pmcid=\"PMC3466591\" pubmed-id=\"23066506\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00065\"/><usage unique-ip=\"2516\" full-text=\"2804\" pdf=\"1583\" abstract=\"195\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"405\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3466783\"><meta-data doi=\"10.7554/eLife.00007\" pmcid=\"PMC3466783\" pubmed-id=\"23066503\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00007\"/><usage unique-ip=\"1331\" full-text=\"1412\" pdf=\"898\" abstract=\"224\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"109\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3467772\"><meta-data doi=\"10.7554/eLife.00270\" pmcid=\"PMC3467772\" pubmed-id=\"23066510\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00270\"/><usage unique-ip=\"1396\" full-text=\"1776\" pdf=\"625\" abstract=\"4\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"0\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3470722\"><meta-data doi=\"10.7554/eLife.00286\" pmcid=\"PMC3470722\" pubmed-id=\"23071903\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00286\"/><usage unique-ip=\"909\" full-text=\"1030\" pdf=\"376\" abstract=\"6\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"0\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3479833\"><meta-data doi=\"10.7554/eLife.00031\" pmcid=\"PMC3479833\" pubmed-id=\"23110253\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00031\"/><usage unique-ip=\"154\" full-text=\"126\" pdf=\"87\" abstract=\"26\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"13\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3470409\"><meta-data doi=\"10.7554/eLife.00048\" pmcid=\"PMC3470409\" pubmed-id=\"23066505\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00048\"/><usage unique-ip=\"1250\" full-text=\"1361\" pdf=\"911\" abstract=\"237\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"317\" supp-data=\"4\" cited-by=\"0\"/></article><article id=\"PMC3482692\"><meta-data doi=\"10.7554/eLife.00102\" pmcid=\"PMC3482692\" pubmed-id=\"23110254\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00102\"/><usage unique-ip=\"259\" full-text=\"232\" pdf=\"133\" abstract=\"36\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"8\" supp-data=\"3\" cited-by=\"0\"/></article><article id=\"PMC3482687\"><meta-data doi=\"10.7554/eLife.00281\" pmcid=\"PMC3482687\" pubmed-id=\"23110255\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00281\"/><usage unique-ip=\"75\" full-text=\"53\" pdf=\"47\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"1\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3482686\"><meta-data doi=\"10.7554/eLife.00005\" pmcid=\"PMC3482686\" pubmed-id=\"23110252\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00005\"/><usage unique-ip=\"324\" full-text=\"249\" pdf=\"263\" abstract=\"71\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"93\" supp-data=\"17\" cited-by=\"0\"/></article></articles></pmc-web-stat>",
               "max_event_date": "2012-10-31T07:34:01.126892",
               "provider": "pmc",
               "aliases": {
                   "pmid": [
                       "23066504",
                       "23066507",
                       "23066508",
                       "23066509",
                       "23066506",
                       "23066503",
                       "23066510",
                       "23071903",
                       "23110253",
                       "23066505",
                       "23110254",
                       "23110255",
                       "23110252"
                   ]
               },
               "provider_raw_version": 1,
               "min_event_date": "2012-10-01T07:34:01.126892",
               "created": "2012-11-29T07:34:01.126892"
            }    

        self.old_doc = {
                   "_id": "pmc201304",
                   "_rev": "1-c9a62778077941736932cfb3510ee382",
                   "raw": "<pmc-web-stat><request year=\"2013\" month=\"04\" jrid=\"elife\" eissn=\"2050-084X\"></request><response status=\"0\" collection=\"eLife\"></response><articles><article id=\"PMC3463246\"><meta-data doi=\"10.7554/eLife.00013\" pmcid=\"PMC3463246\" pubmed-id=\"23066504\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00013\"/><usage unique-ip=\"112\" full-text=\"152\" pdf=\"22\" abstract=\"1\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"31\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3463247\"><meta-data doi=\"10.7554/eLife.00240\" pmcid=\"PMC3463247\" pubmed-id=\"23066507\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00240\"/><usage unique-ip=\"10\" full-text=\"41\" pdf=\"1\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"0\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3465569\"><meta-data doi=\"10.7554/eLife.00242\" pmcid=\"PMC3465569\" pubmed-id=\"23066508\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00242\"/><usage unique-ip=\"27\" full-text=\"26\" pdf=\"3\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"0\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3465570\"><meta-data doi=\"10.7554/eLife.00243\" pmcid=\"PMC3465570\" pubmed-id=\"23066509\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00243\"/><usage unique-ip=\"41\" full-text=\"50\" pdf=\"9\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"8\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3466591\"><meta-data doi=\"10.7554/eLife.00065\" pmcid=\"PMC3466591\" pubmed-id=\"23066506\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00065\"/><usage unique-ip=\"252\" full-text=\"2522\" pdf=\"41\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"72\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3466783\"><meta-data doi=\"10.7554/eLife.00007\" pmcid=\"PMC3466783\" pubmed-id=\"23066503\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00007\"/><usage unique-ip=\"47\" full-text=\"62\" pdf=\"5\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"10\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3467772\"><meta-data doi=\"10.7554/eLife.00270\" pmcid=\"PMC3467772\" pubmed-id=\"23066510\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00270\"/><usage unique-ip=\"28\" full-text=\"32\" pdf=\"2\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"0\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3470409\"><meta-data doi=\"10.7554/eLife.00048\" pmcid=\"PMC3470409\" pubmed-id=\"23066505\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00048\"/><usage unique-ip=\"72\" full-text=\"68\" pdf=\"20\" abstract=\"1\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"26\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3470722\"><meta-data doi=\"10.7554/eLife.00286\" pmcid=\"PMC3470722\" pubmed-id=\"23071903\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00286\"/><usage unique-ip=\"37\" full-text=\"40\" pdf=\"7\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"0\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3479833\"><meta-data doi=\"10.7554/eLife.00031\" pmcid=\"PMC3479833\" pubmed-id=\"23110253\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00031\"/><usage unique-ip=\"31\" full-text=\"41\" pdf=\"3\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"7\" supp-data=\"0\" cited-by=\"1\"/></article><article id=\"PMC3482686\"><meta-data doi=\"10.7554/eLife.00005\" pmcid=\"PMC3482686\" pubmed-id=\"23110252\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00005\"/><usage unique-ip=\"189\" full-text=\"238\" pdf=\"33\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"110\" supp-data=\"2\" cited-by=\"0\"/></article><article id=\"PMC3482687\"><meta-data doi=\"10.7554/eLife.00281\" pmcid=\"PMC3482687\" pubmed-id=\"23110255\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00281\"/><usage unique-ip=\"17\" full-text=\"20\" pdf=\"0\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"0\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3482692\"><meta-data doi=\"10.7554/eLife.00102\" pmcid=\"PMC3482692\" pubmed-id=\"23110254\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00102\"/><usage unique-ip=\"50\" full-text=\"55\" pdf=\"11\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"7\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3485613\"><meta-data doi=\"10.7554/eLife.00301\" pmcid=\"PMC3485613\" pubmed-id=\"23150799\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00301\"/><usage unique-ip=\"41\" full-text=\"43\" pdf=\"7\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"7\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3485615\"><meta-data doi=\"10.7554/eLife.00049\" pmcid=\"PMC3485615\" pubmed-id=\"23150796\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00049\"/><usage unique-ip=\"390\" full-text=\"558\" pdf=\"108\" abstract=\"11\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"132\" supp-data=\"0\" cited-by=\"4\"/></article><article id=\"PMC3490148\"><meta-data doi=\"10.7554/eLife.00302\" pmcid=\"PMC3490148\" pubmed-id=\"23150800\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00302\"/><usage unique-ip=\"47\" full-text=\"54\" pdf=\"4\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"8\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3490149\"><meta-data doi=\"10.7554/eLife.00068\" pmcid=\"PMC3490149\" pubmed-id=\"23150797\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00068\"/><usage unique-ip=\"42\" full-text=\"53\" 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doi=\"10.7554/eLife.00160\" pmcid=\"PMC3539332\" pubmed-id=\"23326640\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00160\"/><usage unique-ip=\"45\" full-text=\"46\" pdf=\"11\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"17\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3539393\"><meta-data doi=\"10.7554/eLife.00170\" pmcid=\"PMC3539393\" pubmed-id=\"23326641\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00170\"/><usage unique-ip=\"67\" full-text=\"80\" pdf=\"12\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"36\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3545443\"><meta-data doi=\"10.7554/eLife.00231\" pmcid=\"PMC3545443\" pubmed-id=\"23326642\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00231\"/><usage unique-ip=\"43\" full-text=\"50\" pdf=\"8\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"22\" supp-data=\"0\" 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cited-by=\"0\"/></article><article id=\"PMC3576711\"><meta-data doi=\"10.7554/eLife.00291\" pmcid=\"PMC3576711\" pubmed-id=\"23426999\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00291\"/><usage unique-ip=\"112\" full-text=\"133\" pdf=\"50\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"60\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3576727\"><meta-data doi=\"10.7554/eLife.00461\" pmcid=\"PMC3576727\" pubmed-id=\"23427024\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00461\"/><usage unique-ip=\"76\" full-text=\"79\" pdf=\"19\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"43\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3576809\"><meta-data doi=\"10.7554/eLife.00290\" pmcid=\"PMC3576809\" pubmed-id=\"23425906\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00290\"/><usage unique-ip=\"46\" full-text=\"58\" pdf=\"4\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"27\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3578201\"><meta-data doi=\"10.7554/eLife.00333\" pmcid=\"PMC3578201\" pubmed-id=\"23550179\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00333\"/><usage unique-ip=\"78\" full-text=\"100\" pdf=\"22\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"39\" supp-data=\"1\" cited-by=\"0\"/></article><article id=\"PMC3579228\"><meta-data doi=\"10.7554/eLife.00488\" pmcid=\"PMC3579228\" pubmed-id=\"0\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00488\"/><usage unique-ip=\"12\" full-text=\"15\" pdf=\"0\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"0\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3582987\"><meta-data doi=\"10.7554/eLife.00593\" pmcid=\"PMC3582987\" pubmed-id=\"23467495\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00593\"/><usage unique-ip=\"26\" full-text=\"29\" pdf=\"7\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"0\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3582988\"><meta-data doi=\"10.7554/eLife.00400\" pmcid=\"PMC3582988\" pubmed-id=\"23467508\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00400\"/><usage unique-ip=\"53\" full-text=\"55\" pdf=\"14\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"23\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3583005\"><meta-data doi=\"10.7554/eLife.00348\" pmcid=\"PMC3583005\" pubmed-id=\"23467541\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00348\"/><usage unique-ip=\"96\" full-text=\"105\" pdf=\"22\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"27\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3589823\"><meta-data doi=\"10.7554/eLife.00615\" pmcid=\"PMC3589823\" pubmed-id=\"23470921\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00615\"/><usage unique-ip=\"22\" full-text=\"26\" pdf=\"2\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"0\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3589824\"><meta-data doi=\"10.7554/eLife.00337\" pmcid=\"PMC3589824\" pubmed-id=\"23471010\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00337\"/><usage unique-ip=\"46\" full-text=\"46\" pdf=\"11\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"5\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3589825\"><meta-data doi=\"10.7554/eLife.00327\" pmcid=\"PMC3589825\" pubmed-id=\"23471103\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00327\"/><usage unique-ip=\"59\" full-text=\"61\" pdf=\"15\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"25\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3591006\"><meta-data doi=\"10.7554/eLife.00133\" pmcid=\"PMC3591006\" pubmed-id=\"23482306\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00133\"/><usage unique-ip=\"68\" full-text=\"72\" pdf=\"22\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"32\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3591093\"><meta-data doi=\"10.7554/eLife.00218\" pmcid=\"PMC3591093\" pubmed-id=\"23483797\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00218\"/><usage unique-ip=\"48\" full-text=\"46\" pdf=\"11\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"23\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3591783\"><meta-data doi=\"10.7554/eLife.00190\" pmcid=\"PMC3591783\" pubmed-id=\"23482940\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00190\"/><usage unique-ip=\"42\" full-text=\"43\" pdf=\"8\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"8\" supp-data=\"2\" cited-by=\"0\"/></article><article id=\"PMC3592195\"><meta-data doi=\"10.7554/eLife.00577\" pmcid=\"PMC3592195\" pubmed-id=\"23538671\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00577\"/><usage unique-ip=\"46\" full-text=\"47\" pdf=\"7\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"10\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3594797\"><meta-data doi=\"10.7554/eLife.00646\" pmcid=\"PMC3594797\" pubmed-id=\"23538735\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00646\"/><usage unique-ip=\"18\" full-text=\"21\" pdf=\"0\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"0\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3601633\"><meta-data doi=\"10.7554/eLife.00638\" pmcid=\"PMC3601633\" pubmed-id=\"23538852\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00638\"/><usage unique-ip=\"39\" full-text=\"41\" pdf=\"7\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"19\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3601634\"><meta-data doi=\"10.7554/eLife.00641\" pmcid=\"PMC3601634\" pubmed-id=\"23539117\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00641\"/><usage unique-ip=\"62\" full-text=\"65\" pdf=\"14\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"16\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3601810\"><meta-data doi=\"10.7554/eLife.00336\" pmcid=\"PMC3601810\" pubmed-id=\"23539289\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00336\"/><usage unique-ip=\"98\" full-text=\"108\" pdf=\"24\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"56\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3601818\"><meta-data doi=\"10.7554/eLife.00378\" pmcid=\"PMC3601818\" pubmed-id=\"23539368\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00378\"/><usage unique-ip=\"78\" full-text=\"89\" pdf=\"21\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"18\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3601819\"><meta-data doi=\"10.7554/eLife.00354\" pmcid=\"PMC3601819\" pubmed-id=\"23539454\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00354\"/><usage unique-ip=\"103\" full-text=\"140\" pdf=\"27\" abstract=\"1\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"36\" supp-data=\"4\" cited-by=\"0\"/></article><article id=\"PMC3602953\"><meta-data doi=\"10.7554/eLife.00605\" pmcid=\"PMC3602953\" pubmed-id=\"23538878\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00605\"/><usage unique-ip=\"65\" full-text=\"76\" pdf=\"17\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"18\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3602954\"><meta-data doi=\"10.7554/eLife.00312\" pmcid=\"PMC3602954\" pubmed-id=\"23538967\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00312\"/><usage unique-ip=\"158\" full-text=\"165\" pdf=\"58\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"70\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3608243\"><meta-data doi=\"10.7554/eLife.00648\" pmcid=\"PMC3608243\" pubmed-id=\"23539513\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00648\"/><usage unique-ip=\"71\" full-text=\"69\" pdf=\"16\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"20\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3608244\"><meta-data doi=\"10.7554/eLife.00642\" pmcid=\"PMC3608244\" pubmed-id=\"23539544\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00642\"/><usage unique-ip=\"40\" full-text=\"49\" pdf=\"7\" abstract=\"1\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"0\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3608245\"><meta-data doi=\"10.7554/eLife.00625\" pmcid=\"PMC3608245\" pubmed-id=\"23539644\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00625\"/><usage unique-ip=\"46\" full-text=\"51\" pdf=\"16\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"7\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3608266\"><meta-data doi=\"10.7554/eLife.00260\" pmcid=\"PMC3608266\" pubmed-id=\"23538384\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00260\"/><usage unique-ip=\"103\" full-text=\"122\" pdf=\"45\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"39\" supp-data=\"6\" cited-by=\"0\"/></article><article id=\"PMC3610343\"><meta-data doi=\"10.7554/eLife.00269\" pmcid=\"PMC3610343\" pubmed-id=\"23543845\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00269\"/><usage unique-ip=\"57\" full-text=\"63\" pdf=\"10\" abstract=\"1\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"9\" supp-data=\"2\" cited-by=\"0\"/></article><article id=\"PMC3614016\"><meta-data doi=\"10.7554/eLife.00278\" pmcid=\"PMC3614016\" pubmed-id=\"23577232\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00278\"/><usage unique-ip=\"39\" full-text=\"42\" pdf=\"7\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"16\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3614024\"><meta-data doi=\"10.7554/eLife.00655\" pmcid=\"PMC3614024\" pubmed-id=\"23577236\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00655\"/><usage unique-ip=\"27\" full-text=\"31\" pdf=\"5\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"2\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3614025\"><meta-data doi=\"10.7554/eLife.00435\" pmcid=\"PMC3614025\" pubmed-id=\"23577234\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00435\"/><usage unique-ip=\"100\" full-text=\"104\" pdf=\"32\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"62\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3614033\"><meta-data doi=\"10.7554/eLife.00367\" pmcid=\"PMC3614033\" pubmed-id=\"23577233\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00367\"/><usage unique-ip=\"49\" full-text=\"64\" pdf=\"15\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"9\" supp-data=\"8\" cited-by=\"0\"/></article><article id=\"PMC3614058\"><meta-data doi=\"10.7554/eLife.00639\" pmcid=\"PMC3614058\" pubmed-id=\"23577235\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00639\"/><usage unique-ip=\"46\" full-text=\"64\" pdf=\"8\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"2\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3622176\"><meta-data doi=\"10.7554/eLife.00692\" pmcid=\"PMC3622176\" pubmed-id=\"23580166\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00692\"/><usage unique-ip=\"27\" full-text=\"33\" pdf=\"5\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"5\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3622177\"><meta-data doi=\"10.7554/eLife.00444\" pmcid=\"PMC3622177\" pubmed-id=\"23580231\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00444\"/><usage unique-ip=\"60\" full-text=\"69\" pdf=\"22\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"26\" supp-data=\"4\" cited-by=\"0\"/></article><article id=\"PMC3622178\"><meta-data doi=\"10.7554/eLife.00426\" pmcid=\"PMC3622178\" pubmed-id=\"23580255\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00426\"/><usage unique-ip=\"63\" full-text=\"88\" pdf=\"18\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"29\" supp-data=\"5\" cited-by=\"0\"/></article><article id=\"PMC3622181\"><meta-data doi=\"10.7554/eLife.00499\" pmcid=\"PMC3622181\" pubmed-id=\"23580326\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00499\"/><usage unique-ip=\"80\" full-text=\"111\" pdf=\"37\" abstract=\"1\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"22\" supp-data=\"0\" cited-by=\"1\"/></article><article id=\"PMC3622228\"><meta-data doi=\"10.7554/eLife.00659\" pmcid=\"PMC3622228\" pubmed-id=\"23580350\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00659\"/><usage unique-ip=\"37\" full-text=\"37\" pdf=\"10\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"11\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3622229\"><meta-data doi=\"10.7554/eLife.00663\" pmcid=\"PMC3622229\" pubmed-id=\"23580362\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00663\"/><usage unique-ip=\"46\" full-text=\"51\" pdf=\"15\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"11\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3628084\"><meta-data doi=\"10.7554/eLife.00415\" pmcid=\"PMC3628084\" pubmed-id=\"23599892\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00415\"/><usage unique-ip=\"40\" full-text=\"40\" pdf=\"10\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"14\" supp-data=\"0\" cited-by=\"1\"/></article><article id=\"PMC3628085\"><meta-data doi=\"10.7554/eLife.00458\" pmcid=\"PMC3628085\" pubmed-id=\"23599893\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00458\"/><usage unique-ip=\"120\" full-text=\"124\" pdf=\"36\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"43\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3628086\"><meta-data doi=\"10.7554/eLife.00362\" pmcid=\"PMC3628086\" pubmed-id=\"23599891\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00362\"/><usage unique-ip=\"91\" full-text=\"120\" pdf=\"24\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"64\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3628087\"><meta-data doi=\"10.7554/eLife.00534\" pmcid=\"PMC3628087\" pubmed-id=\"23599896\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00534\"/><usage unique-ip=\"72\" full-text=\"72\" pdf=\"16\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"19\" supp-data=\"1\" cited-by=\"0\"/></article><article id=\"PMC3628110\"><meta-data doi=\"10.7554/eLife.00482\" pmcid=\"PMC3628110\" pubmed-id=\"23599895\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00482\"/><usage unique-ip=\"44\" full-text=\"51\" pdf=\"1\" abstract=\"1\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"21\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3628404\"><meta-data doi=\"10.7554/eLife.00729\" pmcid=\"PMC3628404\" pubmed-id=\"23599898\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00729\"/><usage unique-ip=\"62\" full-text=\"100\" pdf=\"12\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"8\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3628405\"><meta-data doi=\"10.7554/eLife.00459\" pmcid=\"PMC3628405\" pubmed-id=\"23599894\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00459\"/><usage unique-ip=\"39\" full-text=\"42\" pdf=\"9\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"45\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3628440\"><meta-data doi=\"10.7554/eLife.00676\" pmcid=\"PMC3628440\" pubmed-id=\"23599897\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00676\"/><usage unique-ip=\"18\" full-text=\"23\" pdf=\"3\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"2\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3629793\"><meta-data doi=\"10.7554/eLife.00288\" pmcid=\"PMC3629793\" pubmed-id=\"23606943\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00288\"/><usage unique-ip=\"35\" full-text=\"41\" pdf=\"4\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"11\" supp-data=\"3\" cited-by=\"0\"/></article></articles></pmc-web-stat>",
                   "provider_raw_version": 1,
                   "max_event_date": "2013-04-30T23:59:59.999999",
                   "provider": "pmc",
                   "aliases": {
                       "pmid": [
                           "23066504",
                           "23066507",
                           "23066508",
                           "23066509",
                           "23066506",
                           "23066503"
                       ]
                   },
                   "type": "provider_data_dump",
                   "min_event_date": "2013-04-01T00:00:00",
                   "created": "2013-05-16T07:38:06.831119"
                }        
    def setUp(self):
        self.d = None

        # do the same thing for the redis db, set up the test redis database.  We're using DB Number 8
        self.r = tiredis.from_url("redis://localhost:6379", db=REDIS_UNITTEST_DATABASE_NUMBER)
        self.r.flushdb()

        self.db = setup_postgres_for_unittests(db, app)

        self.aliases = [
            ["doi", "10.123"],
            ["doi", "10.124"],
            ["doi", "10.125"]
        ]
Ejemplo n.º 8
0
    def setUp(self):

        self.db = setup_postgres_for_unittests(db, app)

        # do the same thing for the redis db, set up the test redis database.  We're using DB Number 8
        self.r = tiredis.from_url("redis://localhost:6379", db=REDIS_UNITTEST_DATABASE_NUMBER)
        self.r.flushdb()
        now = datetime.datetime.utcnow()
        self.before = now - datetime.timedelta(days=2)
        self.last_week = now - datetime.timedelta(days=7)
        self.last_year = now - datetime.timedelta(days=370)

        # save basic item beforehand, and some additional items
        self.fake_item_doc = {
            "_id": "tiid1",
            "type": "item",
            "last_modified": now.isoformat(),
            "last_update_run": now.isoformat(),
            "aliases":{"doi":["10.7554/elife.1"]},
            "biblio": {"year":"2012"},
            "metrics": {}
        }
        self.fake_item_obj = item_module.create_objects_from_item_doc(self.fake_item_doc)        
        self.db.session.add(self.fake_item_obj)

        another_elife = copy.copy(self.fake_item_doc)
        another_elife["_id"] = "tiid2"
        another_elife["aliases"] = {"doi":["10.7554/ELIFE.2"]}
        another_elife["last_modified"] = self.before.isoformat()
        another_elife["last_update_run"] = self.before.isoformat()
        another_elife_obj = item_module.create_objects_from_item_doc(another_elife)        
        self.db.session.add(another_elife_obj)

        different_journal = copy.copy(self.fake_item_doc)
        different_journal["_id"] = "tiid3"
        different_journal["aliases"] = {"doi":["10.3897/zookeys.3"], "biblio":[{"year":1999}]}
        different_journal["last_modified"] = now.isoformat()
        different_journal["last_update_run"] = self.last_week.isoformat()
        different_journal_obj = item_module.create_objects_from_item_doc(different_journal)        
        self.db.session.add(different_journal_obj)

        different_journal2 = copy.copy(different_journal)
        different_journal2["_id"] = "tiid4"
        different_journal2["last_update_run"] = self.last_year.isoformat()
        different_journal_obj2 = item_module.create_objects_from_item_doc(different_journal2)        
        self.db.session.add(different_journal_obj2)

        self.db.session.commit()
Ejemplo n.º 9
0
    def setUp(self):

        self.db = setup_postgres_for_unittests(db, app)

        # do the same thing for the redis db, set up the test redis database.  We're using DB Number 8
        self.r = tiredis.from_url("redis://localhost:6379", db=8)
        self.r.flushdb()
        now = datetime.datetime.utcnow()
        self.before = now - datetime.timedelta(days=2)
        self.last_week = now - datetime.timedelta(days=7)
        self.last_year = now - datetime.timedelta(days=370)

        # save basic item beforehand, and some additional items
        self.fake_item_doc = {
            "_id": "tiid1",
            "type": "item",
            "last_modified": now.isoformat(),
            "last_update_run": now.isoformat(),
            "aliases":{"doi":["10.7554/elife.1"]},
            "biblio": {"year":"2012"},
            "metrics": {}
        }
        self.fake_item_obj = item_module.create_objects_from_item_doc(self.fake_item_doc)        
        self.db.session.add(self.fake_item_obj)

        another_elife = copy.copy(self.fake_item_doc)
        another_elife["_id"] = "tiid2"
        another_elife["aliases"] = {"doi":["10.7554/ELIFE.2"]}
        another_elife["last_modified"] = self.before.isoformat()
        another_elife["last_update_run"] = self.before.isoformat()
        another_elife_obj = item_module.create_objects_from_item_doc(another_elife)        
        self.db.session.add(another_elife_obj)

        different_journal = copy.copy(self.fake_item_doc)
        different_journal["_id"] = "tiid3"
        different_journal["aliases"] = {"doi":["10.3897/zookeys.3"], "biblio":[{"year":1999}]}
        different_journal["last_modified"] = now.isoformat()
        different_journal["last_update_run"] = self.last_week.isoformat()
        different_journal_obj = item_module.create_objects_from_item_doc(different_journal)        
        self.db.session.add(different_journal_obj)

        different_journal2 = copy.copy(different_journal)
        different_journal2["_id"] = "tiid4"
        different_journal2["last_update_run"] = self.last_year.isoformat()
        different_journal_obj2 = item_module.create_objects_from_item_doc(different_journal2)        
        self.db.session.add(different_journal_obj2)

        self.db.session.commit()
Ejemplo n.º 10
0
    def setUp(self):
        self.db = setup_postgres_for_unittests(db, app)

        # example from http://docs.cloudmailin.com/http_post_formats/json/
        self.example_payload = {
            "headers": {
                "To": "*****@*****.**",
                "Mime-Version": "1.0",
                "X-Received":
                "by 10.58.45.134 with SMTP id n6mr13476387vem.35.1361476813304; Thu, 21 Feb 2013 12:00:13 -0800 (PST)",
                "Received":
                "by mail-vc0-f202.google.com with SMTP id m8so955261vcd.3 for <*****@*****.**>; Thu, 21 Feb 2013 12:00:13 -0800",
                "From":
                "Google Scholar Alerts <*****@*****.**>",
                "DKIM-Signature":
                "v=1; a=rsa-sha256; c=relaxed/relaxed; d=google.com; s=20120113; h=mime-version:x-received:message-id:date:subject:from:to :content-type; bh=74dhtWOnoX2dYtmZibjD2+Tp65AZ7UnVwRTR7Qwho/o=; b=Fabq5urMfTyUX0s3XgFhVx1pyZ+tW/n38Sm/3T5EXTWeG2k7C6mxbrv1DdmpNpl/a8 Sr70eG6St7oytXii5tg9TrwrlwhftpFZKkJQS8GMWswiEaBkOfnNkoRrN174jRYfBUuZ oKWJr49dxw9hV3uKYoSis0zL6R8P+7GXt1rtqblBELrfIJ3pKC7d7WS65i6hdM2kA+sY va9geqt1fFFN7098U7WELlM2JoXhS4fbIQTev/Z6cF89Sfs4888GXb7PIq0d1kfd6t7c kXK8bV6TkqSP4AxDm646Cv1TR9cfo6+9yCrkK8oW6ihAMzM0Lwobq22NLrRY2QK8494s WAuA==",
                "Date": "Thu, 21 Feb 2013 20:00:13 +0000",
                "Message-ID": "<*****@*****.**>",
                "Content-Type":
                "text/plain; charset=ISO-8859-1; delsp=yes; format=flowed",
                "Subject": "Confirm your Google Scholar Alert"
            },
            "reply_plain": None,
            "attachments": [],
            "plain":
            "Google received a request to start sending Scholar Alerts to  \[email protected] for the query:\nNew articles in Jonathan A. Eisen's profile\n\nClick to confirm this request:\nhttp://scholar.google.ca/scholar_alerts?update_op=confirm_alert&hl=en&alert_id=IMEzMffmofYJ&email_for_op=7be5eb5001593217143f%40cloudmailin.net\n\nClick to cancel this request:\nhttp://scholar.google.ca/scholar_alerts?view_op=cancel_alert_options&hl=en&alert_id=IMEzMffmofYJ&email_for_op=7be5eb5001593217143f%40cloudmailin.net\n\nThanks,\nThe Google Scholar Team",
            "envelope": {
                "to": "*****@*****.**",
                "helo_domain": "mail-vc0-f202.google.com",
                "from":
                "*****@*****.**",
                "remote_ip": "209.85.220.202",
                "spf": {
                    "domain": "scholar-alerts.bounces.google.com",
                    "result": "neutral"
                }
            },
            "html": None
        }
    def setUp(self):
        self.db = setup_postgres_for_unittests(db, app)

        self.test_data = {
            "raw":
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            "max_event_date": "2012-10-31T07:34:01.126892",
            "provider": "pmc",
            "aliases": {
                "pmid": [
                    "23066504", "23066507", "23066508", "23066509", "23066506",
                    "23066503", "23066510", "23071903", "23110253", "23066505",
                    "23110254", "23110255", "23110252"
                ]
            },
            "provider_raw_version": 1,
            "min_event_date": "2012-10-01T07:34:01.126892",
            "created": "2012-11-29T07:34:01.126892"
        }

        self.old_doc = {
            "_id": "pmc201304",
            "_rev": "1-c9a62778077941736932cfb3510ee382",
            "raw":
            "<pmc-web-stat><request year=\"2013\" month=\"04\" jrid=\"elife\" eissn=\"2050-084X\"></request><response status=\"0\" collection=\"eLife\"></response><articles><article id=\"PMC3463246\"><meta-data doi=\"10.7554/eLife.00013\" pmcid=\"PMC3463246\" pubmed-id=\"23066504\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00013\"/><usage unique-ip=\"112\" full-text=\"152\" pdf=\"22\" abstract=\"1\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"31\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3463247\"><meta-data doi=\"10.7554/eLife.00240\" pmcid=\"PMC3463247\" pubmed-id=\"23066507\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00240\"/><usage unique-ip=\"10\" full-text=\"41\" pdf=\"1\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"0\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3465569\"><meta-data doi=\"10.7554/eLife.00242\" pmcid=\"PMC3465569\" pubmed-id=\"23066508\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00242\"/><usage unique-ip=\"27\" full-text=\"26\" pdf=\"3\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"0\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3465570\"><meta-data doi=\"10.7554/eLife.00243\" pmcid=\"PMC3465570\" pubmed-id=\"23066509\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00243\"/><usage unique-ip=\"41\" full-text=\"50\" pdf=\"9\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"8\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3466591\"><meta-data doi=\"10.7554/eLife.00065\" pmcid=\"PMC3466591\" pubmed-id=\"23066506\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00065\"/><usage unique-ip=\"252\" full-text=\"2522\" pdf=\"41\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"72\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3466783\"><meta-data doi=\"10.7554/eLife.00007\" pmcid=\"PMC3466783\" pubmed-id=\"23066503\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00007\"/><usage unique-ip=\"47\" full-text=\"62\" pdf=\"5\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"10\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3467772\"><meta-data doi=\"10.7554/eLife.00270\" pmcid=\"PMC3467772\" pubmed-id=\"23066510\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00270\"/><usage unique-ip=\"28\" full-text=\"32\" pdf=\"2\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"0\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3470409\"><meta-data doi=\"10.7554/eLife.00048\" pmcid=\"PMC3470409\" pubmed-id=\"23066505\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00048\"/><usage unique-ip=\"72\" full-text=\"68\" pdf=\"20\" abstract=\"1\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"26\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3470722\"><meta-data doi=\"10.7554/eLife.00286\" pmcid=\"PMC3470722\" pubmed-id=\"23071903\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00286\"/><usage unique-ip=\"37\" full-text=\"40\" pdf=\"7\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"0\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3479833\"><meta-data doi=\"10.7554/eLife.00031\" pmcid=\"PMC3479833\" pubmed-id=\"23110253\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00031\"/><usage unique-ip=\"31\" full-text=\"41\" pdf=\"3\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"7\" supp-data=\"0\" cited-by=\"1\"/></article><article id=\"PMC3482686\"><meta-data doi=\"10.7554/eLife.00005\" pmcid=\"PMC3482686\" pubmed-id=\"23110252\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00005\"/><usage unique-ip=\"189\" full-text=\"238\" pdf=\"33\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"110\" supp-data=\"2\" cited-by=\"0\"/></article><article id=\"PMC3482687\"><meta-data doi=\"10.7554/eLife.00281\" pmcid=\"PMC3482687\" pubmed-id=\"23110255\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00281\"/><usage unique-ip=\"17\" full-text=\"20\" pdf=\"0\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"0\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3482692\"><meta-data doi=\"10.7554/eLife.00102\" pmcid=\"PMC3482692\" pubmed-id=\"23110254\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00102\"/><usage unique-ip=\"50\" full-text=\"55\" pdf=\"11\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"7\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3485613\"><meta-data doi=\"10.7554/eLife.00301\" pmcid=\"PMC3485613\" pubmed-id=\"23150799\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00301\"/><usage unique-ip=\"41\" full-text=\"43\" pdf=\"7\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"7\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3485615\"><meta-data doi=\"10.7554/eLife.00049\" pmcid=\"PMC3485615\" pubmed-id=\"23150796\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00049\"/><usage unique-ip=\"390\" full-text=\"558\" pdf=\"108\" abstract=\"11\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"132\" supp-data=\"0\" cited-by=\"4\"/></article><article id=\"PMC3490148\"><meta-data doi=\"10.7554/eLife.00302\" pmcid=\"PMC3490148\" pubmed-id=\"23150800\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00302\"/><usage unique-ip=\"47\" full-text=\"54\" pdf=\"4\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"8\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3490149\"><meta-data doi=\"10.7554/eLife.00068\" pmcid=\"PMC3490149\" pubmed-id=\"23150797\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00068\"/><usage unique-ip=\"42\" full-text=\"53\" pdf=\"12\" abstract=\"1\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"9\" supp-data=\"1\" cited-by=\"0\"/></article><article id=\"PMC3491588\"><meta-data doi=\"10.7554/eLife.00003\" pmcid=\"PMC3491588\" pubmed-id=\"23150794\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00003\"/><usage unique-ip=\"62\" full-text=\"58\" pdf=\"20\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"13\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3492862\"><meta-data doi=\"10.7554/eLife.00011\" pmcid=\"PMC3492862\" pubmed-id=\"23150795\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00011\"/><usage unique-ip=\"68\" full-text=\"70\" pdf=\"9\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"18\" supp-data=\"6\" cited-by=\"0\"/></article><article id=\"PMC3494066\"><meta-data doi=\"10.7554/eLife.00173\" pmcid=\"PMC3494066\" pubmed-id=\"23150798\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00173\"/><usage unique-ip=\"39\" full-text=\"47\" pdf=\"3\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"12\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3510452\"><meta-data doi=\"10.7554/eLife.00051\" pmcid=\"PMC3510452\" pubmed-id=\"23240081\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00051\"/><usage unique-ip=\"16\" full-text=\"16\" pdf=\"5\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"0\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3510453\"><meta-data doi=\"10.7554/eLife.00078\" pmcid=\"PMC3510453\" pubmed-id=\"23240084\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00078\"/><usage unique-ip=\"33\" full-text=\"33\" pdf=\"8\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"1\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3510454\"><meta-data doi=\"10.7554/eLife.00171\" pmcid=\"PMC3510454\" pubmed-id=\"23240086\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00171\"/><usage unique-ip=\"28\" full-text=\"34\" pdf=\"4\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"14\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3510455\"><meta-data doi=\"10.7554/eLife.00067\" pmcid=\"PMC3510455\" pubmed-id=\"23240082\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00067\"/><usage unique-ip=\"31\" full-text=\"34\" pdf=\"7\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"10\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3510456\"><meta-data doi=\"10.7554/eLife.00070\" pmcid=\"PMC3510456\" pubmed-id=\"23240083\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00070\"/><usage unique-ip=\"37\" full-text=\"34\" pdf=\"4\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"20\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3510471\"><meta-data doi=\"10.7554/eLife.00365\" pmcid=\"PMC3510471\" pubmed-id=\"23240092\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00365\"/><usage unique-ip=\"13\" full-text=\"14\" pdf=\"1\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"0\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3510472\"><meta-data doi=\"10.7554/eLife.00340\" pmcid=\"PMC3510472\" pubmed-id=\"23240089\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00340\"/><usage unique-ip=\"8\" full-text=\"10\" pdf=\"0\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"0\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3510473\"><meta-data doi=\"10.7554/eLife.00351\" pmcid=\"PMC3510473\" pubmed-id=\"0\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00351\"/><usage unique-ip=\"8\" full-text=\"9\" pdf=\"1\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"0\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3510474\"><meta-data doi=\"10.7554/eLife.00184\" pmcid=\"PMC3510474\" pubmed-id=\"23240087\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00184\"/><usage unique-ip=\"38\" full-text=\"41\" pdf=\"8\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"4\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3510475\"><meta-data doi=\"10.7554/eLife.00347\" pmcid=\"PMC3510475\" pubmed-id=\"23240090\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00347\"/><usage unique-ip=\"17\" full-text=\"18\" pdf=\"2\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"2\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3510476\"><meta-data doi=\"10.7554/eLife.00353\" pmcid=\"PMC3510476\" pubmed-id=\"23240091\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00353\"/><usage unique-ip=\"22\" full-text=\"36\" pdf=\"4\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"4\" supp-data=\"0\" 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unique-ip=\"47\" full-text=\"51\" pdf=\"16\" abstract=\"1\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"18\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3524826\"><meta-data doi=\"10.7554/eLife.00387\" pmcid=\"PMC3524826\" pubmed-id=\"23256047\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00387\"/><usage unique-ip=\"52\" full-text=\"60\" pdf=\"6\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"12\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3524827\"><meta-data doi=\"10.7554/eLife.00385\" pmcid=\"PMC3524827\" pubmed-id=\"23256045\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00385\"/><usage unique-ip=\"13\" full-text=\"16\" pdf=\"2\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"2\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3524939\"><meta-data doi=\"10.7554/eLife.00205\" pmcid=\"PMC3524939\" pubmed-id=\"23256043\" pub-year=\"2012\" volume=\"1\" 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abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"7\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3608266\"><meta-data doi=\"10.7554/eLife.00260\" pmcid=\"PMC3608266\" pubmed-id=\"23538384\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00260\"/><usage unique-ip=\"103\" full-text=\"122\" pdf=\"45\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"39\" supp-data=\"6\" cited-by=\"0\"/></article><article id=\"PMC3610343\"><meta-data doi=\"10.7554/eLife.00269\" pmcid=\"PMC3610343\" pubmed-id=\"23543845\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00269\"/><usage unique-ip=\"57\" full-text=\"63\" pdf=\"10\" abstract=\"1\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"9\" supp-data=\"2\" cited-by=\"0\"/></article><article id=\"PMC3614016\"><meta-data doi=\"10.7554/eLife.00278\" pmcid=\"PMC3614016\" pubmed-id=\"23577232\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00278\"/><usage unique-ip=\"39\" full-text=\"42\" pdf=\"7\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"16\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3614024\"><meta-data doi=\"10.7554/eLife.00655\" pmcid=\"PMC3614024\" pubmed-id=\"23577236\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00655\"/><usage unique-ip=\"27\" full-text=\"31\" pdf=\"5\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"2\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3614025\"><meta-data doi=\"10.7554/eLife.00435\" pmcid=\"PMC3614025\" pubmed-id=\"23577234\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00435\"/><usage unique-ip=\"100\" full-text=\"104\" pdf=\"32\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"62\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3614033\"><meta-data doi=\"10.7554/eLife.00367\" pmcid=\"PMC3614033\" pubmed-id=\"23577233\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00367\"/><usage unique-ip=\"49\" full-text=\"64\" pdf=\"15\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"9\" supp-data=\"8\" cited-by=\"0\"/></article><article id=\"PMC3614058\"><meta-data doi=\"10.7554/eLife.00639\" pmcid=\"PMC3614058\" pubmed-id=\"23577235\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00639\"/><usage unique-ip=\"46\" full-text=\"64\" pdf=\"8\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"2\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3622176\"><meta-data doi=\"10.7554/eLife.00692\" pmcid=\"PMC3622176\" pubmed-id=\"23580166\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00692\"/><usage unique-ip=\"27\" full-text=\"33\" pdf=\"5\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"5\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3622177\"><meta-data doi=\"10.7554/eLife.00444\" pmcid=\"PMC3622177\" pubmed-id=\"23580231\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00444\"/><usage unique-ip=\"60\" full-text=\"69\" pdf=\"22\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"26\" supp-data=\"4\" cited-by=\"0\"/></article><article id=\"PMC3622178\"><meta-data doi=\"10.7554/eLife.00426\" pmcid=\"PMC3622178\" pubmed-id=\"23580255\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00426\"/><usage unique-ip=\"63\" full-text=\"88\" pdf=\"18\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"29\" supp-data=\"5\" cited-by=\"0\"/></article><article id=\"PMC3622181\"><meta-data doi=\"10.7554/eLife.00499\" pmcid=\"PMC3622181\" pubmed-id=\"23580326\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00499\"/><usage unique-ip=\"80\" full-text=\"111\" pdf=\"37\" abstract=\"1\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"22\" supp-data=\"0\" cited-by=\"1\"/></article><article id=\"PMC3622228\"><meta-data doi=\"10.7554/eLife.00659\" pmcid=\"PMC3622228\" pubmed-id=\"23580350\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00659\"/><usage unique-ip=\"37\" full-text=\"37\" pdf=\"10\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"11\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3622229\"><meta-data doi=\"10.7554/eLife.00663\" pmcid=\"PMC3622229\" pubmed-id=\"23580362\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00663\"/><usage unique-ip=\"46\" full-text=\"51\" pdf=\"15\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"11\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3628084\"><meta-data doi=\"10.7554/eLife.00415\" pmcid=\"PMC3628084\" pubmed-id=\"23599892\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00415\"/><usage unique-ip=\"40\" full-text=\"40\" pdf=\"10\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"14\" supp-data=\"0\" cited-by=\"1\"/></article><article id=\"PMC3628085\"><meta-data doi=\"10.7554/eLife.00458\" pmcid=\"PMC3628085\" pubmed-id=\"23599893\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00458\"/><usage unique-ip=\"120\" full-text=\"124\" pdf=\"36\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"43\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3628086\"><meta-data doi=\"10.7554/eLife.00362\" pmcid=\"PMC3628086\" pubmed-id=\"23599891\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00362\"/><usage unique-ip=\"91\" full-text=\"120\" pdf=\"24\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"64\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3628087\"><meta-data doi=\"10.7554/eLife.00534\" pmcid=\"PMC3628087\" pubmed-id=\"23599896\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00534\"/><usage unique-ip=\"72\" full-text=\"72\" pdf=\"16\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"19\" supp-data=\"1\" cited-by=\"0\"/></article><article id=\"PMC3628110\"><meta-data doi=\"10.7554/eLife.00482\" pmcid=\"PMC3628110\" pubmed-id=\"23599895\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00482\"/><usage unique-ip=\"44\" full-text=\"51\" pdf=\"1\" abstract=\"1\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"21\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3628404\"><meta-data doi=\"10.7554/eLife.00729\" pmcid=\"PMC3628404\" pubmed-id=\"23599898\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00729\"/><usage unique-ip=\"62\" full-text=\"100\" pdf=\"12\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"8\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3628405\"><meta-data doi=\"10.7554/eLife.00459\" pmcid=\"PMC3628405\" pubmed-id=\"23599894\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00459\"/><usage unique-ip=\"39\" full-text=\"42\" pdf=\"9\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"45\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3628440\"><meta-data doi=\"10.7554/eLife.00676\" pmcid=\"PMC3628440\" pubmed-id=\"23599897\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00676\"/><usage unique-ip=\"18\" full-text=\"23\" pdf=\"3\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"2\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3629793\"><meta-data doi=\"10.7554/eLife.00288\" pmcid=\"PMC3629793\" pubmed-id=\"23606943\" pub-year=\"2013\" volume=\"2\" issue=\"\" first-page=\"e00288\"/><usage unique-ip=\"35\" full-text=\"41\" pdf=\"4\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"11\" supp-data=\"3\" cited-by=\"0\"/></article></articles></pmc-web-stat>",
            "provider_raw_version": 1,
            "max_event_date": "2013-04-30T23:59:59.999999",
            "provider": "pmc",
            "aliases": {
                "pmid": [
                    "23066504", "23066507", "23066508", "23066509", "23066506",
                    "23066503"
                ]
            },
            "type": "provider_data_dump",
            "min_event_date": "2013-04-01T00:00:00",
            "created": "2013-05-16T07:38:06.831119"
        }
Ejemplo n.º 12
0
    def setUp(self):
        self.d = None

        self.db = setup_postgres_for_unittests(db, app)

        # setup a clean new redis test database.  We're putting unittest redis at DB Number 8.
        self.r = tiredis.from_url("redis://*****:*****@example.com'
        self.test_meta = {
            'max_registered_items': 3,
            'planned_use': 'individual CV',
            'email': self.test_email,
            'notes': '',
            'api_key_owner': 'Julia Smith',
            "example_url": "",
            "organization": "NASA"
        }

        test_meta2 = copy.deepcopy(self.test_meta)
        test_meta2["email"] = '*****@*****.**'
        test_meta2["prefix"] = "SFU"
        self.existing_api_user = ApiUser(**test_meta2)

        self.existing_registered_item = RegisteredItem(
            self.test_alias_registered, self.existing_api_user)

        self.db.session.add(self.existing_api_user)
        self.db.session.add(self.existing_registered_item)
        self.db.session.commit()
Ejemplo n.º 13
0
    def setUp(self):
        self.BIBLIO_DATA = {
            "title": "An extension of de Finetti's theorem",
            "journal": "Advances in Applied Probability",
            "author": [
                "Pitman, J"
            ],
            "authors": "Pitman",
            "collection": "pitnoid",
            "volume": "10",
            "id": "p78",
            "year": "1978",
            "pages": "268 to 270"
        }

        self.ALIAS_DATA = {
            "title":["Why Most Published Research Findings Are False"],
            "url":["http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.0020124"],
            "doi": ["10.1371/journal.pmed.0020124"],
            "biblio": [self.BIBLIO_DATA]
        }


        self.KEY1 = '2012-08-23T14:40:16.888888'
        self.KEY2 = '2012-08-23T14:40:16.999999'
        self.VAL1 = 1
        self.VAL2 = 2

        METRICS_DATA = {
            "provenance_url": "http://api.mendeley.com/research/public-chemical-compound-databases/",
            "values":{
                "raw": self.VAL2,
                "raw_history": {
                    self.KEY1: self.VAL1,
                    self.KEY2: self.VAL2
                }
            }
        }

        METRICS_DATA2 = {
            "provenance_url": "http://api.mendeley.com/research/public-chemical-compound-databases/",
            "values":{
                "raw": self.VAL2,
                "raw_history": {
                    self.KEY1: self.VAL1,
                    self.KEY2: self.VAL2
                }
            }
        }

        METRICS_DATA3 = {
            "provenance_url": "http://api.mendeley.com/research/public-chemical-compound-databases/",
            "values":{
                "raw": self.VAL2,
                "raw_history": {
                    self.KEY1: self.VAL1,
                    self.KEY2: self.VAL2
                }
            }
        }


        self.ITEM_DATA = {
            "_id": "test",
            "created": '2012-08-23T14:40:16.399932',
            "last_modified": '2012-08-23T14:40:16.399932',
            "last_update_run": '2012-08-23T14:40:16.399932',
            "aliases": self.ALIAS_DATA,
            "metrics": {
                "wikipedia:mentions": METRICS_DATA,
                "altmetric_com:tweets": METRICS_DATA2
            },
            "biblio": self.BIBLIO_DATA,
            "type": "item"
        }

        self.TEST_PROVIDER_CONFIG = [
            ("wikipedia", {})
        ]

        self.d = None
        
        self.myrefsets = {"nih": {"2011": {
                        "facebook:comments": {0: [1, 99], 1: [91, 99]}, "mendeley:groups": {0: [1, 99], 3: [91, 99]}
                    }}}

        # setup a clean new redis test database.  We're putting unittest redis at DB Number 8.
        self.r = tiredis.from_url("redis://localhost:6379", db=REDIS_UNITTEST_DATABASE_NUMBER)
        self.r.flushdb()

        self.db = setup_postgres_for_unittests(db, app)
 def test_get_aliases_for_id(self):
     self.db = setup_postgres_for_unittests(db, app)
     new_aliases = self.provider.aliases([self.testitem_aliases])
     print new_aliases
     expected = [('biblio', {'issn': u'15537358', 'repository': u'Public Library of Science (PLoS)', 'title': u'Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article', 'journal': u'PLoS Computational Biology', 'year': '2009', 'free_fulltext_url': 'http://dx.doi.org/10.1371/journal.pcbi.1000361', 'authors': u'Shotton, Portwin, Klyne, Miles'}), ('url', 'http://dx.doi.org/10.1371/journal.pcbi.1000361'), ('url', u'http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000361')]
     assert_equals(sorted(new_aliases), sorted(expected))
 def setUp(self):
     ProviderTestCase.setUp(self)
     self.db = setup_postgres_for_unittests(db, app)
Ejemplo n.º 16
0
    def setUp(self):
        """
        This test item is a lightly-modified version of a real doc from our
        demo collection; it's available at http://total-impact-core.herokuapp.com/collection/kn5auf
        """
        test_item = '''
            {
            "_id": "1aff9dfebea711e1bdf912313d1a5e63",
            "_rev": "968-c7891982fca2ea41346a20b80c2b888d",
            "aliases": {
                "doi": [
                    "10.5061/dryad.j1fd7"
                ],
                "title": [
                    "Data from: Data archiving is a good use of research funds",
                    "data from: data archiving is a good  investment"
                ],
                "url": [
                    "http://datadryad.org/handle/10255/dryad.33537",
                    "http://hdl.handle.net/10255/dryad.33537"
                ]
            },
            "biblio": {
                "authors": "Piwowar, Vision, Whitlock, Piwowar, Vision, Whitlock, Piwowar, Vision, Whitlock",
                "genre": "dataset",
                "h1": "Data from: Data archiving is a good  investment",
                "repository": "Dryad Digital Repository",
                "title": "Data from: Data archiving is a good  investment",
                "year": "2011"
            },
            "created": "2012-06-25T09:21:11.960271",
            "currently_updating": false,
            "last_modified": "2012-11-18T04:57:40.539053",
            "metrics": {
                "delicious:bookmarks": {
                    "provenance_url": "http://www.delicious.com/url/4794ddb7a3e934ba23165af65fcfa9cd",
                    "static_meta": {
                        "description": "The number of bookmarks to this artifact (maximum=100).",
                        "display_name": "bookmarks",
                        "icon": "http://www.delicious.com/favicon.ico",
                        "provider": "Delicious",
                        "provider_url": "http://www.delicious.com/"
                    },
                    "values": {
                        "raw": 1,
                        "raw_history": {
                            "2012-06-23T09:21:16.027149": 1
                        }
                    }
                },
                "dryad:total_downloads": {
                    "provenance_url": "http://dx.doi.org/10.5061/dryad.j1fd7",
                    "static_meta": {
                        "description": "Dryad total downloads: combined number of downloads of the data package and data files",
                        "display_name": "total downloads",
                        "icon": "http:\\/\\/datadryad.org\\/favicon.ico",
                        "provider": "Dryad",
                        "provider_url": "http:\\/\\/www.datadryad.org\\/"
                    },
                    "values": {
                        "dryad": {
                            "CI95_lower": 91,
                            "CI95_upper": 98,
                            "estimate_lower": 96,
                            "estimate_upper": 96
                        },
                        "raw": 207,
                        "raw_history": {
                            "2012-06-25T09:21:16.027149": 132,
                            "2012-06-26T18:05:19.598432": 132,
                            "2012-06-26T20:10:16.858294": 132
                        }
                    }
                }
            },
            "type": "item"
        }
        '''

        self.test_api_user_meta = {
            'max_registered_items': 3,
            'planned_use': 'individual CV',
            'email': "*****@*****.**",
            'notes': '',
            'api_key_owner': 'Julia Smith',
            "example_url": "",
            "organization": "NASA",
            "prefix": "NASA",
        }

        self.db = setup_postgres_for_unittests(db, app)

        item = item_module.create_objects_from_item_doc(json.loads(test_item))
        self.db.session.add(item)

        self.existing_api_user = api_user.ApiUser(**self.test_api_user_meta)
        self.existing_api_user.api_key = "validkey"  #override randomly assigned key
        self.db.session.add(self.existing_api_user)
        self.db.session.commit()

        # do the same thing for the redis db.  We're using DB 8 for unittests.
        self.r = tiredis.from_url("redis://localhost:6379", db=8)
        self.r.flushdb()

        #setup api test client
        self.app = app
        self.app.testing = True
        self.client = self.app.test_client()

        # Mock out relevant methods of the Dryad provider
        self.orig_Dryad_member_items = Dryad.member_items
        Dryad.member_items = MOCK_member_items

        self.aliases = [["doi", "10.123"], ["doi", "10.124"],
                        ["doi", "10.125"]]
Ejemplo n.º 17
0
 def setUp(self):
     self.db = setup_postgres_for_unittests(db, app)
     ProviderTestCase.setUp(self)
Ejemplo n.º 18
0
 def setUp(self):
     self.db = setup_postgres_for_unittests(db, app)
Ejemplo n.º 19
0
    def setUp(self):
        self.BIBLIO_DATA = {
            "title": "An extension of de Finetti's theorem",
            "journal": "Advances in Applied Probability",
            "author": [
                "Pitman, J"
            ],
            "authors": "Pitman",
            "collection": "pitnoid",
            "volume": "10",
            "id": "p78",
            "year": "1978",
            "pages": "268 to 270"
        }

        self.ALIAS_DATA = {
            "title":["Why Most Published Research Findings Are False"],
            "url":["http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.0020124"],
            "doi": ["10.1371/journal.pmed.0020124"],
            "biblio": [self.BIBLIO_DATA]
        }


        self.KEY1 = '2012-08-23T14:40:16.888888'
        self.KEY2 = '2012-08-23T14:40:16.999999'
        self.VAL1 = 1
        self.VAL2 = 2

        METRICS_DATA = {
            "provenance_url": "http://api.mendeley.com/research/public-chemical-compound-databases/",
            "values":{
                "raw": self.VAL2,
                "raw_history": {
                    self.KEY1: self.VAL1,
                    self.KEY2: self.VAL2
                }
            }
        }

        METRICS_DATA2 = {
            "provenance_url": "http://api.mendeley.com/research/public-chemical-compound-databases/",
            "values":{
                "raw": self.VAL2,
                "raw_history": {
                    self.KEY1: self.VAL1,
                    self.KEY2: self.VAL2
                }
            }
        }

        METRICS_DATA3 = {
            "provenance_url": "http://api.mendeley.com/research/public-chemical-compound-databases/",
            "values":{
                "raw": self.VAL2,
                "raw_history": {
                    self.KEY1: self.VAL1,
                    self.KEY2: self.VAL2
                }
            }
        }


        self.ITEM_DATA = {
            "_id": "test",
            "created": '2012-08-23T14:40:16.399932',
            "last_modified": '2012-08-23T14:40:16.399932',
            "aliases": self.ALIAS_DATA,
            "metrics": {
                "wikipedia:mentions": METRICS_DATA,
                "topsy:tweets": METRICS_DATA2
            },
            "biblio": self.BIBLIO_DATA,
            "type": "item"
        }

        self.TEST_PROVIDER_CONFIG = [
            ("wikipedia", {})
        ]

        self.d = None
        
        self.myrefsets = {"nih": {"2011": {
                        "facebook:comments": {0: [1, 99], 1: [91, 99]}, "mendeley:groups": {0: [1, 99], 3: [91, 99]}
                    }}}

        # setup a clean new redis test database.  We're putting unittest redis at DB Number 8.
        self.r = tiredis.from_url("redis://localhost:6379", db=8)
        self.r.flushdb()

        self.db = setup_postgres_for_unittests(db, app)
Ejemplo n.º 20
0
 def setUp(self):
     self.db = setup_postgres_for_unittests(db, app)
Ejemplo n.º 21
0
    def setUp(self):
        ProviderTestCase.setUp(self)

        self.db = setup_postgres_for_unittests(db, app)

        sample_data_dump = open(SAMPLE_EXTRACT_METRICS_PAGE, "r").read()
        sample_data_dump_different_month = open(SAMPLE_EXTRACT_METRICS_PAGE_DIFFERENT_MONTH, "r").read()

        test_monthly_data = [
            {"_id": "abc", 
                "type": "provider_data_dump", 
                "provider": "pmc", 
                "raw": sample_data_dump,
                "provider_raw_version": 1.0,
                "created": "2012-11-29T07:34:01.126892",
                "aliases": {"pmid":["111", "222"]},
                "min_event_date": "2012-10-01T07:34:01.126892",
                "max_event_date": "2012-10-31T07:34:01.126892"
            },
            {"_id": "def", 
                "type": "provider_data_dump", 
                "provider": "pmc", 
                "raw": sample_data_dump_different_month,
                "provider_raw_version": 1.0,
                "created": "2012-11-29T08:34:01.126892",
                "aliases": {"pmid":["111"]},
                "min_event_date": "2012-01-01T07:34:01.126892",
                "max_event_date": "2012-01-31T07:34:01.126892"
            },
            {
               "_id": "abc123",
               "raw": "<pmc-web-stat><request year=\"2012\" month=\"10\" jrid=\"elife\" eissn=\"2050-084X\"></request><response status=\"0\" collection=\"eLife\"></response><articles><article id=\"PMC3463246\"><meta-data doi=\"10.7554/eLife.00013\" pmcid=\"PMC3463246\" pubmed-id=\"23066504\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00013\"/><usage unique-ip=\"1368\" full-text=\"1464\" pdf=\"722\" abstract=\"119\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"144\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3463247\"><meta-data doi=\"10.7554/eLife.00240\" pmcid=\"PMC3463247\" pubmed-id=\"23066507\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00240\"/><usage unique-ip=\"514\" full-text=\"606\" pdf=\"230\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"9\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3465569\"><meta-data doi=\"10.7554/eLife.00242\" pmcid=\"PMC3465569\" pubmed-id=\"23066508\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00242\"/><usage unique-ip=\"473\" full-text=\"503\" pdf=\"181\" abstract=\"2\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"13\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3465570\"><meta-data doi=\"10.7554/eLife.00243\" pmcid=\"PMC3465570\" pubmed-id=\"23066509\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00243\"/><usage unique-ip=\"547\" full-text=\"636\" pdf=\"227\" abstract=\"1\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"56\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3466591\"><meta-data doi=\"10.7554/eLife.00065\" pmcid=\"PMC3466591\" pubmed-id=\"23066506\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00065\"/><usage unique-ip=\"2516\" full-text=\"2804\" pdf=\"1583\" abstract=\"195\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"405\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3466783\"><meta-data doi=\"10.7554/eLife.00007\" pmcid=\"PMC3466783\" pubmed-id=\"23066503\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00007\"/><usage unique-ip=\"1331\" full-text=\"1412\" pdf=\"898\" abstract=\"224\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"109\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3467772\"><meta-data doi=\"10.7554/eLife.00270\" pmcid=\"PMC3467772\" pubmed-id=\"23066510\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00270\"/><usage unique-ip=\"1396\" full-text=\"1776\" pdf=\"625\" abstract=\"4\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"0\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3470722\"><meta-data doi=\"10.7554/eLife.00286\" pmcid=\"PMC3470722\" pubmed-id=\"23071903\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00286\"/><usage unique-ip=\"909\" full-text=\"1030\" pdf=\"376\" abstract=\"6\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"0\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3479833\"><meta-data doi=\"10.7554/eLife.00031\" pmcid=\"PMC3479833\" pubmed-id=\"23110253\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00031\"/><usage unique-ip=\"154\" full-text=\"126\" pdf=\"87\" abstract=\"26\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"13\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3470409\"><meta-data doi=\"10.7554/eLife.00048\" pmcid=\"PMC3470409\" pubmed-id=\"23066505\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00048\"/><usage unique-ip=\"1250\" full-text=\"1361\" pdf=\"911\" abstract=\"237\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"317\" supp-data=\"4\" cited-by=\"0\"/></article><article id=\"PMC3482692\"><meta-data doi=\"10.7554/eLife.00102\" pmcid=\"PMC3482692\" pubmed-id=\"23110254\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00102\"/><usage unique-ip=\"259\" full-text=\"232\" pdf=\"133\" abstract=\"36\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"8\" supp-data=\"3\" cited-by=\"0\"/></article><article id=\"PMC3482687\"><meta-data doi=\"10.7554/eLife.00281\" pmcid=\"PMC3482687\" pubmed-id=\"23110255\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00281\"/><usage unique-ip=\"75\" full-text=\"53\" pdf=\"47\" abstract=\"0\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"1\" supp-data=\"0\" cited-by=\"0\"/></article><article id=\"PMC3482686\"><meta-data doi=\"10.7554/eLife.00005\" pmcid=\"PMC3482686\" pubmed-id=\"23110252\" pub-year=\"2012\" volume=\"1\" issue=\"\" first-page=\"e00005\"/><usage unique-ip=\"324\" full-text=\"249\" pdf=\"263\" abstract=\"71\" scanned-summary=\"0\" scanned-page-browse=\"0\" figure=\"93\" supp-data=\"17\" cited-by=\"0\"/></article></articles></pmc-web-stat>",
               "max_event_date": "2012-10-31T07:34:01.126892",
               "provider": "pmc",
               "aliases": {
                   "pmid": [
                       "23066504",
                       "23066507",
                       "23066508",
                       "23066509",
                       "23066506",
                       "23066503",
                       "23066510",
                       "23071903",
                       "23110253",
                       "23066505",
                       "23110254",
                       "23110255",
                       "23110252"
                   ]
               },
               "provider_raw_version": 1,
               "type": "provider_data_dump",
               "min_event_date": "2012-10-02T07:34:01.126892",
               "created": "2012-11-29T09:34:01.126892"
            }
        ]
        #print test_monthly_data
        for doc in test_monthly_data:
            new_object = provider_batch_data.create_objects_from_doc(doc)
            print new_object

        self.provider = pmc.Pmc()
        print "after pmc"
Ejemplo n.º 22
0
    def setUp(self):
        """
        This test item is a lightly-modified version of a real doc from our
        demo collection; it's available at http://total-impact-core.herokuapp.com/collection/kn5auf
        """
        test_item = '''
            {
            "_id": "1aff9dfebea711e1bdf912313d1a5e63",
            "_rev": "968-c7891982fca2ea41346a20b80c2b888d",
            "aliases": {
                "doi": [
                    "10.5061/dryad.j1fd7"
                ],
                "title": [
                    "Data from: Data archiving is a good use of research funds",
                    "data from: data archiving is a good  investment"
                ],
                "url": [
                    "http://datadryad.org/handle/10255/dryad.33537",
                    "http://hdl.handle.net/10255/dryad.33537"
                ]
            },
            "biblio": {
                "authors": "Piwowar, Vision, Whitlock, Piwowar, Vision, Whitlock, Piwowar, Vision, Whitlock",
                "genre": "dataset",
                "h1": "Data from: Data archiving is a good  investment",
                "repository": "Dryad Digital Repository",
                "title": "Data from: Data archiving is a good  investment",
                "year": "2011"
            },
            "created": "2012-06-25T09:21:11.960271",
            "currently_updating": false,
            "last_modified": "2012-11-18T04:57:40.539053",
            "metrics": {
                "delicious:bookmarks": {
                    "provenance_url": "http://www.delicious.com/url/4794ddb7a3e934ba23165af65fcfa9cd",
                    "static_meta": {
                        "description": "The number of bookmarks to this artifact (maximum=100).",
                        "display_name": "bookmarks",
                        "icon": "http://www.delicious.com/favicon.ico",
                        "provider": "Delicious",
                        "provider_url": "http://www.delicious.com/"
                    },
                    "values": {
                        "raw": 1,
                        "raw_history": {
                            "2012-06-23T09:21:16.027149": 1
                        }
                    }
                },
                "dryad:total_downloads": {
                    "provenance_url": "http://dx.doi.org/10.5061/dryad.j1fd7",
                    "static_meta": {
                        "description": "Dryad total downloads: combined number of downloads of the data package and data files",
                        "display_name": "total downloads",
                        "icon": "http:\\/\\/datadryad.org\\/favicon.ico",
                        "provider": "Dryad",
                        "provider_url": "http:\\/\\/www.datadryad.org\\/"
                    },
                    "values": {
                        "dryad": {
                            "CI95_lower": 91,
                            "CI95_upper": 98,
                            "estimate_lower": 96,
                            "estimate_upper": 96
                        },
                        "raw": 207,
                        "raw_history": {
                            "2012-06-25T09:21:16.027149": 132,
                            "2012-06-26T18:05:19.598432": 132,
                            "2012-06-26T20:10:16.858294": 132
                        }
                    }
                }
            },
            "type": "item"
        }
        '''

        self.test_api_user_meta = {    
                    'max_registered_items': 3, 
                    'planned_use': 'individual CV', 
                    'email': "*****@*****.**", 
                    'notes': '', 
                    'api_key_owner': 'Julia Smith', 
                    "example_url": "", 
                    "organization": "NASA",
                    "prefix": "NASA",
                }

        self.db = setup_postgres_for_unittests(db, app)

        item = item_module.create_objects_from_item_doc(json.loads(test_item))
        self.db.session.add(item)

        self.existing_api_user = api_user.ApiUser(**self.test_api_user_meta)
        self.existing_api_user.api_key = "validkey"  #override randomly assigned key
        self.db.session.add(self.existing_api_user)
        self.db.session.commit()


        # do the same thing for the redis db.  We're using DB 8 for unittests.
        self.r = tiredis.from_url("redis://localhost:6379", db=8)
        self.r.flushdb()

        #setup api test client
        self.app = app
        self.app.testing = True
        self.client = self.app.test_client()

        # Mock out relevant methods of the Dryad provider
        self.orig_Dryad_member_items = Dryad.member_items
        Dryad.member_items = MOCK_member_items

        self.aliases = [
            ["doi", "10.123"],
            ["doi", "10.124"],
            ["doi", "10.125"]
        ]
Ejemplo n.º 23
0
 def test_get_aliases_for_id(self):
     self.db = setup_postgres_for_unittests(db, app)
     new_aliases = self.provider.aliases([self.testitem_aliases])
     print new_aliases
     expected = [('biblio', {'issn': u'15537358', 'repository': u'Public Library of Science (PLoS)', 'title': u'Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article', 'journal': u'PLoS Computational Biology', 'year': '2009', 'free_fulltext_url': 'http://dx.doi.org/10.1371/journal.pcbi.1000361', 'authors': u'Shotton, Portwin, Klyne, Miles'}), ('url', 'http://dx.doi.org/10.1371/journal.pcbi.1000361'), ('url', u'http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000361')]
     assert_equals(sorted(new_aliases), sorted(expected))