def test_10_process_record_03_aam_no_licence(self):
def mock_get_md(*args, **kwargs):
md = epmcmod.EPMCMetadata(json.loads(open(EPMC_MD, "r").read()))
return md, 1.0
def mock_get_ft(*args, **kwargs):
data = open(EPMC_FT, "r").read()
xml = etree.fromstring(data)
l = xml.xpath("//license")
l[0].getparent().remove(l[0])
s = etree.tostring(xml)
return epmc.EPMCFullText(s)
def mock_doaj(*args, **kwargs):
return True
def mock_romeo(*args, **kwargs):
pass
def mock_core(*args, **kwargs):
pass
workflow.get_epmc_md = mock_get_md
workflow.get_epmc_fulltext = mock_get_ft
workflow.doaj_lookup = mock_doaj
workflow.embargo = mock_romeo
workflow.ou_core = mock_core
record = models.Record()
record.pmcid = "PMC4219345"
record.id = record.makeid()
oag = []
msg = workflow.WorkflowMessage(record=record, oag_register=oag)
workflow.process_record(msg)
assert record.confidence == 1.0
assert record.pmcid == "PMC4219345"
assert record.pmid == "24279897"
assert record.doi == "10.1186/1471-2121-14-52"
assert record.in_epmc is True
assert record.is_oa is False
assert len(record.issn) == 1
assert "1471-2121" in record.issn
assert record.id is not None # implies it has been saved
assert record.has_ft_xml is True
assert record.aam is True
assert record.aam_from_xml is True
assert record.licence_type is None
assert record.licence_source is None
assert record.journal_type == "oa"
assert len(oag) == 1
assert oag[0]["id"] == "PMC4219345"
assert oag[0]["type"] == "pmcid"
def test_10_process_record_02_no_md(self):
def mock_get_md(*args, **kwargs):
return None, None
workflow.get_epmc_md = mock_get_md
record = models.Record()
record.pmcid = "PMC4219345"
record.id = record.makeid()
oag = []
msg = workflow.WorkflowMessage(record=record, oag_register=oag)
workflow.process_record(msg)
assert record.confidence is None
assert len(record.provenance) == 1
assert len(oag) == 0
def test_10_process_record_02_no_md(self):
def mock_get_md(*args, **kwargs):
return None, None
workflow.get_epmc_md = mock_get_md
record = models.Record()
record.pmcid = "PMC4219345"
record.id = record.makeid()
oag = []
msg = workflow.WorkflowMessage(record=record, oag_register=oag)
workflow.process_record(msg)
assert record.confidence is None
assert len(record.provenance) == 1
assert len(oag) == 0
def test_10_process_record_01_everything(self):
def mock_get_md(*args, **kwargs):
md = epmcmod.EPMCMetadata(json.loads(open(EPMC_MD, "r").read()))
return md, 1.0
def mock_get_ft(*args, **kwargs):
data = open(EPMC_FT, "r").read()
return epmc.EPMCFullText(data)
def mock_doaj(*args, **kwargs):
return False
def mock_romeo(*args, **kwargs):
pass
def mock_core(*args, **kwargs):
pass
workflow.get_epmc_md = mock_get_md
workflow.get_epmc_fulltext = mock_get_ft
workflow.doaj_lookup = mock_doaj
workflow.embargo = mock_romeo
workflow.ou_core = mock_core
record = models.Record()
record.pmcid = "PMC4219345"
record.id = record.makeid()
oag = []
msg = workflow.WorkflowMessage(record=record, oag_register=oag)
workflow.process_record(msg)
assert record.confidence == 1.0
assert record.pmcid == "PMC4219345"
assert record.pmid == "24279897"
assert record.doi == "10.1186/1471-2121-14-52"
assert record.in_epmc is True
assert record.is_oa is False
assert len(record.issn) == 1
assert "1471-2121" in record.issn
assert record.id is not None # implies it has been saved
assert record.has_ft_xml is True
assert record.aam is True
assert record.aam_from_xml is True
assert record.licence_type == "cc-by"
assert record.licence_source == "epmc_xml"
assert record.journal_type == "hybrid"
assert len(oag) == 0
def test_10_process_record_03_aam_no_licence(self):
def mock_get_md(*args, **kwargs):
md = epmcmod.EPMCMetadata(json.loads(open(EPMC_MD, "r").read()))
return md, 1.0
def mock_get_ft(*args, **kwargs):
data = open(EPMC_FT, "r").read()
xml = etree.fromstring(data)
l = xml.xpath("//license")
l[0].getparent().remove(l[0])
s = etree.tostring(xml)
return epmc.EPMCFullText(s)
def mock_doaj(*args, **kwargs):
return True
workflow.get_epmc_md = mock_get_md
workflow.get_epmc_fulltext = mock_get_ft
workflow.doaj_lookup = mock_doaj
record = models.Record()
record.pmcid = "PMC4219345"
record.id = record.makeid()
oag = []
msg = workflow.WorkflowMessage(record=record, oag_register=oag)
workflow.process_record(msg)
assert record.confidence == 1.0
assert record.pmcid == "PMC4219345"
assert record.pmid == "24279897"
assert record.doi == "10.1186/1471-2121-14-52"
assert record.in_epmc is True
assert record.is_oa is False
assert len(record.issn) == 1
assert "1471-2121" in record.issn
assert record.id is not None # implies it has been saved
assert record.has_ft_xml is True
assert record.aam is True
assert record.aam_from_xml is True
assert record.licence_type is None
assert record.licence_source is None
assert record.journal_type == "oa"
assert len(oag) == 1
assert oag[0]["id"] == "PMC4219345"
assert oag[0]["type"] == "pmcid"
def test_10_process_record_04_licence_no_aam(self):
def mock_get_md(*args, **kwargs):
md = epmcmod.EPMCMetadata(json.loads(open(EPMC_MD, "r").read()))
return md, 1.0
def mock_get_ft(*args, **kwargs):
data = open(EPMC_FT, "r").read()
xml = etree.fromstring(data)
aids = xml.xpath("//article-id[@pub-id-type='manuscript']")
aids[0].getparent().remove(aids[0])
s = etree.tostring(xml)
return epmc.EPMCFullText(s)
def mock_doaj(*args, **kwargs):
return True
workflow.get_epmc_md = mock_get_md
workflow.get_epmc_fulltext = mock_get_ft
workflow.doaj_lookup = mock_doaj
record = models.Record()
record.pmcid = "PMC4219345"
record.id = record.makeid()
oag = []
msg = workflow.WorkflowMessage(record=record, oag_register=oag)
workflow.process_record(msg)
assert record.confidence == 1.0
assert record.pmcid == "PMC4219345"
assert record.pmid == "24279897"
assert record.doi == "10.1186/1471-2121-14-52"
assert record.in_epmc is True
assert record.is_oa is False
assert len(record.issn) == 1
assert "1471-2121" in record.issn
assert record.id is not None # implies it has been saved
assert record.has_ft_xml is True
assert record.aam is False
assert record.aam_from_xml is True
assert record.licence_type == "cc-by"
assert record.licence_source == "epmc_xml"
assert record.journal_type == "oa"
assert len(oag) == 0
def test_10_process_record_05_no_ft(self):
def mock_get_md(*args, **kwargs):
md = epmcmod.EPMCMetadata(json.loads(open(EPMC_MD, "r").read()))
return md, 1.0
def mock_get_ft(*args, **kwargs):
return None
def mock_doaj(*args, **kwargs):
return False
workflow.get_epmc_md = mock_get_md
workflow.get_epmc_fulltext = mock_get_ft
workflow.doaj_lookup = mock_doaj
record = models.Record()
record.pmcid = "PMC4219345"
record.id = record.makeid()
oag = []
msg = workflow.WorkflowMessage(record=record, oag_register=oag)
workflow.process_record(msg)
assert record.confidence == 1.0
assert record.pmcid == "PMC4219345"
assert record.pmid == "24279897"
assert record.doi == "10.1186/1471-2121-14-52"
assert record.in_epmc is True
assert record.is_oa is False
assert len(record.issn) == 1
assert "1471-2121" in record.issn
assert record.id is not None # implies it has been saved
assert record.has_ft_xml is False
assert record.aam is None
assert record.aam_from_xml is False
assert record.licence_type is None
assert record.licence_source is None
assert record.journal_type == "hybrid"
assert len(oag) == 1
assert oag[0]["id"] == "PMC4219345"
assert oag[0]["type"] == "pmcid"
def test_10_process_record_05_no_ft(self):
def mock_get_md(*args, **kwargs):
md = epmcmod.EPMCMetadata(json.loads(open(EPMC_MD, "r").read()))
return md, 1.0
def mock_get_ft(*args, **kwargs):
return None
def mock_doaj(*args, **kwargs):
return False
workflow.get_epmc_md = mock_get_md
workflow.get_epmc_fulltext = mock_get_ft
workflow.doaj_lookup = mock_doaj
record = models.Record()
record.pmcid = "PMC4219345"
record.id = record.makeid()
oag = []
msg = workflow.WorkflowMessage(record=record, oag_register=oag)
workflow.process_record(msg)
assert record.confidence == 1.0
assert record.pmcid == "PMC4219345"
assert record.pmid == "24279897"
assert record.doi == "10.1186/1471-2121-14-52"
assert record.in_epmc is True
assert record.is_oa is False
assert len(record.issn) == 1
assert "1471-2121" in record.issn
assert record.id is not None # implies it has been saved
assert record.has_ft_xml is False
assert record.aam is None
assert record.aam_from_xml is False
assert record.licence_type is None
assert record.licence_source is None
assert record.journal_type == "hybrid"
assert len(oag) == 1
assert oag[0]["id"] == "PMC4219345"
assert oag[0]["type"] == "pmcid"
record.upload_id = job.id
record.upload_pos = 1
if args.type.lower() == "pmcid":
record.pmcid = args.identifier
elif args.type.lower() == "pmid":
record.pmid = args.identifier
elif args.type.lower() == "doi":
record.doi = args.identifier
record.save()
time.sleep(2)
oag_register = []
msg = workflow.WorkflowMessage(job, record, oag_register)
workflow.process_record(msg)
workflow.process_oag(oag_register, job)
time.sleep(2)
i = 0
while True:
i += 1
pcc = job.pc_complete
print i, job.pc_complete, "%",
sys.stdout.flush()
if int(pcc) == 100:
break
time.sleep(2)
out = workflow.output_csv(job)
record.upload_id = job.id
record.upload_pos = 1
if args.type.lower() == "pmcid":
record.pmcid = args.identifier
elif args.type.lower() == "pmid":
record.pmid = args.identifier
elif args.type.lower() == "doi":
record.doi = args.identifier
record.save()
time.sleep(2)
oag_register = []
msg = workflow.WorkflowMessage(job, record, oag_register)
workflow.process_record(msg)
workflow.process_oag(oag_register, job)
time.sleep(2)
i = 0
while True:
i += 1
pcc = job.pc_complete
print i, job.pc_complete, "%",
sys.stdout.flush()
if int(pcc) == 100:
break
time.sleep(2)
out = workflow.output_csv(job)