def test_02_record(self):
r = Record()
r.upload_id = "1234"
r.upload_pos = "234"
r.set_source_data(university="my uni",
pmcid="PMC12345678",
pmid="98765432",
doi="10.whatever",
publisher="wiley",
journal_title="Journal of things",
article_title="A study of sorts",
apc=100,
wellcome_apc=200,
vat=20,
total_cost=300,
grant_code="WELL01",
licence_info="CC BY",
notes="this is a note")
r.pmcid = "PMC12345678"
r.pmid = "98765432"
r.doi = "10.whatever"
r.title = "A study of sorts"
r.has_ft_xml = True
r.aam_from_xml = False
r.aam_from_epmc = True
r.issn = "1234-5678"
r.in_oag = True
r.oag_pmcid = "not_sent"
r.oag_doi = "sent"
r.oag_pmid = "fto"
r.in_epmc = True
r.is_oa = False
r.aam = True
r.licence_type = "CC BY"
r.licence_source = "epmc"
r.journal_type = "hybrid"
r.confidence = "0.8"
r.standard_compliance = True
r.deluxe_compliance = False
r.add_provenance("richard", "provenance 1")
r.add_provenance("wellcome", "provenance 2")
assert r.upload_id == "1234"
assert r.upload_pos == 234
assert r.pmcid == "PMC12345678"
assert r.pmid == "98765432"
assert r.doi == "10.whatever"
assert r.title == "A study of sorts"
assert r.has_ft_xml
assert not r.aam_from_xml
assert r.aam_from_epmc
assert len(r.issn) == 1
assert "1234-5678" in r.issn
assert r.in_epmc
assert not r.is_oa
assert r.aam
assert r.licence_type == "CC BY"
assert r.licence_source == "epmc"
assert r.journal_type == "hybrid"
assert r.confidence == 0.8
assert r.standard_compliance
assert not r.deluxe_compliance
p = r.provenance
assert len(p) == 2
for by, when, note in p:
assert by in ["richard", "wellcome"]
assert note in ["provenance 1", "provenance 2"]
def test_06_duplicates(self):
# first make ourselves a job to work on
job = SpreadsheetJob()
job.save()
# now make a bunch of records, some unique and some duplicate
# unique pmcid
r = Record()
r.upload_id = job.id
r.pmcid = "PMCunique"
r.save()
# duplicate pmcid
r = Record()
r.upload_id = job.id
r.pmcid = "PMCdupe"
r.save()
r = Record()
r.upload_id = job.id
r.pmcid = "PMCdupe"
r.save()
# unique pmid
r = Record()
r.upload_id = job.id
r.pmid = "unique"
r.save()
# duplicate pmid
r = Record()
r.upload_id = job.id
r.pmid = "dupe"
r.save()
r = Record()
r.upload_id = job.id
r.pmid = "dupe"
r.save()
# unique doi
r = Record()
r.upload_id = job.id
r.doi = "10.unique"
r.save()
# duplicate pmcid
r = Record()
r.upload_id = job.id
r.doi = "10.dupe"
r.save()
r = Record()
r.upload_id = job.id
r.doi = "10.dupe"
r.save()
# one that is a duplicate of everything
r = Record()
r.upload_id = job.id
r.pmcid = "PMCdupe"
r.pmid = "dupe"
r.doi = "10.dupe"
r.save()
# one that is confused about its duplication
r = Record()
r.upload_id = job.id
r.pmcid = "PMCdupe"
r.pmid = "dupe"
r.doi = "10.notdupe"
r.save()
time.sleep(2)
dupes = job.list_duplicate_identifiers()
# check the structure of the response
assert "pmcid" in dupes
assert "pmid" in dupes
assert "doi" in dupes
# check the contentes
assert len(dupes["pmcid"]) == 1
assert "PMCdupe" in dupes["pmcid"]
assert len(dupes["pmid"]) == 1
assert "dupe" in dupes["pmid"]
assert len(dupes["doi"]) == 1
assert "10.dupe" in dupes["doi"]
def test_04_pc_complete(self):
job = SpreadsheetJob()
job.save()
# a record with no completeness
r = Record()
r.upload_id = job.id
r.save()
# a record with epmc complete
r2 = Record()
r2.upload_id = job.id
r2.epmc_complete = True
r2.save()
# a record with both complete
r3 = Record()
r3.upload_id = job.id
r3.epmc_complete = True
r3.oag_complete = True
r3.save()
time.sleep(1)
comp = job.pc_complete
assert int(comp) == 50
r.epmc_complete = True
r.save()
time.sleep(1)
comp = job.pc_complete
assert int(comp) == 66
r.oag_complete = True
r2.oag_complete = True
r.save()
r2.save()
time.sleep(1)
comp = job.pc_complete
assert int(comp) == 100
def test_05_compliance(self):
record = Record()
# Truth table for standard and deluxe compliance
#
# Note: CC-BY column means CC-BY or CC0
#
# in EPMC | AAM | CC BY | Licence in EPMC | is OA | S | D
# 0 0 0 0 0 0 0
# 0 0 1 0 0 0 0
# 1 0 0 0 0 0 0
# 1 0 0 0 1 0 0
# 1 0 0 1 1 0 0
# 1 0 1 0 0 1 0
# 1 0 1 1 1 1 1
# 1 1 0 0 0 1 1
# 1 1 1 0 0 1 1
# 1 1 1 1 1 1 1
# check the default values, before we've done anything to the record
assert record.deluxe_compliance is False
assert record.standard_compliance is False
# set the various switches, and then check the results
# in EPMC | AAM | CC BY | Licence in EPMC | is OA | S | D
# 0 0 0 0 0 0 0
record.in_epmc = False
record.aam = False
record.licence_type = "Other"
record.licence_source = "publisher"
record.is_oa = False
assert record.deluxe_compliance is False
assert record.standard_compliance is False
# in EPMC | AAM | CC BY | Licence in EPMC | is OA | S | D
# 0 0 1 0 0 0 0
record.licence_type = "cc-by"
assert record.deluxe_compliance is False
assert record.standard_compliance is False
# in EPMC | AAM | CC BY | Licence in EPMC | is OA | S | D
# 1 0 0 0 0 0 0
record.in_epmc = True
record.licence_type = "Other"
assert record.deluxe_compliance is False
assert record.standard_compliance is False
# in EPMC | AAM | CC BY | Licence in EPMC | is OA | S | D
# 1 0 0 0 1 0 0
record.is_oa = True
assert record.deluxe_compliance is False
assert record.standard_compliance is False
# in EPMC | AAM | CC BY | Licence in EPMC | is OA | S | D
# 1 0 0 1 1 0 0
record.licence_source = "epmc_xml"
assert record.deluxe_compliance is False
assert record.standard_compliance is False
# in EPMC | AAM | CC BY | Licence in EPMC | is OA | S | D
# 1 0 1 0 0 1 0
record.licence_type = "CC0"
record.licence_source = "publisher"
record.is_oa = False
assert record.deluxe_compliance is False
assert record.standard_compliance is True
# in EPMC | AAM | CC BY | Licence in EPMC | is OA | S | D
# 1 0 1 1 1 1 1
record.licence_type = "cc-by"
record.licence_source = "epmc"
record.is_oa = True
assert record.deluxe_compliance is True
assert record.standard_compliance is True
# in EPMC | AAM | CC BY | Licence in EPMC | is OA | S | D
# 1 1 0 0 0 1 1
record.aam = True
record.licence_type = "Other"
record.licence_source = "publisher"
assert record.deluxe_compliance is True
assert record.standard_compliance is True
# in EPMC | AAM | CC BY | Licence in EPMC | is OA | S | D
# 1 1 1 0 0 1 1
record.licence_type = "CC-BY"
assert record.deluxe_compliance is True
assert record.standard_compliance is True
# in EPMC | AAM | CC BY | Licence in EPMC | is OA | S | D
# 1 1 1 1 1 1 1
record.licence_source = "epmc_xml"
record.is_oa = True
assert record.deluxe_compliance is True
assert record.standard_compliance is True
def test_02_record(self):
r = Record()
r.upload_id = "1234"
r.upload_pos = "234"
r.set_source_data(
pmcid="PMC12345678",
pmid="98765432",
doi="10.whatever",
article_title="A study of sorts",
)
r.pmcid = "PMC12345678"
r.pmid = "98765432"
r.doi = "10.whatever"
r.title = "A study of sorts"
r.has_ft_xml = True
r.aam_from_xml = False
r.aam_from_epmc = True
r.issn = "1234-5678"
r.in_oag = True
r.oag_pmcid = "not_sent"
r.oag_doi = "sent"
r.oag_pmid = "fto"
r.in_epmc = True
r.is_oa = False
r.aam = True
r.licence_type = "CC BY"
r.licence_source = "epmc"
r.journal_type = "hybrid"
r.confidence = "0.8"
r.add_provenance("richard", "provenance 1")
r.add_provenance("wellcome", "provenance 2")
r.publisher = "The Publisher"
r.preprint_self_archive = "can"
r.journal_preprint_embargo = "12 months"
r.postprint_self_archive = "may"
r.journal_postprint_embargo = "6 months"
r.publisher_self_archive = "cannot"
r.journal_publisher_embargo = "100 years"
r.in_core = True
assert r.upload_id == "1234"
assert r.upload_pos == 234
assert r.pmcid == "PMC12345678"
assert r.pmid == "98765432"
assert r.doi == "10.whatever"
assert r.title == "A study of sorts"
assert r.has_ft_xml
assert not r.aam_from_xml
assert r.aam_from_epmc
assert len(r.issn) == 1
assert "1234-5678" in r.issn
assert r.in_epmc
assert not r.is_oa
assert r.aam
assert r.licence_type == "CC BY"
assert r.licence_source == "epmc"
assert r.journal_type == "hybrid"
assert r.confidence == 0.8
assert r.preprint_self_archive == "can"
assert r.journal_preprint_embargo == "12 months"
assert r.postprint_self_archive == "may"
assert r.journal_postprint_embargo == "6 months"
assert r.publisher_self_archive == "cannot"
assert r.journal_publisher_embargo == "100 years"
assert r.in_core
p = r.provenance
assert len(p) == 2
for by, when, note in p:
assert by in ["richard", "wellcome"]
assert note in ["provenance 1", "provenance 2"]
def test_06_duplicates(self):
# first make ourselves a job to work on
job = SpreadsheetJob()
job.save()
# now make a bunch of records, some unique and some duplicate
# unique pmcid
r = Record()
r.upload_id = job.id
r.pmcid = "PMCunique"
r.save()
# duplicate pmcid
r = Record()
r.upload_id = job.id
r.pmcid = "PMCdupe"
r.save()
r = Record()
r.upload_id = job.id
r.pmcid = "PMCdupe"
r.save()
# unique pmid
r = Record()
r.upload_id = job.id
r.pmid = "unique"
r.save()
# duplicate pmid
r = Record()
r.upload_id = job.id
r.pmid = "dupe"
r.save()
r = Record()
r.upload_id = job.id
r.pmid = "dupe"
r.save()
# unique doi
r = Record()
r.upload_id = job.id
r.doi = "10.unique"
r.save()
# duplicate pmcid
r = Record()
r.upload_id = job.id
r.doi = "10.dupe"
r.save()
r = Record()
r.upload_id = job.id
r.doi = "10.dupe"
r.save()
# one that is a duplicate of everything
r = Record()
r.upload_id = job.id
r.pmcid = "PMCdupe"
r.pmid = "dupe"
r.doi = "10.dupe"
r.save()
# one that is confused about its duplication
r = Record()
r.upload_id = job.id
r.pmcid = "PMCdupe"
r.pmid = "dupe"
r.doi = "10.notdupe"
r.save()
time.sleep(2)
dupes = job.list_duplicate_identifiers()
# check the structure of the response
assert "pmcid" in dupes
assert "pmid" in dupes
assert "doi" in dupes
# check the contentes
assert len(dupes["pmcid"]) == 1
assert "PMCdupe" in dupes["pmcid"]
assert len(dupes["pmid"]) == 1
assert "dupe" in dupes["pmid"]
assert len(dupes["doi"]) == 1
assert "10.dupe" in dupes["doi"]
def test_02_record(self):
r = Record()
r.upload_id = "1234"
r.upload_pos = "234"
r.set_source_data(university="my uni",
pmcid="PMC12345678",
pmid="98765432",
doi="10.whatever",
publisher="wiley",
journal_title="Journal of things",
article_title="A study of sorts",
apc=100,
wellcome_apc=200,
vat=20,
total_cost=300,
grant_code="WELL01",
licence_info="CC BY",
notes="this is a note")
r.pmcid = "PMC12345678"
r.pmid = "98765432"
r.doi = "10.whatever"
r.title = "A study of sorts"
r.has_ft_xml = True
r.aam_from_xml = False
r.aam_from_epmc = True
r.issn = "1234-5678"
r.in_oag = True
r.oag_pmcid = "not_sent"
r.oag_doi = "sent"
r.oag_pmid = "fto"
r.in_epmc = True
r.is_oa = False
r.aam = True
r.licence_type = "CC BY"
r.licence_source = "epmc"
r.journal_type = "hybrid"
r.confidence = "0.8"
r.standard_compliance = True
r.deluxe_compliance = False
r.add_provenance("richard", "provenance 1")
r.add_provenance("wellcome", "provenance 2")
assert r.upload_id == "1234"
assert r.upload_pos == 234
assert r.pmcid == "PMC12345678"
assert r.pmid == "98765432"
assert r.doi == "10.whatever"
assert r.title == "A study of sorts"
assert r.has_ft_xml
assert not r.aam_from_xml
assert r.aam_from_epmc
assert len(r.issn) == 1
assert "1234-5678" in r.issn
assert r.in_epmc
assert not r.is_oa
assert r.aam
assert r.licence_type == "CC BY"
assert r.licence_source == "epmc"
assert r.journal_type == "hybrid"
assert r.confidence == 0.8
assert r.standard_compliance
assert not r.deluxe_compliance
p = r.provenance
assert len(p) == 2
for by, when, note in p:
assert by in ["richard", "wellcome"]
assert note in ["provenance 1", "provenance 2"]
def test_05_compliance(self):
record = Record()
# Truth table for standard and deluxe compliance
#
# Note: CC-BY column means CC-BY or CC0
#
# in EPMC | AAM | CC BY | Licence in EPMC | is OA | S | D
# 0 0 0 0 0 0 0
# 0 0 1 0 0 0 0
# 1 0 0 0 0 0 0
# 1 0 0 0 1 0 0
# 1 0 0 1 1 0 0
# 1 0 1 0 0 1 0
# 1 0 1 1 1 1 1
# 1 1 0 0 0 1 1
# 1 1 1 0 0 1 1
# 1 1 1 1 1 1 1
# check the default values, before we've done anything to the record
assert record.deluxe_compliance is False
assert record.standard_compliance is False
# set the various switches, and then check the results
# in EPMC | AAM | CC BY | Licence in EPMC | is OA | S | D
# 0 0 0 0 0 0 0
record.in_epmc = False
record.aam = False
record.licence_type = "Other"
record.licence_source = "publisher"
record.is_oa = False
assert record.deluxe_compliance is False
assert record.standard_compliance is False
# in EPMC | AAM | CC BY | Licence in EPMC | is OA | S | D
# 0 0 1 0 0 0 0
record.licence_type = "cc-by"
assert record.deluxe_compliance is False
assert record.standard_compliance is False
# in EPMC | AAM | CC BY | Licence in EPMC | is OA | S | D
# 1 0 0 0 0 0 0
record.in_epmc = True
record.licence_type = "Other"
assert record.deluxe_compliance is False
assert record.standard_compliance is False
# in EPMC | AAM | CC BY | Licence in EPMC | is OA | S | D
# 1 0 0 0 1 0 0
record.is_oa = True
assert record.deluxe_compliance is False
assert record.standard_compliance is False
# in EPMC | AAM | CC BY | Licence in EPMC | is OA | S | D
# 1 0 0 1 1 0 0
record.licence_source = "epmc_xml"
assert record.deluxe_compliance is False
assert record.standard_compliance is False
# in EPMC | AAM | CC BY | Licence in EPMC | is OA | S | D
# 1 0 1 0 0 1 0
record.licence_type = "CC0"
record.licence_source = "publisher"
record.is_oa = False
assert record.deluxe_compliance is False
assert record.standard_compliance is True
# in EPMC | AAM | CC BY | Licence in EPMC | is OA | S | D
# 1 0 1 1 1 1 1
record.licence_type = "cc-by"
record.licence_source = "epmc"
record.is_oa = True
assert record.deluxe_compliance is True
assert record.standard_compliance is True
# in EPMC | AAM | CC BY | Licence in EPMC | is OA | S | D
# 1 1 0 0 0 1 1
record.aam = True
record.licence_type = "Other"
record.licence_source = "publisher"
assert record.deluxe_compliance is True
assert record.standard_compliance is True
# in EPMC | AAM | CC BY | Licence in EPMC | is OA | S | D
# 1 1 1 0 0 1 1
record.licence_type = "CC-BY"
assert record.deluxe_compliance is True
assert record.standard_compliance is True
# in EPMC | AAM | CC BY | Licence in EPMC | is OA | S | D
# 1 1 1 1 1 1 1
record.licence_source = "epmc_xml"
record.is_oa = True
assert record.deluxe_compliance is True
assert record.standard_compliance is True
def test_04_pc_complete(self):
job = SpreadsheetJob()
job.save()
# a record with no completeness
r = Record()
r.upload_id = job.id
r.save()
# a record with epmc complete
r2 = Record()
r2.upload_id = job.id
r2.epmc_complete = True
r2.save()
# a record with both complete
r3 = Record()
r3.upload_id = job.id
r3.epmc_complete = True
r3.oag_complete = True
r3.save()
time.sleep(1)
comp = job.pc_complete
assert int(comp) == 50
r.epmc_complete = True
r.save()
time.sleep(1)
comp = job.pc_complete
assert int(comp) == 66
r.oag_complete = True
r2.oag_complete = True
r.save()
r2.save()
time.sleep(1)
comp = job.pc_complete
assert int(comp) == 100
