def test_02_write_subset(self):
# set up a very simple subset sheet
spec = ["article_title", "pmcid"]
s = StringIO()
ms = sheets.SimpleSheet(writer=s, spec=spec)
# add an object which conforms to the spec of the subset
ms.add_object({
"article_title" : "A",
"pmcid" : "a"
})
# check that the record has been written
size = 0
for o in ms.objects():
size += 1
assert o.get("article_title") == "A"
assert o.get("pmcid") == "a"
assert len(o.keys()) == 2
assert size == 1
# now add an object with insufficient data for all columns
ms.add_object({
"article_title" : "B",
})
# check that the new record has been written correctly (with suitable defaults)
size = 0
found = False
for o in ms.objects():
size += 1
if o.get("article_title") == "B":
found = True
assert o.get("pmcid") == ""
assert size == 2
assert found
# now add an object with too much data for the spec
ms.add_object({
"article_title" : "C",
"pmcid" : "c",
"something_else" : "Gamma"
})
# check that the new record has been written correctly (with suitable defaults)
size = 0
found = False
for o in ms.objects():
size += 1
if o.get("article_title") == "C":
found = True
assert o.get("pmcid") == "c"
assert "something_else" not in o
assert size == 3
assert found
def test_01_read(self):
ms = sheets.SimpleSheet(path=TEST_SUBMISSION)
objects = False
for o in ms.objects():
objects = True
# just check a few fields to make sure the object looks reasonable
assert "pmcid" in o
assert "article_title" in o
assert objects
def test_05_defaults(self):
s = StringIO()
ms = sheets.SimpleSheet(writer=s)
ms.add_object({
"aam" : None,
"licence" : "",
})
size = 0
for o in ms.objects():
size += 1
assert o.get("aam") == "unknown"
assert o.get("licence") == "unknown"
assert size == 1
def test_03_write_full(self):
s = StringIO()
ms = sheets.SimpleSheet(writer=s)
# add an object which conforms to the spec of the subset
ms.add_object({
"article_title" : "A",
"pmcid" : "a",
})
# check that the record has been written
size = 0
for o in ms.objects():
size += 1
assert o.get("article_title") == "A"
assert o.get("pmcid") == "a"
assert o.get("doi") == ""
assert len(o.keys()) == len(ms.OUTPUT_ORDER)
assert size == 1
# now add an object with too much data for the spec
ms.add_object({
"article_title" : "C",
"pmcid" : "c",
"something_else" : "Gamma"
})
# check that the new record has been written correctly (with suitable defaults)
size = 0
found = False
for o in ms.objects():
size += 1
if o.get("article_title") == "C":
found = True
assert o.get("pmcid") == "c"
assert "something_else" not in o
assert size == 2
assert found
def test_04_output(self):
# set up a very simple subset sheet (note it's not in the desired output order)
spec = ["article_title", "doi", "pmcid"]
s = StringIO()
ms = sheets.SimpleSheet(writer=s, spec=spec)
# add an object which conforms to the spec of the subset
ms.add_object({
"article_title" : "A",
"pmcid" : "a",
"doi" : "1"
})
# output the sheet to the StringIO object
ms.save()
# now open the StringIO in the python standard csv reader
s.seek(0)
reader = csv.reader(s)
rows = [row for row in reader]
assert len(rows) == 2
assert rows[0] == ["PMCID", "DOI", "Article title"]
assert rows[1] == ["a", "1", "A"]
def test_06_blank_rows(self):
ms = sheets.SimpleSheet(path=BLANK_LINES)
objects = [o for o in ms.objects()]
assert len(objects) == 20