def test_resolve_protein_type(self):
proteomics = factory.CategoryFactory(
type_group=models.MeasurementType.Group.PROTEINID)
type_A = main_factory.ProteinFactory(accession_code="P12345")
tr = TypeResolver(self.user, proteomics)
found = tr.lookup_type("sp|P12345")
assert found.pk == type_A.pk
def _setup_parse_success(self):
mime = "text/csv"
assay = factory.AssayFactory(study=self.study, protocol=self.protocol)
factory.ProteinFactory(accession_code="P12345")
ParserFactory(
layout=self.layout,
mime_type=mime,
parser_class="edd.load.parsers.skyline.SkylineCsvParser",
)
content = f"""
Replicate Name,Protein Name,Total Area
{assay.name},sp|P12345,42
"""
file = SimpleUploadedFile("example", content.encode("utf-8"), content_type=mime)
self.load.update({"file": file})
return self.load.request
def _setup_parse_excel(self):
mime = "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet"
assay = factory.AssayFactory(study=self.study, protocol=self.protocol)
factory.ProteinFactory(accession_code="P12345")
ParserFactory(
layout=self.layout,
mime_type=mime,
parser_class="edd.load.parsers.skyline.SkylineExcelParser",
)
wb = Workbook()
wb.active.title = "Simple Upload"
wb.active.append(["Replicate Name", "Protein Name", "Total Area"])
wb.active.append([assay.name, "sp|P12345", 42])
with NamedTemporaryFile() as temp:
wb.save(temp)
temp.seek(0)
file = SimpleUploadedFile("example", temp.read(), content_type=mime)
self.load.update({"file": file})
return self.load.request
def test_resolve_broad_type_with_uniprot_existing(self):
broad = factory.CategoryFactory()
type_A = main_factory.ProteinFactory(accession_code="P12345")
tr = TypeResolver(self.user, broad)
found = tr.lookup_type("sp|P12345")
assert found.pk == type_A.pk