def test_delete_m80():
c = Cohort("DeleteMe")
dbFile = os.path.join(c.m80.thawed_dir, "db.sqlite")
assert os.path.exists(dbFile) == True
FreezableAPI.delete("Cohort", "DeleteMe")
assert os.path.exists(dbFile) == False
def RNACohort(RNAAccession1, RNAAccession2):
FreezableAPI.delete("Cohort", "RNACohort")
x = Cohort("RNACohort")
x.add_accession(RNAAccession1)
x.add_accession(RNAAccession2)
yield x
FreezableAPI.delete(x.m80.dtype, x.m80.name)
def test_delete_missing():
c = Cohort("DeleteMe")
dbFile = os.path.join(c.m80.thawed_dir, "db.sqlite")
assert os.path.exists(dbFile) == True
# Giving the wrong information shouldnt do anything
FreezableAPI.delete("Cohort", "DeleteMeee")
assert os.path.exists(dbFile) == True
FreezableAPI.delete("Cohort", "DeleteMe")
assert os.path.exists(dbFile) == False
def simpleCohort():
FreezableAPI.delete("Cohort", "TestCohort")
# Create the simple cohort
a = Accession("Sample1", files=["file1.txt", "file2.txt"], type="WGS")
b = Accession("Sample2", files=["file1.txt", "file2.txt"], type="WGS")
c = Accession("Sample3", files=["file1.txt", "file2.txt"], type="CHIP")
d = Accession("Sample4", files=["file1.txt", "file2.txt"], type="CHIP")
x = Cohort("TestCohort")
for acc in [a, b, c, d]:
x.add_accession(acc)
yield x
FreezableAPI.delete(x.m80.dtype, x.m80.name)
def delete(slug, force):
# Validate the input
if force is False: # pragma: no cover
click.confirm(f'Are you sure you want to delete "{slug}"')
try:
dtype, name, tag = FreezableAPI.parse_slug(slug)
if tag is not None:
raise TagInvalidError()
except TagInvalidError:
click.echo("Cannot delete tags, only entire datasets.")
sys.exit(1)
except FreezableNameInvalidError:
click.echo(
"Please provide a valid dataset name: <dtype>.<name>. E.g. Project.foobar"
"Note: do not include tags")
sys.exit(1)
# Make sure that the dataset is available
if not FreezableAPI.exists(dtype, name):
click.echo(f'"{dtype}.{name}" not in minus80 datasets! '
"check available datasets with the ls command")
sys.exit(1)
else:
FreezableAPI.delete(dtype, name)
sys.exit(0)
def simpleProject(scope="module"):
tmpdir = tempfile.TemporaryDirectory()
x = Project("simpleProject")
x.create_link(Path(tmpdir.name) / "tmp")
yield x
FreezableAPI.delete(x.m80.dtype, x.m80.name)