def test_loadmetadata_from_dataset_create_cli(self):
fn = tempfile.NamedTemporaryFile(suffix=".alignmentset.xml").name
fn2 = tempfile.NamedTemporaryFile(suffix=".alignmentset.xml").name
log.debug(fn)
aln = AlignmentSet(data.getXml(8))
aln.metadata.collections = None
aln.copyTo(fn)
aln.close()
del aln
self.assertTrue(os.path.exists(fn))
aln = AlignmentSet(fn)
self.assertFalse(aln.metadata.collections)
cmd = "dataset create --metadata {m} {o} {i}".format(
o=fn2,
i=fn,
m=("/pbi/dept/secondary/siv/testdata/"
"SA3-Sequel/lambda/roche_SAT/"
"m54013_151205_032353.subreadset.xml"))
log.debug(cmd)
o, r, m = backticks(cmd)
self.assertEqual(r, 0, m)
aln = AlignmentSet(fn2)
self.assertTrue(aln.metadata.collections)
def test_loadmetadata_from_dataset_create_cli(self):
fn = tempfile.NamedTemporaryFile(suffix=".alignmentset.xml").name
fn2 = tempfile.NamedTemporaryFile(suffix=".alignmentset.xml").name
log.debug(fn)
aln = AlignmentSet(data.getXml(8))
aln.metadata.collections = None
aln.copyTo(fn)
aln.close()
del aln
self.assertTrue(os.path.exists(fn))
aln = AlignmentSet(fn)
self.assertFalse(aln.metadata.collections)
cmd = "dataset create --metadata {m} {o} {i}".format(
o=fn2,
i=fn,
m=("/pbi/dept/secondary/siv/testdata/"
"SA3-Sequel/lambda/roche_SAT/"
"m54013_151205_032353.subreadset.xml"))
log.debug(cmd)
o, r, m = backticks(cmd)
self.assertEqual(r, 0, m)
aln = AlignmentSet(fn2)
self.assertTrue(aln.metadata.collections)
def test_absolutize_cli(self):
fn = tempfile.NamedTemporaryFile(suffix=".alignmentset.xml").name
aln = AlignmentSet(data.getXml(7))
aln.copyTo(fn, relative=True)
assert _is_relative(fn)
cmd = "dataset absolutize {d}".format(d=fn)
self._run_cmd_with_output(cmd, fn)
assert not _is_relative(fn)
def test_relativize_cli(self):
fn = tempfile.NamedTemporaryFile(suffix=".alignmentset.xml").name
aln = AlignmentSet(data.getXml(8))
aln.copyTo(fn)
self.assertFalse(_is_relative(fn))
cmd = "dataset relativize {d}".format(d=fn)
log.debug(cmd)
o, r, m = backticks(cmd)
self.assertEqual(r, 0)
self.assertTrue(os.path.exists(fn))
self.assertTrue(_is_relative(fn))
def test_relativize_cli(self):
fn = tempfile.NamedTemporaryFile(suffix=".alignmentset.xml").name
aln = AlignmentSet(data.getXml(8))
aln.copyTo(fn)
self.assertFalse(_is_relative(fn))
cmd = "dataset relativize {d}".format(d=fn)
log.debug(cmd)
o, r, m = backticks(cmd)
self.assertEqual(r, 0)
self.assertTrue(os.path.exists(fn))
self.assertTrue(_is_relative(fn))
def test_newUuid_cli(self):
fn = tempfile.NamedTemporaryFile(suffix=".alignmentset.xml").name
aln = AlignmentSet(data.getXml(8))
aln.copyTo(fn)
pre_uuid = AlignmentSet(fn).uuid
cmd = "dataset newuuid {d}".format(d=fn)
log.debug(cmd)
o, r, m = backticks(cmd)
post_uuid = AlignmentSet(fn).uuid
self.assertEqual(r, 0)
self.assertTrue(os.path.exists(fn))
self.assertNotEqual(pre_uuid, post_uuid)
def test_newUuid_cli(self):
fn = tempfile.NamedTemporaryFile(suffix=".alignmentset.xml").name
aln = AlignmentSet(data.getXml(8))
aln.copyTo(fn)
pre_uuid = AlignmentSet(fn).uuid
cmd = "dataset newuuid {d}".format(d=fn)
log.debug(cmd)
o, r, m = backticks(cmd)
post_uuid = AlignmentSet(fn).uuid
self.assertEqual(r, 0)
self.assertTrue(os.path.exists(fn))
self.assertNotEqual(pre_uuid, post_uuid)
def test_absolutize_cli_3(self):
fn = tempfile.NamedTemporaryFile(suffix=".alignmentset.xml").name
outdir = tempfile.mkdtemp(suffix="dataset-unittest")
outfn = os.path.join(outdir, os.path.split(fn)[1])
aln = AlignmentSet(data.getXml(7))
aln.copyTo(fn, relative=True)
assert _is_relative(fn)
cmd = "dataset absolutize {d} --outdir {o}".format(d=fn, o=outdir)
self._run_cmd_with_output(cmd, fn)
assert os.path.exists(outfn)
assert _is_relative(fn)
assert not _is_relative(outfn)
def test_newUuid_cli(self):
fn = tempfile.NamedTemporaryFile(suffix=".alignmentset.xml").name
aln = AlignmentSet(data.getXml(7))
aln.copyTo(fn)
pre_uuid = AlignmentSet(fn).uuid
cmd = "dataset newuuid {d}".format(d=fn)
self._run_cmd_with_output(cmd, fn)
post_uuid = AlignmentSet(fn).uuid
assert pre_uuid != post_uuid
cmd = "dataset newuuid --updateCounts {d}".format(d=fn)
self._run_cmd_with_output(cmd, fn)
post_uuid = AlignmentSet(fn).uuid
assert pre_uuid != post_uuid
def test_create_cli_generate_indices_4(self):
log.debug("Generate indices, no type specified")
outdir = tempfile.mkdtemp(suffix="dataset-unittest")
ifn = tempfile.NamedTemporaryFile(suffix=".alignmentset.xml",
dir=outdir).name
log.info(ifn)
# copy the resources and xml
aset = AlignmentSet(data.getXml(11))
aset.copyTo(ifn)
aset = AlignmentSet(ifn)
# get the key resource filename
ifn = aset.toExternalFiles()[0]
log.info(ifn)
ofn = self._get_mock_alignment_set_out(outdir)
cmd = ("dataset create --generateIndices {} {}").format(ofn, ifn)
self._run_cmd_with_output(cmd, ofn)
aset = AlignmentSet(ofn, strict=True)
shutil.rmtree(outdir)
def test_loadmetadata_from_dataset_cli(self):
fn = tempfile.NamedTemporaryFile(suffix=".alignmentset.xml").name
log.debug(fn)
aln = AlignmentSet(data.getXml(7))
aln.metadata.collections = None
aln.copyTo(fn)
aln.close()
del aln
assert os.path.exists(fn)
aln = AlignmentSet(fn)
assert not aln.metadata.collections
cmd = "dataset loadmetadata {i} {m}".format(
i=fn,
m=("/pbi/dept/secondary/siv/testdata/"
"SA3-Sequel/lambda/roche_SAT/"
"m54013_151205_032353.subreadset.xml"))
self._check_cmd(cmd)
aln = AlignmentSet(fn)
assert aln.metadata.collections
def test_absolutize_cli(self):
fn = tempfile.NamedTemporaryFile(suffix=".alignmentset.xml").name
aln = AlignmentSet(data.getXml(8))
aln.copyTo(fn, relative=True)
self.assertTrue(_is_relative(fn))
cmd = "dataset absolutize {d}".format(d=fn)
log.debug(cmd)
o, r, m = backticks(cmd)
self.assertEqual(r, 0)
self.assertTrue(os.path.exists(fn))
self.assertFalse(_is_relative(fn))
fn = tempfile.NamedTemporaryFile(suffix=".alignmentset.xml").name
outfn = tempfile.NamedTemporaryFile(suffix=".alignmentset.xml").name
aln = AlignmentSet(data.getXml(8))
aln.copyTo(fn, relative=True)
self.assertTrue(_is_relative(fn))
cmd = "dataset absolutize {d} --outdir {o}".format(d=fn, o=outfn)
log.debug(cmd)
o, r, m = backticks(cmd)
self.assertEqual(r, 0)
self.assertTrue(os.path.exists(fn))
self.assertTrue(os.path.exists(outfn))
self.assertTrue(_is_relative(fn))
self.assertFalse(_is_relative(outfn))
fn = tempfile.NamedTemporaryFile(suffix=".alignmentset.xml").name
outdir = tempfile.mkdtemp(suffix="dataset-unittest")
outfn = os.path.join(outdir, os.path.split(fn)[1])
aln = AlignmentSet(data.getXml(8))
aln.copyTo(fn, relative=True)
self.assertTrue(_is_relative(fn))
cmd = "dataset absolutize {d} --outdir {o}".format(d=fn, o=outdir)
log.debug(cmd)
o, r, m = backticks(cmd)
self.assertEqual(r, 0)
self.assertTrue(os.path.exists(fn))
self.assertTrue(os.path.exists(outfn))
self.assertTrue(_is_relative(fn))
self.assertFalse(_is_relative(outfn))
def test_absolutize_cli(self):
fn = tempfile.NamedTemporaryFile(suffix=".alignmentset.xml").name
aln = AlignmentSet(data.getXml(8))
aln.copyTo(fn, relative=True)
self.assertTrue(_is_relative(fn))
cmd = "dataset absolutize {d}".format(d=fn)
log.debug(cmd)
o, r, m = backticks(cmd)
self.assertEqual(r, 0)
self.assertTrue(os.path.exists(fn))
self.assertFalse(_is_relative(fn))
fn = tempfile.NamedTemporaryFile(suffix=".alignmentset.xml").name
outfn = tempfile.NamedTemporaryFile(suffix=".alignmentset.xml").name
aln = AlignmentSet(data.getXml(8))
aln.copyTo(fn, relative=True)
self.assertTrue(_is_relative(fn))
cmd = "dataset absolutize {d} --outdir {o}".format(d=fn, o=outfn)
log.debug(cmd)
o, r, m = backticks(cmd)
self.assertEqual(r, 0)
self.assertTrue(os.path.exists(fn))
self.assertTrue(os.path.exists(outfn))
self.assertTrue(_is_relative(fn))
self.assertFalse(_is_relative(outfn))
fn = tempfile.NamedTemporaryFile(suffix=".alignmentset.xml").name
outdir = tempfile.mkdtemp(suffix="dataset-unittest")
outfn = os.path.join(outdir, os.path.split(fn)[1])
aln = AlignmentSet(data.getXml(8))
aln.copyTo(fn, relative=True)
self.assertTrue(_is_relative(fn))
cmd = "dataset absolutize {d} --outdir {o}".format(d=fn, o=outdir)
log.debug(cmd)
o, r, m = backticks(cmd)
self.assertEqual(r, 0)
self.assertTrue(os.path.exists(fn))
self.assertTrue(os.path.exists(outfn))
self.assertTrue(_is_relative(fn))
self.assertFalse(_is_relative(outfn))