def testCanConvert(self):
inp = pathmap.nexson_obj('merge/merge-input.v1.2.json')
expected = pathmap.nexson_obj('merge/merge-expected.v1.2.json')
expected = sort_arbitrarily_ordered_nexson(expected)
inp = sort_arbitrarily_ordered_nexson(inp)
self.assertNotEqual(inp, expected)
merge_otus_and_trees(inp)
equal_blob_check(self, '', inp, expected)
def testCanConvert(self):
inp = pathmap.nexson_obj('merge/merge-input.v1.2.json')
expected = pathmap.nexson_obj('merge/merge-expected.v1.2.json')
expected = sort_arbitrarily_ordered_nexson(expected)
inp = sort_arbitrarily_ordered_nexson(inp)
self.assertNotEqual(inp, expected)
merge_otus_and_trees(inp)
equal_blob_check(self, '', inp, expected)
def _get_pair(par, f, s):
bf = os.path.join(par, f)
hbf = os.path.join(par, s)
fp, sp = pathmap.nexson_source_path(bf), pathmap.nexson_source_path(hbf)
if not os.path.exists(fp):
_LOG.warn('\nTest skipped because {s} does not exist'.format(s=fp))
return None, None
if not os.path.exists(sp):
_LOG.warn('\nTest skipped because {s} does not exist'.format(s=sp))
return None, None
return pathmap.nexson_obj(bf), pathmap.nexson_obj(hbf)
def _get_pair(par, f, s):
bf = os.path.join(par, f)
hbf = os.path.join(par, s)
fp, sp = pathmap.nexson_source_path(bf), pathmap.nexson_source_path(hbf)
if not os.path.exists(fp):
_LOG.warn('\nTest skipped because {s} does not exist'.format(s=fp))
return None, None
if not os.path.exists(sp):
_LOG.warn('\nTest skipped because {s} does not exist'.format(s=sp))
return None, None
return pathmap.nexson_obj(bf), pathmap.nexson_obj(hbf)
def testSubTreesConvViaPS(self):
o = pathmap.nexson_obj('10/pg_10.json')
ps = PhyloSchema('newick',
content='subtree',
content_id=('tree3', 'node508'),
version='1.2.1')
x = ps.serialize(o)
self.assertTrue(x.startswith('(')) # pylint: disable=E1103
o = pathmap.nexson_obj('10/pg_10.json')
ps = PhyloSchema('newick',
content='subtree',
content_id=('tree3', 'ingroup'),
version='1.2.1')
x = ps.serialize(o)
self.assertTrue(x.startswith('(')) # pylint: disable=E1103
def testSubTreesConvViaPS(self):
o = pathmap.nexson_obj('10/pg_10.json')
ps = PhyloSchema('newick',
content='subtree',
content_id=('tree3', 'node508'),
version='1.2.1')
x = ps.serialize(o)
self.assertTrue(x.startswith('(')) # pylint: disable=E1103
o = pathmap.nexson_obj('10/pg_10.json')
ps = PhyloSchema('newick',
content='subtree',
content_id=('tree3', 'ingroup'),
version='1.2.1')
x = ps.serialize(o)
self.assertTrue(x.startswith('(')) # pylint: disable=E1103
def testNewickExport(self):
n = pathmap.nexson_obj('10/pg_10.json')
newick = extract_tree(
n, 'tree3',
PhyloSchema('newick',
tip_label='ot:ottTaxonName',
bracket_ingroup=True))
self.assertTrue('[pre-ingroup-marker' in newick)
self.assertTrue('[post-ingroup-marker' in newick)
self.assertTrue(newick.startswith('('))
self.assertTrue('*tip #1 not mapped' in newick)
self.assertTrue('*tip #2 not mapped' in newick)
self.assertTrue('*tip #3 not mapped' not in newick)
newick = extract_tree(
n, 'tree3', PhyloSchema('newick', tip_label='ot:ottTaxonName'))
self.assertTrue('[pre-ingroup-marker' not in newick)
self.assertTrue('[post-ingroup-marker' not in newick)
self.assertTrue('*tip #1 not mapped' in newick)
self.assertTrue('*tip #2 not mapped' in newick)
self.assertTrue('*tip #3 not mapped' not in newick)
self.assertTrue(newick.startswith('('))
newick = extract_tree(
n, 'tree3', PhyloSchema('newick', tip_label='ot:originallabel'))
self.assertTrue('[pre-ingroup-marker' not in newick)
self.assertTrue('[post-ingroup-marker' not in newick)
self.assertTrue('*tip #' not in newick)
def testTreeBaseImport(self):
fp = pathmap.nexml_source_path('S15515.xml')
n = get_ot_study_info_from_treebase_nexml(src=fp,
merge_blocks=True,
sort_arbitrary=True)
expected = pathmap.nexson_obj('S15515.json')
equal_blob_check(self, 'S15515', n, expected)
self.assertTrue(expected == n)
def testTreeBaseImport(self):
fp = pathmap.nexml_source_path('S15515.xml')
n = get_ot_study_info_from_treebase_nexml(src=fp,
merge_blocks=True,
sort_arbitrary=True)
expected = pathmap.nexson_obj('S15515.json')
equal_blob_check(self, 'S15515', n, expected)
self.assertTrue(expected == n)
def testOtuConvViaPS(self):
o = pathmap.nexson_obj('10/pg_10.json')
ps = PhyloSchema('nexson',
content='otu',
content_id='otu190',
version='1.2.1')
x = ps.serialize(o)
self.assertTrue(x.startswith('{')) # pylint: disable=E1103
def testNexusConvByExtViaPS(self):
o = pathmap.nexson_obj('10/pg_10.json')
ps = PhyloSchema(None,
type_ext='.nex',
content='tree',
content_id='tree3')
nex = ps.serialize(o)
self.assertTrue(nex.startswith('#')) # pylint: disable=E1103
def testMimicPhylesystemExport(self):
study_nexson = pathmap.nexson_obj('10/pg_10.json')
src_schema = PhyloSchema('nexson', version='1.2.1')
out_schema = PhyloSchema(schema='newick', content='tree', content_id='bogusID here')
result_data = out_schema.convert(study_nexson, serialize=True, src_schema=src_schema)
self.assertFalse(bool(result_data))
out_schema = PhyloSchema(schema='nexus', content='tree', content_id='bogusID here')
result_data = out_schema.convert(study_nexson, serialize=True, src_schema=src_schema)
self.assertFalse(bool(result_data))
def testNewickExport(self):
n = pathmap.nexson_obj('10/pg_10.json')
newick = extract_tree(n, 'tree3', PhyloSchema('newick', tip_label='ot:ottTaxonName', bracket_ingroup=True))
self.assertTrue('[pre-ingroup-marker' in newick)
self.assertTrue('[post-ingroup-marker' in newick)
self.assertTrue(newick.startswith('('))
newick = extract_tree(n, 'tree3', PhyloSchema('newick', tip_label='ot:ottTaxonName'))
self.assertTrue('[pre-ingroup-marker' not in newick)
self.assertTrue('[post-ingroup-marker' not in newick)
self.assertTrue(newick.startswith('('))
def testIterTree(self):
id_order_list = []
f_list = ['expected', 'input']
for v in ['1.0', '1.2']:
for f in f_list:
inp = pathmap.nexson_obj('merge/merge-{f}.v{v}.json'.format(v=v, f=f))
id_order = []
for t_tuple in iter_trees(inp):
ti = t_tuple[1]
id_order.append(ti)
id_order_list.append(id_order)
for i in range(1, 4):
self.assertEqual(id_order_list[0], id_order_list[i])
def testTreeBaseImport(self):
fp = pathmap.nexml_source_path('S15515.xml')
n = get_ot_study_info_from_treebase_nexml(src=fp,
merge_blocks=True,
sort_arbitrary=True)
# did we successfully coerce its DOI to the required URL form?
self.assertTrue('@href' in n['nexml']['^ot:studyPublication'])
test_doi = n['nexml']['^ot:studyPublication']['@href']
self.assertTrue(test_doi == doi2url(test_doi))
# furthermore, the output should exactly match our test file
expected = pathmap.nexson_obj('S15515.json')
equal_blob_check(self, 'S15515', n, expected)
self.assertTrue(expected == n)
def testTreesCulledNonmatcingConvViaPS(self):
o = pathmap.nexson_obj('9/v1.2.json')
self.assertEqual(len(extract_tree_nexson(o, tree_id=None)), 2)
ps = PhyloSchema('nexson', content='tree', content_id='tree2', version='1.2.1', cull_nonmatching='true')
x = ps.serialize(o)
etn = extract_tree_nexson(o, tree_id=None)
self.assertEqual(len(etn), 1)
self.assertEqual(etn[0][0], 'tree2')
self.assertTrue(x.startswith('{')) # pylint: disable=E1103
rx = json.loads(x)
etn = extract_tree_nexson(rx, tree_id=None)
self.assertEqual(len(etn), 1)
self.assertEqual(etn[0][0], 'tree2')
def testTreesCulledNonmatcingConvViaPS(self):
o = pathmap.nexson_obj('9/v1.2.json')
self.assertEqual(len(extract_tree_nexson(o, tree_id=None)), 2)
ps = PhyloSchema('nexson', content='tree', content_id='tree2', version='1.2.1', cull_nonmatching='true')
x = ps.serialize(o)
etn = extract_tree_nexson(o, tree_id=None)
self.assertEqual(len(etn), 1)
self.assertEqual(etn[0][0], 'tree2')
self.assertTrue(x.startswith('{')) #pylint: disable=E1103
rx = json.loads(x)
etn = extract_tree_nexson(rx, tree_id=None)
self.assertEqual(len(etn), 1)
self.assertEqual(etn[0][0], 'tree2')
def testTreeBaseImport(self):
fp = pathmap.nexml_source_path('S15515.xml')
n = get_ot_study_info_from_treebase_nexml(src=fp,
merge_blocks=True,
sort_arbitrary=True)
# did we successfully coerce its DOI to the required URL form?
self.assertTrue('@href' in n['nexml']['^ot:studyPublication'])
test_doi = n['nexml']['^ot:studyPublication']['@href']
self.assertTrue(test_doi == doi2url(test_doi))
# furthermore, the output should exactly match our test file
expected = pathmap.nexson_obj('S15515.json')
equal_blob_check(self, 'S15515', n, expected)
self.assertTrue(expected == n)
def testTreesCulledNonmatcingConvViaPSV0(self):
'''Verify that the culling does not break the conversion to other forms of NexSON'''
o = pathmap.nexson_obj('9/v1.2.json')
self.assertEqual(len(extract_tree_nexson(o, tree_id=None)), 2)
ps = PhyloSchema('nexson', content='tree', content_id='tree2', version='0.0.0', cull_nonmatching='true')
x = ps.serialize(o)
etn = extract_tree_nexson(o, tree_id=None)
self.assertEqual(len(etn), 1)
self.assertEqual(etn[0][0], 'tree2')
self.assertTrue(x.startswith('{')) #pylint: disable=E1103
rx = json.loads(x)
self.assertEqual(detect_nexson_version(rx), '0.0.0')
etn = extract_tree_nexson(rx, tree_id=None)
self.assertEqual(len(etn), 1)
self.assertEqual(etn[0][0], 'tree2')
def testTreesCulledNonmatcingConvViaPSV0(self):
"""Verify that the culling does not break the conversion to other forms of NexSON"""
o = pathmap.nexson_obj('9/v1.2.json')
self.assertEqual(len(extract_tree_nexson(o, tree_id=None)), 2)
ps = PhyloSchema('nexson', content='tree', content_id='tree2', version='0.0.0', cull_nonmatching='true')
x = ps.serialize(o)
etn = extract_tree_nexson(o, tree_id=None)
self.assertEqual(len(etn), 1)
self.assertEqual(etn[0][0], 'tree2')
self.assertTrue(x.startswith('{')) # pylint: disable=E1103
rx = json.loads(x)
self.assertEqual(detect_nexson_version(rx), '0.0.0')
etn = extract_tree_nexson(rx, tree_id=None)
self.assertEqual(len(etn), 1)
self.assertEqual(etn[0][0], 'tree2')
def testValidFilesPass(self):
format_list = ['1.2']
msg = ''
for d in VALID_NEXSON_DIRS:
for nf in format_list:
frag = os.path.join(d, 'v{f}.json'.format(f=nf))
nexson = pathmap.nexson_obj(frag)
aa = validate_nexson(nexson)
annot = aa[0]
for e in annot.errors:
_LOG.debug('unexpected error from {f}: {m}'.format(f=frag, m=UNICODE(e)))
if len(annot.errors) > 0:
ofn = pathmap.nexson_source_path(frag + '.output')
ew_dict = annot.get_err_warn_summary_dict()
testing_write_json(ew_dict, ofn)
msg = "File failed to validate cleanly. See {o}".format(o=ofn)
self.assertEqual(len(annot.errors), 0, msg)
def testValidFilesPass(self):
format_list = ['1.2']
msg = ''
for d in VALID_NEXSON_DIRS:
for nf in format_list:
frag = os.path.join(d, 'v{f}.json'.format(f=nf))
nexson = pathmap.nexson_obj(frag)
aa = validate_nexson(nexson)
annot = aa[0]
for e in annot.errors:
_LOG.debug('unexpected error from {f}: {m}'.format(
f=frag, m=UNICODE(e)))
if len(annot.errors) > 0:
ofn = pathmap.nexson_source_path(frag + '.output')
ew_dict = annot.get_err_warn_summary_dict()
testing_write_json(ew_dict, ofn)
msg = "File failed to validate cleanly. See {o}".format(
o=ofn)
self.assertEqual(len(annot.errors), 0, msg)
def testValidFilesPass(self):
format_list = ['1.0', '1.2']
TESTS_WITH_GT_ONE_TREE = ['9']
for d in TESTS_WITH_GT_ONE_TREE:
for nf in format_list:
frag = os.path.join(d, 'v{f}.json'.format(f=nf))
nexson = pathmap.nexson_obj(frag)
annotation = ot_validate(nexson)[0]
self.assertTrue(annotation['annotationEvent']['@passedChecks'])
annotation = ot_validate(nexson, max_num_trees_per_study=1)[0]
self.assertFalse(annotation['annotationEvent']['@passedChecks'])
annotation = ot_validate(nexson, max_num_trees_per_study=1)[0]
self.assertFalse(annotation['annotationEvent']['@passedChecks'])
bundle = validate_and_convert_nexson(nexson,
nf,
allow_invalid=True,
max_num_trees_per_study=1)
annotation = bundle[1]
self.assertFalse(annotation['annotationEvent']['@passedChecks'])
def testValidFilesPass(self):
format_list = ['1.0', '1.2']
TESTS_WITH_GT_ONE_TREE = ['9']
for d in TESTS_WITH_GT_ONE_TREE:
for nf in format_list:
frag = os.path.join(d, 'v{f}.json'.format(f=nf))
nexson = pathmap.nexson_obj(frag)
annotation = ot_validate(nexson)[0]
self.assertTrue(annotation['annotationEvent']['@passedChecks'])
annotation = ot_validate(nexson, max_num_trees_per_study=1)[0]
self.assertFalse(annotation['annotationEvent']['@passedChecks'])
annotation = ot_validate(nexson, max_num_trees_per_study=1)[0]
self.assertFalse(annotation['annotationEvent']['@passedChecks'])
bundle = validate_and_convert_nexson(nexson,
nf,
allow_invalid=True,
max_num_trees_per_study=1)
nexson, annotation, validation_log, nexson_adaptor = bundle
self.assertFalse(annotation['annotationEvent']['@passedChecks'])
def testNexmlConvByExtViaPS(self):
o = pathmap.nexson_obj('10/pg_10.json')
ps = PhyloSchema(type_ext='.nexml', otu_label='otttaxonname')
nex = ps.serialize(o, src_schema=PhyloSchema('nexson', version='1.2.1'))
self.assertTrue(nex.startswith('<')) # pylint: disable=E1103
def setUp(self):
self.nexson = pathmap.nexson_obj('pg_329/pg_329.json')
self.np = NexsonProxy(nexson=self.nexson)
def testCanCountTrees(self):
for v in ['0.0', '1.0', '1.2']:
inp = pathmap.nexson_obj('otu/v{v}.json'.format(v=v))
self.assertEqual(1, count_num_trees(inp, v))
def testNexusConvStudyViaPS(self):
o = pathmap.nexson_obj('10/pg_10.json')
ps = PhyloSchema(type_ext='.nex')
nex = ps.convert(o, serialize=True)
self.assertTrue(nex.startswith('#')) # pylint: disable=E1103
def testNexmlConvViaPS(self):
o = pathmap.nexson_obj('10/pg_10.json')
ps = PhyloSchema('nexml')
nex = ps.serialize(o)
self.assertTrue(nex.startswith('<')) # pylint: disable=E1103
def setUp(self):
self.nexson = pathmap.nexson_obj('pg_329/pg_329.json')
self.np = NexsonProxy(nexson=self.nexson)
def setUp(self):
blob = pathmap.nexson_obj('9/v1.2.json')
self.np = NexsonProxy(nexson=blob)
def testTreeExport(self):
n = pathmap.nexson_obj('10/pg_10.json')
newick = extract_tree(
n, 'tree3', PhyloSchema('nexus', tip_label='ot:ottTaxonName'))
self.assertTrue(newick.startswith('#'))
def setUp(self):
blob = pathmap.nexson_obj('9/v1.2.json')
self.np = NexsonProxy(nexson=blob)
def testDetectVersion(self):
o = pathmap.nexson_obj('invalid/bad_version.json.input')
v = detect_nexson_version(o)
self.assertEqual(v, '1.3.1')
def testOtuMapConvViaPS(self):
o = pathmap.nexson_obj('10/pg_10.json')
ps = PhyloSchema('nexson', content='otumap', version='1.2.1')
x = ps.serialize(o)
self.assertTrue(x.startswith('{')) # pylint: disable=E1103
def testNexmlConvViaPS(self):
o = pathmap.nexson_obj('10/pg_10.json')
ps = PhyloSchema('nexml')
nex = ps.serialize(o)
self.assertTrue(nex.startswith('<')) # pylint: disable=E1103
def testNexusConvViaPS(self):
o = pathmap.nexson_obj('10/pg_10.json')
ps = PhyloSchema('nexus', content='tree', content_id='tree3')
nex = ps.convert(o, serialize=True)
self.assertTrue(nex.startswith('#')) # pylint: disable=E1103
def testNexmlConvByExtViaPS(self):
o = pathmap.nexson_obj('10/pg_10.json')
ps = PhyloSchema(type_ext='.nexml', otu_label='otttaxonname')
nex = ps.serialize(o,
src_schema=PhyloSchema('nexson', version='1.2.1'))
self.assertTrue(nex.startswith('<')) # pylint: disable=E1103
def testNexusConvStudyViaPS(self):
o = pathmap.nexson_obj('10/pg_10.json')
ps = PhyloSchema(type_ext='.nex')
nex = ps.convert(o, serialize=True)
self.assertTrue(nex.startswith('#')) # pylint: disable=E1103
def testDetectVersion(self):
o = pathmap.nexson_obj('invalid/bad_version.json.input')
v = detect_nexson_version(o)
self.assertEqual(v, '1.3.1')
def testNewickConvStudyViaPS(self):
o = pathmap.nexson_obj('9/v1.2.json')
ps = PhyloSchema(type_ext='.tre')
nex = ps.convert(o, serialize=True)
self.assertTrue(nex.startswith('(')) # pylint: disable=E1103
def testNexusConvViaPS(self):
o = pathmap.nexson_obj('10/pg_10.json')
ps = PhyloSchema('nexus', content='tree', content_id='tree3')
nex = ps.convert(o, serialize=True)
self.assertTrue(nex.startswith('#')) # pylint: disable=E1103
def testNexusConvByExtViaPS(self):
o = pathmap.nexson_obj('10/pg_10.json')
ps = PhyloSchema(None, type_ext='.nex', content='tree', content_id='tree3')
nex = ps.serialize(o)
self.assertTrue(nex.startswith('#')) # pylint: disable=E1103
def testNewickConvStudyViaPS(self):
o = pathmap.nexson_obj('9/v1.2.json')
ps = PhyloSchema(type_ext='.tre')
nex = ps.convert(o, serialize=True)
self.assertTrue(nex.startswith('(')) # pylint: disable=E1103
def testNewickConvViaPS(self):
o = pathmap.nexson_obj('10/pg_10.json')
ps = PhyloSchema('newick', content='tree', content_id='tree3')
nex = ps.serialize(o)
self.assertTrue(nex.startswith('(')) # pylint: disable=E1103
def testNewickConvViaPS(self):
o = pathmap.nexson_obj('10/pg_10.json')
ps = PhyloSchema('newick', content='tree', content_id='tree3')
nex = ps.serialize(o)
self.assertTrue(nex.startswith('(')) # pylint: disable=E1103
def testTreeExport(self):
n = pathmap.nexson_obj('10/pg_10.json')
newick = extract_tree(n, 'tree3', PhyloSchema('nexus', tip_label='ot:ottTaxonName'))
self.assertTrue(newick.startswith('#'))