|
tests.test_main_cli.HelpTestCase |
test |
tests/test_main_cli.py |
300 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | CLI not working |
Details | tests/test_main_cli.py:299: CLI not working |
Standard output | |
Standard error | |
|
|
tests.util.test_molecule_util.TestInchiMolecule |
test |
tests/util/test_molecule_ut... |
79 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.util.test_rna_seq_util.TestKallisto |
test |
tests/util/test_rna_seq_uti... |
26 |
Pass |
0.839 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.core.test_data_model.TestConsensus |
test |
tests/core/test_data_model.py |
26 |
Pass |
0.002 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.core.test_data_model.TestConsensusMethod |
test |
tests/core/test_data_model.py |
19 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.core.test_data_model.TestEvidence |
test |
tests/core/test_data_model.py |
44 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.core.test_data_model.TestGenetics |
test |
tests/core/test_data_model.py |
333 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.core.test_data_model.TestPolymerSpecie |
test |
tests/core/test_data_model.py |
146 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.core.test_data_model.TestResourceAssignme... |
test |
tests/core/test_data_model.py |
345 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.util.test_file_util.TestFileUtil |
test_access_dict_by_index |
tests/util/test_file_util.py |
56 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.data_source.test_sabio_rk_nosql.TestSabioRk |
test_add_inchi_hash |
tests/data_source/test_sabi... |
338 |
Error |
0.013 |
Result type | |
Message | test setup failure |
Details | cls = <class 'tests.data_source.test_sabio_rk_nosql.TestSabioRk'>
@classmethod
def setUpClass(cls):
cls.cache_dirname = tempfile.mkdtemp()
db = 'test'
username = datanator.config.core.get_config()[
'datanator']['mongodb']['user']
password = datanator.config.core.get_config(
)['datanator']['mongodb']['password']
MongoDB = datanator.config.core.get_config(
)['datanator']['mongodb']['server']
port = datanator.config.core.get_config(
)['datanator']['mongodb']['port']
replSet = datanator.config.core.get_config(
)['datanator']['mongodb']['replSet']
cls.src = sabio_rk.SabioRk(cache_dirname=cls.cache_dirname,
MongoDB=MongoDB, db=db,
verbose=True, max_entries=20, username=username,
> password=password, webservice_batch_size = 10)
E TypeError: __init__() got an unexpected keyword argument 'MongoDB'
tests/data_source/test_sabio_rk_nosql.py:29: TypeError |
Standard output | |
Standard error | |
|
|
tests.test_main_cli.TestBuildController |
test_build_corum |
tests/test_main_cli.py |
55 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | CLI not working |
Details | tests/test_main_cli.py:54: CLI not working |
Standard output | |
Standard error | |
|
|
tests.test_main_cli.TestBuildController |
test_build_ecmdb |
tests/test_main_cli.py |
80 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | CLI not working |
Details | tests/test_main_cli.py:79: CLI not working |
Standard output | |
Standard error | |
|
|
tests.test_main_cli.TestBuildController |
test_build_intact |
tests/test_main_cli.py |
61 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | CLI not working |
Details | tests/test_main_cli.py:60: CLI not working |
Standard output | |
Standard error | |
|
|
tests.test_main_cli.TestBuildController |
test_build_jaspar |
tests/test_main_cli.py |
74 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | CLI not working |
Details | tests/test_main_cli.py:73: CLI not working |
Standard output | |
Standard error | |
|
|
tests.test_main_cli.TestBuildController |
test_build_pax |
tests/test_main_cli.py |
86 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | CLI not working |
Details | tests/test_main_cli.py:85: CLI not working |
Standard output | |
Standard error | |
|
|
tests.test_main_cli.TestBuildController |
test_build_sabio |
tests/test_main_cli.py |
67 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | CLI not working |
Details | tests/test_main_cli.py:66: CLI not working |
Standard output | |
Standard error | |
|
|
tests.data_source.test_sabio_rk_nosql.TestSabioRk |
test_calc_enzyme_molecular_... |
tests/data_source/test_sabi... |
313 |
Error |
0.001 |
Result type | |
Message | test setup failure |
Details | cls = <class 'tests.data_source.test_sabio_rk_nosql.TestSabioRk'>
@classmethod
def setUpClass(cls):
cls.cache_dirname = tempfile.mkdtemp()
db = 'test'
username = datanator.config.core.get_config()[
'datanator']['mongodb']['user']
password = datanator.config.core.get_config(
)['datanator']['mongodb']['password']
MongoDB = datanator.config.core.get_config(
)['datanator']['mongodb']['server']
port = datanator.config.core.get_config(
)['datanator']['mongodb']['port']
replSet = datanator.config.core.get_config(
)['datanator']['mongodb']['replSet']
cls.src = sabio_rk.SabioRk(cache_dirname=cls.cache_dirname,
MongoDB=MongoDB, db=db,
verbose=True, max_entries=20, username=username,
> password=password, webservice_batch_size = 10)
E TypeError: __init__() got an unexpected keyword argument 'MongoDB'
tests/data_source/test_sabio_rk_nosql.py:29: TypeError |
Standard output | |
Standard error | |
|
|
tests.data_source.test_sabio_rk.TestDownloader |
test_calc_inchi_formula_con... |
tests/data_source/test_sabi... |
797 |
Pass |
0.044 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.data_source.test_sabio_rk_nosql.TestSabioRk |
test_calc_inchi_formula_con... |
tests/data_source/test_sabi... |
275 |
Error |
0.001 |
Result type | |
Message | test setup failure |
Details | cls = <class 'tests.data_source.test_sabio_rk_nosql.TestSabioRk'>
@classmethod
def setUpClass(cls):
cls.cache_dirname = tempfile.mkdtemp()
db = 'test'
username = datanator.config.core.get_config()[
'datanator']['mongodb']['user']
password = datanator.config.core.get_config(
)['datanator']['mongodb']['password']
MongoDB = datanator.config.core.get_config(
)['datanator']['mongodb']['server']
port = datanator.config.core.get_config(
)['datanator']['mongodb']['port']
replSet = datanator.config.core.get_config(
)['datanator']['mongodb']['replSet']
cls.src = sabio_rk.SabioRk(cache_dirname=cls.cache_dirname,
MongoDB=MongoDB, db=db,
verbose=True, max_entries=20, username=username,
> password=password, webservice_batch_size = 10)
E TypeError: __init__() got an unexpected keyword argument 'MongoDB'
tests/data_source/test_sabio_rk_nosql.py:29: TypeError |
Standard output | |
Standard error | |
|
|
tests.util.test_reaction_util.TestReaction |
test_calc_reactant_product_... |
tests/util/test_reaction_ut... |
45 |
Pass |
0.015 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.elasticsearch_kl.test_batch_load.TestMong... |
test_connection |
tests/elasticsearch_kl/test... |
30 |
Pass |
0.186 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.util.test_mongo_util.TestMongoUtil |
test_con_db |
tests/util/test_mongo_util.py |
37 |
Pass |
0.021 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.data_source.test_corum_nosql.TestCorumNoSQL |
test_correct_protein_name_list |
tests/data_source/test_coru... |
66 |
Pass |
0.014 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.test_main_cli.DbControllerTestCase |
test_create |
tests/test_main_cli.py |
339 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | CLI not working |
Details | tests/test_main_cli.py:338: CLI not working |
Standard output | |
Standard error | |
|
|
tests.data_source.test_sabio_rk_nosql.TestSabioRk |
test_create_cross_reference... |
tests/data_source/test_sabi... |
51 |
Error |
0.001 |
Result type | |
Message | test setup failure |
Details | cls = <class 'tests.data_source.test_sabio_rk_nosql.TestSabioRk'>
@classmethod
def setUpClass(cls):
cls.cache_dirname = tempfile.mkdtemp()
db = 'test'
username = datanator.config.core.get_config()[
'datanator']['mongodb']['user']
password = datanator.config.core.get_config(
)['datanator']['mongodb']['password']
MongoDB = datanator.config.core.get_config(
)['datanator']['mongodb']['server']
port = datanator.config.core.get_config(
)['datanator']['mongodb']['port']
replSet = datanator.config.core.get_config(
)['datanator']['mongodb']['replSet']
cls.src = sabio_rk.SabioRk(cache_dirname=cls.cache_dirname,
MongoDB=MongoDB, db=db,
verbose=True, max_entries=20, username=username,
> password=password, webservice_batch_size = 10)
E TypeError: __init__() got an unexpected keyword argument 'MongoDB'
tests/data_source/test_sabio_rk_nosql.py:29: TypeError |
Standard output | |
Standard error | |
|
|
tests.data_source.test_sabio_rk_nosql.TestSabioRk |
test_create_kinetic_laws_fr... |
tests/data_source/test_sabi... |
118 |
Error |
0.001 |
Result type | |
Message | test setup failure |
Details | cls = <class 'tests.data_source.test_sabio_rk_nosql.TestSabioRk'>
@classmethod
def setUpClass(cls):
cls.cache_dirname = tempfile.mkdtemp()
db = 'test'
username = datanator.config.core.get_config()[
'datanator']['mongodb']['user']
password = datanator.config.core.get_config(
)['datanator']['mongodb']['password']
MongoDB = datanator.config.core.get_config(
)['datanator']['mongodb']['server']
port = datanator.config.core.get_config(
)['datanator']['mongodb']['port']
replSet = datanator.config.core.get_config(
)['datanator']['mongodb']['replSet']
cls.src = sabio_rk.SabioRk(cache_dirname=cls.cache_dirname,
MongoDB=MongoDB, db=db,
verbose=True, max_entries=20, username=username,
> password=password, webservice_batch_size = 10)
E TypeError: __init__() got an unexpected keyword argument 'MongoDB'
tests/data_source/test_sabio_rk_nosql.py:29: TypeError |
Standard output | |
Standard error | |
|
|
tests.data_source.test_sabio_rk_nosql.TestSabioRk |
test_create_kinetic_law_fro... |
tests/data_source/test_sabi... |
85 |
Error |
0.001 |
Result type | |
Message | test setup failure |
Details | cls = <class 'tests.data_source.test_sabio_rk_nosql.TestSabioRk'>
@classmethod
def setUpClass(cls):
cls.cache_dirname = tempfile.mkdtemp()
db = 'test'
username = datanator.config.core.get_config()[
'datanator']['mongodb']['user']
password = datanator.config.core.get_config(
)['datanator']['mongodb']['password']
MongoDB = datanator.config.core.get_config(
)['datanator']['mongodb']['server']
port = datanator.config.core.get_config(
)['datanator']['mongodb']['port']
replSet = datanator.config.core.get_config(
)['datanator']['mongodb']['replSet']
cls.src = sabio_rk.SabioRk(cache_dirname=cls.cache_dirname,
MongoDB=MongoDB, db=db,
verbose=True, max_entries=20, username=username,
> password=password, webservice_batch_size = 10)
E TypeError: __init__() got an unexpected keyword argument 'MongoDB'
tests/data_source/test_sabio_rk_nosql.py:29: TypeError |
Standard output | |
Standard error | |
|
|
tests.data_source.test_sabio_reaction.TestProte... |
test_create_reactants |
tests/data_source/test_sabi... |
43 |
Pass |
0.014 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.test_main_cli.DbControllerTestCase |
test_create_table_only |
tests/test_main_cli.py |
345 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | CLI not working |
Details | tests/test_main_cli.py:344: CLI not working |
Standard output | |
Standard error | |
|
|
tests.elasticsearch_kl.test_batch_load.TestMong... |
test_data_from_metabolite |
tests/elasticsearch_kl/test... |
40 |
Pass |
0.169 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.elasticsearch_kl.test_batch_load.TestMong... |
test_data_from_metabolites_... |
tests/elasticsearch_kl/test... |
46 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.elasticsearch_kl.test_batch_load.TestMong... |
test_data_from_mongo |
tests/elasticsearch_kl/test... |
35 |
Pass |
20.451 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.util.test_warning_util.TestWarningUtil |
test_disable_warnings_openb... |
tests/util/test_warning_uti... |
24 |
Pass |
0.229 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.util.test_warning_util.TestWarningUtil |
test_disable_warnings_urllib3 |
tests/util/test_warning_uti... |
30 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | todo: implement |
Details | tests/util/test_warning_util.py:29: todo: implement |
Standard output | |
Standard error | |
|
|
tests.util.test_file_util.TestFileUtil |
test_distance_to_common |
tests/util/test_file_util.py |
77 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.test_main_cli.TestDownloadController |
test_download_array_express |
tests/test_main_cli.py |
140 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | skip because too long |
Details | tests/test_main_cli.py:139: skip because too long |
Standard output | |
Standard error | |
|
|
tests.data_source.test_intact_nosql.TestCorumNoSQL |
test_download_content |
tests/data_source/test_inta... |
31 |
Pass |
17.119 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.test_main_cli.TestDownloadController |
test_download_corum |
tests/test_main_cli.py |
104 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | skip because too long |
Details | tests/test_main_cli.py:103: skip because too long |
Standard output | |
Standard error | |
|
|
tests.data_source.test_taxon_tree.TestTaxonTree |
test_download_dump |
tests/data_source/test_taxo... |
33 |
Pass |
6.194 |
Result type | |
Message | |
Details | |
Standard output |
Downloading taxdump zip file ...
... Done!
Unzipping ...
... Done unzipping
|
Standard error | |
|
|
tests.test_main_cli.TestDownloadController |
test_download_ecmdb |
tests/test_main_cli.py |
128 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | skip because too long |
Details | tests/test_main_cli.py:127: skip because too long |
Standard output | |
Standard error | |
|
|
tests.data_source.test_sabio_rk.TestAll |
test_download_full_database |
tests/data_source/test_sabi... |
879 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | Skip this test because it is long |
Details | tests/data_source/test_sabio_rk.py:878: Skip this test because it is long |
Standard output | |
Standard error | |
|
|
tests.test_main_cli.TestDownloadController |
test_download_intact |
tests/test_main_cli.py |
110 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | skip because too long |
Details | tests/test_main_cli.py:109: skip because too long |
Standard output | |
Standard error | |
|
|
tests.test_main_cli.TestDownloadController |
test_download_jaspar |
tests/test_main_cli.py |
122 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | skip because too long |
Details | tests/test_main_cli.py:121: skip because too long |
Standard output | |
Standard error | |
|
|
tests.data_source.test_kegg_orthology.TestKeggO... |
test_download_ko |
tests/data_source/test_kegg... |
78 |
Pass |
0.914 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.test_main_cli.TestDownloadController |
test_download_pax |
tests/test_main_cli.py |
134 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | skip because too long |
Details | tests/test_main_cli.py:133: skip because too long |
Standard output | |
Standard error | |
|
|
tests.data_source.test_kegg_reaction_class.Test... |
test_download_rxn_cls |
tests/data_source/test_kegg... |
80 |
Pass |
0.428 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.test_main_cli.TestDownloadController |
test_download_sabio |
tests/test_main_cli.py |
116 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | skip because too long |
Details | tests/test_main_cli.py:115: skip because too long |
Standard output | |
Standard error | |
|
|
tests.test_main_cli.TestDownloadController |
test_download_uniprot |
tests/test_main_cli.py |
146 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | skip because too long |
Details | tests/test_main_cli.py:145: skip because too long |
Standard output | |
Standard error | |
|
|
tests.data_source.rna_halflife.test_doi_10_1186... |
test_download_xlsx |
tests/data_source/rna_halfl... |
37 |
Pass |
2.272 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.test_main_cli.DbControllerTestCase |
test_drop |
tests/test_main_cli.py |
362 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | CLI not working |
Details | tests/test_main_cli.py:361: CLI not working |
Standard output | |
Standard error | |
|
|
tests.util.test_warning_util.TestWarningUtil |
test_enable_warnings_openbabel |
tests/util/test_warning_uti... |
18 |
Pass |
0.231 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | ==============================
*** Open Babel Warning in InChI code
#0 :Proton(s) added/removed; Omitted undefined stereo
|
|
|
tests.data_source.test_sabio_rk.TestDownloader |
test_enzyme_parameter |
tests/data_source/test_sabi... |
739 |
Pass |
3.277 |
Result type | |
Message | |
Details | |
Standard output | Downloading kinetic laws 1-1 of 1 in SBML format
Downloading compound 1 of 4
Downloading kinetic laws 1-1 of 1 in Excel format
|
Standard error | |
|
|
tests.util.test_rna_seq_util.TestKallisto |
test_error |
tests/util/test_rna_seq_uti... |
53 |
Pass |
0.267 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.util.test_file_util.TestFileUtil |
test_exists_key_value_pair |
tests/util/test_file_util.py |
124 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.data_source.test_sabio_rk.TestStats |
test_export_stats |
tests/data_source/test_sabi... |
855 |
Pass |
0.141 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.data_source.test_sabio_reaction.TestProte... |
test_extract_enzyme_names |
tests/data_source/test_sabi... |
64 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.data_source.test_sabio_reaction.TestProte... |
test_extract_reactant_names |
tests/data_source/test_sabi... |
51 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.util.test_file_util.TestFileUtil |
test_extract_values |
tests/util/test_file_util.py |
32 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.data_source.test_sabio_reaction.TestProte... |
test_fill_collection |
tests/data_source/test_sabi... |
48 |
Pass |
0.430 |
Result type | |
Message | |
Details | |
Standard output | Processing document 2900 out of 60193
|
Standard error | |
|
|
tests.util.test_mongo_util.TestMongoUtil |
test_fill_db |
tests/util/test_mongo_util.py |
40 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | passed |
Details | tests/util/test_mongo_util.py:39: passed |
Standard output | |
Standard error | |
|
|
tests.data_source.rna_halflife.test_doi_10_1186... |
test_fill_gene_protein_name |
tests/data_source/rna_halfl... |
49 |
Pass |
0.019 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.data_source.rna_halflife.test_doi_10_1186... |
test_fill_protein_name |
tests/data_source/rna_halfl... |
55 |
Pass |
0.003 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.data_source.rna_halflife.test_doi_10_1093... |
test_fill_rna_halflife |
tests/data_source/rna_halfl... |
42 |
Failure |
0.009 |
Result type | |
Message | AttributeError: 'QueryUniprot' object has no attribute 'get_gene_protein_name_by_oln' |
Details | self = <test_doi_10_1093_nar_gks1019.TestProteinAggregate testMethod=test_fill_rna_halflife>
def test_fill_rna_halflife(self):
d = {'half_life': [32.3, 12.2, 13.2], 'r_sqaured': [0.9, 0.7, 0.8],
'ordered_locus_name': ['Rv0002', 'something', 'this']}
df_0 = pd.DataFrame(d)
> self.src.fill_rna_halflife(df_0, ['aaa', 102])
tests/data_source/rna_halflife/test_doi_10_1093_nar_gks1019.py:46:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <datanator.data_source.rna_halflife.doi_10_1093_nar_gks1019.Halflife object at 0x7f68048a9668>
df = half_life ... ordered_locus_name
0 32.3 ... Rv0002
1 12.2 ... something
2 13.2 ... this
[3 rows x 3 columns]
species = ['aaa', 102]
def fill_rna_halflife(self, df, species):
"""load data into rna_halflife collection
Args:
df (:obj:`pandas.DataFrame`): dataframe to be loaded into the database
species (:obj:`list`): species name and ncbi_id
"""
row_count = len(df.index)
for i, row in df.iterrows():
if i == self.max_entries:
break
if i % 10 == 0 and self.verbose:
print("Processing locus {} out {}".format(i, row_count))
halflives = {}
oln = row['ordered_locus_name']
halflives['halflife'] = row['half_life'] * 60
halflives['r_sqaured'] = row['r_sqaured']
halflives['unit'] = 's'
halflives['reference'] = [{'doi': '10.1093/nar/gks1019', 'pubmed_id': '23125364'}]
halflives['growth_medium'] = 'Middlebrook 7H9 with the ADC supplement (Difco) and 0.05% Tween80, at 37 degree celcius.'
halflives['ordered_locus_name'] = oln
halflives['species'] = species[0]
halflives['ncbi_taxonomy_id'] = species[1]
> gene_name, protein_name = self.uniprot_query_manager.get_gene_protein_name_by_oln(oln)
E AttributeError: 'QueryUniprot' object has no attribute 'get_gene_protein_name_by_oln'
datanator/data_source/rna_halflife/doi_10_1093_nar_gks1019.py:86: AttributeError |
Standard output | Processing locus 0 out 3
|
Standard error | |
|
|
tests.data_source.rna_halflife.test_doi_10_1093... |
test_fill_uniprot |
tests/data_source/rna_halfl... |
36 |
Skipped |
0.079 |
Result type | pytest.skip |
Message | avoid downloading |
Details | tests/data_source/rna_halflife/test_doi_10_1093_nar_gks1019.py:35: avoid downloading |
Standard output | |
Standard error | |
|
|
tests.util.test_rna_halflife_util.TestRnaHlUtil |
test_fill_uniprot_by_oln |
tests/util/test_rna_halflif... |
30 |
Skipped |
0.008 |
Result type | pytest.skip |
Message | avoid r/w db |
Details | tests/util/test_rna_halflife_util.py:29: avoid r/w db |
Standard output | |
Standard error | |
|
|
tests.data_source.rna_halflife.test_doi_10_1186... |
test_fill_uniprot_by_oln |
tests/data_source/rna_halfl... |
63 |
Failure |
0.001 |
Result type | |
Message | AttributeError: 'QueryUniprot' object has no attribute 'get_gene_protein_name_by_oln' |
Details | self = <test_doi_10_1186_s12864_016_3219_8.TestProteinAggregate testMethod=test_fill_uniprot_by_oln>
def test_fill_uniprot_by_oln(self):
> self.src.fill_uniprot_by_oln('MA0002')
tests/data_source/rna_halflife/test_doi_10_1186_s12864_016_3219_8.py:64:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <datanator.data_source.rna_halflife.doi_10_1186_s12864_016_3219_8.Halflife object at 0x7f6804851940>
oln = 'MA0002'
def fill_uniprot_by_oln(self, oln):
"""Fill uniprot collection using ordered locus name
Args:
oln (:obj:`str`): Ordered locus name
"""
> gene_name, protein_name = self.uniprot_manager.get_gene_protein_name_by_oln(oln, species=188937)
E AttributeError: 'QueryUniprot' object has no attribute 'get_gene_protein_name_by_oln'
datanator/data_source/rna_halflife/doi_10_1186_s12864_016_3219_8.py:204: AttributeError |
Standard output | |
Standard error | |
|
|
tests.util.test_file_util.TestFileUtil |
test_flatten_json |
tests/util/test_file_util.py |
19 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.data_source.test_sabio_rk.TestDownloader |
test_full_kinetic_laws |
tests/data_source/test_sabi... |
814 |
Pass |
1.941 |
Result type | |
Message | |
Details | |
Standard output | Downloading kinetic laws 1-1 of 1 in SBML format
Downloading compound 1 of 4
Downloading kinetic laws 1-1 of 1 in Excel format
|
Standard error | |
|
|
tests.test_main_cli.TestWithTempFile |
test_GenerateTemplateContro... |
tests/test_main_cli.py |
180 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | CLI not working |
Details | tests/test_main_cli.py:179: CLI not working |
Standard output | |
Standard error | |
|
|
tests.test_main_cli.TestWithTempFile |
test_GetDataController |
tests/test_main_cli.py |
162 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | CLI not working |
Details | tests/test_main_cli.py:161: CLI not working |
Standard output | |
Standard error | |
|
|
tests.util.test_taxonomy_util.TestTaxonomyUtil |
test_get_distance_to_common... |
tests/util/test_taxonomy_ut... |
129 |
Pass |
0.068 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.util.test_taxonomy_util.TestTaxonomyUtil |
test_get_distance_to_root |
tests/util/test_taxonomy_ut... |
162 |
Pass |
0.005 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.test_main_cli.TestWithoutTempFile |
test_get_ec_number |
tests/test_main_cli.py |
268 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | CLI not working |
Details | tests/test_main_cli.py:267: CLI not working |
Standard output | |
Standard error | |
|
|
tests.core.test_data_model.TestReaction |
test_get_ec_number |
tests/core/test_data_model.py |
276 |
Pass |
0.002 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.util.test_molecule_util.TestMolecule |
test_get_fingerprint |
tests/util/test_molecule_ut... |
67 |
Pass |
0.010 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.util.test_molecule_util.TestMolecule |
test_get_fingerprint_types |
tests/util/test_molecule_ut... |
60 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.util.test_molecule_util.TestInchiMolecule |
test_get_formula_and_connec... |
tests/util/test_molecule_ut... |
182 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.data_source.test_sabio_reaction.TestProte... |
test_get_id |
tests/data_source/test_sabi... |
38 |
Pass |
0.025 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.util.test_taxonomy_util.TestTaxonomyUtil |
test_get_max_distance_to_co... |
tests/util/test_taxonomy_ut... |
169 |
Pass |
0.004 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.data_source.test_sabio_rk_nosql.TestSabioRk |
test_get_parameter_by_prope... |
tests/data_source/test_sabi... |
161 |
Error |
0.001 |
Result type | |
Message | test setup failure |
Details | cls = <class 'tests.data_source.test_sabio_rk_nosql.TestSabioRk'>
@classmethod
def setUpClass(cls):
cls.cache_dirname = tempfile.mkdtemp()
db = 'test'
username = datanator.config.core.get_config()[
'datanator']['mongodb']['user']
password = datanator.config.core.get_config(
)['datanator']['mongodb']['password']
MongoDB = datanator.config.core.get_config(
)['datanator']['mongodb']['server']
port = datanator.config.core.get_config(
)['datanator']['mongodb']['port']
replSet = datanator.config.core.get_config(
)['datanator']['mongodb']['replSet']
cls.src = sabio_rk.SabioRk(cache_dirname=cls.cache_dirname,
MongoDB=MongoDB, db=db,
verbose=True, max_entries=20, username=username,
> password=password, webservice_batch_size = 10)
E TypeError: __init__() got an unexpected keyword argument 'MongoDB'
tests/data_source/test_sabio_rk_nosql.py:29: TypeError |
Standard output | |
Standard error | |
|
|
tests.core.test_data_model.TestReaction |
test_get_products |
tests/core/test_data_model.py |
259 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.core.test_data_model.TestReaction |
test_get_reactants |
tests/core/test_data_model.py |
255 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.core.test_data_model.TestReaction |
test_get_reactant_product_p... |
tests/core/test_data_model.py |
263 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.data_source.test_sabio_rk_nosql.TestSabioRk |
test_get_specie_from_sbml |
tests/data_source/test_sabi... |
64 |
Error |
0.001 |
Result type | |
Message | test setup failure |
Details | cls = <class 'tests.data_source.test_sabio_rk_nosql.TestSabioRk'>
@classmethod
def setUpClass(cls):
cls.cache_dirname = tempfile.mkdtemp()
db = 'test'
username = datanator.config.core.get_config()[
'datanator']['mongodb']['user']
password = datanator.config.core.get_config(
)['datanator']['mongodb']['password']
MongoDB = datanator.config.core.get_config(
)['datanator']['mongodb']['server']
port = datanator.config.core.get_config(
)['datanator']['mongodb']['port']
replSet = datanator.config.core.get_config(
)['datanator']['mongodb']['replSet']
cls.src = sabio_rk.SabioRk(cache_dirname=cls.cache_dirname,
MongoDB=MongoDB, db=db,
verbose=True, max_entries=20, username=username,
> password=password, webservice_batch_size = 10)
E TypeError: __init__() got an unexpected keyword argument 'MongoDB'
tests/data_source/test_sabio_rk_nosql.py:29: TypeError |
Standard output | |
Standard error | |
|
|
tests.data_source.test_sabio_rk_nosql.TestSabioRk |
test_get_specie_reference_f... |
tests/data_source/test_sabi... |
73 |
Error |
0.001 |
Result type | |
Message | test setup failure |
Details | cls = <class 'tests.data_source.test_sabio_rk_nosql.TestSabioRk'>
@classmethod
def setUpClass(cls):
cls.cache_dirname = tempfile.mkdtemp()
db = 'test'
username = datanator.config.core.get_config()[
'datanator']['mongodb']['user']
password = datanator.config.core.get_config(
)['datanator']['mongodb']['password']
MongoDB = datanator.config.core.get_config(
)['datanator']['mongodb']['server']
port = datanator.config.core.get_config(
)['datanator']['mongodb']['port']
replSet = datanator.config.core.get_config(
)['datanator']['mongodb']['replSet']
cls.src = sabio_rk.SabioRk(cache_dirname=cls.cache_dirname,
MongoDB=MongoDB, db=db,
verbose=True, max_entries=20, username=username,
> password=password, webservice_batch_size = 10)
E TypeError: __init__() got an unexpected keyword argument 'MongoDB'
tests/data_source/test_sabio_rk_nosql.py:29: TypeError |
Standard output | |
Standard error | |
|
|
tests.util.test_calc_tanimoto.TestCalcTanimoto |
test_get_tanimoto |
tests/util/test_calc_tanimo... |
29 |
Pass |
0.029 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.util.test_file_util.TestFileUtil |
test_get_val_from_dict_list |
tests/util/test_file_util.py |
42 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.test_main_cli.BaseControllerTestCase |
test_get_version |
tests/test_main_cli.py |
29 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | CLI not working |
Details | tests/test_main_cli.py:28: CLI not working |
Standard output | |
Standard error | |
|
|
tests.util.test_chem_util.TestChemUtil |
test_hash_inchi |
tests/util/test_chem_util.py |
24 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.core.test_data_model.TestReaction |
test_id |
tests/core/test_data_model.py |
195 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.util.test_index_collection.TestMongoUtil |
test_index_corum |
tests/util/test_index_colle... |
28 |
Skipped |
0.013 |
Result type | pytest.skip |
Message | passed |
Details | tests/util/test_index_collection.py:27: passed |
Standard output | |
Standard error | |
|
|
tests.util.test_index_collection.TestMongoUtil |
test_index_sabio |
tests/util/test_index_colle... |
36 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | passed |
Details | tests/util/test_index_collection.py:35: passed |
Standard output | |
Standard error | |
|
|
tests.util.test_index_collection.TestMongoUtil |
test_index_uniprot |
tests/util/test_index_colle... |
44 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | passed |
Details | tests/util/test_index_collection.py:43: passed |
Standard output | |
Standard error | |
|
|
tests.data_source.test_sabio_rk.TestDownloader |
test_infer_compound_structu... |
tests/data_source/test_sabi... |
756 |
Pass |
1.350 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.data_source.test_sabio_rk_nosql.TestSabioRk |
test_infer_compound_structu... |
tests/data_source/test_sabi... |
193 |
Error |
0.001 |
Result type | |
Message | test setup failure |
Details | cls = <class 'tests.data_source.test_sabio_rk_nosql.TestSabioRk'>
@classmethod
def setUpClass(cls):
cls.cache_dirname = tempfile.mkdtemp()
db = 'test'
username = datanator.config.core.get_config()[
'datanator']['mongodb']['user']
password = datanator.config.core.get_config(
)['datanator']['mongodb']['password']
MongoDB = datanator.config.core.get_config(
)['datanator']['mongodb']['server']
port = datanator.config.core.get_config(
)['datanator']['mongodb']['port']
replSet = datanator.config.core.get_config(
)['datanator']['mongodb']['replSet']
cls.src = sabio_rk.SabioRk(cache_dirname=cls.cache_dirname,
MongoDB=MongoDB, db=db,
verbose=True, max_entries=20, username=username,
> password=password, webservice_batch_size = 10)
E TypeError: __init__() got an unexpected keyword argument 'MongoDB'
tests/data_source/test_sabio_rk_nosql.py:29: TypeError |
Standard output | |
Standard error | |
|
|
tests.util.test_molecule_util.TestMolecule |
test_init |
tests/util/test_molecule_ut... |
36 |
Pass |
0.390 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.core.test_data_model.TestReaction |
test_init |
tests/core/test_data_model.py |
191 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.core.test_data_model.TestResource |
test_init |
tests/core/test_data_model.py |
352 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.util.test_molecule_util.TestInchiMolecule |
test_is_equal |
tests/util/test_molecule_ut... |
137 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.util.test_molecule_util.TestInchiMolecule |
test_is_protonation_isomer |
tests/util/test_molecule_ut... |
174 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.util.test_molecule_util.TestInchiMolecule |
test_is_stereoisomer |
tests/util/test_molecule_ut... |
154 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.util.test_molecule_util.TestInchiMolecule |
test_is_tautomer |
tests/util/test_molecule_ut... |
166 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.util.test_mongo_util.TestMongoUtil |
test_list_all_collections |
tests/util/test_mongo_util.py |
32 |
Pass |
0.019 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.data_source.test_sabio_rk.TestDownloader |
test_loading_enzymes |
tests/data_source/test_sabi... |
530 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | takes too long |
Details | tests/data_source/test_sabio_rk.py:529: takes too long |
Standard output | |
Standard error | |
|
|
tests.data_source.test_protein_aggregate.TestPr... |
test_loadload_kinlaw_from_s... |
tests/data_source/test_prot... |
73 |
Failure |
0.131 |
Result type | |
Message | AssertionError: False is not true |
Details | self = <tests.data_source.test_protein_aggregate.TestProteinAggregate testMethod=test_loadload_kinlaw_from_sabio>
def test_loadload_kinlaw_from_sabio(self):
dic_0 = {'uniprot_id': 'P20932'}
dic_1 = {'uniprot_id': 'id_mock_1', 'protein_name': 'subtilisin'}
dic_2 = {'uniprot_id': 'P16064', 'protein_name': 'subtilisin'}
self.src.col.insert_many([dic_0, dic_1, dic_2])
self.src.load_kinlaw_from_sabio()
result_0 = self.src.col.find_one({'uniprot_id': 'P20932'})
> self.assertTrue('kinetics' in result_0.keys())
E AssertionError: False is not true
tests/data_source/test_protein_aggregate.py:80: AssertionError |
Standard output | |
Standard error | |
|
|
tests.data_source.test_corum_nosql.TestCorumNoSQL |
test_load_all_content |
tests/data_source/test_coru... |
45 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | will not work on circle ci due to file directory setting |
Details | tests/data_source/test_corum_nosql.py:44: will not work on circle ci due to file directory setting |
Standard output | |
Standard error | |
|
|
tests.data_source.test_sabio_rk.TestDownloader |
test_load_and_update_kineti... |
tests/data_source/test_sabi... |
205 |
Pass |
1.757 |
Result type | |
Message | |
Details | |
Standard output | Downloading kinetic laws 1-1 of 1 in SBML format
Downloading compound 1 of 3
Downloading kinetic laws 1-1 of 1 in Excel format
Normalizing kinetic law 1 of 1
Downloading compound 1 of 3
|
Standard error | |
|
|
tests.data_source.test_intact_nosql.TestCorumNoSQL |
test_load_complex |
tests/data_source/test_inta... |
37 |
Pass |
0.329 |
Result type | |
Message | |
Details | |
Standard output | Inserting 1 of 20 complex document
|
Standard error | |
|
|
tests.data_source.test_sabio_rk_nosql.TestSabioRk |
test_load_compounds |
tests/data_source/test_sabi... |
128 |
Error |
0.001 |
Result type | |
Message | test setup failure |
Details | cls = <class 'tests.data_source.test_sabio_rk_nosql.TestSabioRk'>
@classmethod
def setUpClass(cls):
cls.cache_dirname = tempfile.mkdtemp()
db = 'test'
username = datanator.config.core.get_config()[
'datanator']['mongodb']['user']
password = datanator.config.core.get_config(
)['datanator']['mongodb']['password']
MongoDB = datanator.config.core.get_config(
)['datanator']['mongodb']['server']
port = datanator.config.core.get_config(
)['datanator']['mongodb']['port']
replSet = datanator.config.core.get_config(
)['datanator']['mongodb']['replSet']
cls.src = sabio_rk.SabioRk(cache_dirname=cls.cache_dirname,
MongoDB=MongoDB, db=db,
verbose=True, max_entries=20, username=username,
> password=password, webservice_batch_size = 10)
E TypeError: __init__() got an unexpected keyword argument 'MongoDB'
tests/data_source/test_sabio_rk_nosql.py:29: TypeError |
Standard output | |
Standard error | |
|
|
tests.data_source.test_kegg_orthology.TestKeggO... |
test_load_content |
tests/data_source/test_kegg... |
102 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | hold up a min |
Details | tests/data_source/test_kegg_orthology.py:101: hold up a min |
Standard output | |
Standard error | |
|
|
tests.data_source.test_kegg_reaction_class.Test... |
test_load_content |
tests/data_source/test_kegg... |
114 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | hold up a min |
Details | tests/data_source/test_kegg_reaction_class.py:113: hold up a min |
Standard output | |
Standard error | |
|
|
tests.data_source.test_metabolites_meta_collect... |
test_load_content |
tests/data_source/test_meta... |
39 |
Pass |
0.185 |
Result type | |
Message | |
Details | |
Standard output | Getting fields of interest from 0 document in ecmdb
|
Standard error | |
|
|
tests.data_source.test_pax_nosql.TestCorumNoSQL |
test_load_content |
tests/data_source/test_pax_... |
22 |
Pass |
51.306 |
Result type | |
Message | |
Details | |
Standard output | Processing file_id = 1 (out of 5; 0.0% already done)
/tmp/tmp6oxto_jj/paxdb-abundance-files-v4.1/882/882-WHOLE_ORGANISM-integrated.txt
Processing file_id = 2 (out of 5; 20.0% already done)
/tmp/tmp6oxto_jj/paxdb-abundance-files-v4.1/882/882-Desulfo_Lac_Stat_SC_zhang_2006.txt
Processing file_id = 3 (out of 5; 40.0% already done)
/tmp/tmp6oxto_jj/paxdb-abundance-files-v4.1/882/882-Desulfo_Form_Exp_SC_zhang_2006.txt
Processing file_id = 4 (out of 5; 60.0% already done)
/tmp/tmp6oxto_jj/paxdb-abundance-files-v4.1/882/882-Desulfo_Lac_Exp_SC_zhang_2006.txt
Processing file_id = 5 (out of 5; 80.0% already done)
/tmp/tmp6oxto_jj/paxdb-abundance-files-v4.1/882/882-Desulfo_Form_Stat_SC_zhang_2006.txt
|
Standard error | |
|
|
tests.data_source.test_sabio_rk.TestDownloader |
test_load_content |
tests/data_source/test_sabi... |
827 |
Pass |
26.081 |
Result type | |
Message | |
Details | |
Standard output | Downloading the IDs of the kinetic laws ...
Downloaded 63137 IDs
Downloading 9 kinetic laws ...
Downloading kinetic laws 1-9 of 9 in SBML format
done
Downloading 10 compounds ...
Downloading compound 1 of 10
done
Updating 9 kinetic laws ...
Downloading kinetic laws 1-3 of 9 in Excel format
Downloading kinetic laws 4-6 of 9 in Excel format
Downloading kinetic laws 7-9 of 9 in Excel format
done
Inferring structures for 4 compounds ...
Trying to infer the structure of compound 1 of 4
done
Calculating searchable structures for 11 structures ...
Calculating searchable structure for compound 1 of 11
done
Updating 9 kinetic laws ...
Loading enzyme information for 1 of 9 kinetic laws
done
Calculating 9 enzyme molecular weights ...
Calculating molecular weight of enzyme 1 of 9
done
Normalizing 9 parameter values ...
Normalizing kinetic law 1 of 9
done
Downloading the IDs of the kinetic laws ...
Downloaded 63137 IDs
Downloading 9 kinetic laws ...
Downloading kinetic laws 1-9 of 9 in SBML format
done
Downloading 6 compounds ...
Downloading compound 1 of 6
done
Updating 9 kinetic laws ...
Downloading kinetic laws 1-3 of 9 in Excel format
Downloading kinetic laws 4-6 of 9 in Excel format
Downloading kinetic laws 7-9 of 9 in Excel format
done
Inferring structures for 4 compounds ...
Trying to infer the structure of compound 1 of 4
done
Calculating searchable structures for 5 structures ...
Calculating searchable structure for compound 1 of 5
done
Updating 9 kinetic laws ...
Loading enzyme information for 1 of 9 kinetic laws
done
Calculating 18 enzyme molecular weights ...
Calculating molecular weight of enzyme 1 of 18
done
Normalizing 9 parameter values ...
Normalizing kinetic law 1 of 9
done
|
Standard error | ==============================
*** Open Babel Error in InChI code
InChI generation failed
==============================
*** Open Babel Error in InChI code
InChI generation failed
|
|
|
tests.data_source.test_sabio_rk_nosql.TestSabioRk |
test_load_content |
tests/data_source/test_sabi... |
335 |
Error |
0.001 |
Result type | |
Message | test setup failure |
Details | cls = <class 'tests.data_source.test_sabio_rk_nosql.TestSabioRk'>
@classmethod
def setUpClass(cls):
cls.cache_dirname = tempfile.mkdtemp()
db = 'test'
username = datanator.config.core.get_config()[
'datanator']['mongodb']['user']
password = datanator.config.core.get_config(
)['datanator']['mongodb']['password']
MongoDB = datanator.config.core.get_config(
)['datanator']['mongodb']['server']
port = datanator.config.core.get_config(
)['datanator']['mongodb']['port']
replSet = datanator.config.core.get_config(
)['datanator']['mongodb']['replSet']
cls.src = sabio_rk.SabioRk(cache_dirname=cls.cache_dirname,
MongoDB=MongoDB, db=db,
verbose=True, max_entries=20, username=username,
> password=password, webservice_batch_size = 10)
E TypeError: __init__() got an unexpected keyword argument 'MongoDB'
tests/data_source/test_sabio_rk_nosql.py:29: TypeError |
Standard output | |
Standard error | |
|
|
tests.data_source.test_taxon_tree.TestTaxonTree |
test_load_content |
tests/data_source/test_taxo... |
85 |
Pass |
10.179 |
Result type | |
Message | |
Details | |
Standard output |
Downloading taxdump zip file ...
... Done!
Unzipping ...
... Done unzipping
Parsing lineage line 1 of 10...
Parsing lineage line 2 of 10...
Parsing lineage line 3 of 10...
Parsing lineage line 4 of 10...
Parsing lineage line 5 of 10...
Parsing lineage line 6 of 10...
Parsing lineage line 7 of 10...
Parsing lineage line 8 of 10...
Parsing lineage line 9 of 10...
Parsing lineage line 10 of 10...
Indexing tax_id ...
Parsing nodes line 1 of 10 ...
Parsing nodes line 2 of 10 ...
Parsing nodes line 3 of 10 ...
Parsing nodes line 4 of 10 ...
Parsing nodes line 5 of 10 ...
Parsing nodes line 6 of 10 ...
Parsing nodes line 7 of 10 ...
Parsing nodes line 8 of 10 ...
Parsing nodes line 9 of 10 ...
Parsing nodes line 10 of 10 ...
Indexing division_id and gene_code ...
Parsing division line 1 of 10 ...
Parsing division line 2 of 10 ...
Parsing division line 3 of 10 ...
Parsing division line 4 of 10 ...
Parsing division line 5 of 10 ...
Parsing division line 6 of 10 ...
Parsing division line 7 of 10 ...
Parsing division line 8 of 10 ...
Parsing division line 9 of 10 ...
Parsing division line 10 of 10 ...
Parsing names line 1 of 10 ...
Parsing names line 2 of 10 ...
Parsing names line 3 of 10 ...
Parsing names line 4 of 10 ...
Parsing names line 5 of 10 ...
Parsing names line 6 of 10 ...
Parsing names line 7 of 10 ...
Parsing names line 8 of 10 ...
Parsing names line 9 of 10 ...
Parsing names line 10 of 10 ...
Parsing gencode line 1 of 10 ...
Parsing gencode line 2 of 10 ...
Parsing gencode line 3 of 10 ...
Parsing gencode line 4 of 10 ...
Parsing gencode line 5 of 10 ...
Parsing gencode line 6 of 10 ...
Parsing gencode line 7 of 10 ...
Parsing gencode line 8 of 10 ...
Parsing gencode line 9 of 10 ...
Parsing gencode line 10 of 10 ...
|
Standard error | |
|
|
tests.data_source.test_sabio_rk.TestDownloader |
test_load_content_commit_in... |
tests/data_source/test_sabi... |
840 |
Pass |
15.978 |
Result type | |
Message | |
Details | |
Standard output | Downloading the IDs of the kinetic laws ...
Downloaded 63137 IDs
Downloading 9 kinetic laws ...
Downloading kinetic laws 1-9 of 9 in SBML format
done
Downloading 10 compounds ...
Downloading compound 1 of 10
done
Updating 9 kinetic laws ...
Downloading kinetic laws 1-3 of 9 in Excel format
Downloading kinetic laws 4-6 of 9 in Excel format
Downloading kinetic laws 7-9 of 9 in Excel format
done
Inferring structures for 4 compounds ...
Trying to infer the structure of compound 1 of 4
done
Calculating searchable structures for 11 structures ...
Calculating searchable structure for compound 1 of 11
done
Updating 9 kinetic laws ...
Loading enzyme information for 1 of 9 kinetic laws
done
Calculating 9 enzyme molecular weights ...
Calculating molecular weight of enzyme 1 of 9
done
Normalizing 9 parameter values ...
Normalizing kinetic law 1 of 9
done
|
Standard error | ==============================
*** Open Babel Error in InChI code
InChI generation failed
|
|
|
tests.data_source.rna_halflife.test_doi_10_1186... |
test_load_halflife |
tests/data_source/rna_halfl... |
42 |
Failure |
2.451 |
Result type | |
Message | AttributeError: 'QueryUniprot' object has no attribute 'get_gene_protein_name_by_oln' |
Details | self = <test_doi_10_1186_s12864_016_3219_8.TestProteinAggregate testMethod=test_load_halflife>
def test_load_halflife(self):
df = self.src.download_xlsx('MeOH')
> self.src.load_halflife(df)
tests/data_source/rna_halflife/test_doi_10_1186_s12864_016_3219_8.py:44:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
datanator/data_source/rna_halflife/doi_10_1186_s12864_016_3219_8.py:98: in load_halflife
self.fill_uniprot_by_oln(doc['gene_fragment'])
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <datanator.data_source.rna_halflife.doi_10_1186_s12864_016_3219_8.Halflife object at 0x7f6804851940>
oln = 'MA0002'
def fill_uniprot_by_oln(self, oln):
"""Fill uniprot collection using ordered locus name
Args:
oln (:obj:`str`): Ordered locus name
"""
> gene_name, protein_name = self.uniprot_manager.get_gene_protein_name_by_oln(oln, species=188937)
E AttributeError: 'QueryUniprot' object has no attribute 'get_gene_protein_name_by_oln'
datanator/data_source/rna_halflife/doi_10_1186_s12864_016_3219_8.py:204: AttributeError |
Standard output | Processing MeOH row 0 out of 100
|
Standard error | |
|
|
tests.data_source.test_intact_nosql.TestCorumNoSQL |
test_load_interaction |
tests/data_source/test_inta... |
48 |
Pass |
0.188 |
Result type | |
Message | |
Details | |
Standard output | Inserting 1 of 20 intercation document
|
Standard error | |
|
|
tests.data_source.test_sabio_rk.TestDownloader |
test_load_kinetic_laws_and_... |
tests/data_source/test_sabi... |
51 |
Pass |
0.975 |
Result type | |
Message | |
Details | |
Standard output | Downloading kinetic laws 1-1 of 1 in SBML format
Downloading compound 1 of 3
|
Standard error | |
|
|
tests.data_source.test_sabio_rk.TestDownloader |
test_load_kinetic_laws_chec... |
tests/data_source/test_sabi... |
610 |
Pass |
1.919 |
Result type | |
Message | |
Details | |
Standard output | Downloading kinetic laws 1-1 of 1 in SBML format
Downloading compound 1 of 4
Downloading kinetic laws 1-1 of 1 in Excel format
Normalizing kinetic law 1 of 1
|
Standard error | |
|
|
tests.data_source.test_sabio_rk.TestDownloader |
test_load_kinetic_laws_modi... |
tests/data_source/test_sabi... |
424 |
Pass |
0.658 |
Result type | |
Message | |
Details | |
Standard output | Downloading kinetic laws 1-1 of 1 in SBML format
|
Standard error | |
|
|
tests.data_source.test_sabio_rk.TestDownloader |
test_load_kinetic_laws_mult... |
tests/data_source/test_sabi... |
378 |
Pass |
3.315 |
Result type | |
Message | |
Details | |
Standard output | Downloading kinetic laws 1-2 of 2 in SBML format
Downloading compound 1 of 9
Downloading kinetic laws 1-2 of 2 in Excel format
Normalizing kinetic law 1 of 2
|
Standard error | |
|
|
tests.data_source.test_sabio_rk.TestDownloader |
test_load_kinetic_laws_with... |
tests/data_source/test_sabi... |
454 |
Pass |
0.920 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.data_source.test_sabio_rk.TestDownloader |
test_load_kinetic_laws_with... |
tests/data_source/test_sabi... |
433 |
Pass |
1.270 |
Result type | |
Message | |
Details | |
Standard output | Downloading kinetic laws 1-3 of 3 in SBML format
|
Standard error | |
|
|
tests.data_source.test_sabio_rk.TestDownloader |
test_load_kinetic_law_ids |
tests/data_source/test_sabi... |
44 |
Pass |
6.709 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.data_source.test_sabio_rk_nosql.TestSabioRk |
test_load_kinetic_law_ids |
tests/data_source/test_sabi... |
44 |
Error |
0.001 |
Result type | |
Message | test setup failure |
Details | cls = <class 'tests.data_source.test_sabio_rk_nosql.TestSabioRk'>
@classmethod
def setUpClass(cls):
cls.cache_dirname = tempfile.mkdtemp()
db = 'test'
username = datanator.config.core.get_config()[
'datanator']['mongodb']['user']
password = datanator.config.core.get_config(
)['datanator']['mongodb']['password']
MongoDB = datanator.config.core.get_config(
)['datanator']['mongodb']['server']
port = datanator.config.core.get_config(
)['datanator']['mongodb']['port']
replSet = datanator.config.core.get_config(
)['datanator']['mongodb']['replSet']
cls.src = sabio_rk.SabioRk(cache_dirname=cls.cache_dirname,
MongoDB=MongoDB, db=db,
verbose=True, max_entries=20, username=username,
> password=password, webservice_batch_size = 10)
E TypeError: __init__() got an unexpected keyword argument 'MongoDB'
tests/data_source/test_sabio_rk_nosql.py:29: TypeError |
Standard output | |
Standard error | |
|
|
tests.data_source.test_sabio_rk_nosql.TestSabioRk |
test_load_missing_enzyme_in... |
tests/data_source/test_sabi... |
304 |
Error |
0.001 |
Result type | |
Message | test setup failure |
Details | cls = <class 'tests.data_source.test_sabio_rk_nosql.TestSabioRk'>
@classmethod
def setUpClass(cls):
cls.cache_dirname = tempfile.mkdtemp()
db = 'test'
username = datanator.config.core.get_config()[
'datanator']['mongodb']['user']
password = datanator.config.core.get_config(
)['datanator']['mongodb']['password']
MongoDB = datanator.config.core.get_config(
)['datanator']['mongodb']['server']
port = datanator.config.core.get_config(
)['datanator']['mongodb']['port']
replSet = datanator.config.core.get_config(
)['datanator']['mongodb']['replSet']
cls.src = sabio_rk.SabioRk(cache_dirname=cls.cache_dirname,
MongoDB=MongoDB, db=db,
verbose=True, max_entries=20, username=username,
> password=password, webservice_batch_size = 10)
E TypeError: __init__() got an unexpected keyword argument 'MongoDB'
tests/data_source/test_sabio_rk_nosql.py:29: TypeError |
Standard output | |
Standard error | |
|
|
tests.data_source.test_sabio_rk.TestDownloader |
test_load_missing_kinetic_l... |
tests/data_source/test_sabi... |
667 |
Pass |
2.082 |
Result type | |
Message | |
Details | |
Standard output | Downloading kinetic laws 1-1 of 1 in SBML format
Downloading compound 1 of 4
Downloading kinetic laws 1-1 of 1 in Excel format
|
Standard error | |
|
|
tests.data_source.test_sabio_rk.TestDownloader |
test_load_missing_kinetic_l... |
tests/data_source/test_sabi... |
685 |
Pass |
1.572 |
Result type | |
Message | |
Details | |
Standard output | Downloading kinetic laws 1-1 of 1 in SBML format
Downloading compound 1 of 2
Downloading kinetic laws 1-1 of 1 in Excel format
|
Standard error | |
|
|
tests.data_source.test_sabio_rk_nosql.TestSabioRk |
test_load_missing_kinetic_l... |
tests/data_source/test_sabi... |
173 |
Error |
0.001 |
Result type | |
Message | test setup failure |
Details | cls = <class 'tests.data_source.test_sabio_rk_nosql.TestSabioRk'>
@classmethod
def setUpClass(cls):
cls.cache_dirname = tempfile.mkdtemp()
db = 'test'
username = datanator.config.core.get_config()[
'datanator']['mongodb']['user']
password = datanator.config.core.get_config(
)['datanator']['mongodb']['password']
MongoDB = datanator.config.core.get_config(
)['datanator']['mongodb']['server']
port = datanator.config.core.get_config(
)['datanator']['mongodb']['port']
replSet = datanator.config.core.get_config(
)['datanator']['mongodb']['replSet']
cls.src = sabio_rk.SabioRk(cache_dirname=cls.cache_dirname,
MongoDB=MongoDB, db=db,
verbose=True, max_entries=20, username=username,
> password=password, webservice_batch_size = 10)
E TypeError: __init__() got an unexpected keyword argument 'MongoDB'
tests/data_source/test_sabio_rk_nosql.py:29: TypeError |
Standard output | |
Standard error | |
|
|
tests.data_source.test_corum_nosql.TestCorumNoSQL |
test_load_some_content |
tests/data_source/test_coru... |
35 |
Pass |
1.175 |
Result type | |
Message | |
Details | |
Standard output | Download list of all compounds: ...
... Done!
Unzipping and parsing compound list ...
|
Standard error | |
|
|
tests.util.test_rna_halflife_util.TestRnaHlUtil |
test_make_df |
tests/util/test_rna_halflif... |
34 |
Pass |
0.678 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.util.test_file_util.TestFileUtil |
test_make_dict |
tests/util/test_file_util.py |
97 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.util.test_calc_tanimoto.TestCalcTanimoto |
test_many_to_many |
tests/util/test_calc_tanimo... |
52 |
Pass |
1.441 |
Result type | |
Message | |
Details | |
Standard output | Going through document 0 out of 20 in collection metabolites_meta
InChI=1S/C10H12N5O6P/c11-8-5-9(13-2-12-8)15(3-14-5)10-6(16)7-4(20-10)1-19-22(17,18)21-7/h2-4,6-7,10,16H,1H2,(H,17,18)(H2,11,12,13)/t4-,6-,7-,10-/m1/s1
Calculating between given and doc 10 out of 20 in collection metabolites_meta
Going through document 1 out of 20 in collection metabolites_meta
InChI=1S/C10H13N5O4/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(18)6(17)4(1-16)19-10/h2-4,6-7,10,16-18H,1H2,(H2,11,12,13)/t4-,6-,7-,10-/m1/s1
Calculating between given and doc 10 out of 20 in collection metabolites_meta
Going through document 2 out of 20 in collection metabolites_meta
InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Calculating between given and doc 10 out of 20 in collection metabolites_meta
Going through document 3 out of 20 in collection metabolites_meta
InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-6(16)7(25-27(20,21)22)4(24-10)1-23-26(17,18)19/h2-4,6-7,10,16H,1H2,(H2,11,12,13)(H2,17,18,19)(H2,20,21,22)/t4-,6-,7-,10-/m1/s1
Calculating between given and doc 10 out of 20 in collection metabolites_meta
Going through document 4 out of 20 in collection metabolites_meta
InChI=1S/C10H16N2O3S/c13-8(14)4-2-1-3-7-9-6(5-16-7)11-10(15)12-9/h6-7,9H,1-5H2,(H,13,14)(H2,11,12,15)/t6-,7-,9-/m0/s1
Calculating between given and doc 10 out of 20 in collection metabolites_meta
Going through document 5 out of 20 in collection metabolites_meta
InChI=1S/C12H22O11/c13-1-3-5(14)8(17)10(19)12(23-3)21-2-4-6(15)7(16)9(18)11(20)22-4/h3-20H,1-2H2/t3-,4-,5+,6-,7+,8+,9-,10-,11?,12+/m1/s1
Calculating between given and doc 10 out of 20 in collection metabolites_meta
Going through document 6 out of 20 in collection metabolites_meta
InChI=1S/C12H22O11/c13-1-3-5(15)6(16)9(19)12(22-3)23-10-4(2-14)21-11(20)8(18)7(10)17/h3-20H,1-2H2/t3-,4-,5-,6+,7-,8-,9-,10-,11-,12+/m1/s1
Calculating between given and doc 10 out of 20 in collection metabolites_meta
Going through document 7 out of 20 in collection metabolites_meta
InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)
Calculating between given and doc 10 out of 20 in collection metabolites_meta
Going through document 8 out of 20 in collection metabolites_meta
InChI=1S/C3H7NO2/c4-2-1-3(5)6/h1-2,4H2,(H,5,6)
Calculating between given and doc 10 out of 20 in collection metabolites_meta
Going through document 9 out of 20 in collection metabolites_meta
InChI=1S/C4H6O3/c1-2-3(5)4(6)7/h2H2,1H3,(H,6,7)
Calculating between given and doc 10 out of 20 in collection metabolites_meta
Going through document 10 out of 20 in collection metabolites_meta
InChI=1S/C4H6O3/c1-3(5)2-4(6)7/h2H2,1H3,(H,6,7)
Calculating between given and doc 10 out of 20 in collection metabolites_meta
Going through document 11 out of 20 in collection metabolites_meta
InChI=1S/C4H8N2O3/c5-4(9)6-2-1-3(7)8/h1-2H2,(H,7,8)(H3,5,6,9)
Calculating between given and doc 10 out of 20 in collection metabolites_meta
Going through document 12 out of 20 in collection metabolites_meta
InChI=1S/C4H8O2/c1-2-3-4(5)6/h2-3H2,1H3,(H,5,6)
Calculating between given and doc 10 out of 20 in collection metabolites_meta
Going through document 13 out of 20 in collection metabolites_meta
InChI=1S/C4H8O3/c1-3(2-5)4(6)7/h3,5H,2H2,1H3,(H,6,7)
Calculating between given and doc 10 out of 20 in collection metabolites_meta
Going through document 14 out of 20 in collection metabolites_meta
InChI=1S/C5H5N5/c6-4-3-5(9-1-7-3)10-2-8-4/h1-2H,(H3,6,7,8,9,10)
Calculating between given and doc 10 out of 20 in collection metabolites_meta
Going through document 15 out of 20 in collection metabolites_meta
InChI=1S/C5H8O3/c1-3(2)4(6)5(7)8/h3H,1-2H3,(H,7,8)
Calculating between given and doc 10 out of 20 in collection metabolites_meta
Going through document 16 out of 20 in collection metabolites_meta
InChI=1S/C6H8O6/c7-1-2(8)5-3(9)4(10)6(11)12-5/h2,5,7-10H,1H2/t2-,5+/m0/s1
Calculating between given and doc 10 out of 20 in collection metabolites_meta
Going through document 17 out of 20 in collection metabolites_meta
InChI=1S/C9H12N2O5/c12-4-6-5(13)3-8(16-6)11-2-1-7(14)10-9(11)15/h1-2,5-6,8,12-13H,3-4H2,(H,10,14,15)/t5-,6+,8+/m0/s1
Calculating between given and doc 10 out of 20 in collection metabolites_meta
Going through document 18 out of 20 in collection metabolites_meta
InChI=1S/C9H13N3O4/c10-7-1-2-12(9(15)11-7)8-3-5(14)6(4-13)16-8/h1-2,5-6,8,13-14H,3-4H2,(H2,10,11,15)/t5-,6+,8+/m0/s1
Calculating between given and doc 10 out of 20 in collection metabolites_meta
Going through document 19 out of 20 in collection metabolites_meta
InChI=1S/H3N/h1H3
Calculating between given and doc 10 out of 20 in collection metabolites_meta
|
Standard error | |
|
|
tests.util.test_file_util.TestFileUtil |
test_merge_dict |
tests/util/test_file_util.py |
119 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.test_main_cli.DbControllerTestCase |
test_migrate |
tests/test_main_cli.py |
353 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | CLI not working |
Details | tests/test_main_cli.py:352: CLI not working |
Standard output | |
Standard error | |
|
|
tests.test_main_cli.TestWithoutTempFile |
test_molecule_convert_struc... |
tests/test_main_cli.py |
262 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | CLI not working |
Details | tests/test_main_cli.py:261: CLI not working |
Standard output | |
Standard error | |
|
|
tests.test_main_cli.TestWithoutTempFile |
test_molecule_get_structure |
tests/test_main_cli.py |
240 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | CLI not working |
Details | tests/test_main_cli.py:239: CLI not working |
Standard output | |
Standard error | |
|
|
tests.util.test_chem_util.TestChemUtil |
test_morphineInChIKey |
tests/util/test_chem_util.py |
30 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.core.test_data_model.TestReaction |
test_name |
tests/core/test_data_model.py |
199 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.core.test_data_model.TestReaction |
test_normalize |
tests/core/test_data_model.py |
203 |
Pass |
0.002 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.data_source.test_sabio_rk.TestDownloader |
test_normalize_parameter_value |
tests/data_source/test_sabi... |
703 |
Pass |
0.035 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.core.test_data_model.TestObservedResultMe... |
test_ObservedResultMetadata |
tests/core/test_data_model.py |
56 |
Pass |
0.002 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.util.test_calc_tanimoto.TestCalcTanimoto |
test_one_to_many |
tests/util/test_calc_tanimo... |
39 |
Pass |
0.087 |
Result type | |
Message | |
Details | |
Standard output | Calculating between given and doc 10 out of 20 in collection metabolites_meta
10
|
Standard error | |
|
|
tests.data_source.test_sabio_rk.TestDownloader |
test_parse_complex_subunit_... |
tests/data_source/test_sabi... |
472 |
Pass |
0.039 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.data_source.test_sabio_rk_nosql.TestSabioRk |
test_parse_complex_subunit_... |
tests/data_source/test_sabi... |
292 |
Error |
0.001 |
Result type | |
Message | test setup failure |
Details | cls = <class 'tests.data_source.test_sabio_rk_nosql.TestSabioRk'>
@classmethod
def setUpClass(cls):
cls.cache_dirname = tempfile.mkdtemp()
db = 'test'
username = datanator.config.core.get_config()[
'datanator']['mongodb']['user']
password = datanator.config.core.get_config(
)['datanator']['mongodb']['password']
MongoDB = datanator.config.core.get_config(
)['datanator']['mongodb']['server']
port = datanator.config.core.get_config(
)['datanator']['mongodb']['port']
replSet = datanator.config.core.get_config(
)['datanator']['mongodb']['replSet']
cls.src = sabio_rk.SabioRk(cache_dirname=cls.cache_dirname,
MongoDB=MongoDB, db=db,
verbose=True, max_entries=20, username=username,
> password=password, webservice_batch_size = 10)
E TypeError: __init__() got an unexpected keyword argument 'MongoDB'
tests/data_source/test_sabio_rk_nosql.py:29: TypeError |
Standard output | |
Standard error | |
|
|
tests.data_source.test_kegg_orthology.TestKeggO... |
test_parse_definition |
tests/data_source/test_kegg... |
111 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.data_source.test_taxon_tree.TestTaxonTree |
test_parse_division |
tests/data_source/test_taxo... |
74 |
Pass |
0.012 |
Result type | |
Message | |
Details | |
Standard output | Parsing division line 1 of 10 ...
Parsing division line 2 of 10 ...
Parsing division line 3 of 10 ...
Parsing division line 4 of 10 ...
Parsing division line 5 of 10 ...
Parsing division line 6 of 10 ...
Parsing division line 7 of 10 ...
Parsing division line 8 of 10 ...
Parsing division line 9 of 10 ...
Parsing division line 10 of 10 ...
|
Standard error | |
|
|
tests.data_source.test_sabio_rk_nosql.TestSabioRk |
test_parse_enzyme_name |
tests/data_source/test_sabi... |
58 |
Error |
0.001 |
Result type | |
Message | test setup failure |
Details | cls = <class 'tests.data_source.test_sabio_rk_nosql.TestSabioRk'>
@classmethod
def setUpClass(cls):
cls.cache_dirname = tempfile.mkdtemp()
db = 'test'
username = datanator.config.core.get_config()[
'datanator']['mongodb']['user']
password = datanator.config.core.get_config(
)['datanator']['mongodb']['password']
MongoDB = datanator.config.core.get_config(
)['datanator']['mongodb']['server']
port = datanator.config.core.get_config(
)['datanator']['mongodb']['port']
replSet = datanator.config.core.get_config(
)['datanator']['mongodb']['replSet']
cls.src = sabio_rk.SabioRk(cache_dirname=cls.cache_dirname,
MongoDB=MongoDB, db=db,
verbose=True, max_entries=20, username=username,
> password=password, webservice_batch_size = 10)
E TypeError: __init__() got an unexpected keyword argument 'MongoDB'
tests/data_source/test_sabio_rk_nosql.py:29: TypeError |
Standard output | |
Standard error | |
|
|
tests.data_source.test_taxon_tree.TestTaxonTree |
test_parse_fullname_line |
tests/data_source/test_taxo... |
40 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.data_source.test_taxon_tree.TestTaxonTree |
test_parse_fullname_taxid |
tests/data_source/test_taxo... |
61 |
Pass |
1.151 |
Result type | |
Message | |
Details | |
Standard output | Parsing lineage line 1 of 10...
Parsing lineage line 2 of 10...
Parsing lineage line 3 of 10...
Parsing lineage line 4 of 10...
Parsing lineage line 5 of 10...
Parsing lineage line 6 of 10...
Parsing lineage line 7 of 10...
Parsing lineage line 8 of 10...
Parsing lineage line 9 of 10...
Parsing lineage line 10 of 10...
|
Standard error | |
|
|
tests.data_source.test_taxon_tree.TestTaxonTree |
test_parse_gencode |
tests/data_source/test_taxo... |
82 |
Pass |
0.011 |
Result type | |
Message | |
Details | |
Standard output | Parsing gencode line 1 of 10 ...
Parsing gencode line 2 of 10 ...
Parsing gencode line 3 of 10 ...
Parsing gencode line 4 of 10 ...
Parsing gencode line 5 of 10 ...
Parsing gencode line 6 of 10 ...
Parsing gencode line 7 of 10 ...
Parsing gencode line 8 of 10 ...
Parsing gencode line 9 of 10 ...
Parsing gencode line 10 of 10 ...
|
Standard error | |
|
|
tests.data_source.test_kegg_orthology.TestKeggO... |
test_parse_ko_txt |
tests/data_source/test_kegg... |
85 |
Pass |
1.930 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.data_source.test_corum_nosql.TestCorumNoSQL |
test_parse_list |
tests/data_source/test_coru... |
60 |
Pass |
0.014 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.data_source.test_taxon_tree.TestTaxonTree |
test_parse_names |
tests/data_source/test_taxo... |
78 |
Pass |
1.140 |
Result type | |
Message | |
Details | |
Standard output | Parsing names line 1 of 10 ...
Parsing names line 2 of 10 ...
Parsing names line 3 of 10 ...
Parsing names line 4 of 10 ...
Parsing names line 5 of 10 ...
Parsing names line 6 of 10 ...
Parsing names line 7 of 10 ...
Parsing names line 8 of 10 ...
Parsing names line 9 of 10 ...
Parsing names line 10 of 10 ...
|
Standard error | |
|
|
tests.data_source.test_taxon_tree.TestTaxonTree |
test_parse_nodes |
tests/data_source/test_taxo... |
67 |
Pass |
0.853 |
Result type | |
Message | |
Details | |
Standard output | Parsing nodes line 1 of 10 ...
Parsing nodes line 2 of 10 ...
Parsing nodes line 3 of 10 ...
Parsing nodes line 4 of 10 ...
Parsing nodes line 5 of 10 ...
Parsing nodes line 6 of 10 ...
Parsing nodes line 7 of 10 ...
Parsing nodes line 8 of 10 ...
Parsing nodes line 9 of 10 ...
Parsing nodes line 10 of 10 ...
|
Standard error | |
|
|
tests.data_source.test_kegg_reaction_class.Test... |
test_parse_rc_multiline |
tests/data_source/test_kegg... |
93 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.data_source.test_kegg_reaction_class.Test... |
test_parse_rc_orthology |
tests/data_source/test_kegg... |
102 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.data_source.test_kegg_reaction_class.Test... |
test_parse_root_json |
tests/data_source/test_kegg... |
87 |
Pass |
4.128 |
Result type | |
Message | |
Details | |
Standard output |
Downloading root kegg reactions file ...
|
Standard error | |
|
|
tests.data_source.test_taxon_tree.TestTaxonTree |
test_parse_taxid_line |
tests/data_source/test_taxo... |
55 |
Pass |
0.172 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.util.test_mongo_util.TestMongoUtil |
test_print_schema |
tests/util/test_mongo_util.py |
48 |
Pass |
0.006 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.data_source.test_uniprot_nosql.TestUnipro... |
test_proper_loading |
tests/data_source/test_unip... |
25 |
Pass |
0.572 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.data_source.test_sqlite_to_json.TestSQLTo... |
test_query_table |
tests/data_source/test_sqli... |
33 |
Error |
0.001 |
Result type | |
Message | test setup failure |
Details | cls = <class 'tests.data_source.test_sqlite_to_json.TestSQLToJSON'>
@classmethod
def setUpClass(cls):
cls.cache_dirname = tempfile.mkdtemp()
cls.query = "select * from "
cls.quilt_package = 'datanator'
cls.system_path = 'SabioRk.sqlite'
cls.src = sqlite_to_json.SQLToJSON(
> cls.query, cls.cache_dirname, cls.quilt_package, cls.system_path)
E TypeError: __init__() takes from 2 to 3 positional arguments but 5 were given
tests/data_source/test_sqlite_to_json.py:20: TypeError |
Standard output | |
Standard error | |
|
|
tests.util.test_molecule_util.TestInchiMolecule |
test_remove_layer |
tests/util/test_molecule_ut... |
132 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.util.test_file_util.TestFileUtil |
test_replace_dict_key |
tests/util/test_file_util.py |
62 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.data_source.test_metabolites_meta_collect... |
test_replace_key_in_similar... |
tests/data_source/test_meta... |
51 |
Pass |
0.294 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.util.test_file_util.TestFileUtil |
test_replace_list_dict_key |
tests/util/test_file_util.py |
68 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.test_main_cli.DbControllerTestCase |
test_restore |
tests/test_main_cli.py |
371 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | CLI not working |
Details | tests/test_main_cli.py:370: CLI not working |
Standard output | |
Standard error | |
|
|
tests.util.test_file_util.TestFileUtil |
test_search_dict_list |
tests/util/test_file_util.py |
104 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.util.test_taxonomy_util.TestTaxonomyUtil |
test_setup_database |
tests/util/test_taxonomy_ut... |
16 |
Pass |
0.527 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.util.test_chem_util.TestChemUtil |
test_simplify_inchi |
tests/util/test_chem_util.py |
18 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.data_source.test_sqlite_to_json.TestSQLTo... |
test_table |
tests/data_source/test_sqli... |
27 |
Error |
0.001 |
Result type | |
Message | test setup failure |
Details | cls = <class 'tests.data_source.test_sqlite_to_json.TestSQLToJSON'>
@classmethod
def setUpClass(cls):
cls.cache_dirname = tempfile.mkdtemp()
cls.query = "select * from "
cls.quilt_package = 'datanator'
cls.system_path = 'SabioRk.sqlite'
cls.src = sqlite_to_json.SQLToJSON(
> cls.query, cls.cache_dirname, cls.quilt_package, cls.system_path)
E TypeError: __init__() takes from 2 to 3 positional arguments but 5 were given
tests/data_source/test_sqlite_to_json.py:20: TypeError |
Standard output | |
Standard error | |
|
|
tests.test_main_cli.TestWithoutTempFile |
test_taxonomy_get_common_an... |
tests/test_main_cli.py |
212 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | CLI not working |
Details | tests/test_main_cli.py:211: CLI not working |
Standard output | |
Standard error | |
|
|
tests.test_main_cli.TestWithoutTempFile |
test_taxonomy_get_distance_... |
tests/test_main_cli.py |
222 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | CLI not working |
Details | tests/test_main_cli.py:221: CLI not working |
Standard output | |
Standard error | |
|
|
tests.test_main_cli.TestWithoutTempFile |
test_taxonomy_get_distance_... |
tests/test_main_cli.py |
231 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | CLI not working |
Details | tests/test_main_cli.py:230: CLI not working |
Standard output | |
Standard error | |
|
|
tests.test_main_cli.TestWithoutTempFile |
test_taxonomy_get_parents |
tests/test_main_cli.py |
203 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | CLI not working |
Details | tests/test_main_cli.py:202: CLI not working |
Standard output | |
Standard error | |
|
|
tests.test_main_cli.TestWithoutTempFile |
test_taxonomy_get_rank |
tests/test_main_cli.py |
189 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | CLI not working |
Details | tests/test_main_cli.py:188: CLI not working |
Standard output | |
Standard error | |
|
|
tests.util.test_taxonomy_util.TestTaxonomyUtil |
test_Taxon_get_common_ancestor |
tests/util/test_taxonomy_ut... |
104 |
Pass |
0.056 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.util.test_taxonomy_util.TestTaxonomyUtil |
test_Taxon_get_ncbi_id |
tests/util/test_taxonomy_ut... |
77 |
Pass |
0.002 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.util.test_taxonomy_util.TestTaxonomyUtil |
test_Taxon_get_parent_taxa |
tests/util/test_taxonomy_ut... |
84 |
Pass |
0.013 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.util.test_taxonomy_util.TestTaxonomyUtil |
test_Taxon_get_rank |
tests/util/test_taxonomy_ut... |
99 |
Pass |
0.003 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.util.test_taxonomy_util.TestTaxonomyUtil |
test_Taxon_init_from_id |
tests/util/test_taxonomy_ut... |
56 |
Pass |
0.004 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.util.test_taxonomy_util.TestTaxonomyUtil |
test_Taxon_init_from_name |
tests/util/test_taxonomy_ut... |
19 |
Pass |
0.003 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.core.test_data_model.TestSpecie |
test_to_inchi |
tests/core/test_data_model.py |
116 |
Pass |
0.005 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.core.test_data_model.TestSpecie |
test_to_mol |
tests/core/test_data_model.py |
121 |
Pass |
0.004 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.core.test_data_model.TestSpecie |
test_to_openbabel |
tests/core/test_data_model.py |
126 |
Pass |
0.002 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.core.test_data_model.TestSpecie |
test_to_pybel |
tests/core/test_data_model.py |
130 |
Pass |
0.002 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.core.test_data_model.TestSpecie |
test_to_smiles |
tests/core/test_data_model.py |
134 |
Pass |
0.002 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.util.test_file_util.TestFileUtil |
test_unpack_list |
tests/util/test_file_util.py |
50 |
Pass |
0.001 |
Result type | |
Message | |
Details | |
Standard output | |
Standard error | |
|
|
tests.data_source.test_sabio_rk.TestAll |
test_update_all_and_backup |
tests/data_source/test_sabi... |
871 |
Skipped |
0.001 |
Result type | pytest.skip |
Message | Skip this test because it is long |
Details | tests/data_source/test_sabio_rk.py:870: Skip this test because it is long |
Standard output | |
Standard error | |
|
|
tests.data_source.test_metabolite_nosql.TestMet... |
test_write_to_json |
tests/data_source/test_meta... |
42 |
Skipped |
0.013 |
Result type | pytest.skip |
Message | ecmdb.ca and ymdb.ca xml server http 500 error |
Details | tests/data_source/test_metabolite_nosql.py:41: ecmdb.ca and ymdb.ca xml server http 500 error |
Standard output | |
Standard error | |
|