tests/test_main_cli.py:299: CLI not working

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

tests/test_main_cli.py:54: CLI not working

tests/test_main_cli.py:79: CLI not working

tests/test_main_cli.py:60: CLI not working

tests/test_main_cli.py:73: CLI not working

tests/test_main_cli.py:85: CLI not working

tests/test_main_cli.py:66: CLI not working

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

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

tests/test_main_cli.py:338: CLI not working

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

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

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

tests/test_main_cli.py:344: CLI not working

tests/util/test_warning_util.py:29: todo: implement

tests/test_main_cli.py:139: skip because too long

tests/test_main_cli.py:103: skip because too long

 Downloading taxdump zip file ...
 ... Done!
Unzipping ...
... Done unzipping

tests/test_main_cli.py:127: skip because too long

tests/data_source/test_sabio_rk.py:878: Skip this test because it is long

tests/test_main_cli.py:109: skip because too long

tests/test_main_cli.py:121: skip because too long

tests/test_main_cli.py:133: skip because too long

tests/test_main_cli.py:115: skip because too long

tests/test_main_cli.py:145: skip because too long

tests/test_main_cli.py:361: CLI not working

==============================
*** Open Babel Warning  in InChI code
  #0 :Proton(s) added/removed; Omitted undefined stereo

  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

Processing document 2900 out of 60193

tests/util/test_mongo_util.py:39: passed

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

Processing locus 0 out 3

tests/data_source/rna_halflife/test_doi_10_1093_nar_gks1019.py:35: avoid downloading

tests/util/test_rna_halflife_util.py:29: avoid r/w db

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

  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

tests/test_main_cli.py:179: CLI not working

tests/test_main_cli.py:161: CLI not working

tests/test_main_cli.py:267: CLI not working

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

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

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

tests/test_main_cli.py:28: CLI not working

tests/util/test_index_collection.py:27: passed

tests/util/test_index_collection.py:35: passed

tests/util/test_index_collection.py:43: passed

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

tests/data_source/test_sabio_rk.py:529: takes too long

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

tests/data_source/test_corum_nosql.py:44: will not work on circle ci due to file directory setting

  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

Inserting 1 of 20 complex document

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

tests/data_source/test_kegg_orthology.py:101: hold up a min

tests/data_source/test_kegg_reaction_class.py:113: hold up a min

Getting fields of interest from 0 document in ecmdb

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

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

==============================
*** Open Babel Error  in InChI code
  InChI generation failed
==============================
*** Open Babel Error  in InChI code
  InChI generation failed

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

 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 ...

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

==============================
*** Open Babel Error  in InChI code
  InChI generation failed

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

Processing MeOH row 0 out of 100

Inserting 1 of 20 intercation document

  Downloading kinetic laws 1-1 of 1 in SBML format
  Downloading compound 1 of 3

  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

  Downloading kinetic laws 1-1 of 1 in SBML format

  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

  Downloading kinetic laws 1-3 of 3 in SBML format

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

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

  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

  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

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

Download list of all compounds: ...
... Done!
Unzipping and parsing compound list ...

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

tests/test_main_cli.py:352: CLI not working

tests/test_main_cli.py:261: CLI not working

tests/test_main_cli.py:239: CLI not working

     Calculating between given and doc 10 out of 20 in collection metabolites_meta
10

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

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 ...

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

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...

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 ...

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 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 ...

 Downloading root kegg reactions file ...

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

tests/test_main_cli.py:370: CLI not working

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

tests/test_main_cli.py:211: CLI not working

tests/test_main_cli.py:221: CLI not working

tests/test_main_cli.py:230: CLI not working

tests/test_main_cli.py:202: CLI not working

tests/test_main_cli.py:188: CLI not working

tests/data_source/test_sabio_rk.py:870: Skip this test because it is long

tests/data_source/test_metabolite_nosql.py:41: ecmdb.ca and ymdb.ca xml server http 500 error