Exemplo n.º 1
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def tearDownModule():
    # remove index created
    global INI_CONFIG
    os.remove(MY_INI_FILE)
    # requests.delete(ElasticSettings.url() + '/' + INI_CONFIG['DEFAULT']['CRITERIA_IDX_STUDY'])

    PydginTestSettings.tearDownIdx(['DISEASE', 'STUDY_CRITERIA_STUDY_FOR_DISEASE'])
Exemplo n.º 2
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def tearDownModule():
    ''' Remove test indices '''
    PydginTestSettings.tearDownIdx(['STUDY', 'DISEASE', 'GENE', 'STUDY_HITS', 'PUBLICATION',
                                    'REGION', 'REGION_CRITERIA_IS_REGION_IN_MHC',
                                    'REGION_CRITERIA_IS_REGION_FOR_DISEASE',
                                    'GENE_CRITERIA_GENE_IN_REGION',
                                    'MARKER', 'MARKER_CRITERIA_IS_MARKER_IN_MHC',
                                    'STUDY_CRITERIA_STUDY_FOR_DISEASE'])
Exemplo n.º 3
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def tearDownModule():
    # remove index created
    global INI_CONFIG
    os.remove(MY_INI_FILE)
    # requests.delete(ElasticSettings.url() + '/' + INI_CONFIG['DEFAULT']['CRITERIA_IDX_GENE'])

    PydginTestSettings.tearDownIdx(['DISEASE', 'GENE_CRITERIA_IS_GENE_IN_MHC', 'GENE_CRITERIA_CAND_GENE_IN_STUDY',
                                    'GENE_CRITERIA_GENE_IN_REGION', 'GENE_CRITERIA_CAND_GENE_IN_REGION'])
Exemplo n.º 4
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def setUpModule():
    ''' Load test indices (study) '''
    PydginTestSettings.setupIdx(['STUDY', 'DISEASE', 'GENE', 'STUDY_HITS', 'PUBLICATION',
                                 'REGION', 'REGION_CRITERIA_IS_REGION_IN_MHC',
                                 'REGION_CRITERIA_IS_REGION_FOR_DISEASE',
                                 'GENE_CRITERIA_GENE_IN_REGION',
                                 'MARKER', 'MARKER_CRITERIA_IS_MARKER_IN_MHC',
                                 'STUDY_CRITERIA_STUDY_FOR_DISEASE'])
Exemplo n.º 5
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def tearDownModule():
    # remove index created
    global INI_CONFIG
    os.remove(MY_INI_FILE)
    # requests.delete(ElasticSettings.url() + '/' + INI_CONFIG['DEFAULT']['CRITERIA_IDX_MARKER'])

    PydginTestSettings.tearDownIdx(['MARKER', 'DISEASE',
                                    'MARKER_CRITERIA_IS_MARKER_IN_MHC', 'MARKER_CRITERIA_IS_AN_INDEX_SNP',
                                    'MARKER_CRITERIA_MARKER_IS_GWAS_SIGNIFICANT_STUDY',
                                    'MARKER_CRITERIA_RSQ_WITH_INDEX_SNP'])
Exemplo n.º 6
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def setUpModule():
    ''' Change ini config (MY_INI_FILE) to use the test suffix when
    creating pipeline indices. '''
    global INI_CONFIG
    ini_file = os.path.join(os.path.dirname(__file__), 'test_criteria.ini')

    if os.path.isfile(MY_INI_FILE):
        INI_CONFIG = IniParser().read_ini(MY_INI_FILE)
        return

    with open(MY_INI_FILE, 'w') as new_file:
        with open(ini_file) as old_file:
            for line in old_file:
                new_file.write(line.replace('auto_tests', IDX_SUFFIX))

    INI_CONFIG = IniParser().read_ini(MY_INI_FILE)

    PydginTestSettings.setupIdx(['DISEASE', 'STUDY_CRITERIA_STUDY_FOR_DISEASE'])
Exemplo n.º 7
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def tearDownModule():
    """ Remove test indices """
    PydginTestSettings.tearDownIdx(["GENE", "STUDY_HITS", "PUBLICATION", "DISEASE", "MARKER"])
Exemplo n.º 8
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def setUpModule():
    """ create elastic indices for querying """
    PydginTestSettings.setupIdx(["GENE", "STUDY_HITS", "PUBLICATION", "DISEASE", "MARKER"])
Exemplo n.º 9
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 def tearDown(cls):
     PydginTestSettings.tearDownIdx(['STUDY_HITS', 'DISEASE_LOCUS', 'REGION'])
Exemplo n.º 10
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 def setUp(cls):
     idx = ElasticSettings.idx(RegionTest.IDX_KEY, 'STUDY_HITS')
     (RegionTest.idx, RegionTest.idx_type) = idx.split('/')
     PydginTestSettings.setupIdx(['STUDY_HITS', 'DISEASE_LOCUS', 'REGION'])
Exemplo n.º 11
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def tearDownModule():
    ''' Remove test indices '''
    PydginTestSettings.tearDownIdx(['GENE', 'MARKER', 'STUDY_HITS', 'DISEASE_LOCUS', 'REGION', 'DISEASE', 'IC_STATS'])
Exemplo n.º 12
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def setUpModule():
    ''' create elastic indices for querying '''
    PydginTestSettings.setupIdx(['GENE', 'MARKER', 'STUDY_HITS', 'DISEASE_LOCUS', 'REGION', 'DISEASE', 'IC_STATS'])
Exemplo n.º 13
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def setUpModule():
    ''' create elastic indices for querying '''
    PydginTestSettings.setupIdx(['GENE_INTERACTIONS', 'GENE', 'GENE_PATHWAY', 'DISEASE', 'PUBLICATION',
                                 'GENE_CRITERIA_IS_GENE_IN_MHC', 'GENE_CRITERIA_CAND_GENE_IN_STUDY',
                                 'GENE_CRITERIA_GENE_IN_REGION', 'GENE_CRITERIA_CAND_GENE_IN_REGION'])
Exemplo n.º 14
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 def tearDown(cls):
     PydginTestSettings.tearDownIdx(['DISEASE'])
Exemplo n.º 15
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def setUpModule():
    ''' Load test indices (marker) '''
    PydginTestSettings.setupIdx(['MARKER', 'MARKER_IC', 'DISEASE',
                                 'MARKER_CRITERIA_IS_MARKER_IN_MHC', 'MARKER_CRITERIA_IS_AN_INDEX_SNP',
                                 'MARKER_CRITERIA_MARKER_IS_GWAS_SIGNIFICANT_STUDY',
                                 'MARKER_CRITERIA_RSQ_WITH_INDEX_SNP'])
Exemplo n.º 16
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def tearDownModule():
    ''' Remove test indices '''
    PydginTestSettings.tearDownIdx(['GENE', 'DISEASE', 'PUBLICATION',
                                    'GENE_CRITERIA_IS_GENE_IN_MHC', 'GENE_CRITERIA_CAND_GENE_IN_STUDY',
                                    'GENE_CRITERIA_GENE_IN_REGION', 'GENE_CRITERIA_CAND_GENE_IN_REGION'])
Exemplo n.º 17
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def tearDownModule():
    ''' Remove test indices '''
    PydginTestSettings.tearDownIdx(['GENE', 'STUDY_HITS', 'PUBLICATION', 'DISEASE', 'MARKER', 'STUDY'])
Exemplo n.º 18
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def setUpModule():
    ''' create elastic indices for querying '''
    PydginTestSettings.setupIdx(['GENE', 'STUDY_HITS', 'PUBLICATION', 'DISEASE', 'MARKER', 'STUDY'])
Exemplo n.º 19
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def setUpModule():
    ''' Load test indices (region) '''
    PydginTestSettings.setupIdx(['REGION', 'STUDY_HITS', 'DISEASE',
                                 'REGION_CRITERIA_IS_REGION_IN_MHC', 'REGION_CRITERIA_IS_REGION_FOR_DISEASE'])
Exemplo n.º 20
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def tearDownModule():
    ''' Remove test indices '''
    PydginTestSettings.tearDownIdx(['GENE', 'DISEASE', 'PUBLICATION'])
Exemplo n.º 21
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def tearDownModule():
    ''' Remove test indices '''
    PydginTestSettings.tearDownIdx(['REGION', 'DISEASE',
                                    'REGION_CRITERIA_IS_REGION_IN_MHC', 'REGION_CRITERIA_IS_REGION_FOR_DISEASE'])
Exemplo n.º 22
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def tearDownModule():
    ''' Remove test indices '''
    PydginTestSettings.tearDownIdx(['MARKER', 'DISEASE',
                                    'MARKER_CRITERIA_IS_MARKER_IN_MHC', 'MARKER_CRITERIA_IS_AN_INDEX_SNP',
                                    'MARKER_CRITERIA_MARKER_IS_GWAS_SIGNIFICANT_STUDY',
                                    'MARKER_CRITERIA_RSQ_WITH_INDEX_SNP'])
Exemplo n.º 23
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 def setUp(cls):
     DiseaseTest.idx = ElasticSettings.idx('DISEASE')
     PydginTestSettings.setupIdx(['DISEASE'])