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'])
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'])
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'])
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'])
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'])
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'])
def tearDownModule(): """ Remove test indices """ PydginTestSettings.tearDownIdx(["GENE", "STUDY_HITS", "PUBLICATION", "DISEASE", "MARKER"])
def setUpModule(): """ create elastic indices for querying """ PydginTestSettings.setupIdx(["GENE", "STUDY_HITS", "PUBLICATION", "DISEASE", "MARKER"])
def tearDown(cls): PydginTestSettings.tearDownIdx(['STUDY_HITS', 'DISEASE_LOCUS', 'REGION'])
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'])
def tearDownModule(): ''' Remove test indices ''' PydginTestSettings.tearDownIdx(['GENE', 'MARKER', 'STUDY_HITS', 'DISEASE_LOCUS', 'REGION', 'DISEASE', 'IC_STATS'])
def setUpModule(): ''' create elastic indices for querying ''' PydginTestSettings.setupIdx(['GENE', 'MARKER', 'STUDY_HITS', 'DISEASE_LOCUS', 'REGION', 'DISEASE', 'IC_STATS'])
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'])
def tearDown(cls): PydginTestSettings.tearDownIdx(['DISEASE'])
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'])
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'])
def tearDownModule(): ''' Remove test indices ''' PydginTestSettings.tearDownIdx(['GENE', 'STUDY_HITS', 'PUBLICATION', 'DISEASE', 'MARKER', 'STUDY'])
def setUpModule(): ''' create elastic indices for querying ''' PydginTestSettings.setupIdx(['GENE', 'STUDY_HITS', 'PUBLICATION', 'DISEASE', 'MARKER', 'STUDY'])
def setUpModule(): ''' Load test indices (region) ''' PydginTestSettings.setupIdx(['REGION', 'STUDY_HITS', 'DISEASE', 'REGION_CRITERIA_IS_REGION_IN_MHC', 'REGION_CRITERIA_IS_REGION_FOR_DISEASE'])
def tearDownModule(): ''' Remove test indices ''' PydginTestSettings.tearDownIdx(['GENE', 'DISEASE', 'PUBLICATION'])
def tearDownModule(): ''' Remove test indices ''' PydginTestSettings.tearDownIdx(['REGION', 'DISEASE', 'REGION_CRITERIA_IS_REGION_IN_MHC', 'REGION_CRITERIA_IS_REGION_FOR_DISEASE'])
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'])
def setUp(cls): DiseaseTest.idx = ElasticSettings.idx('DISEASE') PydginTestSettings.setupIdx(['DISEASE'])