Merge remote-tracking branch 'pjotrp/testing' into testing

1 files changed, 610 insertions, 0 deletions

diff --git a/unused.txt b/unused.txt
new file mode 100644
index 00000000..8eab64ea
--- /dev/null
+++ b/unused.txt
@@ -0,0 +1,610 @@
+wqflask/base/data_set.py:32: unused import 'itemgetter' (90% confidence)
+wqflask/base/data_set.py:271: unused attribute 'genetic_type' (60% confidence)
+wqflask/base/data_set.py:273: unused attribute 'genetic_type' (60% confidence)
+wqflask/base/data_set.py:281: unused attribute 'accession_id' (60% confidence)
+wqflask/base/data_set.py:282: unused attribute 'mapping_id' (60% confidence)
+wqflask/base/data_set.py:282: unused attribute 'mapping_names' (60% confidence)
+wqflask/base/data_set.py:319: unused function 'get_specified_markers' (60% confidence)
+wqflask/base/data_set.py:460: unused variable 'dataset_sub_menu' (60% confidence)
+wqflask/base/data_set.py:463: unused variable 'tissue_position' (60% confidence)
+wqflask/base/data_set.py:467: unused variable 'tissue_position' (60% confidence)
+wqflask/base/data_set.py:660: unused class 'PhenotypeDataSet' (60% confidence)
+wqflask/base/data_set.py:722: unused function 'get_trait_list' (60% confidence)
+wqflask/base/data_set.py:751: unreachable code after 'continue' (100% confidence)
+wqflask/base/data_set.py:773: unused attribute 'LRS_score_value' (60% confidence)
+wqflask/base/data_set.py:775: unused attribute 'LRS_location_value' (60% confidence)
+wqflask/base/data_set.py:794: unused variable 'LRS_location_value' (60% confidence)
+wqflask/base/data_set.py:797: unused variable 'LRS_location_value' (60% confidence)
+wqflask/base/data_set.py:799: unused variable 'LRS_location_value' (60% confidence)
+wqflask/base/data_set.py:802: unused attribute 'LRS_score_value' (60% confidence)
+wqflask/base/data_set.py:802: unused variable 'LRS_score_value' (60% confidence)
+wqflask/base/data_set.py:828: unused class 'GenotypeDataSet' (60% confidence)
+wqflask/base/data_set.py:864: unused function 'get_trait_list' (60% confidence)
+wqflask/base/data_set.py:884: unused variable 'trait_location_repr' (60% confidence)
+wqflask/base/data_set.py:897: unused attribute 'location_value' (60% confidence)
+wqflask/base/data_set.py:923: unused class 'MrnaAssayDataSet' (60% confidence)
+wqflask/base/data_set.py:992: unused function 'get_trait_list_1' (60% confidence)
+wqflask/base/data_set.py:1038: unused variable 'trait_location_repr' (60% confidence)
+wqflask/base/data_set.py:1057: unused attribute 'location_value' (60% confidence)
+wqflask/base/data_set.py:1079: unused attribute 'LRS_score_value' (60% confidence)
+wqflask/base/data_set.py:1081: unused attribute 'LRS_location_value' (60% confidence)
+wqflask/base/data_set.py:1097: unused variable 'lrs_location_value' (60% confidence)
+wqflask/base/data_set.py:1099: unused attribute 'LRS_score_value' (60% confidence)
+wqflask/base/data_set.py:1115: unused function 'get_sequence' (60% confidence)
+wqflask/base/data_set.py:1167: unused class 'TempDataSet' (60% confidence)
+wqflask/base/data_set.py:1207: unused function 'get_group' (60% confidence)
+wqflask/base/data_set.py:1218: unused attribute 'group_id' (60% confidence)
+wqflask/base/mrna_assay_tissue_data.py:21: unused attribute 'have_data' (60% confidence)
+wqflask/base/species.py:21: unused attribute 'genome_mb_length' (60% confidence)
+wqflask/base/species.py:45: unused function 'set_cm_length' (60% confidence)
+wqflask/base/species.py:77: unused attribute 'mb_graph_interval' (60% confidence)
+wqflask/base/species.py:79: unused attribute 'mb_graph_interval' (60% confidence)
+wqflask/base/species.py:94: unused function 'get_genome_cm_length' (60% confidence)
+wqflask/base/species.py:99: unused function 'get_cm_length_list' (60% confidence)
+wqflask/base/template.py:27: unused variable 'template' (60% confidence)
+wqflask/base/trait.py:28: unused function 'print_mem' (60% confidence)
+wqflask/base/trait.py:58: unused attribute 'pvalue' (60% confidence)
+wqflask/base/trait.py:66: unused attribute 'LRS_score_value' (60% confidence)
+wqflask/base/trait.py:68: unused attribute 'LRS_location_value' (60% confidence)
+wqflask/base/trait.py:86: unused function 'get_name' (60% confidence)
+wqflask/base/trait.py:97: unused function 'get_given_name' (60% confidence)
+wqflask/base/trait.py:118: unused function 'display_name' (60% confidence)
+wqflask/base/trait.py:148: unused function 'export_data' (60% confidence)
+wqflask/base/trait.py:189: unused property 'name_header_fmt' (60% confidence)
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+wqflask/base/trait.py:232: unused property 'location_fmt' (60% confidence)
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+wqflask/base/trait.py:309: unused function 'get_sample_data' (60% confidence)
+wqflask/base/trait.py:546: unused attribute 'homologeneid' (60% confidence)
+wqflask/base/trait.py:575: unused attribute 'homologeneid' (60% confidence)
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+wqflask/base/trait.py:615: unused attribute 'location_value' (60% confidence)
+wqflask/base/trait.py:624: unused attribute 'location_value' (60% confidence)
+wqflask/base/trait.py:629: unused attribute 'LRS_score_value' (60% confidence)
+wqflask/base/trait.py:631: unused attribute 'LRS_location_value' (60% confidence)
+wqflask/base/trait.py:646: unused attribute 'pvalue' (60% confidence)
+wqflask/base/trait.py:664: unused attribute 'pvalue' (60% confidence)
+wqflask/base/trait.py:704: unused variable 'LRS_location_value' (60% confidence)
+wqflask/base/trait.py:707: unused variable 'LRS_location_value' (60% confidence)
+wqflask/base/trait.py:709: unused variable 'LRS_location_value' (60% confidence)
+wqflask/base/trait.py:714: unused attribute 'LRS_score_value' (60% confidence)
+wqflask/base/trait.py:714: unused variable 'LRS_score_value' (60% confidence)
+wqflask/base/webqtlCaseData.py:42: unused attribute 'this_id' (60% confidence)
+wqflask/base/webqtlCaseData.py:59: unused property 'class_outlier' (60% confidence)
+wqflask/base/webqtlCaseData.py:67: unused property 'display_value' (60% confidence)
+wqflask/base/webqtlCaseData.py:74: unused property 'display_variance' (60% confidence)
+wqflask/base/webqtlConfig.py:24: unused variable 'MULTIPLEMAPPINGLIMIT' (60% confidence)
+wqflask/base/webqtlConfig.py:27: unused variable 'MAXCORR' (60% confidence)
+wqflask/base/webqtlConfig.py:36: unused variable 'MAXLIFE' (60% confidence)
+wqflask/base/webqtlConfig.py:42: unused variable 'NCBI_LOCUSID' (60% confidence)
+wqflask/base/webqtlConfig.py:43: unused variable 'UCSC_REFSEQ' (60% confidence)
+wqflask/base/webqtlConfig.py:44: unused variable 'GENBANK_ID' (60% confidence)
+wqflask/base/webqtlConfig.py:45: unused variable 'OMIM_ID' (60% confidence)
+wqflask/base/webqtlConfig.py:46: unused variable 'UNIGEN_ID' (60% confidence)
+wqflask/base/webqtlConfig.py:47: unused variable 'HOMOLOGENE_ID' (60% confidence)
+wqflask/base/webqtlConfig.py:49: unused variable 'UCSC_POS' (60% confidence)
+wqflask/base/webqtlConfig.py:53: unused variable 'UCSC_GENOME' (60% confidence)
+wqflask/base/webqtlConfig.py:54: unused variable 'ENSEMBLE_BLAT' (60% confidence)
+wqflask/base/webqtlConfig.py:55: unused variable 'DBSNP' (60% confidence)
+wqflask/base/webqtlConfig.py:56: unused variable 'UCSC_RUDI_TRACK_URL' (60% confidence)
+wqflask/base/webqtlConfig.py:57: unused variable 'GENOMEBROWSER_URL' (60% confidence)
+wqflask/base/webqtlConfig.py:58: unused variable 'ENSEMBLETRANSCRIPT_URL' (60% confidence)
+wqflask/base/webqtlFormData.py:53: unused variable 'mod_python_session' (60% confidence)
+wqflask/base/webqtlFormData.py:54: unused variable 'FieldStorage_formdata' (60% confidence)
+wqflask/base/webqtlFormData.py:61: unused attribute 'varianceDispName' (60% confidence)
+wqflask/base/webqtlFormData.py:74: unused attribute 'refURL' (60% confidence)
+wqflask/base/webqtlFormData.py:76: unused attribute 'refURL' (60% confidence)
+wqflask/base/webqtlFormData.py:328: unused function 'Sample' (60% confidence)
+wqflask/basicStatistics/BasicStatisticsFunctions.py:21: unused function 'basicStatsTable' (60% confidence)
+wqflask/basicStatistics/BasicStatisticsFunctions.py:101: unused function 'plotNormalProbability' (60% confidence)
+wqflask/basicStatistics/BasicStatisticsFunctions.py:155: unused function 'plotBarGraph' (60% confidence)
+wqflask/basicStatistics/corestats.py:61: unused function 'median' (60% confidence)
+wqflask/maintenance/convert_geno_to_bimbam.py:74: unused attribute 'geno_fh' (60% confidence)
+wqflask/maintenance/convert_geno_to_bimbam.py:82: unused variable 'row_count' (60% confidence)
+wqflask/maintenance/gen_select_dataset.py:69: unused variable 'db_uri' (60% confidence)
+wqflask/maintenance/gen_select_dataset.py:302: unused function '_test_it' (60% confidence)
+wqflask/maintenance/get_group_samplelists.py:9: unused function 'process_genofiles' (60% confidence)
+wqflask/mock/es_double.py:1: unused class 'ESDouble' (60% confidence)
+wqflask/run_gunicorn.py:17: unused function 'hello' (60% confidence)
+wqflask/utility/after.py:18: unused function 'call_after_request_callbacks' (60% confidence)
+wqflask/utility/AJAX_table.py:41: unused class 'AJAX_table' (60% confidence)
+wqflask/utility/benchmark.py:6: unused import 'LOG_BENCH' (90% confidence)
+wqflask/utility/elasticsearch_tools.py:51: unused variable 'te' (60% confidence)
+wqflask/utility/genofile_parser.py:75: unused variable 'row_count' (60% confidence)
+wqflask/utility/logger.py:36: unused import 'LOG_FORMAT' (90% confidence)
+wqflask/utility/logger.py:59: unused function 'debug20' (60% confidence)
+wqflask/utility/logger.py:84: unused function 'infof' (60% confidence)
+wqflask/utility/Plot.py:167: unused function 'erf' (60% confidence)
+wqflask/utility/Plot.py:182: unused function 'calMeanVar' (60% confidence)
+wqflask/utility/Plot.py:370: unused variable 'tstrain' (60% confidence)
+wqflask/utility/Plot.py:449: unused function 'plotSecurity' (60% confidence)
+wqflask/utility/Plot.py:594: unused variable 'Xll' (60% confidence)
+wqflask/utility/Plot.py:595: unused variable 'Xur' (60% confidence)
+wqflask/utility/Plot.py:914: unused function 'plotXYSVG' (60% confidence)
+wqflask/utility/Plot.py:914: unused variable 'plotColor' (60% confidence)
+wqflask/utility/Plot.py:923: unused variable 'dataXAlt' (60% confidence)
+wqflask/utility/Plot.py:924: unused variable 'dataYAlt' (60% confidence)
+wqflask/utility/Plot.py:929: unused variable 'dataXAlt' (60% confidence)
+wqflask/utility/Plot.py:930: unused variable 'dataYAlt' (60% confidence)
+wqflask/utility/Plot.py:1030: unused attribute 'argv' (60% confidence)
+wqflask/utility/Plot.py:1117: unused variable 'bufferSpace' (60% confidence)
+wqflask/utility/Plot.py:1156: unused function 'colorSpectrumOld' (60% confidence)
+wqflask/utility/Plot.py:1234: unused function 'colorSpectrumSVG' (60% confidence)
+wqflask/utility/Plot.py:1257: unused function 'BWSpectrum' (60% confidence)
+wqflask/utility/svg.py:116: unused attribute 'setrecursionlimit' (60% confidence)
+wqflask/utility/svg.py:174: unused function '_pointlist' (60% confidence)
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+wqflask/utility/svg.py:192: unused function 'relmove' (60% confidence)
+wqflask/utility/svg.py:198: unused function 'relline' (60% confidence)
+wqflask/utility/svg.py:201: unused function 'hline' (60% confidence)
+wqflask/utility/svg.py:204: unused function 'relhline' (60% confidence)
+wqflask/utility/svg.py:207: unused function 'vline' (60% confidence)
+wqflask/utility/svg.py:210: unused function 'relvline' (60% confidence)
+wqflask/utility/svg.py:213: unused function 'bezier' (60% confidence)
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+wqflask/utility/svg.py:219: unused function 'smbezier' (60% confidence)
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+wqflask/utility/svg.py:228: unused function 'relqbezier' (60% confidence)
+wqflask/utility/svg.py:231: unused function 'smqbezier' (60% confidence)
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+wqflask/utility/svg.py:240: unused function 'relellarc' (60% confidence)
+wqflask/utility/svg.py:359: unused class 'spannedtext' (60% confidence)
+wqflask/utility/svg.py:382: unused function 'addtext' (60% confidence)
+wqflask/utility/svg.py:384: unused function 'addtspan' (60% confidence)
+wqflask/utility/svg.py:386: unused function 'addtref' (60% confidence)
+wqflask/utility/svg.py:494: unused class 'polyline' (60% confidence)
+wqflask/utility/svg.py:508: unused class 'polygon' (60% confidence)
+wqflask/utility/svg.py:560: unused class 'textpath' (60% confidence)
+wqflask/utility/svg.py:612: unused class 'lineargradient' (60% confidence)
+wqflask/utility/svg.py:631: unused class 'radialgradient' (60% confidence)
+wqflask/utility/svg.py:652: unused class 'stop' (60% confidence)
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+wqflask/utility/svg.py:671: unused class 'image' (60% confidence)
+wqflask/utility/svg.py:747: unused class 'defs' (60% confidence)
+wqflask/utility/svg.py:755: unused class 'switch' (60% confidence)
+wqflask/utility/svg.py:793: unused class 'view' (60% confidence)
+wqflask/utility/svg.py:802: unused class 'script' (60% confidence)
+wqflask/utility/svg.py:811: unused class 'animate' (60% confidence)
+wqflask/utility/svg.py:837: unused class 'animateTransform' (60% confidence)
+wqflask/utility/svg.py:853: unused class 'animateColor' (60% confidence)
+wqflask/utility/svg.py:1022: unused function 'validate' (60% confidence)
+wqflask/utility/temp_data.py:13: unused function 'store' (60% confidence)
+wqflask/utility/tools.py:182: unused function 'locate_phewas' (60% confidence)
+wqflask/utility/tools.py:235: unused variable 'HOME' (60% confidence)
+wqflask/utility/tools.py:243: unused variable 'LOG_BENCH' (60% confidence)
+wqflask/utility/tools.py:244: unused variable 'LOG_FORMAT' (60% confidence)
+wqflask/utility/tools.py:248: unused variable 'GENENETWORK_FILES' (60% confidence)
+wqflask/utility/tools.py:251: unused variable 'JS_GN_PATH' (60% confidence)
+wqflask/utility/webqtlUtil.py:69: unused variable 'IMGSTEP1' (60% confidence)
+wqflask/utility/webqtlUtil.py:70: unused variable 'IMGSTEP2' (60% confidence)
+wqflask/utility/webqtlUtil.py:71: unused variable 'IMGSTEP3' (60% confidence)
+wqflask/utility/webqtlUtil.py:72: unused variable 'IMGNEXT' (60% confidence)
+wqflask/utility/webqtlUtil.py:87: unused variable 'PROGRESSBAR' (60% confidence)
+wqflask/utility/webqtlUtil.py:157: unused function 'decodeEscape' (60% confidence)
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+wqflask/utility/webqtlUtil.py:220: unused function 'transpose' (60% confidence)
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+wqflask/utility/webqtlUtil.py:241: unused function 'generate_session' (60% confidence)
+wqflask/utility/webqtlUtil.py:245: unused function 'cvt2Dict' (60% confidence)
+wqflask/utility/webqtlUtil.py:251: unused function 'dump_session' (60% confidence)
+wqflask/utility/webqtlUtil.py:276: unused function 'FloatAsFloat' (60% confidence)
+wqflask/utility/webqtlUtil.py:283: unused function 'RemoveZero' (60% confidence)
+wqflask/utility/webqtlUtil.py:306: unused function 'FloatList2String' (60% confidence)
+wqflask/utility/webqtlUtil.py:332: unused function 'FileDataProcess' (60% confidence)
+wqflask/utility/webqtlUtil.py:372: unused function 'cmpScanResult' (60% confidence)
+wqflask/utility/webqtlUtil.py:384: unused function 'cmpScanResult2' (60% confidence)
+wqflask/utility/webqtlUtil.py:596: unused function 'calCorrelationRankText' (60% confidence)
+wqflask/utility/webqtlUtil.py:715: unused function 'calCorrelationText' (60% confidence)
+wqflask/utility/webqtlUtil.py:761: unused function 'cmpCorr' (60% confidence)
+wqflask/utility/webqtlUtil.py:772: unused function 'cmpLitCorr' (60% confidence)
+wqflask/utility/webqtlUtil.py:783: unused function 'cmpPValue' (60% confidence)
+wqflask/utility/webqtlUtil.py:811: unused function 'cmpLRSFull' (60% confidence)
+wqflask/utility/webqtlUtil.py:822: unused function 'cmpLRSInteract' (60% confidence)
+wqflask/utility/webqtlUtil.py:834: unused function 'cmpPos' (60% confidence)
+wqflask/utility/webqtlUtil.py:858: unused function 'cmpGenoPos' (60% confidence)
+wqflask/utility/webqtlUtil.py:895: unused class 'VisualizeException' (60% confidence)
+wqflask/utility/webqtlUtil.py:912: unused function 'safeFloat' (60% confidence)
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+wqflask/utility/webqtlUtil.py:941: unused function 'intToYesNo' (60% confidence)
+wqflask/utility/webqtlUtil.py:949: unused function 'formatField' (60% confidence)
+wqflask/utility/webqtlUtil.py:971: unused variable 'last_idx' (60% confidence)
+wqflask/utility/webqtlUtil.py:981: unused variable 'last_idx' (60% confidence)
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+wqflask/wqflask/collect.py:43: unused function 'get_collection' (60% confidence)
+wqflask/wqflask/collect.py:225: unused function 'collections_add' (60% confidence)
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+wqflask/wqflask/collect.py:285: unused variable 'current_collections' (60% confidence)
+wqflask/wqflask/collect.py:291: unused function 'list_collections' (60% confidence)
+wqflask/wqflask/collect.py:368: unused function 'view_collection' (60% confidence)
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+wqflask/wqflask/correlation/corr_scatter_plot.py:28: unused attribute 'height' (60% confidence)
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+wqflask/wqflask/correlation/corr_scatter_plot.py:69: unused variable 'std_err' (60% confidence)
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+wqflask/wqflask/correlation/correlation_functions.py:124: unused function 'findIdenticalControlTraits' (60% confidence)
+wqflask/wqflask/correlation/correlation_functions.py:150: unused function 'findIdenticalTraits' (60% confidence)
+wqflask/wqflask/correlation/correlation_functions.py:185: unused function 'determinePartialsByR' (60% confidence)
+wqflask/wqflask/correlation/correlation_functions.py:497: unused function 'calZeroOrderCorr' (60% confidence)
+wqflask/wqflask/correlation/correlation_functions.py:502: unused variable 'primary_var' (60% confidence)
+wqflask/wqflask/correlation/correlation_functions.py:681: unused function 'getTissueProbeSetXRefInfo' (60% confidence)
+wqflask/wqflask/correlation/correlation_functions.py:727: unused variable 'resultCount' (60% confidence)
+wqflask/wqflask/correlation/correlation_functions.py:759: unused function 'get_symbol_value_pairs' (60% confidence)
+wqflask/wqflask/correlation/correlation_functions.py:881: unused function 'getCorrPvArray' (60% confidence)
+wqflask/wqflask/correlation/correlation_functions.py:941: unused function 'calculateCorrOfAllTissueTrait' (60% confidence)
+wqflask/wqflask/correlation/show_corr_results.py:26: unused import 'gc' (90% confidence)
+wqflask/wqflask/correlation/show_corr_results.py:67: unused variable 'METHOD_SAMPLE_PEARSON' (60% confidence)
+wqflask/wqflask/correlation/show_corr_results.py:68: unused variable 'METHOD_SAMPLE_RANK' (60% confidence)
+wqflask/wqflask/correlation/show_corr_results.py:77: unused function 'print_mem' (60% confidence)
+wqflask/wqflask/correlation/show_corr_results.py:81: unused class 'AuthException' (60% confidence)
+wqflask/wqflask/correlation/show_corr_results.py:86: unused variable 'corr_min_informative' (60% confidence)
+wqflask/wqflask/correlation/show_corr_results.py:178: unused variable 'cache_available' (60% confidence)
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