$ make unit-test PYTHONWARNINGS=ignore:ResourceWarning coverage run \ --source=app,cli,common,compute,converters,data_anndata,data_common,data_cxg \ --omit=.coverage,data_common/fbs/NetEncoding,venv \ -m unittest discover \ --start-directory test/ \ --top-level-directory ../ \ --verbose /home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/anndata/_core/anndata.py:21: FutureWarning: pandas.core.indersion. The public classes are available in the top-level namespace. from pandas.core.index import RangeIndex server.test.test_anndata_adaptor (unittest.loader._FailedTest) ... ERROR test_delayed_load_data (server.test.test_anndata_adaptor_data_load.DataLoadAdaptorTest) ... /home/kli3/anaconda3/envs/cellxgentions/local.py:33: FutureWarning: The default value of auto_mkdir=True has been deprecated and will be changed to auto_mkdir=F FutureWarning, ok test_diffexp_topN (server.test.test_anndata_adaptor_data_load.DataLoadAdaptorTest) ... ok test_posix_file (server.test.test_anndata_adaptor_data_load.DataLocatorAdaptorTest) ... ok test_url_http (server.test.test_anndata_adaptor_data_load.DataLocatorAdaptorTest) ... ok test_url_https (server.test.test_anndata_adaptor_data_load.DataLocatorAdaptorTest) ... ok /home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/anndata/_core/anndata.py:21: FutureWarning: pandas.core.indersion. The public classes are available in the top-level namespace. from pandas.core.index import RangeIndex [cellxgene] Starting the CLI... [cellxgene] Warning: The default value of auto_mkdir=True has been deprecated and will be changed to auto_mkdir=False by defau [cellxgene] Loading data from pbmc3k.h5ad. [cellxgene] Launching! Please go to http://127.0.0.1:5010 in your browser. [cellxgene] Type CTRL-C at any time to exit. * Serving Flask app "server.app.app" (lazy loading) * Environment: production WARNING: This is a development server. Do not use it in a production deployment. Use a production WSGI server instead. * Debug mode: off * Running on http://127.0.0.1:5010/ (Press CTRL+C to quit) 127.0.0.1 - - [08/May/2020 10:27:48] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:48] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:48] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:48] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:49] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:49] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:49] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:49] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:49] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:49] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:49] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:49] "GET /api/v0.2/schema HTTP/1.1" 200 - 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127.0.0.1 - - [08/May/2020 10:27:49] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:49] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:49] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:49] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:49] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:49] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:49] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:49] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:49] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:49] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:49] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:49] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:49] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:49] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:49] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:49] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:49] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:49] "GET /api/v0.2/schema HTTP/1.1" 200 - test_bad_filter (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:27:49] "PUT /api/v0.2/data/var HTTP/ ok test_config (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:27:49] "GET /api/v0.2/config HTTP/1.1" 2 ok test_data_get_fbs (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:27:49] "GET /api/v0.2/data/var HTT ok test_data_get_filter_fbs (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:27:49] "GET /api/v0.2/data/ ok test_data_mimetype_error (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:27:49] "PUT /api/v0.2/data/ ok test_data_put_fbs (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:27:49] "PUT /api/v0.2/data/var HTT ok test_data_put_filter_fbs (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:27:49] "PUT /api/v0.2/data/ ok test_data_put_single_var (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:27:49] "PUT /api/v0.2/data/ ok test_diff_exp (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:27:49] "POST /api/v0.2/diffexp/obs HTT ok test_diff_exp_indices (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:27:49] "POST /api/v0.2/diffexp ok test_fbs_default (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:27:50] "PUT /api/v0.2/data/var HTTP 127.0.0.1 - - [08/May/2020 10:27:50] "PUT /api/v0.2/data/var HTTP/1.1" 200 - ok test_get_annotations_obs_error (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:27:50] "GET /api/v0.2 400 - ok test_get_annotations_obs_fbs (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:27:50] "GET /api/v0.2/a ok test_get_annotations_obs_keys_fbs (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:27:50] "GET /api/vtion-name=percent_mito HTTP/1.1" 200 - ok test_get_annotations_var_error (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:27:50] "GET /api/v0.2 400 - ok test_get_annotations_var_fbs (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:27:50] "GET /api/v0.2/a ok test_get_annotations_var_keys_fbs (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:27:50] "GET /api/v.1" 200 - ok test_get_layout_fbs (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:27:50] "GET /api/v0.2/layout/obs ok test_initialize (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:27:50] "GET /api/v0.2/schema HTTP/1. ok test_static (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:27:50] "GET /static/assets/favicon.ico H ok /home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/anndata/_core/anndata.py:21: FutureWarning: pandas.core.indersion. The public classes are available in the top-level namespace. from pandas.core.index import RangeIndex [cellxgene] Starting the CLI... [cellxgene] Warning: The default value of auto_mkdir=True has been deprecated and will be changed to auto_mkdir=False by defau [cellxgene] Loading data from pbmc3k.h5ad. [cellxgene] Launching! Please go to http://127.0.0.1:5012 in your browser. [cellxgene] Type CTRL-C at any time to exit. * Serving Flask app "server.app.app" (lazy loading) * Environment: production WARNING: This is a development server. Do not use it in a production deployment. 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127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:55] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:56] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:56] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:56] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:56] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:56] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:56] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:56] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:56] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:56] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:56] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:56] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:56] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:56] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:56] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:56] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:56] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:56] "GET /api/v0.2/schema HTTP/1.1" 200 - test_bad_filter (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 10:27:56] "PUT /api/v0.2/dat ok test_config (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 10:27:56] "GET /api/v0.2/config ok test_data_get_fbs (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 10:27:56] "GET /api/v0.2/d ok test_data_get_filter_fbs (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 10:27:56] "GET /api ok test_data_mimetype_error (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 10:27:56] "PUT /api ok test_data_put_fbs (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 10:27:56] "PUT /api/v0.2/d ok test_data_put_filter_fbs (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 10:27:56] "PUT /api ok test_data_put_single_var (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 10:27:56] "PUT /api ok test_diff_exp (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 10:27:56] "POST /api/v0.2/diff ok test_diff_exp_indices (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 10:27:56] "POST /api/v ok test_fbs_default (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 10:27:56] "PUT /api/v0.2/da 127.0.0.1 - - [08/May/2020 10:27:56] "PUT /api/v0.2/data/var HTTP/1.1" 200 - ok test_get_annotations_obs_error (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 10:27:56] "GEy HTTP/1.1" 400 - ok test_get_annotations_obs_fbs (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 10:27:56] "GET ok test_get_annotations_obs_keys_fbs (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 10:27:56] enes&annotation-name=percent_mito HTTP/1.1" 200 - ok test_get_annotations_var_error (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 10:27:56] "GEy HTTP/1.1" 400 - ok test_get_annotations_var_fbs (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 10:27:56] "GET ok test_get_annotations_var_keys_fbs (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 10:27:56] ells HTTP/1.1" 200 - ok test_get_layout_fbs (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 10:27:56] "GET /api/v0.2 ok test_get_schema_existing_writable (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 10:27:56] ok test_get_user_annotations_existing_obs_keys_fbs (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2ation-name=cluster-test HTTP/1.1" 200 - ok test_initialize (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 10:27:56] "GET /api/v0.2/sch ok test_put_user_annotations_obs_fbs (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 10:27:56] on-name=test_annotations HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:56] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:27:56] "GET /api/v0.2/annotations/obs?annotation-name=cat_A HTTP/1.1" 200 - ok test_static (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 10:27:56] "GET /static/assets/fa ok /home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/anndata/_core/anndata.py:21: FutureWarning: pandas.core.indersion. The public classes are available in the top-level namespace. from pandas.core.index import RangeIndex [cellxgene] Starting the CLI... [cellxgene] Warning: The default value of auto_mkdir=True has been deprecated and will be changed to auto_mkdir=False by defau [cellxgene] Loading data from pbmc3k.cxg. [cellxgene] Launching! Please go to http://127.0.0.1:5011 in your browser. [cellxgene] Type CTRL-C at any time to exit. * Serving Flask app "server.app.app" (lazy loading) * Environment: production WARNING: This is a development server. Do not use it in a production deployment. Use a production WSGI server instead. * Debug mode: off * Running on http://127.0.0.1:5011/ (Press CTRL+C to quit) 127.0.0.1 - - [08/May/2020 10:28:00] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:00] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:00] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:00] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:00] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/schema HTTP/1.1" 200 - test_bad_filter (server.test.test_api.EndPointsCxg) ... 127.0.0.1 - - [08/May/2020 10:28:01] "PUT /api/v0.2/data/var HTTP/1.1" ok test_config (server.test.test_api.EndPointsCxg) ... 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/config HTTP/1.1" 200 - ok test_data_get_fbs (server.test.test_api.EndPointsCxg) ... 127.0.0.1 - - [08/May/2020 10:28:01] "GET /api/v0.2/data/var HTTP/1. ok test_data_get_filter_fbs (server.test.test_api.EndPointsCxg) ... [2020-05-08 10:28:02,138] ERROR in app: Exception on /api/v0. Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1950, in full_dispatch_request rv = self.dispatch_request() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1936, in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py", line 468, in wrapper resp = resource(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/views.py", line 89, in view return self.dispatch_request(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py", line 583, in dispatch_r resp = meth(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 35, in wrapper response = make_response(f(*args, **kwargs)) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 116, in wrapped_function return func(self, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 207, in get return common_rest.data_var_get(request, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/common/rest.py", line 217, in data_var_get data_adaptor.data_frame_to_fbs_matrix(filter, axis=Axis.VAR), File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_common/data_adaptor.py", line 275, in d X = self.get_X_array(obs_selector, var_selector) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_cxg/cxg_adaptor.py", line 204, in get_X data = X.multi_index[obs_items, var_items][""] KeyError: '' 127.0.0.1 - - [08/May/2020 10:28:02] "GET /api/v0.2/data/var?var:name_0=SIK1 HTTP/1.1" 500 - FAIL test_data_mimetype_error (server.test.test_api.EndPointsCxg) ... 127.0.0.1 - - [08/May/2020 10:28:02] "PUT /api/v0.2/data/var ok test_data_put_fbs (server.test.test_api.EndPointsCxg) ... 127.0.0.1 - - [08/May/2020 10:28:02] "PUT /api/v0.2/data/var HTTP/1. ok test_data_put_filter_fbs (server.test.test_api.EndPointsCxg) ... [2020-05-08 10:28:02,276] ERROR in app: Exception on /api/v0. Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1950, in full_dispatch_request rv = self.dispatch_request() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1936, in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py", line 468, in wrapper resp = resource(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/views.py", line 89, in view return self.dispatch_request(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py", line 583, in dispatch_r resp = meth(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 35, in wrapper response = make_response(f(*args, **kwargs)) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 116, in wrapped_function return func(self, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 202, in put return common_rest.data_var_put(request, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/common/rest.py", line 201, in data_var_put data_adaptor.data_frame_to_fbs_matrix(filter, axis=Axis.VAR), File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_common/data_adaptor.py", line 275, in d X = self.get_X_array(obs_selector, var_selector) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_cxg/cxg_adaptor.py", line 204, in get_X data = X.multi_index[obs_items, var_items][""] KeyError: '' 127.0.0.1 - - [08/May/2020 10:28:02] "PUT /api/v0.2/data/var HTTP/1.1" 500 - FAIL test_data_put_single_var (server.test.test_api.EndPointsCxg) ... [2020-05-08 10:28:02,328] ERROR in app: Exception on /api/v0. Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1950, in full_dispatch_request rv = self.dispatch_request() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1936, in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py", line 468, in wrapper resp = resource(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/views.py", line 89, in view return self.dispatch_request(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py", line 583, in dispatch_r resp = meth(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 35, in wrapper response = make_response(f(*args, **kwargs)) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 116, in wrapped_function return func(self, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 202, in put return common_rest.data_var_put(request, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/common/rest.py", line 201, in data_var_put data_adaptor.data_frame_to_fbs_matrix(filter, axis=Axis.VAR), File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_common/data_adaptor.py", line 275, in d X = self.get_X_array(obs_selector, var_selector) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_cxg/cxg_adaptor.py", line 204, in get_X data = X.multi_index[obs_items, var_items][""] KeyError: '' 127.0.0.1 - - [08/May/2020 10:28:02] "PUT /api/v0.2/data/var HTTP/1.1" 500 - FAIL test_diff_exp (server.test.test_api.EndPointsCxg) ... [2020-05-08 10:28:02,531] ERROR in app: Exception on /api/v0.2/diffexp/o Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/compute/diffexp_cxg.py", line 84, in diffexp result = future.result() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/concurrent/futures/_base.py", line 435, in result return self.__get_result() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result raise self._exception File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/concurrent/futures/thread.py", line 57, in run result = self.fn(*self.args, **self.kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/compute/diffexp_cxg.py", line 110, in _mean_ X = matrix.multi_index[row_selector_AB, col_range[0] : col_range[1] - 1][""] KeyError: '' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1950, in full_dispatch_request rv = self.dispatch_request() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1936, in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py", line 468, in wrapper resp = resource(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/views.py", line 89, in view return self.dispatch_request(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py", line 583, in dispatch_r resp = meth(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 35, in wrapper response = make_response(f(*args, **kwargs)) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 116, in wrapped_function return func(self, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 214, in post return common_rest.diffexp_obs_post(request, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/common/rest.py", line 250, in diffexp_obs_po diffexp = data_adaptor.diffexp_topN(set1_filter, set2_filter, count) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_common/data_adaptor.py", line 307, in d result = self.compute_diffexp_ttest(obs_mask_A, obs_mask_B, top_n, self.config.diffexp__lfc_cutoff) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_cxg/cxg_adaptor.py", line 195, in compu return diffexp_cxg.diffexp_ttest(self, maskA, maskB, top_n, lfc_cutoff) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/compute/diffexp_cxg.py", line 93, in diffexp raise ComputeError(str(e)) server.common.errors.ComputeError: '' 127.0.0.1 - - [08/May/2020 10:28:02] "POST /api/v0.2/diffexp/obs HTTP/1.1" 500 - FAIL test_diff_exp_indices (server.test.test_api.EndPointsCxg) ... [2020-05-08 10:28:02,639] ERROR in app: Exception on /api/v0.2/d Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/compute/diffexp_cxg.py", line 84, in diffexp result = future.result() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/concurrent/futures/_base.py", line 435, in result return self.__get_result() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result raise self._exception File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/concurrent/futures/thread.py", line 57, in run result = self.fn(*self.args, **self.kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/compute/diffexp_cxg.py", line 110, in _mean_ X = matrix.multi_index[row_selector_AB, col_range[0] : col_range[1] - 1][""] KeyError: '' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1950, in full_dispatch_request rv = self.dispatch_request() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1936, in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py", line 468, in wrapper resp = resource(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/views.py", line 89, in view return self.dispatch_request(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py", line 583, in dispatch_r resp = meth(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 35, in wrapper response = make_response(f(*args, **kwargs)) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 116, in wrapped_function return func(self, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 214, in post return common_rest.diffexp_obs_post(request, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/common/rest.py", line 250, in diffexp_obs_po diffexp = data_adaptor.diffexp_topN(set1_filter, set2_filter, count) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_common/data_adaptor.py", line 307, in d result = self.compute_diffexp_ttest(obs_mask_A, obs_mask_B, top_n, self.config.diffexp__lfc_cutoff) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_cxg/cxg_adaptor.py", line 195, in compu return diffexp_cxg.diffexp_ttest(self, maskA, maskB, top_n, lfc_cutoff) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/compute/diffexp_cxg.py", line 93, in diffexp raise ComputeError(str(e)) server.common.errors.ComputeError: '' 127.0.0.1 - - [08/May/2020 10:28:02] "POST /api/v0.2/diffexp/obs HTTP/1.1" 500 - FAIL test_fbs_default (server.test.test_api.EndPointsCxg) ... 127.0.0.1 - - [08/May/2020 10:28:02] "PUT /api/v0.2/data/var HTTP/1.1 [2020-05-08 10:28:02,690] ERROR in app: Exception on /api/v0.2/data/var [PUT] Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1950, in full_dispatch_request rv = self.dispatch_request() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1936, in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py", line 468, in wrapper resp = resource(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/views.py", line 89, in view return self.dispatch_request(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py", line 583, in dispatch_r resp = meth(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 35, in wrapper response = make_response(f(*args, **kwargs)) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 116, in wrapped_function return func(self, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 202, in put return common_rest.data_var_put(request, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/common/rest.py", line 201, in data_var_put data_adaptor.data_frame_to_fbs_matrix(filter, axis=Axis.VAR), File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_common/data_adaptor.py", line 275, in d X = self.get_X_array(obs_selector, var_selector) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_cxg/cxg_adaptor.py", line 204, in get_X data = X.multi_index[obs_items, var_items][""] KeyError: '' 127.0.0.1 - - [08/May/2020 10:28:02] "PUT /api/v0.2/data/var HTTP/1.1" 500 - FAIL test_get_annotations_obs_error (server.test.test_api.EndPointsCxg) ... 127.0.0.1 - - [08/May/2020 10:28:02] "GET /api/v0.2/ann - ok test_get_annotations_obs_fbs (server.test.test_api.EndPointsCxg) ... 127.0.0.1 - - [08/May/2020 10:28:02] "GET /api/v0.2/annot ok test_get_annotations_obs_keys_fbs (server.test.test_api.EndPointsCxg) ... 127.0.0.1 - - [08/May/2020 10:28:02] "GET /api/v0.2/-name=percent_mito HTTP/1.1" 200 - ok test_get_annotations_var_error (server.test.test_api.EndPointsCxg) ... 127.0.0.1 - - [08/May/2020 10:28:02] "GET /api/v0.2/ann - ok test_get_annotations_var_fbs (server.test.test_api.EndPointsCxg) ... 127.0.0.1 - - [08/May/2020 10:28:02] "GET /api/v0.2/annot ok test_get_annotations_var_keys_fbs (server.test.test_api.EndPointsCxg) ... 127.0.0.1 - - [08/May/2020 10:28:02] "GET /api/v0.2/200 - ok test_get_layout_fbs (server.test.test_api.EndPointsCxg) ... [2020-05-08 10:28:02,925] ERROR in app: Exception on /api/v0.2/lay Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1950, in full_dispatch_request rv = self.dispatch_request() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1936, in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py", line 468, in wrapper resp = resource(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/views.py", line 89, in view return self.dispatch_request(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py", line 583, in dispatch_r resp = meth(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 35, in wrapper response = make_response(f(*args, **kwargs)) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 116, in wrapped_function return func(self, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 221, in get return common_rest.layout_obs_get(request, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/common/rest.py", line 273, in layout_obs_get data_adaptor.layout_to_fbs_matrix(fields), HTTPStatus.OK, {"Content-Type": "application/octet-stream"} File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_common/data_adaptor.py", line 352, in l embedding = self.get_embedding_array(ename, 2) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_cxg/cxg_adaptor.py", line 185, in get_e return array[:, 0:dims] File "tiledb/libtiledb.pyx", line 4002, in tiledb.libtiledb.DenseArrayImpl.__getitem__ File "tiledb/libtiledb.pyx", line 4107, in tiledb.libtiledb.DenseArrayImpl.subarray File "tiledb/libtiledb.pyx", line 4153, in tiledb.libtiledb.DenseArrayImpl._read_dense_subarray File "tiledb/libtiledb.pyx", line 3172, in tiledb.libtiledb.ArraySchema.attr File "tiledb/libtiledb.pyx", line 3149, in tiledb.libtiledb.ArraySchema._attr_name File "tiledb/libtiledb.pyx", line 457, in tiledb.libtiledb.check_error File "tiledb/libtiledb.pyx", line 453, in tiledb.libtiledb._raise_ctx_err File "tiledb/libtiledb.pyx", line 438, in tiledb.libtiledb._raise_tiledb_error tiledb.libtiledb.TileDBError: [TileDB::ArraySchema] Error: Attribute name: does not exist for array file:///home/katasets/pbmc3k.cxg/emb/draw_graph_fr 127.0.0.1 - - [08/May/2020 10:28:02] "GET /api/v0.2/layout/obs HTTP/1.1" 500 - FAIL test_initialize (server.test.test_api.EndPointsCxg) ... 127.0.0.1 - - [08/May/2020 10:28:02] "GET /api/v0.2/schema HTTP/1.1" 2 ok test_static (server.test.test_api.EndPointsCxg) ... 127.0.0.1 - - [08/May/2020 10:28:02] "GET /static/assets/favicon.ico HTTP/ ok /home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/anndata/_core/anndata.py:21: FutureWarning: pandas.core.indersion. The public classes are available in the top-level namespace. from pandas.core.index import RangeIndex [cellxgene] Starting the CLI... [cellxgene] Warning: The default value of auto_mkdir=True has been deprecated and will be changed to auto_mkdir=False by defau [cellxgene] Loading data from . [cellxgene] Launching! Please go to http://127.0.0.1:5013 in your browser. [cellxgene] Type CTRL-C at any time to exit. * Serving Flask app "server.app.app" (lazy loading) * Environment: production WARNING: This is a development server. Do not use it in a production deployment. Use a production WSGI server instead. * Debug mode: off * Running on http://127.0.0.1:5013/ (Press CTRL+C to quit) 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:08] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:08] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:08] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:08] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:08] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:08] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:08] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:08] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:08] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:08] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:08] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:08] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:08] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:08] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:08] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:08] "GET /api/v0.2/schema HTTP/1.1" 200 - test_bad_filter (server.test.test_api.EndPointsCxgAnnotations) ... 127.0.0.1 - - [08/May/2020 10:28:08] "PUT /api/v0.2/data/va ok test_config (server.test.test_api.EndPointsCxgAnnotations) ... 127.0.0.1 - - [08/May/2020 10:28:08] "GET /api/v0.2/config HTTP ok test_data_get_fbs (server.test.test_api.EndPointsCxgAnnotations) ... 127.0.0.1 - - [08/May/2020 10:28:08] "GET /api/v0.2/data/ ok test_data_get_filter_fbs (server.test.test_api.EndPointsCxgAnnotations) ... [2020-05-08 10:28:08,305] ERROR in app: Exception Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1950, in full_dispatch_request rv = self.dispatch_request() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1936, in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py", line 468, in wrapper resp = resource(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/views.py", line 89, in view return self.dispatch_request(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py", line 583, in dispatch_r resp = meth(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 35, in wrapper response = make_response(f(*args, **kwargs)) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 116, in wrapped_function return func(self, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 207, in get return common_rest.data_var_get(request, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/common/rest.py", line 217, in data_var_get data_adaptor.data_frame_to_fbs_matrix(filter, axis=Axis.VAR), File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_common/data_adaptor.py", line 275, in d X = self.get_X_array(obs_selector, var_selector) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_cxg/cxg_adaptor.py", line 204, in get_X data = X.multi_index[obs_items, var_items][""] KeyError: '' 127.0.0.1 - - [08/May/2020 10:28:08] "GET /api/v0.2/data/var?var:name_0=SIK1 HTTP/1.1" 500 - FAIL test_data_mimetype_error (server.test.test_api.EndPointsCxgAnnotations) ... 127.0.0.1 - - [08/May/2020 10:28:08] "PUT /api/v0. ok test_data_put_fbs (server.test.test_api.EndPointsCxgAnnotations) ... 127.0.0.1 - - [08/May/2020 10:28:08] "PUT /api/v0.2/data/ ok test_data_put_filter_fbs (server.test.test_api.EndPointsCxgAnnotations) ... [2020-05-08 10:28:08,409] ERROR in app: Exception Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1950, in full_dispatch_request rv = self.dispatch_request() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1936, in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py", line 468, in wrapper resp = resource(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/views.py", line 89, in view return self.dispatch_request(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py", line 583, in dispatch_r resp = meth(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 35, in wrapper response = make_response(f(*args, **kwargs)) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 116, in wrapped_function return func(self, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 202, in put return common_rest.data_var_put(request, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/common/rest.py", line 201, in data_var_put data_adaptor.data_frame_to_fbs_matrix(filter, axis=Axis.VAR), File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_common/data_adaptor.py", line 275, in d X = self.get_X_array(obs_selector, var_selector) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_cxg/cxg_adaptor.py", line 204, in get_X data = X.multi_index[obs_items, var_items][""] KeyError: '' 127.0.0.1 - - [08/May/2020 10:28:08] "PUT /api/v0.2/data/var HTTP/1.1" 500 - FAIL test_data_put_single_var (server.test.test_api.EndPointsCxgAnnotations) ... [2020-05-08 10:28:08,460] ERROR in app: Exception Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1950, in full_dispatch_request rv = self.dispatch_request() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1936, in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py", line 468, in wrapper resp = resource(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/views.py", line 89, in view return self.dispatch_request(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py", line 583, in dispatch_r resp = meth(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 35, in wrapper response = make_response(f(*args, **kwargs)) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 116, in wrapped_function return func(self, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 202, in put return common_rest.data_var_put(request, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/common/rest.py", line 201, in data_var_put data_adaptor.data_frame_to_fbs_matrix(filter, axis=Axis.VAR), File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_common/data_adaptor.py", line 275, in d X = self.get_X_array(obs_selector, var_selector) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_cxg/cxg_adaptor.py", line 204, in get_X data = X.multi_index[obs_items, var_items][""] KeyError: '' 127.0.0.1 - - [08/May/2020 10:28:08] "PUT /api/v0.2/data/var HTTP/1.1" 500 - FAIL test_diff_exp (server.test.test_api.EndPointsCxgAnnotations) ... [2020-05-08 10:28:08,656] ERROR in app: Exception on /api/v0. Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/compute/diffexp_cxg.py", line 84, in diffexp result = future.result() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/concurrent/futures/_base.py", line 435, in result return self.__get_result() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result raise self._exception File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/concurrent/futures/thread.py", line 57, in run result = self.fn(*self.args, **self.kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/compute/diffexp_cxg.py", line 110, in _mean_ X = matrix.multi_index[row_selector_AB, col_range[0] : col_range[1] - 1][""] KeyError: '' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1950, in full_dispatch_request rv = self.dispatch_request() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1936, in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py", line 468, in wrapper resp = resource(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/views.py", line 89, in view return self.dispatch_request(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py", line 583, in dispatch_r resp = meth(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 35, in wrapper response = make_response(f(*args, **kwargs)) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 116, in wrapped_function return func(self, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 214, in post return common_rest.diffexp_obs_post(request, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/common/rest.py", line 250, in diffexp_obs_po diffexp = data_adaptor.diffexp_topN(set1_filter, set2_filter, count) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_common/data_adaptor.py", line 307, in d result = self.compute_diffexp_ttest(obs_mask_A, obs_mask_B, top_n, self.config.diffexp__lfc_cutoff) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_cxg/cxg_adaptor.py", line 195, in compu return diffexp_cxg.diffexp_ttest(self, maskA, maskB, top_n, lfc_cutoff) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/compute/diffexp_cxg.py", line 93, in diffexp raise ComputeError(str(e)) server.common.errors.ComputeError: '' 127.0.0.1 - - [08/May/2020 10:28:08] "POST /api/v0.2/diffexp/obs HTTP/1.1" 500 - FAIL test_diff_exp_indices (server.test.test_api.EndPointsCxgAnnotations) ... [2020-05-08 10:28:08,749] ERROR in app: Exception on Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/compute/diffexp_cxg.py", line 84, in diffexp result = future.result() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/concurrent/futures/_base.py", line 435, in result return self.__get_result() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result raise self._exception File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/concurrent/futures/thread.py", line 57, in run result = self.fn(*self.args, **self.kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/compute/diffexp_cxg.py", line 110, in _mean_ X = matrix.multi_index[row_selector_AB, col_range[0] : col_range[1] - 1][""] KeyError: '' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1950, in full_dispatch_request rv = self.dispatch_request() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1936, in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py", line 468, in wrapper resp = resource(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/views.py", line 89, in view return self.dispatch_request(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py", line 583, in dispatch_r resp = meth(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 35, in wrapper response = make_response(f(*args, **kwargs)) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 116, in wrapped_function return func(self, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 214, in post return common_rest.diffexp_obs_post(request, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/common/rest.py", line 250, in diffexp_obs_po diffexp = data_adaptor.diffexp_topN(set1_filter, set2_filter, count) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_common/data_adaptor.py", line 307, in d result = self.compute_diffexp_ttest(obs_mask_A, obs_mask_B, top_n, self.config.diffexp__lfc_cutoff) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_cxg/cxg_adaptor.py", line 195, in compu return diffexp_cxg.diffexp_ttest(self, maskA, maskB, top_n, lfc_cutoff) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/compute/diffexp_cxg.py", line 93, in diffexp raise ComputeError(str(e)) server.common.errors.ComputeError: '' 127.0.0.1 - - [08/May/2020 10:28:08] "POST /api/v0.2/diffexp/obs HTTP/1.1" 500 - FAIL test_fbs_default (server.test.test_api.EndPointsCxgAnnotations) ... 127.0.0.1 - - [08/May/2020 10:28:08] "PUT /api/v0.2/data/v [2020-05-08 10:28:08,808] ERROR in app: Exception on /api/v0.2/data/var [PUT] Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1950, in full_dispatch_request rv = self.dispatch_request() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1936, in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py", line 468, in wrapper resp = resource(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/views.py", line 89, in view return self.dispatch_request(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py", line 583, in dispatch_r resp = meth(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 35, in wrapper response = make_response(f(*args, **kwargs)) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 116, in wrapped_function return func(self, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 202, in put return common_rest.data_var_put(request, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/common/rest.py", line 201, in data_var_put data_adaptor.data_frame_to_fbs_matrix(filter, axis=Axis.VAR), File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_common/data_adaptor.py", line 275, in d X = self.get_X_array(obs_selector, var_selector) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_cxg/cxg_adaptor.py", line 204, in get_X data = X.multi_index[obs_items, var_items][""] KeyError: '' 127.0.0.1 - - [08/May/2020 10:28:08] "PUT /api/v0.2/data/var HTTP/1.1" 500 - FAIL test_get_annotations_obs_error (server.test.test_api.EndPointsCxgAnnotations) ... 127.0.0.1 - - [08/May/2020 10:28:08] "GET /aTP/1.1" 400 - ok test_get_annotations_obs_fbs (server.test.test_api.EndPointsCxgAnnotations) ... 127.0.0.1 - - [08/May/2020 10:28:08] "GET /api ok test_get_annotations_obs_keys_fbs (server.test.test_api.EndPointsCxgAnnotations) ... 127.0.0.1 - - [08/May/2020 10:28:08] "GET&annotation-name=percent_mito HTTP/1.1" 200 - ok test_get_annotations_var_error (server.test.test_api.EndPointsCxgAnnotations) ... 127.0.0.1 - - [08/May/2020 10:28:08] "GET /aTP/1.1" 400 - ok test_get_annotations_var_fbs (server.test.test_api.EndPointsCxgAnnotations) ... 127.0.0.1 - - [08/May/2020 10:28:08] "GET /api ok test_get_annotations_var_keys_fbs (server.test.test_api.EndPointsCxgAnnotations) ... 127.0.0.1 - - [08/May/2020 10:28:09] "GET HTTP/1.1" 200 - ok test_get_layout_fbs (server.test.test_api.EndPointsCxgAnnotations) ... [2020-05-08 10:28:09,054] ERROR in app: Exception on /a Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1950, in full_dispatch_request rv = self.dispatch_request() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1936, in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py", line 468, in wrapper resp = resource(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/views.py", line 89, in view return self.dispatch_request(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py", line 583, in dispatch_r resp = meth(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 35, in wrapper response = make_response(f(*args, **kwargs)) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 116, in wrapped_function return func(self, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 221, in get return common_rest.layout_obs_get(request, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/common/rest.py", line 273, in layout_obs_get data_adaptor.layout_to_fbs_matrix(fields), HTTPStatus.OK, {"Content-Type": "application/octet-stream"} File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_common/data_adaptor.py", line 352, in l embedding = self.get_embedding_array(ename, 2) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_cxg/cxg_adaptor.py", line 185, in get_e return array[:, 0:dims] File "tiledb/libtiledb.pyx", line 4002, in tiledb.libtiledb.DenseArrayImpl.__getitem__ File "tiledb/libtiledb.pyx", line 4107, in tiledb.libtiledb.DenseArrayImpl.subarray File "tiledb/libtiledb.pyx", line 4153, in tiledb.libtiledb.DenseArrayImpl._read_dense_subarray File "tiledb/libtiledb.pyx", line 3172, in tiledb.libtiledb.ArraySchema.attr File "tiledb/libtiledb.pyx", line 3149, in tiledb.libtiledb.ArraySchema._attr_name File "tiledb/libtiledb.pyx", line 457, in tiledb.libtiledb.check_error File "tiledb/libtiledb.pyx", line 453, in tiledb.libtiledb._raise_ctx_err File "tiledb/libtiledb.pyx", line 438, in tiledb.libtiledb._raise_tiledb_error tiledb.libtiledb.TileDBError: [TileDB::ArraySchema] Error: Attribute name: does not exist for array file:///home/katasets/pbmc3k.cxg/emb/draw_graph_fr 127.0.0.1 - - [08/May/2020 10:28:09] "GET /api/v0.2/layout/obs HTTP/1.1" 500 - FAIL test_get_schema_existing_writable (server.test.test_api.EndPointsCxgAnnotations) ... 127.0.0.1 - - [08/May/2020 10:28:09] "GET ok test_get_user_annotations_existing_obs_keys_fbs (server.test.test_api.EndPointsCxgAnnotations) ... 127.0.0.1 - - [08/May/2020 n-name=cluster-test HTTP/1.1" 200 - ok test_initialize (server.test.test_api.EndPointsCxgAnnotations) ... 127.0.0.1 - - [08/May/2020 10:28:09] "GET /api/v0.2/schema ok test_put_user_annotations_obs_fbs (server.test.test_api.EndPointsCxgAnnotations) ... 127.0.0.1 - - [08/May/2020 10:28:09] "PUTame=test_annotations HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:09] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:09] "GET /api/v0.2/annotations/obs?annotation-name=cat_A HTTP/1.1" 200 - ok test_static (server.test.test_api.EndPointsCxgAnnotations) ... 127.0.0.1 - - [08/May/2020 10:28:09] "GET /static/assets/favico ok test_update (server.test.test_app_config.AppConfigTest) ... ok test_make_index_unique (server.test.test_cli_prepare.CLIPrepareTests) ... ok test_assert_verstion_gt (server.test.test_cli_upgrade.CLIUpgradeTests) ... ok test_split_version_str (server.test.test_cli_upgrade.CLIUpgradeTests) ... ok test_validate_version_str (server.test.test_cli_upgrade.CLIUpgradeTests) ... ok test_anndata_default (server.test.test_diffexp.DiffExpTest) Test an anndata adaptor with its default diffexp algorithm (diffexp_generic) ... FAIL test_cxg_default (server.test.test_diffexp.DiffExpTest) Test a cxg adaptor with its default diffexp algorithm (diffexp_cxg) ... ERROR test_cxg_generic (server.test.test_diffexp.DiffExpTest) Test a cxg adaptor with the generic adaptor ... ERROR test_encode_DataFrame (server.test.test_fbs.FbsTests) ... ok test_encode_boundary (server.test.test_fbs.FbsTests) test various boundary checks ... ok test_encode_ndarray (server.test.test_fbs.FbsTests) ... ok test_encode_sparse (server.test.test_fbs.FbsTests) ... ok test_roundtrip (server.test.test_fbs.FbsTests) ... ok test_queryparam_to_filter_errors (server.test.test_filter.FilterParseTests) ... ok test_queryparam_to_filter_escaping (server.test.test_filter.FilterParseTests) ... ok test_queryparam_to_filter_parse (server.test.test_filter.FilterParseTests) ... ok test_access_error (server.test.test_matrixcache.MatrixCacheTest) ... ok test_basic (server.test.test_matrixcache.MatrixCacheTest) ... ok test_timelimit (server.test.test_matrixcache.MatrixCacheTest) ... ok server.test.test_nan_anndata_adaptor (unittest.loader._FailedTest) ... ERROR /home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/anndata/_core/anndata.py:21: FutureWarning: pandas.core.indersion. The public classes are available in the top-level namespace. from pandas.core.index import RangeIndex [cellxgene] Starting the CLI... [cellxgene] Warning: The default value of auto_mkdir=True has been deprecated and will be changed to auto_mkdir=False by defau [cellxgene] Loading data from nan.h5ad. [cellxgene] Warning: Annotation var_with_nans will be converted to 32 bit float and may lose precision. [cellxgene] Launching! Please go to http://127.0.0.1:5006 in your browser. [cellxgene] Type CTRL-C at any time to exit. * Serving Flask app "server.app.app" (lazy loading) * Environment: production WARNING: This is a development server. Do not use it in a production deployment. Use a production WSGI server instead. * Debug mode: off * Running on http://127.0.0.1:5006/ (Press CTRL+C to quit) 127.0.0.1 - - [08/May/2020 10:28:17] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:17] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:17] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:17] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:17] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:17] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:17] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:17] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:17] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:17] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:17] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:17] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:17] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:17] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:17] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:17] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:17] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:17] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:17] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:17] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:17] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:17] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:17] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:17] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:17] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 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HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:28:18] "GET /api/v0.2/schema HTTP/1.1" 200 - test_annotation_obs (server.test.test_nan_rest.WithNaNs) ... 127.0.0.1 - - [08/May/2020 10:28:18] "GET /api/v0.2/annotations/o ok test_annotation_var (server.test.test_nan_rest.WithNaNs) ... 127.0.0.1 - - [08/May/2020 10:28:18] "GET /api/v0.2/annotations/v ok test_data (server.test.test_nan_rest.WithNaNs) ... 127.0.0.1 - - [08/May/2020 10:28:18] "PUT /api/v0.2/data/var HTTP/1.1" 200 ok test_initialize (server.test.test_nan_rest.WithNaNs) ... 127.0.0.1 - - [08/May/2020 10:28:18] "GET /api/v0.2/schema HTTP/1.1" ok test_config (server.test.test_writable_annotation.WritableAnnotationTest) ... ok test_error_checks (server.test.test_writable_annotation.WritableAnnotationTest) ... ok test_file_rotation_to_max_9 (server.test.test_writable_annotation.WritableAnnotationTest) ... ok test_put_get_roundtrip (server.test.test_writable_annotation.WritableAnnotationTest) ... ok test_write_to_file (server.test.test_writable_annotation.WritableAnnotationTest) ... ok ====================================================================== ERROR: server.test.test_anndata_adaptor (unittest.loader._FailedTest) ---------------------------------------------------------------------- ImportError: Failed to import test module: server.test.test_anndata_adaptor Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/unittest/loader.py", line 436, in _find_test_path module = self._get_module_from_name(name) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/unittest/loader.py", line 377, in _get_module_from_name __import__(name) File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_anndata_adaptor.py", line 3, in import pytest ModuleNotFoundError: No module named 'pytest' ====================================================================== ERROR: test_cxg_default (server.test.test_diffexp.DiffExpTest) Test a cxg adaptor with its default diffexp algorithm (diffexp_cxg) ---------------------------------------------------------------------- Traceback (most recent call last): KeyError: '' During handling of the above exception, another exception occurred: Traceback (most recent call last): server.common.errors.ComputeError: '' ====================================================================== ERROR: test_cxg_generic (server.test.test_diffexp.DiffExpTest) Test a cxg adaptor with the generic adaptor ---------------------------------------------------------------------- Traceback (most recent call last): KeyError: '' ====================================================================== ERROR: server.test.test_nan_anndata_adaptor (unittest.loader._FailedTest) ---------------------------------------------------------------------- ImportError: Failed to import test module: server.test.test_nan_anndata_adaptor Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/unittest/loader.py", line 436, in _find_test_path module = self._get_module_from_name(name) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/unittest/loader.py", line 377, in _get_module_from_name __import__(name) File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_nan_anndata_adaptor.py", line 1, in import pytest ModuleNotFoundError: No module named 'pytest' ====================================================================== FAIL: test_data_get_filter_fbs (server.test.test_api.EndPointsCxg) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_api.py", line 239, in test_data_get_filter_fbs self.assertEqual(result.status_code, HTTPStatus.OK) AssertionError: 500 != ====================================================================== FAIL: test_data_put_filter_fbs (server.test.test_api.EndPointsCxg) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_api.py", line 222, in test_data_put_filter_fbs self.assertEqual(result.status_code, HTTPStatus.OK) AssertionError: 500 != ====================================================================== FAIL: test_data_put_single_var (server.test.test_api.EndPointsCxg) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_api.py", line 252, in test_data_put_single_var self.assertEqual(result.status_code, HTTPStatus.OK) AssertionError: 500 != ====================================================================== FAIL: test_diff_exp (server.test.test_api.EndPointsCxg) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_api.py", line 126, in test_diff_exp self.assertEqual(result.status_code, HTTPStatus.OK) AssertionError: 500 != ====================================================================== FAIL: test_diff_exp_indices (server.test.test_api.EndPointsCxg) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_api.py", line 141, in test_diff_exp_indices self.assertEqual(result.status_code, HTTPStatus.OK) AssertionError: 500 != ====================================================================== FAIL: test_fbs_default (server.test.test_api.EndPointsCxg) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_api.py", line 200, in test_fbs_default self.assertEqual(result.headers["Content-Type"], "application/octet-stream") AssertionError: 'application/json' != 'application/octet-stream' - application/json + application/octet-stream ====================================================================== FAIL: test_get_layout_fbs (server.test.test_api.EndPointsCxg) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_api.py", line 54, in test_get_layout_fbs self.assertEqual(result.status_code, HTTPStatus.OK) AssertionError: 500 != ====================================================================== FAIL: test_data_get_filter_fbs (server.test.test_api.EndPointsCxgAnnotations) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_api.py", line 239, in test_data_get_filter_fbs self.assertEqual(result.status_code, HTTPStatus.OK) AssertionError: 500 != ====================================================================== FAIL: test_data_put_filter_fbs (server.test.test_api.EndPointsCxgAnnotations) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_api.py", line 222, in test_data_put_filter_fbs self.assertEqual(result.status_code, HTTPStatus.OK) AssertionError: 500 != ====================================================================== FAIL: test_data_put_single_var (server.test.test_api.EndPointsCxgAnnotations) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_api.py", line 252, in test_data_put_single_var self.assertEqual(result.status_code, HTTPStatus.OK) AssertionError: 500 != ====================================================================== FAIL: test_diff_exp (server.test.test_api.EndPointsCxgAnnotations) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_api.py", line 126, in test_diff_exp self.assertEqual(result.status_code, HTTPStatus.OK) AssertionError: 500 != ====================================================================== FAIL: test_diff_exp_indices (server.test.test_api.EndPointsCxgAnnotations) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_api.py", line 141, in test_diff_exp_indices self.assertEqual(result.status_code, HTTPStatus.OK) AssertionError: 500 != ====================================================================== FAIL: test_fbs_default (server.test.test_api.EndPointsCxgAnnotations) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_api.py", line 200, in test_fbs_default self.assertEqual(result.headers["Content-Type"], "application/octet-stream") AssertionError: 'application/json' != 'application/octet-stream' - application/json + application/octet-stream ====================================================================== FAIL: test_get_layout_fbs (server.test.test_api.EndPointsCxgAnnotations) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_api.py", line 54, in test_get_layout_fbs self.assertEqual(result.status_code, HTTPStatus.OK) AssertionError: 500 != ====================================================================== FAIL: test_anndata_default (server.test.test_diffexp.DiffExpTest) Test an anndata adaptor with its default diffexp algorithm (diffexp_generic) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_diffexp.py", line 57, in test_anndata_default self.check_1_10_2_10(results) File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_diffexp.py", line 47, in check_1_10_2_10 self.assertAlmostEqual(result[1], expect[1]) AssertionError: 0.5201582 != 0.5201581 within 7 places (7.165374760198517e-08 difference) ---------------------------------------------------------------------- Ran 121 tests in 46.913s FAILED (failures=15, errors=4) make: *** [Makefile:10: unit-test] Error 1 (cellxgenevis) [kli3@yarrow01 server]$ conda install coverage ^C CondaError: KeyboardInterrupt (cellxgenevis) [kli3@yarrow01 server]$ (cellxgenevis) [kli3@yarrow01 server]$ (cellxgenevis) [kli3@yarrow01 server]$ (cellxgenevis) [kli3@yarrow01 server]$ ll total 928 drwxrwxr-x. 2 kli3 1000515 53 May 7 18:20 app drwxrwxr-x. 3 kli3 1000515 195 May 8 10:27 cli drwxrwxr-x. 4 kli3 1000515 413 May 8 10:27 common drwxrwxr-x. 3 kli3 1000515 153 May 8 10:27 compute drwxrwxr-x. 2 kli3 1000515 28 May 7 18:20 converters drwxrwxr-x. 3 kli3 1000515 94 May 8 10:27 data_anndata drwxrwxr-x. 4 kli3 1000515 203 May 8 10:27 data_common drwxrwxr-x. 3 kli3 1000515 119 May 8 10:27 data_cxg drwxrwxr-x. 3 kli3 1000515 144 May 7 18:20 eb -rw-rw-r--. 1 kli3 1000515 23 May 7 18:20 __init__.py -rw-rw-r--. 1 kli3 1000515 177 May 8 09:22 __init__.pyc drwxrwxr-x. 2 kli3 1000515 126 May 7 18:20 locust -rw-rw-r--. 1 kli3 1000515 339 May 7 18:20 __main__.py -rw-rw-r--. 1 kli3 1000515 424 May 8 10:05 Makefile drwxrwxr-x. 2 kli3 1000515 41 May 8 10:27 __pycache__ -rw-rw-r--. 1 kli3 1000515 108 May 7 18:20 requirements-dev.txt -rw-rw-r--. 1 kli3 1000515 41 May 7 18:20 requirements-prepare.txt -rw-rw-r--. 1 kli3 1000515 347 May 7 18:20 requirements.txt drwxrwxr-x. 4 kli3 1000515 882 May 8 10:27 test (cellxgenevis) [kli3@yarrow01 server]$ more requirements.txt anndata>=0.6.20 boto3>=1.12.18 click>=6.7 fastobo>=0.6.1 Flask>=1.0.2 Flask-Compress>=1.4.0 Flask-Cors>=3.0.6 Flask-RESTful>=0.3.6 flask-server-timing>=0.1.2 flask-talisman>=0.7.0 flatbuffers>=1.10.0 flatten-dict>=0.2.0 fsspec>=0.4.4 numpy>=1.16.0 packaging>=20.0 pandas>=0.24.2 PyYAML>=5.3 scipy>=1.3.0 requests>=2.22.0 tiledb>=0.5.3 s3fs>=0.4.2 (cellxgenevis) [kli3@yarrow01 server]$ more requirements-prepare.txt scanpy>=1.3.7 python-igraph louvain>=0.6 (cellxgenevis) [kli3@yarrow01 server]$ more requirements-dev.txt black bumpversion>=0.5 parameterized>=0.7.0 pytest>=3.6.3 twine>=1.12.1 codecov>=2.0.15 -r requirements.txt (cellxgenevis) [kli3@yarrow01 server]$ conda install pytest Collecting package metadata (current_repodata.json): done Solving environment: done ## Package Plan ## environment location: /home/kli3/anaconda3/envs/cellxgenevis added / updated specs: - pytest The following packages will be downloaded: package | build ---------------------------|----------------- more-itertools-8.2.0 | py_0 35 KB conda-forge pluggy-0.13.1 | py37hc8dfbb8_1 29 KB conda-forge py-1.8.1 | py_0 66 KB conda-forge pytest-5.4.2 | py37hc8dfbb8_0 383 KB conda-forge ------------------------------------------------------------ Total: 512 KB The following NEW packages will be INSTALLED: attrs conda-forge/noarch::attrs-19.3.0-py_0 importlib-metadata conda-forge/linux-64::importlib-metadata-1.6.0-py37hc8dfbb8_0 importlib_metadata conda-forge/noarch::importlib_metadata-1.6.0-0 more-itertools conda-forge/noarch::more-itertools-8.2.0-py_0 packaging conda-forge/noarch::packaging-20.1-py_0 pluggy conda-forge/linux-64::pluggy-0.13.1-py37hc8dfbb8_1 py conda-forge/noarch::py-1.8.1-py_0 pyparsing conda-forge/noarch::pyparsing-2.4.7-pyh9f0ad1d_0 pytest conda-forge/linux-64::pytest-5.4.2-py37hc8dfbb8_0 six conda-forge/noarch::six-1.14.0-py_1 wcwidth conda-forge/noarch::wcwidth-0.1.9-pyh9f0ad1d_0 zipp conda-forge/noarch::zipp-3.1.0-py_0 Proceed ([y]/n)? y Downloading and Extracting Packages py-1.8.1 | 66 KB | ########################################################## | 100% pytest-5.4.2 | 383 KB | ########################################################## | 100% more-itertools-8.2.0 | 35 KB | ########################################################## | 100% pluggy-0.13.1 | 29 KB | ########################################################## | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done (cellxgenevis) [kli3@yarrow01 server]$ make unit-test |less -S (cellxgenevis) [kli3@yarrow01 server]$ pwd /home/kli3/git/cellxgene_VIP/cellxgene/server (cellxgenevis) [kli3@yarrow01 server]$ make unit-test > log.txt /home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/anndata/_core/anndata.py:21: Futur eWarning: pandas.core.index is deprecated and will be removed in a future version. The public classe s are available in the top-level namespace. from pandas.core.index import RangeIndex server.test.test_anndata_adaptor (unittest.loader._FailedTest) ... ERROR test_delayed_load_data (server.test.test_anndata_adaptor_data_load.DataLoadAdaptorTest) ... /home/kli 3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/fsspec/implementations/local.py:33: FutureW arning: The default value of auto_mkdir=True has been deprecated and will be changed to auto_mkdir=Fa lse by default in a future release. FutureWarning, ok test_diffexp_topN (server.test.test_anndata_adaptor_data_load.DataLoadAdaptorTest) ... ok test_posix_file (server.test.test_anndata_adaptor_data_load.DataLocatorAdaptorTest) ... ok test_url_http (server.test.test_anndata_adaptor_data_load.DataLocatorAdaptorTest) ... ok test_url_https (server.test.test_anndata_adaptor_data_load.DataLocatorAdaptorTest) ... ok /home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/anndata/_core/anndata.py:21: Futur eWarning: pandas.core.index is deprecated and will be removed in a future version. The public classe s are available in the top-level namespace. from pandas.core.index import RangeIndex [cellxgene] Warning: The default value of auto_mkdir=True has been deprecated and will be changed to auto_mkdir=False by default in a future release. * Running on http://127.0.0.1:5010/ (Press CTRL+C to quit) 127.0.0.1 - - [08/May/2020 10:42:06] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:06] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:06] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:06] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:06] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:06] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:06] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:06] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:06] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:06] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:06] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:06] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:06] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:06] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:06] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:06] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:06] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:06] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:06] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:06] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:07] "GET /api/v0.2/schema HTTP/1.1" 200 - test_bad_filter (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:42:07] "PUT /api/v0.2/data/var HTTP/1.1" 400 - ok test_config (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:42:07] "GET /ap i/v0.2/config HTTP/1.1" 200 - ok test_data_get_fbs (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:42:07] "G ET /api/v0.2/data/var HTTP/1.1" 400 - ok test_data_get_filter_fbs (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:42 :07] "GET /api/v0.2/data/var?var:name_0=SIK1 HTTP/1.1" 200 - ok test_data_mimetype_error (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:42 :07] "PUT /api/v0.2/data/var HTTP/1.1" 406 - ok test_data_put_fbs (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:42:07] "P UT /api/v0.2/data/var HTTP/1.1" 400 - ok test_data_put_filter_fbs (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:42 :07] "PUT /api/v0.2/data/var HTTP/1.1" 200 - ok test_data_put_single_var (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:42 :07] "PUT /api/v0.2/data/var HTTP/1.1" 200 - ok test_diff_exp (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:42:07] "POST /api/v0.2/diffexp/obs HTTP/1.1" 200 - ok test_diff_exp_indices (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:42:07 ] "POST /api/v0.2/diffexp/obs HTTP/1.1" 200 - ok test_fbs_default (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:42:07] "PU T /api/v0.2/data/var HTTP/1.1" 400 - 127.0.0.1 - - [08/May/2020 10:42:07] "PUT /api/v0.2/data/var HTTP/1.1" 200 - ok test_get_annotations_obs_error (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:42:08] "GET /api/v0.2/annotations/obs?annotation-name=notakey HTTP/1.1" 400 - ok test_get_annotations_obs_fbs (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 1 0:42:08] "GET /api/v0.2/annotations/obs HTTP/1.1" 200 - ok test_get_annotations_obs_keys_fbs (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2 020 10:42:08] "GET /api/v0.2/annotations/obs?annotation-name=n_genes&annotation-name=percent_mito HTT P/1.1" 200 - ok test_get_annotations_var_error (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:42:08] "GET /api/v0.2/annotations/var?annotation-name=notakey HTTP/1.1" 400 - ok test_get_annotations_var_fbs (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 1 0:42:08] "GET /api/v0.2/annotations/var HTTP/1.1" 200 - ok test_get_annotations_var_keys_fbs (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2 020 10:42:08] "GET /api/v0.2/annotations/var?annotation-name=n_cells HTTP/1.1" 200 - ok test_get_layout_fbs (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:42:08] "GET /api/v0.2/layout/obs HTTP/1.1" 200 - ok test_initialize (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:42:08] "GET /api/v0.2/schema HTTP/1.1" 200 - ok test_static (server.test.test_api.EndPointsAnndata) ... 127.0.0.1 - - [08/May/2020 10:42:08] "GET /st atic/assets/favicon.ico HTTP/1.1" 200 - ok /home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/anndata/_core/anndata.py:21: Futur eWarning: pandas.core.index is deprecated and will be removed in a future version. The public classe s are available in the top-level namespace. from pandas.core.index import RangeIndex [cellxgene] Warning: The default value of auto_mkdir=True has been deprecated and will be changed to auto_mkdir=False by default in a future release. * Running on http://127.0.0.1:5012/ (Press CTRL+C to quit) 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 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127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:13] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:14] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:14] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:14] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:14] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:14] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:14] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:14] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:14] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:14] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:14] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:14] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:14] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:14] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:14] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:14] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:14] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:14] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:14] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:14] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:14] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:14] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:14] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:14] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:14] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:14] "GET /api/v0.2/schema HTTP/1.1" 200 - test_bad_filter (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 10: 42:14] "PUT /api/v0.2/data/var HTTP/1.1" 400 - ok test_config (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 10:42:1 4] "GET /api/v0.2/config HTTP/1.1" 200 - ok test_data_get_fbs (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 1 0:42:14] "GET /api/v0.2/data/var HTTP/1.1" 400 - ok test_data_get_filter_fbs (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May /2020 10:42:14] "GET /api/v0.2/data/var?var:name_0=SIK1 HTTP/1.1" 200 - ok test_data_mimetype_error (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May /2020 10:42:14] "PUT /api/v0.2/data/var HTTP/1.1" 406 - ok test_data_put_fbs (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 1 0:42:14] "PUT /api/v0.2/data/var HTTP/1.1" 400 - ok test_data_put_filter_fbs (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May /2020 10:42:14] "PUT /api/v0.2/data/var HTTP/1.1" 200 - ok test_data_put_single_var (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May /2020 10:42:14] "PUT /api/v0.2/data/var HTTP/1.1" 200 - ok test_diff_exp (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 10:42 :14] "POST /api/v0.2/diffexp/obs HTTP/1.1" 200 - ok test_diff_exp_indices (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/20 20 10:42:14] "POST /api/v0.2/diffexp/obs HTTP/1.1" 200 - ok test_fbs_default (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 10 :42:14] "PUT /api/v0.2/data/var HTTP/1.1" 400 - 127.0.0.1 - - [08/May/2020 10:42:14] "PUT /api/v0.2/data/var HTTP/1.1" 200 - ok test_get_annotations_obs_error (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [ 08/May/2020 10:42:14] "GET /api/v0.2/annotations/obs?annotation-name=notakey HTTP/1.1" 400 - ok test_get_annotations_obs_fbs (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08 /May/2020 10:42:14] "GET /api/v0.2/annotations/obs HTTP/1.1" 200 - ok test_get_annotations_obs_keys_fbs (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 10:42:14] "GET /api/v0.2/annotations/obs?annotation-name=n_genes&annotation-name=perce nt_mito HTTP/1.1" 200 - ok test_get_annotations_var_error (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [ 08/May/2020 10:42:14] "GET /api/v0.2/annotations/var?annotation-name=notakey HTTP/1.1" 400 - ok test_get_annotations_var_fbs (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08 /May/2020 10:42:14] "GET /api/v0.2/annotations/var HTTP/1.1" 200 - ok test_get_annotations_var_keys_fbs (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 10:42:14] "GET /api/v0.2/annotations/var?annotation-name=n_cells HTTP/1.1" 200 - ok test_get_layout_fbs (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 10:42:14] "GET /api/v0.2/layout/obs HTTP/1.1" 200 - ok test_get_schema_existing_writable (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 10:42:14] "GET /api/v0.2/schema HTTP/1.1" 200 - ok test_get_user_annotations_existing_obs_keys_fbs (server.test.test_api.EndPointsAnndataAnnotations) .. . 127.0.0.1 - - [08/May/2020 10:42:14] "GET /api/v0.2/annotations/obs?annotation-name=cluster-test HT TP/1.1" 200 - ok test_initialize (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 10: 42:14] "GET /api/v0.2/schema HTTP/1.1" 200 - ok test_put_user_annotations_obs_fbs (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 10:42:14] "PUT /api/v0.2/annotations/obs?annotation-collection-name=test_annotations H TTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:14] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:14] "GET /api/v0.2/annotations/obs?annotation-name=cat_A HTTP/1.1" 2 00 - ok test_static (server.test.test_api.EndPointsAnndataAnnotations) ... 127.0.0.1 - - [08/May/2020 10:42:1 4] "GET /static/assets/favicon.ico HTTP/1.1" 200 - ok /home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/anndata/_core/anndata.py:21: Futur eWarning: pandas.core.index is deprecated and will be removed in a future version. The public classe s are available in the top-level namespace. from pandas.core.index import RangeIndex [cellxgene] Warning: The default value of auto_mkdir=True has been deprecated and will be changed to auto_mkdir=False by default in a future release. * Running on http://127.0.0.1:5011/ (Press CTRL+C to quit) 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:18] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:19] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:19] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:19] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:19] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:19] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:19] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:19] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:19] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:19] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:19] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:19] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:19] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:19] "GET /api/v0.2/schema HTTP/1.1" 200 - test_bad_filter (server.test.test_api.EndPointsCxg) ... 127.0.0.1 - - [08/May/2020 10:42:19] "PUT /ap i/v0.2/data/var HTTP/1.1" 400 - ok test_config (server.test.test_api.EndPointsCxg) ... 127.0.0.1 - - [08/May/2020 10:42:19] "GET /api/v0 .2/config HTTP/1.1" 200 - ok test_data_get_fbs (server.test.test_api.EndPointsCxg) ... 127.0.0.1 - - [08/May/2020 10:42:19] "GET / api/v0.2/data/var HTTP/1.1" 400 - ok test_data_get_filter_fbs (server.test.test_api.EndPointsCxg) ... [2020-05-08 10:42:19,309] ERROR in a pp: Exception on /api/v0.2/data/var [GET] Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1950, in full_dispatch_request rv = self.dispatch_request() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1936, in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py" , line 468, in wrapper resp = resource(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/views.py", line 89, in view return self.dispatch_request(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py" , line 583, in dispatch_request resp = meth(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 3 5, in wrapper response = make_response(f(*args, **kwargs)) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 1 16, in wrapped_function return func(self, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 2 07, in get return common_rest.data_var_get(request, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/common/rest.py", li ne 217, in data_var_get data_adaptor.data_frame_to_fbs_matrix(filter, axis=Axis.VAR), File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_common/data_ad aptor.py", line 275, in data_frame_to_fbs_matrix X = self.get_X_array(obs_selector, var_selector) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_cxg/cxg_adapto r.py", line 204, in get_X_array data = X.multi_index[obs_items, var_items][""] KeyError: '' 127.0.0.1 - - [08/May/2020 10:42:19] "GET /api/v0.2/data/var?var:name_0=SIK1 HTTP/1.1" 500 - FAIL test_data_mimetype_error (server.test.test_api.EndPointsCxg) ... 127.0.0.1 - - [08/May/2020 10:42:19] "PUT /api/v0.2/data/var HTTP/1.1" 406 - ok test_data_put_fbs (server.test.test_api.EndPointsCxg) ... 127.0.0.1 - - [08/May/2020 10:42:19] "PUT / api/v0.2/data/var HTTP/1.1" 400 - ok test_data_put_filter_fbs (server.test.test_api.EndPointsCxg) ... [2020-05-08 10:42:19,418] ERROR in a pp: Exception on /api/v0.2/data/var [PUT] Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1950, in full_dispatch_request rv = self.dispatch_request() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1936, in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py" , line 468, in wrapper resp = resource(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/views.py", line 89, in view return self.dispatch_request(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py" , line 583, in dispatch_request resp = meth(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 3 5, in wrapper response = make_response(f(*args, **kwargs)) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 1 16, in wrapped_function return func(self, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 2 02, in put return common_rest.data_var_put(request, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/common/rest.py", li ne 201, in data_var_put data_adaptor.data_frame_to_fbs_matrix(filter, axis=Axis.VAR), File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_common/data_ad aptor.py", line 275, in data_frame_to_fbs_matrix X = self.get_X_array(obs_selector, var_selector) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_cxg/cxg_adapto r.py", line 204, in get_X_array data = X.multi_index[obs_items, var_items][""] KeyError: '' 127.0.0.1 - - [08/May/2020 10:42:19] "PUT /api/v0.2/data/var HTTP/1.1" 500 - FAIL test_data_put_single_var (server.test.test_api.EndPointsCxg) ... [2020-05-08 10:42:19,468] ERROR in a pp: Exception on /api/v0.2/data/var [PUT] Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1950, in full_dispatch_request rv = self.dispatch_request() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1936, in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py" , line 468, in wrapper resp = resource(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/views.py", line 89, in view return self.dispatch_request(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py" , line 583, in dispatch_request resp = meth(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 3 5, in wrapper response = make_response(f(*args, **kwargs)) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 1 16, in wrapped_function return func(self, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 2 02, in put return common_rest.data_var_put(request, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/common/rest.py", li ne 201, in data_var_put data_adaptor.data_frame_to_fbs_matrix(filter, axis=Axis.VAR), File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_common/data_ad aptor.py", line 275, in data_frame_to_fbs_matrix X = self.get_X_array(obs_selector, var_selector) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_cxg/cxg_adapto r.py", line 204, in get_X_array data = X.multi_index[obs_items, var_items][""] KeyError: '' 127.0.0.1 - - [08/May/2020 10:42:19] "PUT /api/v0.2/data/var HTTP/1.1" 500 - FAIL test_diff_exp (server.test.test_api.EndPointsCxg) ... [2020-05-08 10:42:19,682] ERROR in app: Excepti on on /api/v0.2/diffexp/obs [POST] Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/compute/diffexp_cxg .py", line 84, in diffexp_ttest result = future.result() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/concurrent/futures/_base.py", line 435, in result return self.__get_result() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result raise self._exception File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/concurrent/futures/thread.py", line 57, in run result = self.fn(*self.args, **self.kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/compute/diffexp_cxg .py", line 110, in _mean_var_ab X = matrix.multi_index[row_selector_AB, col_range[0] : col_range[1] - 1][""] KeyError: '' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1950, in full_dispatch_request rv = self.dispatch_request() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1936, in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py" , line 468, in wrapper resp = resource(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/views.py", line 89, in view return self.dispatch_request(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py" , line 583, in dispatch_request resp = meth(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 3 5, in wrapper response = make_response(f(*args, **kwargs)) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 1 16, in wrapped_function return func(self, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 2 14, in post return common_rest.diffexp_obs_post(request, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/common/rest.py", li ne 250, in diffexp_obs_post diffexp = data_adaptor.diffexp_topN(set1_filter, set2_filter, count) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_common/data_ad aptor.py", line 307, in diffexp_topN result = self.compute_diffexp_ttest(obs_mask_A, obs_mask_B, top_n, self.config.diffexp__lfc_cutof f) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_cxg/cxg_adapto r.py", line 195, in compute_diffexp_ttest return diffexp_cxg.diffexp_ttest(self, maskA, maskB, top_n, lfc_cutoff) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/compute/diffexp_cxg .py", line 93, in diffexp_ttest raise ComputeError(str(e)) server.common.errors.ComputeError: '' 127.0.0.1 - - [08/May/2020 10:42:19] "POST /api/v0.2/diffexp/obs HTTP/1.1" 500 - FAIL test_diff_exp_indices (server.test.test_api.EndPointsCxg) ... [2020-05-08 10:42:19,762] ERROR in app: Exception on /api/v0.2/diffexp/obs [POST] Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/compute/diffexp_cxg .py", line 84, in diffexp_ttest result = future.result() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/concurrent/futures/_base.py", line 435, in result return self.__get_result() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result raise self._exception File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/concurrent/futures/thread.py", line 57, in run result = self.fn(*self.args, **self.kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/compute/diffexp_cxg .py", line 110, in _mean_var_ab X = matrix.multi_index[row_selector_AB, col_range[0] : col_range[1] - 1][""] KeyError: '' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1950, in full_dispatch_request rv = self.dispatch_request() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1936, in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py" , line 468, in wrapper resp = resource(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/views.py", line 89, in view return self.dispatch_request(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py" , line 583, in dispatch_request resp = meth(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 3 5, in wrapper response = make_response(f(*args, **kwargs)) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 1 16, in wrapped_function return func(self, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 2 14, in post return common_rest.diffexp_obs_post(request, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/common/rest.py", li ne 250, in diffexp_obs_post diffexp = data_adaptor.diffexp_topN(set1_filter, set2_filter, count) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_common/data_ad aptor.py", line 307, in diffexp_topN result = self.compute_diffexp_ttest(obs_mask_A, obs_mask_B, top_n, self.config.diffexp__lfc_cutof f) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_cxg/cxg_adapto r.py", line 195, in compute_diffexp_ttest return diffexp_cxg.diffexp_ttest(self, maskA, maskB, top_n, lfc_cutoff) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/compute/diffexp_cxg .py", line 93, in diffexp_ttest raise ComputeError(str(e)) server.common.errors.ComputeError: '' 127.0.0.1 - - [08/May/2020 10:42:19] "POST /api/v0.2/diffexp/obs HTTP/1.1" 500 - FAIL test_fbs_default (server.test.test_api.EndPointsCxg) ... 127.0.0.1 - - [08/May/2020 10:42:19] "PUT /a pi/v0.2/data/var HTTP/1.1" 400 - [2020-05-08 10:42:19,809] ERROR in app: Exception on /api/v0.2/data/var [PUT] Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1950, in full_dispatch_request rv = self.dispatch_request() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1936, in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py" , line 468, in wrapper resp = resource(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/views.py", line 89, in view return self.dispatch_request(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py" , line 583, in dispatch_request resp = meth(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 3 5, in wrapper response = make_response(f(*args, **kwargs)) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 1 16, in wrapped_function return func(self, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 2 02, in put return common_rest.data_var_put(request, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/common/rest.py", li ne 201, in data_var_put data_adaptor.data_frame_to_fbs_matrix(filter, axis=Axis.VAR), File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_common/data_ad aptor.py", line 275, in data_frame_to_fbs_matrix X = self.get_X_array(obs_selector, var_selector) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_cxg/cxg_adapto r.py", line 204, in get_X_array data = X.multi_index[obs_items, var_items][""] KeyError: '' 127.0.0.1 - - [08/May/2020 10:42:19] "PUT /api/v0.2/data/var HTTP/1.1" 500 - FAIL test_get_annotations_obs_error (server.test.test_api.EndPointsCxg) ... 127.0.0.1 - - [08/May/2020 10: 42:19] "GET /api/v0.2/annotations/obs?annotation-name=notakey HTTP/1.1" 400 - ok test_get_annotations_obs_fbs (server.test.test_api.EndPointsCxg) ... 127.0.0.1 - - [08/May/2020 10:42 :19] "GET /api/v0.2/annotations/obs HTTP/1.1" 200 - ok test_get_annotations_obs_keys_fbs (server.test.test_api.EndPointsCxg) ... 127.0.0.1 - - [08/May/2020 10:42:19] "GET /api/v0.2/annotations/obs?annotation-name=n_genes&annotation-name=percent_mito HTTP/1. 1" 200 - ok test_get_annotations_var_error (server.test.test_api.EndPointsCxg) ... 127.0.0.1 - - [08/May/2020 10: 42:19] "GET /api/v0.2/annotations/var?annotation-name=notakey HTTP/1.1" 400 - ok test_get_annotations_var_fbs (server.test.test_api.EndPointsCxg) ... 127.0.0.1 - - [08/May/2020 10:42 :19] "GET /api/v0.2/annotations/var HTTP/1.1" 200 - ok test_get_annotations_var_keys_fbs (server.test.test_api.EndPointsCxg) ... 127.0.0.1 - - [08/May/2020 10:42:20] "GET /api/v0.2/annotations/var?annotation-name=n_cells HTTP/1.1" 200 - ok test_get_layout_fbs (server.test.test_api.EndPointsCxg) ... [2020-05-08 10:42:20,043] ERROR in app: E xception on /api/v0.2/layout/obs [GET] Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1950, in full_dispatch_request rv = self.dispatch_request() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1936, in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py" , line 468, in wrapper resp = resource(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/views.py", line 89, in view return self.dispatch_request(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py" , line 583, in dispatch_request resp = meth(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 3 5, in wrapper response = make_response(f(*args, **kwargs)) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 1 16, in wrapped_function return func(self, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 2 21, in get return common_rest.layout_obs_get(request, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/common/rest.py", li ne 273, in layout_obs_get data_adaptor.layout_to_fbs_matrix(fields), HTTPStatus.OK, {"Content-Type": "application/octet-str eam"} File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_common/data_ad aptor.py", line 352, in layout_to_fbs_matrix embedding = self.get_embedding_array(ename, 2) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_cxg/cxg_adapto r.py", line 185, in get_embedding_array return array[:, 0:dims] File "tiledb/libtiledb.pyx", line 4002, in tiledb.libtiledb.DenseArrayImpl.__getitem__ File "tiledb/libtiledb.pyx", line 4107, in tiledb.libtiledb.DenseArrayImpl.subarray File "tiledb/libtiledb.pyx", line 4153, in tiledb.libtiledb.DenseArrayImpl._read_dense_subarray File "tiledb/libtiledb.pyx", line 3172, in tiledb.libtiledb.ArraySchema.attr File "tiledb/libtiledb.pyx", line 3149, in tiledb.libtiledb.ArraySchema._attr_name File "tiledb/libtiledb.pyx", line 457, in tiledb.libtiledb.check_error File "tiledb/libtiledb.pyx", line 453, in tiledb.libtiledb._raise_ctx_err File "tiledb/libtiledb.pyx", line 438, in tiledb.libtiledb._raise_tiledb_error tiledb.libtiledb.TileDBError: [TileDB::ArraySchema] Error: Attribute name: does not exist for array file:///home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_datasets/pbmc3k.cxg/emb/dra w_graph_fr 127.0.0.1 - - [08/May/2020 10:42:20] "GET /api/v0.2/layout/obs HTTP/1.1" 500 - FAIL test_initialize (server.test.test_api.EndPointsCxg) ... 127.0.0.1 - - [08/May/2020 10:42:20] "GET /ap i/v0.2/schema HTTP/1.1" 200 - ok test_static (server.test.test_api.EndPointsCxg) ... 127.0.0.1 - - [08/May/2020 10:42:20] "GET /static /assets/favicon.ico HTTP/1.1" 200 - ok /home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/anndata/_core/anndata.py:21: Futur eWarning: pandas.core.index is deprecated and will be removed in a future version. The public classe s are available in the top-level namespace. from pandas.core.index import RangeIndex [cellxgene] Warning: The default value of auto_mkdir=True has been deprecated and will be changed to auto_mkdir=False by default in a future release. * Running on http://127.0.0.1:5013/ (Press CTRL+C to quit) 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:23] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:24] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:24] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:24] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:24] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:24] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:24] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:24] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:24] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:24] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:24] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:24] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:24] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:24] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:24] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:24] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:24] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:24] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:24] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:24] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:24] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:24] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:24] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:24] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:24] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:24] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:24] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:24] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:24] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:24] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:24] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:24] "GET /api/v0.2/schema HTTP/1.1" 200 - test_bad_filter (server.test.test_api.EndPointsCxgAnnotations) ... 127.0.0.1 - - [08/May/2020 10:42:2 4] "PUT /api/v0.2/data/var HTTP/1.1" 400 - ok test_config (server.test.test_api.EndPointsCxgAnnotations) ... 127.0.0.1 - - [08/May/2020 10:42:24] " GET /api/v0.2/config HTTP/1.1" 200 - ok test_data_get_fbs (server.test.test_api.EndPointsCxgAnnotations) ... 127.0.0.1 - - [08/May/2020 10:42 :24] "GET /api/v0.2/data/var HTTP/1.1" 400 - ok test_data_get_filter_fbs (server.test.test_api.EndPointsCxgAnnotations) ... [2020-05-08 10:42:24,523] ERROR in app: Exception on /api/v0.2/data/var [GET] Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1950, in full_dispatch_request rv = self.dispatch_request() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1936, in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py" , line 468, in wrapper resp = resource(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/views.py", line 89, in view return self.dispatch_request(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py" , line 583, in dispatch_request resp = meth(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 3 5, in wrapper response = make_response(f(*args, **kwargs)) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 1 16, in wrapped_function return func(self, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 2 07, in get return common_rest.data_var_get(request, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/common/rest.py", li ne 217, in data_var_get data_adaptor.data_frame_to_fbs_matrix(filter, axis=Axis.VAR), File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_common/data_ad aptor.py", line 275, in data_frame_to_fbs_matrix X = self.get_X_array(obs_selector, var_selector) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_cxg/cxg_adapto r.py", line 204, in get_X_array data = X.multi_index[obs_items, var_items][""] KeyError: '' 127.0.0.1 - - [08/May/2020 10:42:24] "GET /api/v0.2/data/var?var:name_0=SIK1 HTTP/1.1" 500 - FAIL test_data_mimetype_error (server.test.test_api.EndPointsCxgAnnotations) ... 127.0.0.1 - - [08/May/202 0 10:42:24] "PUT /api/v0.2/data/var HTTP/1.1" 406 - ok test_data_put_fbs (server.test.test_api.EndPointsCxgAnnotations) ... 127.0.0.1 - - [08/May/2020 10:42 :24] "PUT /api/v0.2/data/var HTTP/1.1" 400 - ok test_data_put_filter_fbs (server.test.test_api.EndPointsCxgAnnotations) ... [2020-05-08 10:42:24,611] ERROR in app: Exception on /api/v0.2/data/var [PUT] Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1950, in full_dispatch_request rv = self.dispatch_request() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1936, in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py" , line 468, in wrapper resp = resource(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/views.py", line 89, in view return self.dispatch_request(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py" , line 583, in dispatch_request resp = meth(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 3 5, in wrapper response = make_response(f(*args, **kwargs)) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 1 16, in wrapped_function return func(self, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 2 02, in put return common_rest.data_var_put(request, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/common/rest.py", li ne 201, in data_var_put data_adaptor.data_frame_to_fbs_matrix(filter, axis=Axis.VAR), File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_common/data_ad aptor.py", line 275, in data_frame_to_fbs_matrix X = self.get_X_array(obs_selector, var_selector) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_cxg/cxg_adapto r.py", line 204, in get_X_array data = X.multi_index[obs_items, var_items][""] KeyError: '' 127.0.0.1 - - [08/May/2020 10:42:24] "PUT /api/v0.2/data/var HTTP/1.1" 500 - FAIL test_data_put_single_var (server.test.test_api.EndPointsCxgAnnotations) ... [2020-05-08 10:42:24,660] ERROR in app: Exception on /api/v0.2/data/var [PUT] Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1950, in full_dispatch_request rv = self.dispatch_request() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1936, in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py" , line 468, in wrapper resp = resource(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/views.py", line 89, in view return self.dispatch_request(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py" , line 583, in dispatch_request resp = meth(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 3 5, in wrapper response = make_response(f(*args, **kwargs)) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 1 16, in wrapped_function return func(self, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 2 02, in put return common_rest.data_var_put(request, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/common/rest.py", li ne 201, in data_var_put data_adaptor.data_frame_to_fbs_matrix(filter, axis=Axis.VAR), File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_common/data_ad aptor.py", line 275, in data_frame_to_fbs_matrix X = self.get_X_array(obs_selector, var_selector) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_cxg/cxg_adapto r.py", line 204, in get_X_array data = X.multi_index[obs_items, var_items][""] KeyError: '' 127.0.0.1 - - [08/May/2020 10:42:24] "PUT /api/v0.2/data/var HTTP/1.1" 500 - FAIL test_diff_exp (server.test.test_api.EndPointsCxgAnnotations) ... [2020-05-08 10:42:24,838] ERROR in a pp: Exception on /api/v0.2/diffexp/obs [POST] Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/compute/diffexp_cxg .py", line 84, in diffexp_ttest result = future.result() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/concurrent/futures/_base.py", line 435, in result return self.__get_result() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result raise self._exception File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/concurrent/futures/thread.py", line 57, in run result = self.fn(*self.args, **self.kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/compute/diffexp_cxg .py", line 110, in _mean_var_ab X = matrix.multi_index[row_selector_AB, col_range[0] : col_range[1] - 1][""] KeyError: '' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1950, in full_dispatch_request rv = self.dispatch_request() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1936, in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py" , line 468, in wrapper resp = resource(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/views.py", line 89, in view return self.dispatch_request(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py" , line 583, in dispatch_request resp = meth(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 3 5, in wrapper response = make_response(f(*args, **kwargs)) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 1 16, in wrapped_function return func(self, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 2 14, in post return common_rest.diffexp_obs_post(request, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/common/rest.py", li ne 250, in diffexp_obs_post diffexp = data_adaptor.diffexp_topN(set1_filter, set2_filter, count) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_common/data_ad aptor.py", line 307, in diffexp_topN result = self.compute_diffexp_ttest(obs_mask_A, obs_mask_B, top_n, self.config.diffexp__lfc_cutof f) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_cxg/cxg_adapto r.py", line 195, in compute_diffexp_ttest return diffexp_cxg.diffexp_ttest(self, maskA, maskB, top_n, lfc_cutoff) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/compute/diffexp_cxg .py", line 93, in diffexp_ttest raise ComputeError(str(e)) server.common.errors.ComputeError: '' 127.0.0.1 - - [08/May/2020 10:42:24] "POST /api/v0.2/diffexp/obs HTTP/1.1" 500 - FAIL test_diff_exp_indices (server.test.test_api.EndPointsCxgAnnotations) ... [2020-05-08 10:42:24,932] ER ROR in app: Exception on /api/v0.2/diffexp/obs [POST] Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/compute/diffexp_cxg .py", line 84, in diffexp_ttest result = future.result() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/concurrent/futures/_base.py", line 435, in result return self.__get_result() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result raise self._exception File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/concurrent/futures/thread.py", line 57, in run result = self.fn(*self.args, **self.kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/compute/diffexp_cxg .py", line 110, in _mean_var_ab X = matrix.multi_index[row_selector_AB, col_range[0] : col_range[1] - 1][""] KeyError: '' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1950, in full_dispatch_request rv = self.dispatch_request() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1936, in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py" , line 468, in wrapper resp = resource(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/views.py", line 89, in view return self.dispatch_request(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py" , line 583, in dispatch_request resp = meth(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 3 5, in wrapper response = make_response(f(*args, **kwargs)) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 1 16, in wrapped_function return func(self, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 2 14, in post return common_rest.diffexp_obs_post(request, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/common/rest.py", li ne 250, in diffexp_obs_post diffexp = data_adaptor.diffexp_topN(set1_filter, set2_filter, count) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_common/data_ad aptor.py", line 307, in diffexp_topN result = self.compute_diffexp_ttest(obs_mask_A, obs_mask_B, top_n, self.config.diffexp__lfc_cutof f) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_cxg/cxg_adapto r.py", line 195, in compute_diffexp_ttest return diffexp_cxg.diffexp_ttest(self, maskA, maskB, top_n, lfc_cutoff) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/compute/diffexp_cxg .py", line 93, in diffexp_ttest raise ComputeError(str(e)) server.common.errors.ComputeError: '' 127.0.0.1 - - [08/May/2020 10:42:24] "POST /api/v0.2/diffexp/obs HTTP/1.1" 500 - FAIL test_fbs_default (server.test.test_api.EndPointsCxgAnnotations) ... 127.0.0.1 - - [08/May/2020 10:42: 24] "PUT /api/v0.2/data/var HTTP/1.1" 400 - [2020-05-08 10:42:24,987] ERROR in app: Exception on /api/v0.2/data/var [PUT] Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1950, in full_dispatch_request rv = self.dispatch_request() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1936, in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py" , line 468, in wrapper resp = resource(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/views.py", line 89, in view return self.dispatch_request(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py" , line 583, in dispatch_request resp = meth(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 3 5, in wrapper response = make_response(f(*args, **kwargs)) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 1 16, in wrapped_function return func(self, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 2 02, in put return common_rest.data_var_put(request, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/common/rest.py", li ne 201, in data_var_put data_adaptor.data_frame_to_fbs_matrix(filter, axis=Axis.VAR), File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_common/data_ad aptor.py", line 275, in data_frame_to_fbs_matrix X = self.get_X_array(obs_selector, var_selector) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_cxg/cxg_adapto r.py", line 204, in get_X_array data = X.multi_index[obs_items, var_items][""] KeyError: '' 127.0.0.1 - - [08/May/2020 10:42:24] "PUT /api/v0.2/data/var HTTP/1.1" 500 - FAIL test_get_annotations_obs_error (server.test.test_api.EndPointsCxgAnnotations) ... 127.0.0.1 - - [08/M ay/2020 10:42:25] "GET /api/v0.2/annotations/obs?annotation-name=notakey HTTP/1.1" 400 - ok test_get_annotations_obs_fbs (server.test.test_api.EndPointsCxgAnnotations) ... 127.0.0.1 - - [08/May /2020 10:42:25] "GET /api/v0.2/annotations/obs HTTP/1.1" 200 - ok test_get_annotations_obs_keys_fbs (server.test.test_api.EndPointsCxgAnnotations) ... 127.0.0.1 - - [0 8/May/2020 10:42:25] "GET /api/v0.2/annotations/obs?annotation-name=n_genes&annotation-name=percent_m ito HTTP/1.1" 200 - ok test_get_annotations_var_error (server.test.test_api.EndPointsCxgAnnotations) ... 127.0.0.1 - - [08/M ay/2020 10:42:25] "GET /api/v0.2/annotations/var?annotation-name=notakey HTTP/1.1" 400 - ok test_get_annotations_var_fbs (server.test.test_api.EndPointsCxgAnnotations) ... 127.0.0.1 - - [08/May /2020 10:42:25] "GET /api/v0.2/annotations/var HTTP/1.1" 200 - ok test_get_annotations_var_keys_fbs (server.test.test_api.EndPointsCxgAnnotations) ... 127.0.0.1 - - [0 8/May/2020 10:42:25] "GET /api/v0.2/annotations/var?annotation-name=n_cells HTTP/1.1" 200 - ok test_get_layout_fbs (server.test.test_api.EndPointsCxgAnnotations) ... [2020-05-08 10:42:25,243] ERRO R in app: Exception on /api/v0.2/layout/obs [GET] Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1950, in full_dispatch_request rv = self.dispatch_request() File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/app.py", line 1936, in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py" , line 468, in wrapper resp = resource(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask/views.py", line 89, in view return self.dispatch_request(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/flask_restful/__init__.py" , line 583, in dispatch_request resp = meth(*args, **kwargs) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 3 5, in wrapper response = make_response(f(*args, **kwargs)) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 1 16, in wrapped_function return func(self, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/app/app.py", line 2 21, in get return common_rest.layout_obs_get(request, data_adaptor) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/common/rest.py", li ne 273, in layout_obs_get data_adaptor.layout_to_fbs_matrix(fields), HTTPStatus.OK, {"Content-Type": "application/octet-str eam"} File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_common/data_ad aptor.py", line 352, in layout_to_fbs_matrix embedding = self.get_embedding_array(ename, 2) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/server/data_cxg/cxg_adapto r.py", line 185, in get_embedding_array return array[:, 0:dims] File "tiledb/libtiledb.pyx", line 4002, in tiledb.libtiledb.DenseArrayImpl.__getitem__ File "tiledb/libtiledb.pyx", line 4107, in tiledb.libtiledb.DenseArrayImpl.subarray File "tiledb/libtiledb.pyx", line 4153, in tiledb.libtiledb.DenseArrayImpl._read_dense_subarray File "tiledb/libtiledb.pyx", line 3172, in tiledb.libtiledb.ArraySchema.attr File "tiledb/libtiledb.pyx", line 3149, in tiledb.libtiledb.ArraySchema._attr_name File "tiledb/libtiledb.pyx", line 457, in tiledb.libtiledb.check_error File "tiledb/libtiledb.pyx", line 453, in tiledb.libtiledb._raise_ctx_err File "tiledb/libtiledb.pyx", line 438, in tiledb.libtiledb._raise_tiledb_error tiledb.libtiledb.TileDBError: [TileDB::ArraySchema] Error: Attribute name: does not exist for array file:///home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_datasets/pbmc3k.cxg/emb/dra w_graph_fr 127.0.0.1 - - [08/May/2020 10:42:25] "GET /api/v0.2/layout/obs HTTP/1.1" 500 - FAIL test_get_schema_existing_writable (server.test.test_api.EndPointsCxgAnnotations) ... 127.0.0.1 - - [0 8/May/2020 10:42:25] "GET /api/v0.2/schema HTTP/1.1" 200 - ok test_get_user_annotations_existing_obs_keys_fbs (server.test.test_api.EndPointsCxgAnnotations) ... 12 7.0.0.1 - - [08/May/2020 10:42:25] "GET /api/v0.2/annotations/obs?annotation-name=cluster-test HTTP/1 .1" 200 - ok test_initialize (server.test.test_api.EndPointsCxgAnnotations) ... 127.0.0.1 - - [08/May/2020 10:42:2 5] "GET /api/v0.2/schema HTTP/1.1" 200 - ok test_put_user_annotations_obs_fbs (server.test.test_api.EndPointsCxgAnnotations) ... 127.0.0.1 - - [0 8/May/2020 10:42:25] "PUT /api/v0.2/annotations/obs?annotation-collection-name=test_annotations HTTP/ 1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:25] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:25] "GET /api/v0.2/annotations/obs?annotation-name=cat_A HTTP/1.1" 2 00 - ok test_static (server.test.test_api.EndPointsCxgAnnotations) ... 127.0.0.1 - - [08/May/2020 10:42:25] " GET /static/assets/favicon.ico HTTP/1.1" 200 - ok test_update (server.test.test_app_config.AppConfigTest) ... ok test_make_index_unique (server.test.test_cli_prepare.CLIPrepareTests) ... ok test_assert_verstion_gt (server.test.test_cli_upgrade.CLIUpgradeTests) ... ok test_split_version_str (server.test.test_cli_upgrade.CLIUpgradeTests) ... ok test_validate_version_str (server.test.test_cli_upgrade.CLIUpgradeTests) ... ok test_anndata_default (server.test.test_diffexp.DiffExpTest) Test an anndata adaptor with its default diffexp algorithm (diffexp_generic) ... FAIL test_cxg_default (server.test.test_diffexp.DiffExpTest) Test a cxg adaptor with its default diffexp algorithm (diffexp_cxg) ... ERROR test_cxg_generic (server.test.test_diffexp.DiffExpTest) Test a cxg adaptor with the generic adaptor ... ERROR test_encode_DataFrame (server.test.test_fbs.FbsTests) ... ok test_encode_boundary (server.test.test_fbs.FbsTests) test various boundary checks ... ok test_encode_ndarray (server.test.test_fbs.FbsTests) ... ok test_encode_sparse (server.test.test_fbs.FbsTests) ... ok test_roundtrip (server.test.test_fbs.FbsTests) ... ok test_queryparam_to_filter_errors (server.test.test_filter.FilterParseTests) ... ok test_queryparam_to_filter_escaping (server.test.test_filter.FilterParseTests) ... ok test_queryparam_to_filter_parse (server.test.test_filter.FilterParseTests) ... ok test_access_error (server.test.test_matrixcache.MatrixCacheTest) ... ok test_basic (server.test.test_matrixcache.MatrixCacheTest) ... ok test_timelimit (server.test.test_matrixcache.MatrixCacheTest) ... ok test_annotation (server.test.test_nan_anndata_adaptor.NaNTest) ... [cellxgene] Warning: Annotation va r_with_nans will be converted to 32 bit float and may lose precision. ok test_dataframe (server.test.test_nan_anndata_adaptor.NaNTest) ... [cellxgene] Warning: Annotation var _with_nans will be converted to 32 bit float and may lose precision. ok test_dataframe_obs_not_implemented (server.test.test_nan_anndata_adaptor.NaNTest) ... [cellxgene] War ning: Annotation var_with_nans will be converted to 32 bit float and may lose precision. ok test_init (server.test.test_nan_anndata_adaptor.NaNTest) ... [cellxgene] Warning: Annotation var_with _nans will be converted to 32 bit float and may lose precision. ok test_load (server.test.test_nan_anndata_adaptor.NaNTest) ... [cellxgene] Warning: Annotation var_with _nans will be converted to 32 bit float and may lose precision. ok /home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/site-packages/anndata/_core/anndata.py:21: Futur eWarning: pandas.core.index is deprecated and will be removed in a future version. The public classe s are available in the top-level namespace. from pandas.core.index import RangeIndex [cellxgene] Warning: The default value of auto_mkdir=True has been deprecated and will be changed to auto_mkdir=False by default in a future release. [cellxgene] Warning: Annotation var_with_nans will be converted to 32 bit float and may lose precisio n. * Running on http://127.0.0.1:5006/ (Press CTRL+C to quit) 127.0.0.1 - - [08/May/2020 10:42:32] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:32] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:32] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:32] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:32] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:33] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:34] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:34] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:34] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:34] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:34] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:34] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:34] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:34] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:34] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:34] "GET /api/v0.2/schema HTTP/1.1" 200 - 127.0.0.1 - - [08/May/2020 10:42:34] "GET /api/v0.2/schema HTTP/1.1" 200 - test_annotation_obs (server.test.test_nan_rest.WithNaNs) ... 127.0.0.1 - - [08/May/2020 10:42:34] "GE T /api/v0.2/annotations/obs HTTP/1.1" 200 - ok test_annotation_var (server.test.test_nan_rest.WithNaNs) ... 127.0.0.1 - - [08/May/2020 10:42:34] "GE T /api/v0.2/annotations/var HTTP/1.1" 200 - ok test_data (server.test.test_nan_rest.WithNaNs) ... 127.0.0.1 - - [08/May/2020 10:42:34] "PUT /api/v0. 2/data/var HTTP/1.1" 200 - ok test_initialize (server.test.test_nan_rest.WithNaNs) ... 127.0.0.1 - - [08/May/2020 10:42:34] "GET /a pi/v0.2/schema HTTP/1.1" 200 - ok test_config (server.test.test_writable_annotation.WritableAnnotationTest) ... ok test_error_checks (server.test.test_writable_annotation.WritableAnnotationTest) ... ok test_file_rotation_to_max_9 (server.test.test_writable_annotation.WritableAnnotationTest) ... ok test_put_get_roundtrip (server.test.test_writable_annotation.WritableAnnotationTest) ... ok test_write_to_file (server.test.test_writable_annotation.WritableAnnotationTest) ... ok ====================================================================== ERROR: server.test.test_anndata_adaptor (unittest.loader._FailedTest) ---------------------------------------------------------------------- ImportError: Failed to import test module: server.test.test_anndata_adaptor Traceback (most recent call last): File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/unittest/loader.py", line 436, in _find_ test_path module = self._get_module_from_name(name) File "/home/kli3/anaconda3/envs/cellxgenevis/lib/python3.7/unittest/loader.py", line 377, in _get_m odule_from_name __import__(name) File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_anndata_adaptor.py", line 8, in from parameterized import parameterized_class ModuleNotFoundError: No module named 'parameterized' ====================================================================== ERROR: test_cxg_default (server.test.test_diffexp.DiffExpTest) Test a cxg adaptor with its default diffexp algorithm (diffexp_cxg) ---------------------------------------------------------------------- Traceback (most recent call last): KeyError: '' During handling of the above exception, another exception occurred: Traceback (most recent call last): server.common.errors.ComputeError: '' ====================================================================== ERROR: test_cxg_generic (server.test.test_diffexp.DiffExpTest) Test a cxg adaptor with the generic adaptor ---------------------------------------------------------------------- Traceback (most recent call last): KeyError: '' ====================================================================== FAIL: test_data_get_filter_fbs (server.test.test_api.EndPointsCxg) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_api.py", line 239, in test_data_get_f ilter_fbs self.assertEqual(result.status_code, HTTPStatus.OK) AssertionError: 500 != ====================================================================== FAIL: test_data_put_filter_fbs (server.test.test_api.EndPointsCxg) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_api.py", line 222, in test_data_put_f ilter_fbs self.assertEqual(result.status_code, HTTPStatus.OK) AssertionError: 500 != ====================================================================== FAIL: test_data_put_single_var (server.test.test_api.EndPointsCxg) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_api.py", line 252, in test_data_put_s ingle_var self.assertEqual(result.status_code, HTTPStatus.OK) AssertionError: 500 != ====================================================================== FAIL: test_diff_exp (server.test.test_api.EndPointsCxg) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_api.py", line 126, in test_diff_exp self.assertEqual(result.status_code, HTTPStatus.OK) AssertionError: 500 != ====================================================================== FAIL: test_diff_exp_indices (server.test.test_api.EndPointsCxg) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_api.py", line 141, in test_diff_exp_i ndices self.assertEqual(result.status_code, HTTPStatus.OK) AssertionError: 500 != ====================================================================== FAIL: test_fbs_default (server.test.test_api.EndPointsCxg) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_api.py", line 200, in test_fbs_defaul t self.assertEqual(result.headers["Content-Type"], "application/octet-stream") AssertionError: 'application/json' != 'application/octet-stream' - application/json + application/octet-stream ====================================================================== FAIL: test_get_layout_fbs (server.test.test_api.EndPointsCxg) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_api.py", line 54, in test_get_layout_ fbs self.assertEqual(result.status_code, HTTPStatus.OK) AssertionError: 500 != ====================================================================== FAIL: test_data_get_filter_fbs (server.test.test_api.EndPointsCxgAnnotations) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_api.py", line 239, in test_data_get_f ilter_fbs self.assertEqual(result.status_code, HTTPStatus.OK) AssertionError: 500 != ====================================================================== FAIL: test_data_put_filter_fbs (server.test.test_api.EndPointsCxgAnnotations) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_api.py", line 222, in test_data_put_f ilter_fbs self.assertEqual(result.status_code, HTTPStatus.OK) AssertionError: 500 != ====================================================================== FAIL: test_data_put_single_var (server.test.test_api.EndPointsCxgAnnotations) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_api.py", line 252, in test_data_put_s ingle_var self.assertEqual(result.status_code, HTTPStatus.OK) AssertionError: 500 != ====================================================================== FAIL: test_diff_exp (server.test.test_api.EndPointsCxgAnnotations) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_api.py", line 126, in test_diff_exp self.assertEqual(result.status_code, HTTPStatus.OK) AssertionError: 500 != ====================================================================== FAIL: test_diff_exp_indices (server.test.test_api.EndPointsCxgAnnotations) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_api.py", line 141, in test_diff_exp_i ndices self.assertEqual(result.status_code, HTTPStatus.OK) AssertionError: 500 != ====================================================================== FAIL: test_fbs_default (server.test.test_api.EndPointsCxgAnnotations) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_api.py", line 200, in test_fbs_defaul t self.assertEqual(result.headers["Content-Type"], "application/octet-stream") AssertionError: 'application/json' != 'application/octet-stream' - application/json + application/octet-stream ====================================================================== FAIL: test_get_layout_fbs (server.test.test_api.EndPointsCxgAnnotations) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_api.py", line 54, in test_get_layout_ fbs self.assertEqual(result.status_code, HTTPStatus.OK) AssertionError: 500 != ====================================================================== FAIL: test_anndata_default (server.test.test_diffexp.DiffExpTest) Test an anndata adaptor with its default diffexp algorithm (diffexp_generic) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_diffexp.py", line 57, in test_anndata _default self.check_1_10_2_10(results) File "/home/kli3/git/cellxgene_VIP/cellxgene/server/test/test_diffexp.py", line 47, in check_1_10_2 _10 self.assertAlmostEqual(result[1], expect[1]) AssertionError: 0.5201582 != 0.5201581 within 7 places (7.165374760198517e-08 difference) ---------------------------------------------------------------------- Ran 125 tests in 41.943s FAILED (failures=15, errors=3) make: *** [Makefile:10: unit-test] Error 1