Mercurial > repos > iuc > scanpy_remove_confounders

changeset 22:c5541bfb8feb draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 90275e51aa271edacdd9d277c441e38e99502c53
author iuc
date Mon, 28 Oct 2024 18:07:34 +0000
parents acc4732fae0b
children
files old_output.json test-data/krumsiek11_ranked_gene_groups.h5ad test-data/test.h5ad
diffstat 3 files changed, 0 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/old_output.json	Mon Oct 28 18:06:52 2024 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-{"version": "0.1", "tests": [{"id": "functional.test_toolbox.TestForTool_scanpy_plot.test_tool_000000", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy0", "test_index": 0, "time_seconds": 28.03529191017151, "inputs": {"adata": {"src": "hda", "id": "2891970512fa2d5a"}, "advanced_common|show_log": true, "format": "png", "method|method": "pl.scatter", "method|plot|color_map": "inferno", "method|plot|frameon": true, "method|plot|legend_fontsize": "1", "method|plot|legend_fontweight": "normal", "method|plot|legend_loc": "right margin", "method|plot|palette": "inferno", "method|plot|projection": "2d", "method|plot|size": "1", "method|sort_order": true, "method|type|basis": "umap", "method|type|color": "HES4", "method|type|type": "basis", "method|use_raw": true}, "job": {"command_line": "cp '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/files/7/b/c/dataset_7bc02b2c-0d82-4456-abcd-7ec123a4006d.dat' 'anndata.h5ad' && cat '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/job_working_directory/000/2/configs/tmpinudjtrk' > '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/files/b/a/7/dataset_ba72e443-4078-464d-8f69-93ff16fb341d.dat' && python '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/job_working_directory/000/2/configs/tmpinudjtrk' >> '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/files/b/a/7/dataset_ba72e443-4078-464d-8f69-93ff16fb341d.dat' && ls . >> '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/files/b/a/7/dataset_ba72e443-4078-464d-8f69-93ff16fb341d.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt'  | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\"  | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n-    \\2|g' | sed 's|, |\\n-    |g'", "command_version": "scanpy version: 1.7.1\n", "create_time": "2021-03-15T16:18:49.439040", "exit_code": 0, "external_id": "46459", "galaxy_version": "21.01", "history_id": "2891970512fa2d5a", "id": "5729865256bc2525", "inputs": {"adata": {"id": "2891970512fa2d5a", "src": "hda", "uuid": "7bc02b2c-0d82-4456-abcd-7ec123a4006d"}}, "job_messages": [], "job_metrics": [], "job_stderr": "", "job_stdout": "", "model_class": "Job", "outputs": {"hidden_output": {"id": "54f2a3a23292eb07", "src": "hda", "uuid": "ba72e443-4078-464d-8f69-93ff16fb341d"}, "out_png": {"id": "5729865256bc2525", "src": "hda", "uuid": "79c9b4aa-c8ce-4f05-a32c-918bd718908c"}}, "params": {"__input_ext": "\"input\"", "advanced_common": "{\"show_log\": \"true\"}", "chromInfo": "\"/Users/mvandenb/src/galaxy/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "format": "\"png\"", "method": "{\"__current_case__\": 0, \"groups\": \"\", \"method\": \"pl.scatter\", \"plot\": {\"color_map\": \"inferno\", \"components\": [], \"frameon\": \"true\", \"legend_fontsize\": \"1\", \"legend_fontweight\": \"normal\", \"legend_loc\": \"right margin\", \"palette\": \"inferno\", \"projection\": \"2d\", \"size\": \"1.0\", \"title\": \"\"}, \"sort_order\": \"true\", \"type\": {\"__current_case__\": 1, \"basis\": \"umap\", \"color\": \"HES4\", \"type\": \"basis\"}, \"use_raw\": \"true\"}"}, "state": "ok", "stderr": "WARNING: saving figure to file umap.png\n", "stdout": "", "tool_id": "scanpy_plot", "tool_stderr": "WARNING: saving figure to file umap.png\n", "tool_stdout": "", "update_time": "2021-03-15T16:19:05.199885", "user_email": "test@bx.psu.edu"}, "status": "success"}}, {"id": "functional.test_toolbox.TestForTool_scanpy_plot.test_tool_000009", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy0", "test_index": 9, "time_seconds": 21.56184482574463, "inputs": {"adata": {"src": "hda", "id": "8155e4b4bf1581ff"}, "advanced_common|show_log": true, "format": "png", "method|highly_variable_genes": true, "method|log": false, "method|method": "pl.highly_variable_genes"}, "job": {"command_line": "cp '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/files/9/a/a/dataset_9aa6e338-6993-44f9-80d5-45eac03e8909.dat' 'anndata.h5ad' && cat '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/job_working_directory/000/4/configs/tmpr8qxfwok' > '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/files/6/f/e/dataset_6feb2e49-12e4-40b4-a05e-6b3cac160e18.dat' && python '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/job_working_directory/000/4/configs/tmpr8qxfwok' >> '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/files/6/f/e/dataset_6feb2e49-12e4-40b4-a05e-6b3cac160e18.dat' && ls . >> '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/files/6/f/e/dataset_6feb2e49-12e4-40b4-a05e-6b3cac160e18.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt'  | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\"  | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n-    \\2|g' | sed 's|, |\\n-    |g'", "command_version": "scanpy version: 1.7.1\n", "create_time": "2021-03-15T16:19:18.809400", "exit_code": 1, "external_id": "46704", "galaxy_version": "21.01", "history_id": "5729865256bc2525", "id": "8155e4b4bf1581ff", "inputs": {"adata": {"id": "8155e4b4bf1581ff", "src": "hda", "uuid": "9aa6e338-6993-44f9-80d5-45eac03e8909"}}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}], "job_metrics": [], "job_stderr": "", "job_stdout": "", "model_class": "Job", "outputs": {"hidden_output": {"id": "fa6d20d0fb68383f", "src": "hda", "uuid": "6feb2e49-12e4-40b4-a05e-6b3cac160e18"}, "out_png": {"id": "7b55dbb89df8f4e5", "src": "hda", "uuid": "a302936c-0321-456e-bdd7-7e85556a34e0"}}, "params": {"__input_ext": "\"input\"", "advanced_common": "{\"show_log\": \"true\"}", "chromInfo": "\"/Users/mvandenb/src/galaxy/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "format": "\"png\"", "method": "{\"__current_case__\": 7, \"highly_variable_genes\": \"true\", \"log\": \"false\", \"method\": \"pl.highly_variable_genes\"}"}, "state": "error", "stderr": "Traceback (most recent call last):\n  File \"/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/job_working_directory/000/4/configs/tmpr8qxfwok\", line 15, in <module>\n    sc.pl.highly_variable_genes(\n  File \"/usr/local/lib/python3.8/site-packages/scanpy/plotting/_preprocessing.py\", line 42, in highly_variable_genes\n    seurat_v3_flavor = adata_or_result.uns[\"hvg\"][\"flavor\"] == \"seurat_v3\"\n  File \"/usr/local/lib/python3.8/site-packages/anndata/compat/_overloaded_dict.py\", line 100, in __getitem__\n    return self.data[key]\nKeyError: 'hvg'\n", "stdout": "", "tool_id": "scanpy_plot", "tool_stderr": "Traceback (most recent call last):\n  File \"/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/job_working_directory/000/4/configs/tmpr8qxfwok\", line 15, in <module>\n    sc.pl.highly_variable_genes(\n  File \"/usr/local/lib/python3.8/site-packages/scanpy/plotting/_preprocessing.py\", line 42, in highly_variable_genes\n    seurat_v3_flavor = adata_or_result.uns[\"hvg\"][\"flavor\"] == \"seurat_v3\"\n  File \"/usr/local/lib/python3.8/site-packages/anndata/compat/_overloaded_dict.py\", line 100, in __getitem__\n    return self.data[key]\nKeyError: 'hvg'\n", "tool_stdout": "", "update_time": "2021-03-15T16:19:31.053717", "user_email": "test@bx.psu.edu"}, "output_problems": ["Job in error state.", "Job in error state.", "Job in error state."], "status": "failure", "problem_type": "galaxy.tool_util.verify.interactor.JobOutputsError", "problem_log": "  File \"/Users/mvandenb/.pyenv/versions/3.8.2/lib/python3.8/unittest/case.py\", line 60, in testPartExecutor\n    yield\n  File \"/Users/mvandenb/.pyenv/versions/3.8.2/lib/python3.8/unittest/case.py\", line 676, in run\n    self._callTestMethod(testMethod)\n  File \"/Users/mvandenb/.pyenv/versions/3.8.2/lib/python3.8/unittest/case.py\", line 633, in _callTestMethod\n    method()\n  File \"/Users/mvandenb/src/galaxy/test/functional/test_toolbox.py\", line 98, in test_tool\n    self.do_it(tool_version=tool_version, test_index=test_index)\n  File \"/Users/mvandenb/src/galaxy/test/functional/test_toolbox.py\", line 35, in do_it\n    verify_tool(tool_id, self.galaxy_interactor, resource_parameters=resource_parameters, test_index=test_index, tool_version=tool_version, register_job_data=register_job_data)\n  File \"/Users/mvandenb/src/galaxy/lib/galaxy/tool_util/verify/interactor.py\", line 1050, in verify_tool\n    raise e\n  File \"/Users/mvandenb/src/galaxy/lib/galaxy/tool_util/verify/interactor.py\", line 1046, in verify_tool\n    job_stdio = _verify_outputs(testdef, test_history, jobs, tool_id, data_list, data_collection_list, galaxy_interactor, quiet=quiet)\n  File \"/Users/mvandenb/src/galaxy/lib/galaxy/tool_util/verify/interactor.py\", line 1222, in _verify_outputs\n    raise JobOutputsError(found_exceptions, job_stdio)\nJob in error state.\nJob in error state.\nJob in error state.\n-------------------- >> begin captured stdout << ---------------------\nProblem in history with id 5729865256bc2525 - summary of history's datasets and jobs below.\n--------------------------------------\n| 1 - pp.highly_variable_genes.seurat.blobs.h5ad (HID - NAME) \n| Dataset State:\n|  ok\n| Dataset Blurb:\n|  Anndata file (58.5 KB)\n| Dataset Info:\n|  uploaded h5ad file\n| Peek:\n|  [n_obs x n_vars]\n|  640 x 11\n|  [obs]: 2 layers\n|  blobs, index\n|  [var]: 5 layers\n|  dispersions, dispersions_norm, highly_variable, index, means\n|  [uns]: 1 layer\n|  blobs_categories\n| Dataset Job Standard Output:\n|  *Standard output was empty.*\n| Dataset Job Standard Error:\n|  *Standard error was empty.*\n|\n--------------------------------------\n| 2 - Plot (pl.highly_variable_genes) on data 1 (HID - NAME) \n| Dataset State:\n|  error\n| Dataset Blurb:\n|  error\n| Dataset Info:\n|  Traceback (most recent call last):\n|  File \"/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/job_working_directory/000/4/configs/tmpr8qxfwok\", line 15, in <module>\n|  sc.pl.highly_variable_genes(\n|  File \"/usr/local/lib/python3.8/site-\n| Peek:\n|  *Peek unavilable.*\n| Dataset Job Standard Output:\n|  *Standard output was empty.*\n| Dataset Job Standard Error:\n|  Traceback (most recent call last):\n|  File \"/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/job_working_directory/000/4/configs/tmpr8qxfwok\", line 15, in <module>\n|  sc.pl.highly_variable_genes(\n|  File \"/usr/local/lib/python3.8/site-packages/scanpy/plotting/_preprocessing.py\", line 42, in highly_variable_genes\n|  seurat_v3_flavor = adata_or_result.uns[\"hvg\"][\"flavor\"] == \"seurat_v3\"\n|  File \"/usr/local/lib/python3.8/site-packages/anndata/compat/_overloaded_dict.py\", line 100, in __getitem__\n|  return self.data[key]\n|  KeyError: 'hvg'\n|\n--------------------------------------\n| 3 - Log file (HID - NAME) \n| Dataset State:\n|  error\n| Dataset Blurb:\n|  error\n| Dataset Info:\n|  Traceback (most recent call last):\n|  File \"/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/job_working_directory/000/4/configs/tmpr8qxfwok\", line 15, in <module>\n|  sc.pl.highly_variable_genes(\n|  File \"/usr/local/lib/python3.8/site-\n| Peek:\n|  *Peek unavilable.*\n| Dataset Job Standard Output:\n|  *Standard output was empty.*\n| Dataset Job Standard Error:\n|  Traceback (most recent call last):\n|  File \"/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/job_working_directory/000/4/configs/tmpr8qxfwok\", line 15, in <module>\n|  sc.pl.highly_variable_genes(\n|  File \"/usr/local/lib/python3.8/site-packages/scanpy/plotting/_preprocessing.py\", line 42, in highly_variable_genes\n|  seurat_v3_flavor = adata_or_result.uns[\"hvg\"][\"flavor\"] == \"seurat_v3\"\n|  File \"/usr/local/lib/python3.8/site-packages/anndata/compat/_overloaded_dict.py\", line 100, in __getitem__\n|  return self.data[key]\n|  KeyError: 'hvg'\n|\n--------------------------------------\n| Job 8155e4b4bf1581ff\n| State: \n|  error\n| Update Time:\n|  2021-03-15T16:19:31.053717\n| Create Time:\n|  2021-03-15T16:19:18.809400\n|\n--------------------------------------\n| Job 54f2a3a23292eb07\n| State: \n|  ok\n| Update Time:\n|  2021-03-15T16:19:18.686983\n| Create Time:\n|  2021-03-15T16:19:11.155708\n|\n--------------------------------------\nProblem in history with id 5729865256bc2525 - summary of history's datasets and jobs below.\n--------------------------------------\n| 1 - pp.highly_variable_genes.seurat.blobs.h5ad (HID - NAME) \n| Dataset State:\n|  ok\n| Dataset Blurb:\n|  Anndata file (58.5 KB)\n| Dataset Info:\n|  uploaded h5ad file\n| Peek:\n|  [n_obs x n_vars]\n|  640 x 11\n|  [obs]: 2 layers\n|  blobs, index\n|  [var]: 5 layers\n|  dispersions, dispersions_norm, highly_variable, index, means\n|  [uns]: 1 layer\n|  blobs_categories\n| Dataset Job Standard Output:\n|  *Standard output was empty.*\n| Dataset Job Standard Error:\n|  *Standard error was empty.*\n|\n--------------------------------------\n| 2 - Plot (pl.highly_variable_genes) on data 1 (HID - NAME) \n| Dataset State:\n|  error\n| Dataset Blurb:\n|  error\n| Dataset Info:\n|  Traceback (most recent call last):\n|  File \"/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/job_working_directory/000/4/configs/tmpr8qxfwok\", line 15, in <module>\n|  sc.pl.highly_variable_genes(\n|  File \"/usr/local/lib/python3.8/site-\n| Peek:\n|  *Peek unavilable.*\n| Dataset Job Standard Output:\n|  *Standard output was empty.*\n| Dataset Job Standard Error:\n|  Traceback (most recent call last):\n|  File \"/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/job_working_directory/000/4/configs/tmpr8qxfwok\", line 15, in <module>\n|  sc.pl.highly_variable_genes(\n|  File \"/usr/local/lib/python3.8/site-packages/scanpy/plotting/_preprocessing.py\", line 42, in highly_variable_genes\n|  seurat_v3_flavor = adata_or_result.uns[\"hvg\"][\"flavor\"] == \"seurat_v3\"\n|  File \"/usr/local/lib/python3.8/site-packages/anndata/compat/_overloaded_dict.py\", line 100, in __getitem__\n|  return self.data[key]\n|  KeyError: 'hvg'\n|\n--------------------------------------\n| 3 - Log file (HID - NAME) \n| Dataset State:\n|  error\n| Dataset Blurb:\n|  error\n| Dataset Info:\n|  Traceback (most recent call last):\n|  File \"/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/job_working_directory/000/4/configs/tmpr8qxfwok\", line 15, in <module>\n|  sc.pl.highly_variable_genes(\n|  File \"/usr/local/lib/python3.8/site-\n| Peek:\n|  *Peek unavilable.*\n| Dataset Job Standard Output:\n|  *Standard output was empty.*\n| Dataset Job Standard Error:\n|  Traceback (most recent call last):\n|  File \"/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/job_working_directory/000/4/configs/tmpr8qxfwok\", line 15, in <module>\n|  sc.pl.highly_variable_genes(\n|  File \"/usr/local/lib/python3.8/site-packages/scanpy/plotting/_preprocessing.py\", line 42, in highly_variable_genes\n|  seurat_v3_flavor = adata_or_result.uns[\"hvg\"][\"flavor\"] == \"seurat_v3\"\n|  File \"/usr/local/lib/python3.8/site-packages/anndata/compat/_overloaded_dict.py\", line 100, in __getitem__\n|  return self.data[key]\n|  KeyError: 'hvg'\n|\n--------------------------------------\n| Job 8155e4b4bf1581ff\n| State: \n|  error\n| Update Time:\n|  2021-03-15T16:19:31.053717\n| Create Time:\n|  2021-03-15T16:19:18.809400\n|\n--------------------------------------\n| Job 54f2a3a23292eb07\n| State: \n|  ok\n| Update Time:\n|  2021-03-15T16:19:18.686983\n| Create Time:\n|  2021-03-15T16:19:11.155708\n|\n--------------------------------------\nProblem in history with id 5729865256bc2525 - summary of history's datasets and jobs below.\n--------------------------------------\n| 1 - pp.highly_variable_genes.seurat.blobs.h5ad (HID - NAME) \n| Dataset State:\n|  ok\n| Dataset Blurb:\n|  Anndata file (58.5 KB)\n| Dataset Info:\n|  uploaded h5ad file\n| Peek:\n|  [n_obs x n_vars]\n|  640 x 11\n|  [obs]: 2 layers\n|  blobs, index\n|  [var]: 5 layers\n|  dispersions, dispersions_norm, highly_variable, index, means\n|  [uns]: 1 layer\n|  blobs_categories\n| Dataset Job Standard Output:\n|  *Standard output was empty.*\n| Dataset Job Standard Error:\n|  *Standard error was empty.*\n|\n--------------------------------------\n| 2 - Plot (pl.highly_variable_genes) on data 1 (HID - NAME) \n| Dataset State:\n|  error\n| Dataset Blurb:\n|  error\n| Dataset Info:\n|  Traceback (most recent call last):\n|  File \"/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/job_working_directory/000/4/configs/tmpr8qxfwok\", line 15, in <module>\n|  sc.pl.highly_variable_genes(\n|  File \"/usr/local/lib/python3.8/site-\n| Peek:\n|  *Peek unavilable.*\n| Dataset Job Standard Output:\n|  *Standard output was empty.*\n| Dataset Job Standard Error:\n|  Traceback (most recent call last):\n|  File \"/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/job_working_directory/000/4/configs/tmpr8qxfwok\", line 15, in <module>\n|  sc.pl.highly_variable_genes(\n|  File \"/usr/local/lib/python3.8/site-packages/scanpy/plotting/_preprocessing.py\", line 42, in highly_variable_genes\n|  seurat_v3_flavor = adata_or_result.uns[\"hvg\"][\"flavor\"] == \"seurat_v3\"\n|  File \"/usr/local/lib/python3.8/site-packages/anndata/compat/_overloaded_dict.py\", line 100, in __getitem__\n|  return self.data[key]\n|  KeyError: 'hvg'\n|\n--------------------------------------\n| 3 - Log file (HID - NAME) \n| Dataset State:\n|  error\n| Dataset Blurb:\n|  error\n| Dataset Info:\n|  Traceback (most recent call last):\n|  File \"/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/job_working_directory/000/4/configs/tmpr8qxfwok\", line 15, in <module>\n|  sc.pl.highly_variable_genes(\n|  File \"/usr/local/lib/python3.8/site-\n| Peek:\n|  *Peek unavilable.*\n| Dataset Job Standard Output:\n|  *Standard output was empty.*\n| Dataset Job Standard Error:\n|  Traceback (most recent call last):\n|  File \"/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/job_working_directory/000/4/configs/tmpr8qxfwok\", line 15, in <module>\n|  sc.pl.highly_variable_genes(\n|  File \"/usr/local/lib/python3.8/site-packages/scanpy/plotting/_preprocessing.py\", line 42, in highly_variable_genes\n|  seurat_v3_flavor = adata_or_result.uns[\"hvg\"][\"flavor\"] == \"seurat_v3\"\n|  File \"/usr/local/lib/python3.8/site-packages/anndata/compat/_overloaded_dict.py\", line 100, in __getitem__\n|  return self.data[key]\n|  KeyError: 'hvg'\n|\n--------------------------------------\n| Job 8155e4b4bf1581ff\n| State: \n|  error\n| Update Time:\n|  2021-03-15T16:19:31.053717\n| Create Time:\n|  2021-03-15T16:19:18.809400\n|\n--------------------------------------\n| Job 54f2a3a23292eb07\n| State: \n|  ok\n| Update Time:\n|  2021-03-15T16:19:18.686983\n| Create Time:\n|  2021-03-15T16:19:11.155708\n|\n--------------------------------------\n\n--------------------- >> end captured stdout << ----------------------\n-------------------- >> begin captured logging << --------------------\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/tools/scanpy_plot/test_data?tool_version=1.7.1+galaxy0 HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"POST /api/histories HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: 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/api/histories/5729865256bc2525/contents/8155e4b4bf1581ff HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/histories/5729865256bc2525/contents/8155e4b4bf1581ff/provenance HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/histories/5729865256bc2525/contents/7b55dbb89df8f4e5 HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/histories/5729865256bc2525/contents/7b55dbb89df8f4e5/provenance HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/histories/5729865256bc2525/contents/fa6d20d0fb68383f HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/histories/5729865256bc2525/contents/fa6d20d0fb68383f/provenance HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs?history_id=5729865256bc2525 HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/8155e4b4bf1581ff HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/histories/5729865256bc2525/contents HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/histories/5729865256bc2525/contents/8155e4b4bf1581ff HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/histories/5729865256bc2525/contents/8155e4b4bf1581ff/provenance HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/histories/5729865256bc2525/contents/7b55dbb89df8f4e5 HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/histories/5729865256bc2525/contents/7b55dbb89df8f4e5/provenance HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/histories/5729865256bc2525/contents/fa6d20d0fb68383f HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/histories/5729865256bc2525/contents/fa6d20d0fb68383f/provenance HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs?history_id=5729865256bc2525 HTTP/1.1\" 200 None\n--------------------- >> end captured logging << ---------------------"}}, {"id": "functional.test_toolbox.TestForTool_scanpy_plot.test_tool_000020", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy0", "test_index": 20, "time_seconds": 19.550668954849243, "inputs": {"adata": {"src": "hda", "id": "683bc220e21425bb"}, "advanced_common|show_log": true, "format": "png", "method|genes|n_genes": "10", "method|genes|select": "n_genes", "method|method": "pl.rank_genes_groups_violin", "method|split": true, "method|use_raw": false, "method|violin_plot|scale": "width", "method|violin_plot|stripplot|stripplot": "True"}, "job": {"command_line": "cp '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/files/1/c/9/dataset_1c93b18d-87b5-4bc1-a937-bc85649cb0d5.dat' 'anndata.h5ad' && cat '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/job_working_directory/000/6/configs/tmpppckod_k' > '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/files/8/4/8/dataset_84842696-6f5d-416f-8553-5341e2d192ee.dat' && python '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/job_working_directory/000/6/configs/tmpppckod_k' >> '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/files/8/4/8/dataset_84842696-6f5d-416f-8553-5341e2d192ee.dat' && ls . >> '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/files/8/4/8/dataset_84842696-6f5d-416f-8553-5341e2d192ee.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt'  | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\"  | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n-    \\2|g' | sed 's|, |\\n-    |g'", "command_version": "scanpy version: 1.7.1\n", "create_time": "2021-03-15T16:19:38.291924", "exit_code": 1, "external_id": "46913", "galaxy_version": "21.01", "history_id": "54f2a3a23292eb07", "id": "fa6d20d0fb68383f", "inputs": {"adata": {"id": "683bc220e21425bb", "src": "hda", "uuid": "1c93b18d-87b5-4bc1-a937-bc85649cb0d5"}}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}], "job_metrics": [], "job_stderr": "", "job_stdout": "", "model_class": "Job", "outputs": {"hidden_output": {"id": "a90a30fafe298e1e", "src": "hda", "uuid": "84842696-6f5d-416f-8553-5341e2d192ee"}}, "params": {"__input_ext": "\"input\"", "advanced_common": "{\"show_log\": \"true\"}", "chromInfo": "\"/Users/mvandenb/src/galaxy/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "format": "\"png\"", "method": "{\"__current_case__\": 23, \"gene_symbols\": \"\", \"genes\": {\"__current_case__\": 0, \"n_genes\": \"10\", \"select\": \"n_genes\"}, \"groups\": \"\", \"method\": \"pl.rank_genes_groups_violin\", \"split\": \"true\", \"use_raw\": \"false\", \"violin_plot\": {\"scale\": \"width\", \"stripplot\": {\"__current_case__\": 0, \"jitter\": {\"__current_case__\": 0, \"jitter\": \"True\", \"size\": \"1.0\"}, \"stripplot\": \"True\"}}}"}, "state": "error", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n/usr/local/lib/python3.8/site-packages/pandas/core/arrays/categorical.py:2487: FutureWarning: The `inplace` parameter in pandas.Categorical.remove_unused_categories is deprecated and will be removed in a future version.\n  res = method(*args, **kwargs)\nTraceback (most recent call last):\n  File \"/usr/local/lib/python3.8/site-packages/pandas/core/frame.py\", line 3292, in _ensure_valid_index\n    value = Series(value)\n  File \"/usr/local/lib/python3.8/site-packages/pandas/core/series.py\", line 364, in __init__\n    data = sanitize_array(data, index, dtype, copy, raise_cast_failure=True)\n  File \"/usr/local/lib/python3.8/site-packages/pandas/core/construction.py\", line 529, in sanitize_array\n    raise ValueError(\"Data must be 1-dimensional\")\nValueError: Data must be 1-dimensional\n\nThe above exception was the direct cause of the following exception:\n\nTraceback (most recent call last):\n  File \"/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/job_working_directory/000/6/configs/tmpppckod_k\", line 15, in <module>\n    sc.pl.rank_genes_groups_violin(\n  File \"/usr/local/lib/python3.8/site-packages/scanpy/plotting/_tools/__init__.py\", line 909, in rank_genes_groups_violin\n    df[g] = X_col\n  File \"/usr/local/lib/python3.8/site-packages/pandas/core/frame.py\", line 3163, in __setitem__\n    self._set_item(key, value)\n  File \"/usr/local/lib/python3.8/site-packages/pandas/core/frame.py\", line 3241, in _set_item\n    self._ensure_valid_index(value)\n  File \"/usr/local/lib/python3.8/site-packages/pandas/core/frame.py\", line 3294, in _ensure_valid_index\n    raise ValueError(\nValueError: Cannot set a frame with no defined index and a value that cannot be converted to a Series\n", "stdout": "", "tool_id": "scanpy_plot", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n/usr/local/lib/python3.8/site-packages/pandas/core/arrays/categorical.py:2487: FutureWarning: The `inplace` parameter in pandas.Categorical.remove_unused_categories is deprecated and will be removed in a future version.\n  res = method(*args, **kwargs)\nTraceback (most recent call last):\n  File \"/usr/local/lib/python3.8/site-packages/pandas/core/frame.py\", line 3292, in _ensure_valid_index\n    value = Series(value)\n  File \"/usr/local/lib/python3.8/site-packages/pandas/core/series.py\", line 364, in __init__\n    data = sanitize_array(data, index, dtype, copy, raise_cast_failure=True)\n  File \"/usr/local/lib/python3.8/site-packages/pandas/core/construction.py\", line 529, in sanitize_array\n    raise ValueError(\"Data must be 1-dimensional\")\nValueError: Data must be 1-dimensional\n\nThe above exception was the direct cause of the following exception:\n\nTraceback (most recent call last):\n  File \"/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/job_working_directory/000/6/configs/tmpppckod_k\", line 15, in <module>\n    sc.pl.rank_genes_groups_violin(\n  File \"/usr/local/lib/python3.8/site-packages/scanpy/plotting/_tools/__init__.py\", line 909, in rank_genes_groups_violin\n    df[g] = X_col\n  File \"/usr/local/lib/python3.8/site-packages/pandas/core/frame.py\", line 3163, in __setitem__\n    self._set_item(key, value)\n  File \"/usr/local/lib/python3.8/site-packages/pandas/core/frame.py\", line 3241, in _set_item\n    self._ensure_valid_index(value)\n  File \"/usr/local/lib/python3.8/site-packages/pandas/core/frame.py\", line 3294, in _ensure_valid_index\n    raise ValueError(\nValueError: Cannot set a frame with no defined index and a value that cannot be converted to a Series\n", "tool_stdout": "", "update_time": "2021-03-15T16:19:51.110981", "user_email": "test@bx.psu.edu"}, "output_problems": ["Job in error state.", "Job in error state.", "Failed to find identifier 'cell_type_Ery' in the tool generated collection elements []"], "status": "failure", "problem_type": "galaxy.tool_util.verify.interactor.JobOutputsError", "problem_log": "  File \"/Users/mvandenb/.pyenv/versions/3.8.2/lib/python3.8/unittest/case.py\", line 60, in testPartExecutor\n    yield\n  File \"/Users/mvandenb/.pyenv/versions/3.8.2/lib/python3.8/unittest/case.py\", line 676, in run\n    self._callTestMethod(testMethod)\n  File \"/Users/mvandenb/.pyenv/versions/3.8.2/lib/python3.8/unittest/case.py\", line 633, in _callTestMethod\n    method()\n  File \"/Users/mvandenb/src/galaxy/test/functional/test_toolbox.py\", line 98, in test_tool\n    self.do_it(tool_version=tool_version, test_index=test_index)\n  File \"/Users/mvandenb/src/galaxy/test/functional/test_toolbox.py\", line 35, in do_it\n    verify_tool(tool_id, self.galaxy_interactor, resource_parameters=resource_parameters, test_index=test_index, tool_version=tool_version, register_job_data=register_job_data)\n  File \"/Users/mvandenb/src/galaxy/lib/galaxy/tool_util/verify/interactor.py\", line 1050, in verify_tool\n    raise e\n  File \"/Users/mvandenb/src/galaxy/lib/galaxy/tool_util/verify/interactor.py\", line 1046, in verify_tool\n    job_stdio = _verify_outputs(testdef, test_history, jobs, tool_id, data_list, data_collection_list, galaxy_interactor, quiet=quiet)\n  File \"/Users/mvandenb/src/galaxy/lib/galaxy/tool_util/verify/interactor.py\", line 1222, in _verify_outputs\n    raise JobOutputsError(found_exceptions, job_stdio)\nJob in error state.\nJob in error state.\nFailed to find identifier 'cell_type_Ery' in the tool generated collection elements []\n-------------------- >> begin captured stdout << ---------------------\nProblem in history with id 54f2a3a23292eb07 - summary of history's datasets and jobs below.\n--------------------------------------\n| 1 - tl.rank_genes_groups.krumsiek11.h5ad (HID - NAME) \n| Dataset State:\n|  ok\n| Dataset Blurb:\n|  Anndata file (77.2 KB)\n| Dataset Info:\n|  uploaded h5ad file\n| Peek:\n|  [n_obs x n_vars]\n|  640 x 11\n|  [obs]: 3 layers\n|  __categories, cell_type, index\n|  [var]: 1 layer\n|  index\n|  [uns]: 4 layers\n|  cell_type_colors, highlights, iroot, rank_genes_groups\n| Dataset Job Standard Output:\n|  *Standard output was empty.*\n| Dataset Job Standard Error:\n|  *Standard error was empty.*\n|\n--------------------------------------\n| 2 - Plot (pl.rank_genes_groups_violin) on data 1 (HID - NAME) \n| Dataset Collection: {'collection_type': 'list', 'contents_url': '/api/dataset_collections/2891970512fa2d5a/contents/2891970512fa2d5a', 'deleted': False, 'element_count': 0, 'elements': [], 'hid': 2, 'history_content_type': 'dataset_collection', 'history_id': '54f2a3a23292eb07', 'id': '2891970512fa2d5a', 'job_source_id': 'fa6d20d0fb68383f', 'job_source_type': 'Job', 'model_class': 'HistoryDatasetCollectionAssociation', 'name': 'Plot (pl.rank_genes_groups_violin) on data 1', 'populated': True, 'populated_state': 'ok', 'populated_state_message': None, 'tags': [], 'type': 'collection', 'url': '/api/histories/54f2a3a23292eb07/contents/dataset_collections/2891970512fa2d5a', 'visible': True}\n|\n--------------------------------------\n| 3 - Log file (HID - NAME) \n| Dataset State:\n|  error\n| Dataset Blurb:\n|  error\n| Dataset Info:\n|  Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n|  /usr/local/lib/python3.8/site-packages/pandas/core/arrays/categorical.py:2487: FutureWarning: The `inplace` parameter in pandas.Categorical.remove_unused_categories is\n| Peek:\n|  *Peek unavilable.*\n| Dataset Job Standard Output:\n|  *Standard output was empty.*\n| Dataset Job Standard Error:\n|  Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n|  /usr/local/lib/python3.8/site-packages/pandas/core/arrays/categorical.py:2487: FutureWarning: The `inplace` parameter in pandas.Categorical.remove_unused_categories is deprecated and will be removed in a future version.\n|  res = method(*args, **kwargs)\n|  Traceback (most recent call last):\n|  File \"/usr/local/lib/python3.8/site-packages/pandas/core/frame.py\", line 3292, in _ensure_valid_index\n|  value = Series(value)\n|  File \"/usr/local/lib/python3.8/site-packages/pandas/core/series.py\", line 364, in __init__\n|  data = sanitize_array(data, index, dtype, copy, raise_cast_failure=True)\n|  File \"/usr/local/lib/python3.8/site-packages/pandas/core/construction.py\", line 529, in sanitize_array\n|  raise ValueError(\"Data must be 1-dimensional\")\n|  ValueError: Data must be 1-dimensional\n|  The above exception was the direct cause of the following exception:\n|  Traceback (most recent call last):\n|  File \"/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/job_working_directory/000/6/configs/tmpppckod_k\", line 15, in <module>\n|  sc.pl.rank_genes_groups_violin(\n|  File \"/usr/local/lib/python3.8/site-packages/scanpy/plotting/_tools/__init__.py\", line 909, in rank_genes_groups_violin\n|  df[g] = X_col\n|  File \"/usr/local/lib/python3.8/site-packages/pandas/core/frame.py\", line 3163, in __setitem__\n|  self._set_item(key, value)\n|  File \"/usr/local/lib/python3.8/site-packages/pandas/core/frame.py\", line 3241, in _set_item\n|  self._ensure_valid_index(value)\n|  File \"/usr/local/lib/python3.8/site-packages/pandas/core/frame.py\", line 3294, in _ensure_valid_index\n|  raise ValueError(\n|  ValueError: Cannot set a frame with no defined index and a value that cannot be converted to a Series\n|\n--------------------------------------\n| Job fa6d20d0fb68383f\n| State: \n|  error\n| Update Time:\n|  2021-03-15T16:19:51.110981\n| Create Time:\n|  2021-03-15T16:19:38.291924\n|\n--------------------------------------\n| Job 7b55dbb89df8f4e5\n| State: \n|  ok\n| Update Time:\n|  2021-03-15T16:19:38.091214\n| Create Time:\n|  2021-03-15T16:19:32.766189\n|\n--------------------------------------\nProblem in history with id 54f2a3a23292eb07 - summary of history's datasets and jobs below.\n--------------------------------------\n| 1 - tl.rank_genes_groups.krumsiek11.h5ad (HID - NAME) \n| Dataset State:\n|  ok\n| Dataset Blurb:\n|  Anndata file (77.2 KB)\n| Dataset Info:\n|  uploaded h5ad file\n| Peek:\n|  [n_obs x n_vars]\n|  640 x 11\n|  [obs]: 3 layers\n|  __categories, cell_type, index\n|  [var]: 1 layer\n|  index\n|  [uns]: 4 layers\n|  cell_type_colors, highlights, iroot, rank_genes_groups\n| Dataset Job Standard Output:\n|  *Standard output was empty.*\n| Dataset Job Standard Error:\n|  *Standard error was empty.*\n|\n--------------------------------------\n| 2 - Plot (pl.rank_genes_groups_violin) on data 1 (HID - NAME) \n| Dataset Collection: {'collection_type': 'list', 'contents_url': '/api/dataset_collections/2891970512fa2d5a/contents/2891970512fa2d5a', 'deleted': False, 'element_count': 0, 'elements': [], 'hid': 2, 'history_content_type': 'dataset_collection', 'history_id': '54f2a3a23292eb07', 'id': '2891970512fa2d5a', 'job_source_id': 'fa6d20d0fb68383f', 'job_source_type': 'Job', 'model_class': 'HistoryDatasetCollectionAssociation', 'name': 'Plot (pl.rank_genes_groups_violin) on data 1', 'populated': True, 'populated_state': 'ok', 'populated_state_message': None, 'tags': [], 'type': 'collection', 'url': '/api/histories/54f2a3a23292eb07/contents/dataset_collections/2891970512fa2d5a', 'visible': True}\n|\n--------------------------------------\n| 3 - Log file (HID - NAME) \n| Dataset State:\n|  error\n| Dataset Blurb:\n|  error\n| Dataset Info:\n|  Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n|  /usr/local/lib/python3.8/site-packages/pandas/core/arrays/categorical.py:2487: FutureWarning: The `inplace` parameter in pandas.Categorical.remove_unused_categories is\n| Peek:\n|  *Peek unavilable.*\n| Dataset Job Standard Output:\n|  *Standard output was empty.*\n| Dataset Job Standard Error:\n|  Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n|  /usr/local/lib/python3.8/site-packages/pandas/core/arrays/categorical.py:2487: FutureWarning: The `inplace` parameter in pandas.Categorical.remove_unused_categories is deprecated and will be removed in a future version.\n|  res = method(*args, **kwargs)\n|  Traceback (most recent call last):\n|  File \"/usr/local/lib/python3.8/site-packages/pandas/core/frame.py\", line 3292, in _ensure_valid_index\n|  value = Series(value)\n|  File \"/usr/local/lib/python3.8/site-packages/pandas/core/series.py\", line 364, in __init__\n|  data = sanitize_array(data, index, dtype, copy, raise_cast_failure=True)\n|  File \"/usr/local/lib/python3.8/site-packages/pandas/core/construction.py\", line 529, in sanitize_array\n|  raise ValueError(\"Data must be 1-dimensional\")\n|  ValueError: Data must be 1-dimensional\n|  The above exception was the direct cause of the following exception:\n|  Traceback (most recent call last):\n|  File \"/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/job_working_directory/000/6/configs/tmpppckod_k\", line 15, in <module>\n|  sc.pl.rank_genes_groups_violin(\n|  File \"/usr/local/lib/python3.8/site-packages/scanpy/plotting/_tools/__init__.py\", line 909, in rank_genes_groups_violin\n|  df[g] = X_col\n|  File \"/usr/local/lib/python3.8/site-packages/pandas/core/frame.py\", line 3163, in __setitem__\n|  self._set_item(key, value)\n|  File \"/usr/local/lib/python3.8/site-packages/pandas/core/frame.py\", line 3241, in _set_item\n|  self._ensure_valid_index(value)\n|  File \"/usr/local/lib/python3.8/site-packages/pandas/core/frame.py\", line 3294, in _ensure_valid_index\n|  raise ValueError(\n|  ValueError: Cannot set a frame with no defined index and a value that cannot be converted to a Series\n|\n--------------------------------------\n| Job fa6d20d0fb68383f\n| State: \n|  error\n| Update Time:\n|  2021-03-15T16:19:51.110981\n| Create Time:\n|  2021-03-15T16:19:38.291924\n|\n--------------------------------------\n| Job 7b55dbb89df8f4e5\n| State: \n|  ok\n| Update Time:\n|  2021-03-15T16:19:38.091214\n| Create Time:\n|  2021-03-15T16:19:32.766189\n|\n--------------------------------------\n\n--------------------- >> end captured stdout << ----------------------\n-------------------- >> begin captured logging << --------------------\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/tools/scanpy_plot/test_data?tool_version=1.7.1+galaxy0 HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"POST /api/histories HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/tools/scanpy_plot/test_data_download?filename=tl.rank_genes_groups.krumsiek11.h5ad HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"POST /api/tools HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/7b55dbb89df8f4e5 HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/7b55dbb89df8f4e5 HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/7b55dbb89df8f4e5 HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/7b55dbb89df8f4e5 HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/7b55dbb89df8f4e5 HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/7b55dbb89df8f4e5 HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/7b55dbb89df8f4e5 HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/7b55dbb89df8f4e5 HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/7b55dbb89df8f4e5 HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/7b55dbb89df8f4e5 HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/7b55dbb89df8f4e5 HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/7b55dbb89df8f4e5 HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/7b55dbb89df8f4e5 HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/7b55dbb89df8f4e5 HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/7b55dbb89df8f4e5 HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/7b55dbb89df8f4e5 HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/7b55dbb89df8f4e5 HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/7b55dbb89df8f4e5 HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"POST /api/tools HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/fa6d20d0fb68383f HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/fa6d20d0fb68383f HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/fa6d20d0fb68383f HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/fa6d20d0fb68383f HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/fa6d20d0fb68383f HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/fa6d20d0fb68383f 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new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/fa6d20d0fb68383f HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/fa6d20d0fb68383f HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/fa6d20d0fb68383f HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/fa6d20d0fb68383f HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/fa6d20d0fb68383f HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 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http://127.0.0.1:9844 \"GET /api/jobs/fa6d20d0fb68383f HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/fa6d20d0fb68383f HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/fa6d20d0fb68383f HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/fa6d20d0fb68383f HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/fa6d20d0fb68383f HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/fa6d20d0fb68383f 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127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/fa6d20d0fb68383f HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/fa6d20d0fb68383f HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/fa6d20d0fb68383f HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/fa6d20d0fb68383f HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/histories/54f2a3a23292eb07/contents HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/histories/54f2a3a23292eb07/contents/683bc220e21425bb HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/histories/54f2a3a23292eb07/contents/683bc220e21425bb/provenance HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/histories/54f2a3a23292eb07/contents/dataset_collections/2891970512fa2d5a HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/histories/54f2a3a23292eb07/contents/a90a30fafe298e1e HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/histories/54f2a3a23292eb07/contents/a90a30fafe298e1e/provenance HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs?history_id=54f2a3a23292eb07 HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/fa6d20d0fb68383f?full=true HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs/fa6d20d0fb68383f HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/histories/54f2a3a23292eb07/contents HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/histories/54f2a3a23292eb07/contents/683bc220e21425bb HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/histories/54f2a3a23292eb07/contents/683bc220e21425bb/provenance HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/histories/54f2a3a23292eb07/contents/dataset_collections/2891970512fa2d5a HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/histories/54f2a3a23292eb07/contents/a90a30fafe298e1e HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/histories/54f2a3a23292eb07/contents/a90a30fafe298e1e/provenance HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/jobs?history_id=54f2a3a23292eb07 HTTP/1.1\" 200 None\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \"GET /api/dataset_collections/2891970512fa2d5a?instance_type=history HTTP/1.1\" 200 None\n--------------------- >> end captured logging << ---------------------"}}], "summary": {"num_tests": 3, "num_failures": 2, "num_errors": 0, "num_skips": 0}, "exit_code": 1}
\ No newline at end of file
Binary file test-data/krumsiek11_ranked_gene_groups.h5ad has changed
Binary file test-data/test.h5ad has changed