view tool_test_output.json @ 1:2e7bc1bb2dbe draft default tip

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{"tests": [{"data": {"status": "failure", "inputs": {"input": {"src": "hda", "id": "2891970512fa2d5a"}, "cond": "c2"}, "output_problems": ["Job in error state."], "job": {"inputs": {"input": {"src": "hda", "id": "2891970512fa2d5a"}}, "update_time": "2015-01-08T22:31:55.343681", "tool_id": "Summary_Statistics1", "outputs": {"out_file1": {"src": "hda", "id": "5729865256bc2525"}}, "stdout": "Error in dyn.load(file, DLLpath = DLLpath, ...) : \n  kann shared object '/home/bag/projects/code/galaxy-central/tool_deps/R_3_0_1/3.0.1/iuc/package_r_3_0_1/1c0e86a44f73/lib/R/library/stats/libs/stats.so' nicht laden:\n  /home/bag/projects/code/galaxy-central/tool_deps/R/3.1.2/iuc/package_r_3_1_2/f0626dac6765/lib/R/lib/libRlapack.so: undefined symbol: _gfortran_pow_r8_i4\nBeim Start - Warnmeldung:\n \nFehler: 'rho' must be an environment not NULL: detected in C-level eval\n", "command_line": "python /home/bag/projects/code/galaxytools/rpy_statistics_collection/gsummary.py /tmp/tmprD44IMfiles/000/dataset_1.dat /tmp/tmprD44IMfiles/000/dataset_2.dat \"c2\"", "exit_code": 139, "state": "error", "create_time": "2015-01-08T22:31:51.004258", "params": {"chromInfo": "\"/home/bag/projects/code/galaxy-central/tool-data/shared/ucsc/chrom/hg17.len\"", "cond": "\"c2\"", "dbkey": "\"hg17\""}, "stderr": "Segmentation fault (core dumped)\n", "job_metrics": [], "model_class": "Job", "id": "5729865256bc2525"}, "problem_log": "Traceback (most recent call last):\n  File \"/usr/lib/python2.7/unittest/case.py\", line 329, in run\n    testMethod()\n  File \"/home/bag/projects/code/galaxy-central/test/functional/test_toolbox.py\", line 182, in test_tool\n    self.do_it( td )\n  File \"/home/bag/projects/code/galaxy-central/test/functional/test_toolbox.py\", line 65, in do_it\n    raise e\nJobOutputsError: Job in error state.\n-------------------- >> begin captured stdout << ---------------------\nHistory with id 2891970512fa2d5a in error - summary of datasets in error below.\n--------------------------------------\n| 2 - Summary Statistics on data 1 (HID - NAME) \n| Dataset Blurb:\n|  error\n| Dataset Info:\n|  Error in dyn.load(file, DLLpath = DLLpath, ...) :\n|  kann shared object '/home/bag/projects/code/galaxy-central/tool_deps/R_3_0_1/3.0.1/iuc/package_r_3_0_1/1c0e86a44f73/lib/R/library/stats/libs/stats.so' nicht laden:\n|  /home/bag/projects/code/galaxy-cent\n| Dataset Job Standard Output:\n|  Error in dyn.load(file, DLLpath = DLLpath, ...) :\n|  kann shared object '/home/bag/projects/code/galaxy-central/tool_deps/R_3_0_1/3.0.1/iuc/package_r_3_0_1/1c0e86a44f73/lib/R/library/stats/libs/stats.so' nicht laden:\n|  /home/bag/projects/code/galaxy-central/tool_deps/R/3.1.2/iuc/package_r_3_1_2/f0626dac6765/lib/R/lib/libRlapack.so: undefined symbol: _gfortran_pow_r8_i4\n|  Beim Start - Warnmeldung:\n|  \n|  Fehler: 'rho' must be an environment not NULL: detected in C-level eval\n| Dataset Job Standard Error:\n|  Segmentation fault (core dumped)\n|\n--------------------------------------\n\n--------------------- >> end captured stdout << ----------------------\n-------------------- >> begin captured logging << --------------------\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/users?key=test_key HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key\nrequests.packages.urllib3.connectionpool: DEBUG: \"POST /api/users HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key\nrequests.packages.urllib3.connectionpool: DEBUG: \"POST /api/users/2891970512fa2d5a/api_key HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"POST /api/histories HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.tools.actions.upload_common: INFO: tool upload1 created job id 1\nrequests.packages.urllib3.connectionpool: DEBUG: \"POST /api/tools HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs: DEBUG: (1) Working directory for job is: /tmp/tmprD44IM/job_working_directory/000/1\ngalaxy.jobs.handler: DEBUG: (1) Dispatching to local runner\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=1ad2653278529aa1e63296a7e0b9dc50 HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=1ad2653278529aa1e63296a7e0b9dc50 HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs: DEBUG: (1) Persisting job destination (destination id: local:///)\ngalaxy.jobs.handler: INFO: (1) Job dispatched\ngalaxy.jobs.runners: DEBUG: (1) command is: python /home/bag/projects/code/galaxy-central/tools/data_source/upload.py /home/bag/projects/code/galaxy-central /tmp/tmprD44IM/tmp/tmpBJjmke /tmp/tmprD44IM/tmp/tmpzDrmot 1:/tmp/tmprD44IM/job_working_directory/000/1/dataset_1_files:/tmp/tmprD44IMfiles/000/dataset_1.dat; return_code=$?; cd /home/bag/projects/code/galaxy-central; /home/bag/projects/code/galaxy-central/set_metadata.sh /tmp/tmprD44IMfiles /tmp/tmprD44IM/job_working_directory/000/1 . /tmp/tmp_QrpB0/functional_tests_wsgi.ini /tmp/tmprD44IM/tmp/tmpBJjmke /tmp/tmprD44IM/job_working_directory/000/1/galaxy.json /tmp/tmprD44IM/job_working_directory/000/1/metadata_in_HistoryDatasetAssociation_1_od2880,/tmp/tmprD44IM/job_working_directory/000/1/metadata_kwds_HistoryDatasetAssociation_1_LAC5zI,/tmp/tmprD44IM/job_working_directory/000/1/metadata_out_HistoryDatasetAssociation_1_oWzbfn,/tmp/tmprD44IM/job_working_directory/000/1/metadata_results_HistoryDatasetAssociation_1_dxBMBo,,/tmp/tmprD44IM/job_working_directory/000/1/metadata_override_HistoryDatasetAssociation_1_kZQ7D7; sh -c \"exit $return_code\"\ngalaxy.jobs.runners.local: DEBUG: (1) executing job script: /tmp/tmprD44IM/job_working_directory/000/1/galaxy_1.sh\ngalaxy.jobs: DEBUG: (1) Persisting job destination (destination id: local:///)\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=1ad2653278529aa1e63296a7e0b9dc50 HTTP/1.1\" 200 None\ngalaxy.jobs.runners.local: DEBUG: execution finished: /tmp/tmprD44IM/job_working_directory/000/1/galaxy_1.sh\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=1ad2653278529aa1e63296a7e0b9dc50 HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.datatypes.metadata: DEBUG: loading metadata from file for: HistoryDatasetAssociation 1\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=1ad2653278529aa1e63296a7e0b9dc50 HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs: DEBUG: job 1 ended\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=1ad2653278529aa1e63296a7e0b9dc50 HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"POST /api/tools HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs: DEBUG: (2) Working directory for job is: /tmp/tmprD44IM/job_working_directory/000/2\ngalaxy.jobs.handler: DEBUG: (2) Dispatching to local runner\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/jobs/5729865256bc2525?key=1ad2653278529aa1e63296a7e0b9dc50 HTTP/1.1\" 200 None\ngalaxy.jobs: DEBUG: (2) Persisting job destination (destination id: local:///)\ngalaxy.jobs.handler: INFO: (2) Job dispatched\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/jobs/5729865256bc2525?key=1ad2653278529aa1e63296a7e0b9dc50 HTTP/1.1\" 200 None\ngalaxy.jobs.runners: DEBUG: (2) command is: python /home/bag/projects/code/galaxytools/rpy_statistics_collection/gsummary.py /tmp/tmprD44IMfiles/000/dataset_1.dat /tmp/tmprD44IMfiles/000/dataset_2.dat \"c2\"; return_code=$?; cd /home/bag/projects/code/galaxy-central; /home/bag/projects/code/galaxy-central/set_metadata.sh /tmp/tmprD44IMfiles /tmp/tmprD44IM/job_working_directory/000/2 . /tmp/tmp_QrpB0/functional_tests_wsgi.ini /tmp/tmprD44IM/tmp/tmpBJjmke /tmp/tmprD44IM/job_working_directory/000/2/galaxy.json /tmp/tmprD44IM/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_2_MCE7SE,/tmp/tmprD44IM/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_AtXwgq,/tmp/tmprD44IM/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_2_NX8vCK,/tmp/tmprD44IM/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_2_Z2348A,,/tmp/tmprD44IM/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_2_CBptA2; sh -c \"exit $return_code\"\ngalaxy.jobs.runners.local: DEBUG: (2) executing job script: /tmp/tmprD44IM/job_working_directory/000/2/galaxy_2.sh\ngalaxy.jobs: DEBUG: (2) Persisting job destination (destination id: local:///)\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/jobs/5729865256bc2525?key=1ad2653278529aa1e63296a7e0b9dc50 HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/jobs/5729865256bc2525?key=1ad2653278529aa1e63296a7e0b9dc50 HTTP/1.1\" 200 None\ngalaxy.jobs.runners.local: DEBUG: execution finished: /tmp/tmprD44IM/job_working_directory/000/2/galaxy_2.sh\ngalaxy.jobs: DEBUG: setting dataset state to ERROR\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/jobs/5729865256bc2525?key=1ad2653278529aa1e63296a7e0b9dc50 HTTP/1.1\" 200 None\ngalaxy.jobs: DEBUG: job 2 ended\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/jobs/5729865256bc2525?key=1ad2653278529aa1e63296a7e0b9dc50 HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a/contents?key=1ad2653278529aa1e63296a7e0b9dc50 HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525?key=1ad2653278529aa1e63296a7e0b9dc50 HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525/provenance?key=1ad2653278529aa1e63296a7e0b9dc50 HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/jobs/5729865256bc2525?full=true&key=1ad2653278529aa1e63296a7e0b9dc50 HTTP/1.1\" 200 None\n--------------------- >> end captured logging << ---------------------\n", "problem_type": "functional.test_toolbox.JobOutputsError"}, "id": "functional.test_toolbox.TestForTool_Summary_Statistics1.test_tool_000000", "has_data": true}], "version": "0.1", "summary": {"num_skips": 0, "num_errors": 0, "num_failures": 1, "num_tests": 1}}