# HG changeset patch # User fubar # Date 1446420400 18000 # Node ID d351a1ec1e18412c578a453e223928d7e3e79d86 # Parent 31be675baa50f0422db320283f2f2a0c635a10f2 GRRR!!! as at nov 2015, glmnet fails to load methods. see https://github.com/dhimmel/elevcan/issues/1 diff -r 31be675baa50 -r d351a1ec1e18 .Rhistory --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.Rhistory Sun Nov 01 18:26:40 2015 -0500 @@ -0,0 +1,5 @@ +library('glmnet') +library('lars') +library('survival') +library('pec') +message=function(x) {print.noquote(paste(x,sep=''))} diff -r 31be675baa50 -r d351a1ec1e18 rglasso_cox.xml --- a/rglasso_cox.xml Sat Oct 31 07:20:03 2015 -0400 +++ b/rglasso_cox.xml Sun Nov 01 18:26:40 2015 -0500 @@ -13,6 +13,8 @@ + + + + + + Tool Test Results (powered by Planemo) + + + + + + + + + + + + + + +
+
+
+ + +
+
+ +

Overview

+
+
+
+

Tests

+

The remainder of this contains a description for each test executed to run these jobs.

+
+
+
+ + + + + + + \ No newline at end of file diff -r 31be675baa50 -r d351a1ec1e18 tool_test_output.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_test_output.json Sun Nov 01 18:26:40 2015 -0500 @@ -0,0 +1,1 @@ +{"tests": [{"data": {"status": "failure", "inputs": {"force_xvar_cols": "3", "xvar_cols": ["3", "4", "5"], "input1": {"src": "hda", "id": "2891970512fa2d5a"}, "nfold": "10", "title": "Cox glmnet test", "model|output_pred": "F", "do_standard": "True", "model|output_full": "F", "model|predict_at": "", "model|fam": "cox", "logxform_cols": "", "model|cox_id": "1", "model|cox_status": "2", "alpha": "0.95", "model|cox_time": "1"}, "output_problems": ["History item different than expected\nOutput file did not contain expected text 'rhubarb' (ouptut '')", "History item different than expected, difference (using diff):\n( /home/rlazarus/tools-iuc/tools/rglasso/test-data/coxlassotest.html v. /tmp/tmp1act3b/tmp/tmpM1zEZTcoxlassotest.html )\n--- local_file\n+++ history_data\n@@ -8,160 +8,27 @@\n \n
\n \n-
Galaxy Tool \"rglasso\" run at 18/02/2015 22:06:08

\n-
cox images and outputs
\n-(Click on a thumbnail image to download the corresponding original PDF image)
\n-
\n-\n-\n-\n-\n-\n-\n-
\"Image\"Image
\n-\n-
cox log output
\n-\n-
\n-\n-[1] @@@ Cox model will be predicted at times = 3.724234,1325.40516225,2373.090418,3650.1730825,4989.405682\n********\n*SNIP *\n********\n-\n-7: In box(...) : \"label\" is not a graphical parameter\n-\n-8: In title(...) : \"label\" is not a graphical parameter\n-\n-\n-
\n-\n+/tmp/tmp1act3b/job_working_directory/000/2/dataset_2_files/rglasso_runner.log is empty
\n
All output files available for downloading
\n \n
\n \n-\n-\n-\n-\n \n-\n-\n+\n+\n
Output File Name (click to view)Size
cox_Coxglmnettest_glmnet_cvdeviance.pdf6.4 KB
cox_Coxglmnettest_glmnetdev.pdf5.3 KB
cox_cross_validation_model_counts.xls42 B
cox_rglasso.log522 B
rglasso.Rscript21.5 KB
rglasso_error.log803 B
rglasso_runner.log1.7 KB
rglasso_error.log86 B
rglasso_runner.log49 B

\n
\n \n"], "job": {"inputs": {"input1": {"src": "hda", "id": "2891970512fa2d5a", "uuid": "1c4d3d04-75b4-4c7c-b738-ab0257ce0c35"}}, "update_time": "2015-11-01T22:53:13.211964", "tool_id": "rglasso_cox", "outputs": {"html_file": {"src": "hda", "id": "5729865256bc2525", "uuid": "3ecbbcb5-6058-4429-bc8d-6281b5c9e9be"}, "model_file": {"src": "hda", "id": "54f2a3a23292eb07", "uuid": "1833924e-4f31-4d15-903d-252d32488b15"}}, "stdout": "", "command_line": "python /home/rlazarus/tools-iuc/tools/rglasso/rgToolFactory.py --script_path \"/tmp/tmp1act3b/job_working_directory/000/2/tmpI7mLI2\" --interpreter \"Rscript\" --tool_name \"rglasso\" --output_dir \"/tmp/tmp1act3b/job_working_directory/000/2/dataset_2_files\" --output_html \"/tmp/tmp1act3b/files/000/dataset_2.dat\" --make_HTML \"yes\"", "exit_code": 1, "state": "ok", "create_time": "2015-11-01T22:53:08.474952", "params": {"force_xvar_cols": "[\"3\"]", "mdsplots": "\"False\"", "nfold": "\"10\"", "title": "\"Cox glmnet test\"", "do_standard": "\"True\"", "optLambda": "\"lambda.1se\"", "xvar_cols": "[\"3\", \"4\", \"5\"]", "dbkey": "\"hg17\"", "logxform_cols": "[]", "alpha": "\"0.95\"", "model": "{\"__current_case__\": 3, \"output_pred\": \"F\", \"cox_time\": \"1\", \"fam\": \"cox\", \"predict_at\": \"\", \"cox_id\": \"1\", \"cox_status\": \"2\", \"output_full\": \"F\"}", "chromInfo": "\"/home/rlazarus/galaxy/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "", "job_metrics": [], "model_class": "Job", "external_id": "27854", "id": "5729865256bc2525", "user_email": "test@bx.psu.edu"}, "problem_log": " File \"/usr/lib/python2.7/unittest/case.py\", line 331, in run\n testMethod()\n File \"/home/rlazarus/galaxy/test/functional/test_toolbox.py\", line 289, in test_tool\n self.do_it( td )\n File \"/home/rlazarus/galaxy/test/functional/test_toolbox.py\", line 73, in do_it\n raise e\n'History item different than expected\\nOutput file did not contain expected text \\'rhubarb\\' (ouptut \\'\\')\\nHistory item different than expected, difference (using diff):\\n( /home/rlazarus/tools-iuc/tools/rglasso/test-data/coxlassotest.html v. /tmp/tmp1act3b/tmp/tmpM1zEZTcoxlassotest.html )\\n--- local_file\\n+++ history_data\\n@@ -8,160 +8,27 @@\\n \\n
\\n \\n-
Galaxy Tool \"rglasso\" run at 18/02/2015 22:06:08

\\n-
cox images and outputs
\\n-(Click on a thumbnail image to download the corresponding original PDF image)
\\n-
\\n-\\n-\\n-\\n-\\n-\\n-\\n-
\"Image\"Image
\\n-\\n-
cox log output
\\n-\\n-
\\n-\\n-[1] @@@ Cox model will be predicted at times = 3.724234,1325.40516225,2373.090418,3650.1730825,4989.405682\\n********\\n*SNIP *\\n********\\n-\\n-7: In box(...) : \"label\" is not a graphical parameter\\n-\\n-8: In title(...) : \"label\" is not a graphical parameter\\n-\\n-\\n-
\\n-\\n+/tmp/tmp1act3b/job_working_directory/000/2/dataset_2_files/rglasso_runner.log is empty
\\n
All output files available for downloading
\\n \\n
\\n \\n-\\n-\\n-\\n-\\n \\n-\\n-\\n+\\n+\\n
Output File Name (click to view)Size
cox_Coxglmnettest_glmnet_cvdeviance.pdf6.4 KB
cox_Coxglmnettest_glmnetdev.pdf5.3 KB
cox_cross_validation_model_counts.xls42 B
cox_rglasso.log522 B
rglasso.Rscript21.5 KB
rglasso_error.log803 B
rglasso_runner.log1.7 KB
rglasso_error.log86 B
rglasso_runner.log49 B

\\n
\\n \\n\\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\\ngalaxy.tools.execute: DEBUG: Tool [upload1] created job [1] (535.979 ms)\\ngalaxy.jobs: DEBUG: (1) Working directory for job is: /tmp/tmp1act3b/job_working_directory/000/1\\ngalaxy.jobs.handler: DEBUG: (1) Dispatching to local runner\\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) Persisting job destination (destination id: local:///)\\ngalaxy.jobs.runners: DEBUG: Job [1] queued (338.266 ms)\\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=3d8ec2f04896f6b3eee771fcb4ad58bb HTTP/1.1\" 200 None\\ngalaxy.jobs.handler: INFO: (1) Job dispatched\\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=3d8ec2f04896f6b3eee771fcb4ad58bb 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=3d8ec2f04896f6b3eee771fcb4ad58bb HTTP/1.1\" 200 None\\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\\ngalaxy.tools.deps: DEBUG: Building dependency shell command for dependency \\'samtools\\'\\ngalaxy.tools.deps: WARNING: Failed to resolve dependency on \\'samtools\\', ignoring\\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=3d8ec2f04896f6b3eee771fcb4ad58bb HTTP/1.1\" 200 None\\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\\ngalaxy.jobs.runners: DEBUG: (1) command is: python /home/rlazarus/galaxy/tools/data_source/upload.py /home/rlazarus/galaxy /tmp/tmp1act3b/tmp/tmpeK8ceT /tmp/tmp1act3b/tmp/tmp_u4ilL 1:/tmp/tmp1act3b/job_working_directory/000/1/dataset_1_files:/tmp/tmp1act3b/files/000/dataset_1.dat; return_code=$?; python \"/tmp/tmp1act3b/job_working_directory/000/1/set_metadata_W_dDn4.py\" \"/tmp/tmp1act3b/tmp/tmpeK8ceT\" \"/tmp/tmp1act3b/job_working_directory/000/1/galaxy.json\" \"/tmp/tmp1act3b/job_working_directory/000/1/metadata_in_HistoryDatasetAssociation_1_7KGRiW,/tmp/tmp1act3b/job_working_directory/000/1/metadata_kwds_HistoryDatasetAssociation_1_1AqRY_,/tmp/tmp1act3b/job_working_directory/000/1/metadata_out_HistoryDatasetAssociation_1_8gFKoI,/tmp/tmp1act3b/job_working_directory/000/1/metadata_results_HistoryDatasetAssociation_1_WaL55c,/tmp/tmp1act3b/files/000/dataset_1.dat,/tmp/tmp1act3b/job_working_directory/000/1/metadata_override_HistoryDatasetAssociation_1_pbPQn2\" 5242880; sh -c \"exit $return_code\"\\ngalaxy.jobs.runners.local: DEBUG: (1) executing job script: /tmp/tmp1act3b/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=3d8ec2f04896f6b3eee771fcb4ad58bb HTTP/1.1\" 200 None\\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\\ngalaxy.jobs.runners.local: DEBUG: execution finished: /tmp/tmp1act3b/job_working_directory/000/1/galaxy_1.sh\\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=3d8ec2f04896f6b3eee771fcb4ad58bb 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=3d8ec2f04896f6b3eee771fcb4ad58bb HTTP/1.1\" 200 None\\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\\ngalaxy.jobs: DEBUG: job 1 ended (finish() executed in (731.866 ms))\\ngalaxy.tools.actions: INFO: Handled output (99.066 ms)\\ngalaxy.tools.actions: INFO: Handled output (58.023 ms)\\ngalaxy.tools.actions: INFO: Verified access to datasets (13.814 ms)\\ngalaxy.tools.execute: DEBUG: Tool [rglasso_cox] created job [2] (612.189 ms)\\nrequests.packages.urllib3.connectionpool: DEBUG: \"POST /api/tools 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=3d8ec2f04896f6b3eee771fcb4ad58bb 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=3d8ec2f04896f6b3eee771fcb4ad58bb HTTP/1.1\" 200 None\\ngalaxy.jobs: DEBUG: (2) Working directory for job is: /tmp/tmp1act3b/job_working_directory/000/2\\ngalaxy.jobs.handler: DEBUG: (2) Dispatching to local runner\\ngalaxy.jobs: DEBUG: (2) Persisting job destination (destination id: local:///)\\ngalaxy.jobs.runners: DEBUG: Job [2] queued (196.526 ms)\\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\\ngalaxy.jobs.handler: INFO: (2) Job dispatched\\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/jobs/5729865256bc2525?key=3d8ec2f04896f6b3eee771fcb4ad58bb HTTP/1.1\" 200 None\\ngalaxy.util.object_wrapper: WARNING: Unable to create dynamic subclass for , None: metaclass conflict: the metaclass of a derived class must be a (non-strict) subclass of the metaclasses of all its bases\\ngalaxy.tools.deps: DEBUG: Building dependency shell command for dependency \\'R\\'\\ngalaxy.tools.deps: WARNING: Failed to resolve dependency on \\'R\\', ignoring\\ngalaxy.tools.deps: DEBUG: Building dependency shell command for dependency \\'graphicsmagick\\'\\ngalaxy.tools.deps: WARNING: Failed to resolve dependency on \\'graphicsmagick\\', ignoring\\ngalaxy.tools.deps: DEBUG: Building dependency shell command for dependency \\'ghostscript\\'\\ngalaxy.tools.deps: WARNING: Failed to resolve dependency on \\'ghostscript\\', ignoring\\ngalaxy.tools.deps: DEBUG: Building dependency shell command for dependency \\'glmnet_lars_3_2\\'\\ngalaxy.tools.deps: WARNING: Failed to resolve dependency on \\'glmnet_lars_3_2\\', ignoring\\ngalaxy.jobs.runners: DEBUG: (2) command is: python /home/rlazarus/tools-iuc/tools/rglasso/rgToolFactory.py --script_path \"/tmp/tmp1act3b/job_working_directory/000/2/tmpI7mLI2\" --interpreter \"Rscript\" --tool_name \"rglasso\" --output_dir \"/tmp/tmp1act3b/job_working_directory/000/2/dataset_2_files\" --output_html \"/tmp/tmp1act3b/files/000/dataset_2.dat\" --make_HTML \"yes\"; return_code=$?; python \"/tmp/tmp1act3b/job_working_directory/000/2/set_metadata_7vae5k.py\" \"/tmp/tmp1act3b/tmp/tmpeK8ceT\" \"/tmp/tmp1act3b/job_working_directory/000/2/galaxy.json\" \"/tmp/tmp1act3b/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_2_oZQ1tt,/tmp/tmp1act3b/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_6Rj50u,/tmp/tmp1act3b/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_2_wwwPW5,/tmp/tmp1act3b/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_2_R7LNrr,/tmp/tmp1act3b/files/000/dataset_2.dat,/tmp/tmp1act3b/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_2_Q1xZen\" \"/tmp/tmp1act3b/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_3_EDLEac,/tmp/tmp1act3b/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_3_gtysqk,/tmp/tmp1act3b/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_3_aAuG54,/tmp/tmp1act3b/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_3_xsrfi3,/tmp/tmp1act3b/files/000/dataset_3.dat,/tmp/tmp1act3b/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_3_2kPRZE\" 5242880; sh -c \"exit $return_code\"\\ngalaxy.jobs.runners.local: DEBUG: (2) executing job script: /tmp/tmp1act3b/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=3d8ec2f04896f6b3eee771fcb4ad58bb HTTP/1.1\" 200 None\\ngalaxy.jobs.runners.local: DEBUG: execution finished: /tmp/tmp1act3b/job_working_directory/000/2/galaxy_2.sh\\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/jobs/5729865256bc2525?key=3d8ec2f04896f6b3eee771fcb4ad58bb HTTP/1.1\" 200 None\\ngalaxy.datatypes.metadata: DEBUG: loading metadata from file for: HistoryDatasetAssociation 2\\ngalaxy.jobs: DEBUG: job 2 ended (finish() executed in (590.407 ms))\\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/jobs/5729865256bc2525?key=3d8ec2f04896f6b3eee771fcb4ad58bb 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=3d8ec2f04896f6b3eee771fcb4ad58bb 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=3d8ec2f04896f6b3eee771fcb4ad58bb 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/54f2a3a23292eb07/display?raw=true&key=3d8ec2f04896f6b3eee771fcb4ad58bb 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=3d8ec2f04896f6b3eee771fcb4ad58bb 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/display?raw=true&key=3d8ec2f04896f6b3eee771fcb4ad58bb HTTP/1.1\" 200 None\\nbase.twilltestcase: DEBUG: keepoutdir: /tmp/tmp1act3b/jobfiles, ofn: /tmp/tmp1act3b/jobfiles/coxlassotest.html\\nbase.twilltestcase: DEBUG: ## GALAXY_TEST_SAVE=/tmp/tmp1act3b/jobfiles. saved /tmp/tmp1act3b/jobfiles/coxlassotest.html\\nbase.twilltestcase: INFO: ## files diff on /home/rlazarus/tools-iuc/tools/rglasso/test-data/coxlassotest.html and /tmp/tmp1act3b/tmp/tmpM1zEZTcoxlassotest.html lines_diff=16, found diff = 145\\n--------------------- >> end captured logging << ---------------------'", "problem_type": "functional.test_toolbox.JobOutputsError"}, "id": "functional.test_toolbox.TestForTool_rglasso_cox.test_tool_000000", "has_data": true}], "version": "0.1", "summary": {"num_skips": 0, "num_errors": 0, "num_failures": 1, "num_tests": 1}} \ No newline at end of file