Mercurial > repos > tduigou > save_to_db
diff output.json @ 0:034686b5bc15 draft
planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
| author | tduigou |
|---|---|
| date | Thu, 24 Apr 2025 09:56:36 +0000 |
| parents | |
| children | eca0d710bbe9 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/output.json Thu Apr 24 09:56:36 2025 +0000 @@ -0,0 +1,129 @@ +{ + "summary": { + "num_errors": 0, + "num_failures": 0, + "num_skips": 0, + "num_tests": 1 + }, + "tests": [ + { + "data": { + "inputs": { + "annotation_column": "annotation", + "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db", + "fragment_column": "fragment", + "genbank_files": [ + { + "id": "0ed824750a9f5374", + "src": "hda" + }, + { + "id": "93c5e169024bda92", + "src": "hda" + }, + { + "id": "7e79446a5abd8b5f", + "src": "hda" + }, + { + "id": "81603bca0e110055", + "src": "hda" + }, + { + "id": "f1c08c8102faa4bc", + "src": "hda" + } + ], + "sequence_column": "sequence", + "table": "sample" + }, + "job": { + "command_line": "python '/home/rkhaled/galaxytools/tools/save_to_db/save_to_db.py' --input '/tmp/tmp_mv7gt3c/files/5/2/2/dataset_5228856a-39be-4f27-afa9-d1f613dea185.dat,/tmp/tmp_mv7gt3c/files/f/a/a/dataset_faa1d0aa-2bb0-47c0-bc3e-949253dd5c3c.dat,/tmp/tmp_mv7gt3c/files/9/6/1/dataset_961fe859-a187-4b45-98ac-bc9c8bd29463.dat,/tmp/tmp_mv7gt3c/files/a/5/c/dataset_a5c56d98-0435-435b-ad8a-01906b2ab961.dat,/tmp/tmp_mv7gt3c/files/2/a/7/dataset_2a788c0d-f89d-4961-95c4-423fd51249f0.dat' --sequence_column 'sequence' --annotation_column 'annotation' --db_uri 'postgresql://postgres:RK17__at__localhost:5432/test_fragments_db' --table 'sample' --fragment_column 'fragment' --output '/tmp/tmp_mv7gt3c/job_working_directory/000/6/outputs/dataset_c2d55cf8-9c51-42f9-84da-9aa06323c7ce.dat' --file_name_mapping '/tmp/tmp_mv7gt3c/files/5/2/2/dataset_5228856a-39be-4f27-afa9-d1f613dea185.dat:p7_L7Ae-Weiss.gb,/tmp/tmp_mv7gt3c/files/f/a/a/dataset_faa1d0aa-2bb0-47c0-bc3e-949253dd5c3c.dat:p6_Nt-IgKLsequence.gb,/tmp/tmp_mv7gt3c/files/9/6/1/dataset_961fe859-a187-4b45-98ac-bc9c8bd29463.dat:p6_Kozak-ATG.gb,/tmp/tmp_mv7gt3c/files/a/5/c/dataset_a5c56d98-0435-435b-ad8a-01906b2ab961.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmp_mv7gt3c/files/2/a/7/dataset_2a788c0d-f89d-4961-95c4-423fd51249f0.dat:HC_Amp_ccdB.gb'", + "command_version": "", + "copied_from_job_id": null, + "create_time": "2025-04-24T09:49:34.459208", + "dependencies": [], + "exit_code": 0, + "external_id": "84720", + "galaxy_version": "24.2", + "handler": null, + "history_id": "0ed824750a9f5374", + "id": "016b212ed10ed695", + "inputs": { + "genbank_files": { + "id": "0ed824750a9f5374", + "src": "hda", + "uuid": "5228856a-39be-4f27-afa9-d1f613dea185" + }, + "genbank_files1": { + "id": "0ed824750a9f5374", + "src": "hda", + "uuid": "5228856a-39be-4f27-afa9-d1f613dea185" + }, + "genbank_files2": { + "id": "93c5e169024bda92", + "src": "hda", + "uuid": "faa1d0aa-2bb0-47c0-bc3e-949253dd5c3c" + }, + "genbank_files3": { + "id": "7e79446a5abd8b5f", + "src": "hda", + "uuid": "961fe859-a187-4b45-98ac-bc9c8bd29463" + }, + "genbank_files4": { + "id": "81603bca0e110055", + "src": "hda", + "uuid": "a5c56d98-0435-435b-ad8a-01906b2ab961" + }, + "genbank_files5": { + "id": "f1c08c8102faa4bc", + "src": "hda", + "uuid": "2a788c0d-f89d-4961-95c4-423fd51249f0" + } + }, + "job_messages": [], + "job_metrics": [], + "job_runner_name": null, + "job_stderr": "", + "job_stdout": "", + "model_class": "Job", + "output_collections": {}, + "outputs": { + "output": { + "id": "016b212ed10ed695", + "src": "hda", + "uuid": "c2d55cf8-9c51-42f9-84da-9aa06323c7ce" + } + }, + "params": { + "__input_ext": "\"input\"", + "annotation_column": "\"annotation\"", + "chromInfo": "\"/tmp/tmp_mv7gt3c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "db_uri": "\"postgresql://postgres:RK17@localhost:5432/test_fragments_db\"", + "dbkey": "\"?\"", + "fragment_column": "\"fragment\"", + "sequence_column": "\"sequence\"", + "table": "\"sample\"" + }, + "state": "ok", + "stderr": "", + "stdout": "Container 'test_fragments_db' is already running.\nConnected to database.\nProcessing file: dataset_5228856a-39be-4f27-afa9-d1f613dea185.dat\nProcessing file: dataset_faa1d0aa-2bb0-47c0-bc3e-949253dd5c3c.dat\nProcessing file: dataset_961fe859-a187-4b45-98ac-bc9c8bd29463.dat\nProcessing file: dataset_a5c56d98-0435-435b-ad8a-01906b2ab961.dat\nProcessing file: dataset_2a788c0d-f89d-4961-95c4-423fd51249f0.dat\nInserted 5 fragments.\nFragment names written to '/tmp/tmp_mv7gt3c/job_working_directory/000/6/outputs/dataset_c2d55cf8-9c51-42f9-84da-9aa06323c7ce.dat'.\n", + "tool_id": "save_to_db", + "tool_stderr": "", + "tool_stdout": "Container 'test_fragments_db' is already running.\nConnected to database.\nProcessing file: dataset_5228856a-39be-4f27-afa9-d1f613dea185.dat\nProcessing file: dataset_faa1d0aa-2bb0-47c0-bc3e-949253dd5c3c.dat\nProcessing file: dataset_961fe859-a187-4b45-98ac-bc9c8bd29463.dat\nProcessing file: dataset_a5c56d98-0435-435b-ad8a-01906b2ab961.dat\nProcessing file: dataset_2a788c0d-f89d-4961-95c4-423fd51249f0.dat\nInserted 5 fragments.\nFragment names written to '/tmp/tmp_mv7gt3c/job_working_directory/000/6/outputs/dataset_c2d55cf8-9c51-42f9-84da-9aa06323c7ce.dat'.\n", + "update_time": "2025-04-24T09:49:41.678113", + "user_email": "planemo@galaxyproject.org", + "user_id": "0ed824750a9f5374" + }, + "status": "success", + "test_index": 0, + "time_seconds": 26.82854700088501, + "tool_id": "save_to_db", + "tool_version": "0.1.0+galaxy0" + }, + "has_data": true, + "id": "save_to_db-0" + } + ], + "version": "0.1" +} \ No newline at end of file
