Mercurial > repos > tduigou > seq_to_db
diff output.json @ 2:d77ff06f5dc9 draft default tip
planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit d8cc8b87fdb0374745b5420f2da7f08ae905c222-dirty
| author | tduigou |
|---|---|
| date | Wed, 16 Jul 2025 14:51:52 +0000 |
| parents | 5db1c2b9edb8 |
| children |
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--- a/output.json Fri Jul 11 14:16:33 2025 +0000 +++ b/output.json Wed Jul 16 14:51:52 2025 +0000 @@ -1,241 +1,67 @@ { "summary": { "num_errors": 0, - "num_failures": 1, + "num_failures": 0, "num_skips": 0, - "num_tests": 2 + "num_tests": 1 }, "tests": [ { "data": { "inputs": { "genbank_files": { - "id": "5035e3bab9835d6e", + "id": "c483dc6e4815613d", "src": "hdca" }, "json_generating": false, "json_use|json_conf": { - "id": "48861e2bb98fa8f3", + "id": "aa2843b1b277b7a7", "src": "hda" }, "json_use|use_json_paramers": true }, "job": { - "command_line": "python '/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py' --input '/tmp/tmp_qydb9xn/files/8/c/6/dataset_8c6c4607-b545-411e-8565-3c6ca3472443.dat,/tmp/tmp_qydb9xn/files/e/b/6/dataset_eb604a05-357c-45df-ae5a-81ddb65244e3.dat,/tmp/tmp_qydb9xn/files/3/6/6/dataset_366741cf-94b2-42de-8d64-7f00e58563e0.dat,/tmp/tmp_qydb9xn/files/f/f/1/dataset_ff11bb17-ed2d-415e-96cf-e5ed35c7d997.dat,/tmp/tmp_qydb9xn/files/5/8/6/dataset_5861c673-e009-436c-9020-a23df5356851.dat' --use_json_paramers 'true' --json_conf '/tmp/tmp_qydb9xn/files/8/c/a/dataset_8ca49aab-9732-422b-bd76-9975c97f5f2a.dat' --output '/tmp/tmp_qydb9xn/job_working_directory/000/7/outputs/dataset_b5f885e2-68c2-4441-9ade-922799b2cfd6.dat' --file_name_mapping '/tmp/tmp_qydb9xn/files/8/c/6/dataset_8c6c4607-b545-411e-8565-3c6ca3472443.dat:p7_L7Ae-Weiss.gb,/tmp/tmp_qydb9xn/files/e/b/6/dataset_eb604a05-357c-45df-ae5a-81ddb65244e3.dat:p6_Nt-IgKLsequence.gb,/tmp/tmp_qydb9xn/files/3/6/6/dataset_366741cf-94b2-42de-8d64-7f00e58563e0.dat:p6_Kozak-ATG.gb,/tmp/tmp_qydb9xn/files/f/f/1/dataset_ff11bb17-ed2d-415e-96cf-e5ed35c7d997.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmp_qydb9xn/files/5/8/6/dataset_5861c673-e009-436c-9020-a23df5356851.dat:HC_Amp_ccdB.gb' --json_generating 'false' --json_output 'XXXX' && echo \"DEBUG\" && cat \"XXXX\"", + "command_line": "python '/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py' --input '/tmp/tmpac_768cd/files/d/4/1/dataset_d41458b9-ed0a-4b73-83bd-c0b05e03f3ca.dat,/tmp/tmpac_768cd/files/3/2/3/dataset_3234dfd4-c4b6-42fb-b254-e23532f04d7a.dat,/tmp/tmpac_768cd/files/5/c/3/dataset_5c34ee15-4ade-4ee7-9068-607cee72ba4f.dat,/tmp/tmpac_768cd/files/7/9/7/dataset_7970a203-ec8d-40ea-845f-eaa66f55ac7b.dat,/tmp/tmpac_768cd/files/b/c/5/dataset_bc5a286c-1a56-4506-90e2-1687f93f24d0.dat' --use_json_paramers 'true' --json_conf '/tmp/tmpac_768cd/files/5/7/3/dataset_57302268-f98c-4e9d-9812-c2e5bda507f5.dat' --output '/tmp/tmpac_768cd/job_working_directory/000/7/outputs/dataset_8bb5f859-22ca-4d7f-bb07-cfbb3ca3a04f.dat' --file_name_mapping '/tmp/tmpac_768cd/files/d/4/1/dataset_d41458b9-ed0a-4b73-83bd-c0b05e03f3ca.dat:p7_L7Ae-Weiss.gb,/tmp/tmpac_768cd/files/3/2/3/dataset_3234dfd4-c4b6-42fb-b254-e23532f04d7a.dat:p6_Nt-IgKLsequence.gb,/tmp/tmpac_768cd/files/5/c/3/dataset_5c34ee15-4ade-4ee7-9068-607cee72ba4f.dat:p6_Kozak-ATG.gb,/tmp/tmpac_768cd/files/7/9/7/dataset_7970a203-ec8d-40ea-845f-eaa66f55ac7b.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmpac_768cd/files/b/c/5/dataset_bc5a286c-1a56-4506-90e2-1687f93f24d0.dat:HC_Amp_ccdB.gb' --json_generating 'false' --json_output 'XXXX'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-07-11T14:13:47.541606", + "create_time": "2025-07-16T14:50:01.488998", "dependencies": [], - "exit_code": 1, - "external_id": "133184", + "exit_code": 0, + "external_id": "166724", "galaxy_version": "25.0", "handler": null, - "history_id": "5035e3bab9835d6e", - "id": "cf8d16af14dc294f", + "history_id": "c483dc6e4815613d", + "id": "bcb3b45a1cc4a671", "inputs": { "genbank_files1": { - "id": "5035e3bab9835d6e", + "id": "c483dc6e4815613d", "src": "hda", - "uuid": "8c6c4607-b545-411e-8565-3c6ca3472443" + "uuid": "d41458b9-ed0a-4b73-83bd-c0b05e03f3ca" }, "genbank_files2": { - "id": "6a141869249298e9", + "id": "c4d3b2f0c36d8241", "src": "hda", - "uuid": "eb604a05-357c-45df-ae5a-81ddb65244e3" + "uuid": "3234dfd4-c4b6-42fb-b254-e23532f04d7a" }, "genbank_files3": { - "id": "8ca00df555c44d56", + "id": "69de8fd4747f3c3b", "src": "hda", - "uuid": "366741cf-94b2-42de-8d64-7f00e58563e0" + "uuid": "5c34ee15-4ade-4ee7-9068-607cee72ba4f" }, "genbank_files4": { - "id": "be795001aeb7b4a0", + "id": "941f1e1f3cfa391c", "src": "hda", - "uuid": "ff11bb17-ed2d-415e-96cf-e5ed35c7d997" + "uuid": "7970a203-ec8d-40ea-845f-eaa66f55ac7b" }, "genbank_files5": { - "id": "8fbddce2c6d1629d", + "id": "3a97944c68e74177", "src": "hda", - "uuid": "5861c673-e009-436c-9020-a23df5356851" + "uuid": "bc5a286c-1a56-4506-90e2-1687f93f24d0" }, "json_use|json_conf": { - "id": "48861e2bb98fa8f3", - "src": "hda", - "uuid": "8ca49aab-9732-422b-bd76-9975c97f5f2a" - } - }, - "job_messages": [ - { - "code_desc": "", - "desc": "Fatal error: Exit code 1 ()", - "error_level": 3.0, - "exit_code": 1, - "type": "exit_code" - } - ], - "job_metrics": [], - "job_runner_name": null, - "job_stderr": "", - "job_stdout": "", - "model_class": "Job", - "output_collections": {}, - "outputs": { - "output": { - "id": "cf8d16af14dc294f", + "id": "aa2843b1b277b7a7", "src": "hda", - "uuid": "b5f885e2-68c2-4441-9ade-922799b2cfd6" - } - }, - "params": { - "__input_ext": "\"input\"", - "chromInfo": "\"/tmp/tmp_qydb9xn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", - "dbkey": "\"?\"", - "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}", - "json_generating": "false", - "json_use": "{\"__current_case__\": 1, \"json_conf\": {\"values\": [{\"id\": 6, \"src\": \"hda\"}]}, \"use_json_paramers\": true}" - }, - "state": "error", - "stderr": "cat: XXXX: No such file or directory\n", - "stdout": "Execution blocked by config (execution = false)\nDEBUG\n", - "tool_id": "seq_to_db", - "tool_stderr": "cat: XXXX: No such file or directory\n", - "tool_stdout": "Execution blocked by config (execution = false)\nDEBUG\n", - "update_time": "2025-07-11T14:13:54.198241", - "user_email": "planemo@galaxyproject.org", - "user_id": "5035e3bab9835d6e" - }, - "output_problems": [ - "Job in error state.. tool_id: seq_to_db, exit_code: 1, stderr: cat: XXXX: No such file or directory\n.", - "Job in error state.. tool_id: seq_to_db, exit_code: 1, stderr: cat: XXXX: No such file or directory\n." - ], - "status": "failure", - "test_index": 1, - "time_seconds": 28.040581941604614, - "tool_id": "seq_to_db", - "tool_version": "0.2.0+galaxy1" - }, - "has_data": true, - "id": "seq_to_db-1" - }, - { - "data": { - "inputs": { - "genbank_files": { - "id": "6a141869249298e9", - "src": "hdca" - }, - "json_use|annotation_column": "annotation", - "json_use|db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db", - "json_use|execution_enable": true, - "json_use|fragment_column": "fragment", - "json_use|sequence_column": "sequence", - "json_use|table": "sample", - "json_use|use_json_paramers": false - }, - "job": { - "command_line": "python '/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py' --input '/tmp/tmp_qydb9xn/files/e/2/4/dataset_e2429fd0-5082-415d-869b-2f7c67516829.dat,/tmp/tmp_qydb9xn/files/8/5/2/dataset_85256206-1030-4b72-bc8d-786951caba8a.dat,/tmp/tmp_qydb9xn/files/d/d/a/dataset_ddae9a40-9b20-4439-8022-532bb18a89a9.dat,/tmp/tmp_qydb9xn/files/1/b/2/dataset_1b2fd1a2-9b4f-42f0-a66c-6d7f5b6d935f.dat,/tmp/tmp_qydb9xn/files/3/a/9/dataset_3a93ffcc-6958-4761-a4c3-1f6e5b64bbb6.dat' --use_json_paramers 'false' --sequence_column 'sequence' --annotation_column 'annotation' --db_uri 'postgresql://postgres:RK17__at__localhost:5432/test_fragments_db' --table 'sample' --fragment_column 'fragment' --execution_enable 'true' --output '/tmp/tmp_qydb9xn/job_working_directory/000/13/outputs/dataset_c78df7ec-701b-4f3e-8081-d63aa4a4ba90.dat' --file_name_mapping '/tmp/tmp_qydb9xn/files/e/2/4/dataset_e2429fd0-5082-415d-869b-2f7c67516829.dat:p7_L7Ae-Weiss.gb,/tmp/tmp_qydb9xn/files/8/5/2/dataset_85256206-1030-4b72-bc8d-786951caba8a.dat:p6_Nt-IgKLsequence.gb,/tmp/tmp_qydb9xn/files/d/d/a/dataset_ddae9a40-9b20-4439-8022-532bb18a89a9.dat:p6_Kozak-ATG.gb,/tmp/tmp_qydb9xn/files/1/b/2/dataset_1b2fd1a2-9b4f-42f0-a66c-6d7f5b6d935f.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmp_qydb9xn/files/3/a/9/dataset_3a93ffcc-6958-4761-a4c3-1f6e5b64bbb6.dat:HC_Amp_ccdB.gb' --json_generating 'true' --json_output '/tmp/tmp_qydb9xn/job_working_directory/000/13/outputs/dataset_705e4a52-0582-42c5-afba-22b1cbe3eb9f.dat' && echo \"DEBUG\" && cat \"/tmp/tmp_qydb9xn/job_working_directory/000/13/outputs/dataset_705e4a52-0582-42c5-afba-22b1cbe3eb9f.dat\"", - "command_version": "", - "copied_from_job_id": null, - "create_time": "2025-07-11T14:14:15.037467", - "dependencies": [ - { - "cacheable": false, - "dependency_resolver": { - "auto_init": true, - "auto_install": true, - "can_uninstall_dependencies": true, - "ensure_channels": "conda-forge,bioconda", - "model_class": "CondaDependencyResolver", - "prefix": "/home/rkhaled/miniconda3", - "read_only": false, - "resolver_type": "conda", - "resolves_simple_dependencies": true, - "use_local": false, - "versionless": false - }, - "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966", - "exact": true, - "model_class": "MergedCondaDependency", - "name": "pandas", - "version": "2.2.3" - }, - { - "cacheable": false, - "dependency_resolver": { - "auto_init": true, - "auto_install": true, - "can_uninstall_dependencies": true, - "ensure_channels": "conda-forge,bioconda", - "model_class": "CondaDependencyResolver", - "prefix": "/home/rkhaled/miniconda3", - "read_only": false, - "resolver_type": "conda", - "resolves_simple_dependencies": true, - "use_local": false, - "versionless": false - }, - "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966", - "exact": true, - "model_class": "MergedCondaDependency", - "name": "sqlalchemy", - "version": "2.0.40" - }, - { - "cacheable": false, - "dependency_resolver": { - "auto_init": true, - "auto_install": true, - "can_uninstall_dependencies": true, - "ensure_channels": "conda-forge,bioconda", - "model_class": "CondaDependencyResolver", - "prefix": "/home/rkhaled/miniconda3", - "read_only": false, - "resolver_type": "conda", - "resolves_simple_dependencies": true, - "use_local": false, - "versionless": false - }, - "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966", - "exact": true, - "model_class": "MergedCondaDependency", - "name": "psycopg2", - "version": "2.9.9" - } - ], - "exit_code": 0, - "external_id": "133675", - "galaxy_version": "25.0", - "handler": null, - "history_id": "6a141869249298e9", - "id": "179da9a21af79ae5", - "inputs": { - "genbank_files1": { - "id": "e058757b81e0ebed", - "src": "hda", - "uuid": "e2429fd0-5082-415d-869b-2f7c67516829" - }, - "genbank_files2": { - "id": "10993b807f8c1a73", - "src": "hda", - "uuid": "85256206-1030-4b72-bc8d-786951caba8a" - }, - "genbank_files3": { - "id": "d964653210776bae", - "src": "hda", - "uuid": "ddae9a40-9b20-4439-8022-532bb18a89a9" - }, - "genbank_files4": { - "id": "1187622ddb220809", - "src": "hda", - "uuid": "1b2fd1a2-9b4f-42f0-a66c-6d7f5b6d935f" - }, - "genbank_files5": { - "id": "0ec72b924a1ee71e", - "src": "hda", - "uuid": "3a93ffcc-6958-4761-a4c3-1f6e5b64bbb6" + "uuid": "57302268-f98c-4e9d-9812-c2e5bda507f5" } }, "job_messages": [], @@ -246,43 +72,38 @@ "model_class": "Job", "output_collections": {}, "outputs": { - "json_output": { - "id": "8d85a3e6aa2938f6", + "output": { + "id": "bcb3b45a1cc4a671", "src": "hda", - "uuid": "705e4a52-0582-42c5-afba-22b1cbe3eb9f" - }, - "output": { - "id": "179da9a21af79ae5", - "src": "hda", - "uuid": "c78df7ec-701b-4f3e-8081-d63aa4a4ba90" + "uuid": "8bb5f859-22ca-4d7f-bb07-cfbb3ca3a04f" } }, "params": { "__input_ext": "\"input\"", - "chromInfo": "\"/tmp/tmp_qydb9xn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmpac_768cd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", - "genbank_files": "{\"values\": [{\"id\": 2, \"src\": \"hdca\"}]}", - "json_generating": "true", - "json_use": "{\"__current_case__\": 0, \"annotation_column\": \"annotation\", \"db_uri\": \"postgresql://postgres:RK17@localhost:5432/test_fragments_db\", \"execution_enable\": true, \"fragment_column\": \"fragment\", \"sequence_column\": \"sequence\", \"table\": \"sample\", \"use_json_paramers\": false}" + "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}", + "json_generating": "false", + "json_use": "{\"__current_case__\": 1, \"json_conf\": {\"values\": [{\"id\": 6, \"src\": \"hda\"}]}, \"use_json_paramers\": true}" }, "state": "ok", "stderr": "", - "stdout": "JSON configuration written to: /tmp/tmp_qydb9xn/job_working_directory/000/13/outputs/dataset_705e4a52-0582-42c5-afba-22b1cbe3eb9f.dat\nConnected to database.\nProcessing file: dataset_e2429fd0-5082-415d-869b-2f7c67516829.dat(p7_L7Ae-Weiss)\nProcessing file: dataset_85256206-1030-4b72-bc8d-786951caba8a.dat(p6_Nt-IgKLsequence)\nProcessing file: dataset_ddae9a40-9b20-4439-8022-532bb18a89a9.dat(p6_Kozak-ATG)\nProcessing file: dataset_1b2fd1a2-9b4f-42f0-a66c-6d7f5b6d935f.dat(p4_Kt-L7Ae-Weiss)\nProcessing file: dataset_3a93ffcc-6958-4761-a4c3-1f6e5b64bbb6.dat(HC_Amp_ccdB)\nInserted 5 fragments.\nFragment names written to '/tmp/tmp_qydb9xn/job_working_directory/000/13/outputs/dataset_c78df7ec-701b-4f3e-8081-d63aa4a4ba90.dat'.\nDEBUG\n{\n \"table\": \"sample\",\n \"sequence_column\": \"sequence\",\n \"annotation_column\": \"annotation\",\n \"fragment_column\": \"fragment\",\n \"db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n \"execution\": \"true\"\n}", + "stdout": "Connected to database.\nProcessing file: dataset_d41458b9-ed0a-4b73-83bd-c0b05e03f3ca.dat(p7_L7Ae-Weiss)\nProcessing file: dataset_3234dfd4-c4b6-42fb-b254-e23532f04d7a.dat(p6_Nt-IgKLsequence)\nProcessing file: dataset_5c34ee15-4ade-4ee7-9068-607cee72ba4f.dat(p6_Kozak-ATG)\nProcessing file: dataset_7970a203-ec8d-40ea-845f-eaa66f55ac7b.dat(p4_Kt-L7Ae-Weiss)\nProcessing file: dataset_bc5a286c-1a56-4506-90e2-1687f93f24d0.dat(HC_Amp_ccdB)\nInserted 5 fragments.\nFragment names written to '/tmp/tmpac_768cd/job_working_directory/000/7/outputs/dataset_8bb5f859-22ca-4d7f-bb07-cfbb3ca3a04f.dat'.\n", "tool_id": "seq_to_db", "tool_stderr": "", - "tool_stdout": "JSON configuration written to: /tmp/tmp_qydb9xn/job_working_directory/000/13/outputs/dataset_705e4a52-0582-42c5-afba-22b1cbe3eb9f.dat\nConnected to database.\nProcessing file: dataset_e2429fd0-5082-415d-869b-2f7c67516829.dat(p7_L7Ae-Weiss)\nProcessing file: dataset_85256206-1030-4b72-bc8d-786951caba8a.dat(p6_Nt-IgKLsequence)\nProcessing file: dataset_ddae9a40-9b20-4439-8022-532bb18a89a9.dat(p6_Kozak-ATG)\nProcessing file: dataset_1b2fd1a2-9b4f-42f0-a66c-6d7f5b6d935f.dat(p4_Kt-L7Ae-Weiss)\nProcessing file: dataset_3a93ffcc-6958-4761-a4c3-1f6e5b64bbb6.dat(HC_Amp_ccdB)\nInserted 5 fragments.\nFragment names written to '/tmp/tmp_qydb9xn/job_working_directory/000/13/outputs/dataset_c78df7ec-701b-4f3e-8081-d63aa4a4ba90.dat'.\nDEBUG\n{\n \"table\": \"sample\",\n \"sequence_column\": \"sequence\",\n \"annotation_column\": \"annotation\",\n \"fragment_column\": \"fragment\",\n \"db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n \"execution\": \"true\"\n}", - "update_time": "2025-07-11T14:14:21.313512", + "tool_stdout": "Connected to database.\nProcessing file: dataset_d41458b9-ed0a-4b73-83bd-c0b05e03f3ca.dat(p7_L7Ae-Weiss)\nProcessing file: dataset_3234dfd4-c4b6-42fb-b254-e23532f04d7a.dat(p6_Nt-IgKLsequence)\nProcessing file: dataset_5c34ee15-4ade-4ee7-9068-607cee72ba4f.dat(p6_Kozak-ATG)\nProcessing file: dataset_7970a203-ec8d-40ea-845f-eaa66f55ac7b.dat(p4_Kt-L7Ae-Weiss)\nProcessing file: dataset_bc5a286c-1a56-4506-90e2-1687f93f24d0.dat(HC_Amp_ccdB)\nInserted 5 fragments.\nFragment names written to '/tmp/tmpac_768cd/job_working_directory/000/7/outputs/dataset_8bb5f859-22ca-4d7f-bb07-cfbb3ca3a04f.dat'.\n", + "update_time": "2025-07-16T14:50:07.342567", "user_email": "planemo@galaxyproject.org", - "user_id": "5035e3bab9835d6e" + "user_id": "c483dc6e4815613d" }, "status": "success", - "test_index": 2, - "time_seconds": 26.91756534576416, + "test_index": 0, + "time_seconds": 35.08016586303711, "tool_id": "seq_to_db", - "tool_version": "0.2.0+galaxy1" + "tool_version": "0.3.0+galaxy2" }, "has_data": true, - "id": "seq_to_db-2" + "id": "seq_to_db-0" } ], "version": "0.1"