Mercurial > repos > tduigou > json_db_config_generating
diff output.json @ 1:2909e53fac5b draft
planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
| author | tduigou |
|---|---|
| date | Mon, 02 Jun 2025 14:54:24 +0000 |
| parents | 95757ea6c333 |
| children | 8eb6c417d4f5 |
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--- a/output.json Mon Jun 02 13:39:41 2025 +0000 +++ b/output.json Mon Jun 02 14:54:24 2025 +0000 @@ -9,25 +9,25 @@ { "data": { "inputs": { - "annotation_column": "annotation", - "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db", - "execution": true, - "fragment_column": "fragment", - "sequence_column": "sequence", - "table_name": "sample" + "db_request|db_config|annotation_column": "annotation", + "db_request|db_config|db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db", + "db_request|db_config|fragment_column": "fragment", + "db_request|db_config|sequence_column": "sequence", + "db_request|db_config|table_name": "sample", + "db_request|execution": "true" }, "job": { - "command_line": "python3 -c \"import json; params = { 'execution': 'true', 'JSON_db_uri': 'postgresql://postgres:RK17__at__localhost:5432/test_fragments_db', 'JSON_table': 'sample', 'JSON_fragment_column': 'fragment', 'JSON_sequence_column': 'sequence', 'JSON_annotation_column': 'annotation' }; f = open('/tmp/tmphuox1me_/job_working_directory/000/1/outputs/dataset_a57d4381-ba51-4c7e-8409-1ec0f85d3ba2.dat', 'w'); json.dump(params, f, indent=4); f.close()\" && echo DEBUG && cat '/tmp/tmphuox1me_/job_working_directory/000/1/outputs/dataset_a57d4381-ba51-4c7e-8409-1ec0f85d3ba2.dat'", + "command_line": "python3 -c \"import json; params = { 'execution': 'true', 'JSON_db_uri': 'postgresql://postgres:RK17__at__localhost:5432/test_fragments_db', 'JSON_table': 'sample', 'JSON_fragment_column': 'fragment', 'JSON_sequence_column': 'sequence', 'JSON_annotation_column': 'annotation' }; f = open('/tmp/tmp91u1vmdr/job_working_directory/000/1/outputs/dataset_b781e9dc-83b4-4c3f-99ef-6c1eb6078f62.dat', 'w'); json.dump(params, f, indent=4); f.close()\" && echo DEBG && cat '/tmp/tmp91u1vmdr/job_working_directory/000/1/outputs/dataset_b781e9dc-83b4-4c3f-99ef-6c1eb6078f62.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-06-02T13:36:45.666819", + "create_time": "2025-06-02T14:52:18.811266", "dependencies": [], "exit_code": 0, - "external_id": "240263", + "external_id": "274048", "galaxy_version": "24.2", "handler": null, - "history_id": "abb9783f010dde16", - "id": "abb9783f010dde16", + "history_id": "a0c0127196534838", + "id": "a0c0127196534838", "inputs": {}, "job_messages": [], "job_metrics": [], @@ -38,35 +38,30 @@ "output_collections": {}, "outputs": { "output_json": { - "id": "abb9783f010dde16", + "id": "a0c0127196534838", "src": "hda", - "uuid": "a57d4381-ba51-4c7e-8409-1ec0f85d3ba2" + "uuid": "b781e9dc-83b4-4c3f-99ef-6c1eb6078f62" } }, "params": { "__input_ext": "\"input\"", - "annotation_column": "\"annotation\"", - "chromInfo": "\"/tmp/tmphuox1me_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", - "db_uri": "\"postgresql://postgres:RK17@localhost:5432/test_fragments_db\"", - "dbkey": "\"?\"", - "execution": "true", - "fragment_column": "\"fragment\"", - "sequence_column": "\"sequence\"", - "table_name": "\"sample\"" + "chromInfo": "\"/tmp/tmp91u1vmdr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "db_request": "{\"__current_case__\": 0, \"db_config\": {\"annotation_column\": \"annotation\", \"db_uri\": \"postgresql://postgres:RK17@localhost:5432/test_fragments_db\", \"fragment_column\": \"fragment\", \"sequence_column\": \"sequence\", \"table_name\": \"sample\"}, \"execution\": \"true\"}", + "dbkey": "\"?\"" }, "state": "ok", "stderr": "", - "stdout": "DEBUG\n{\n \"execution\": \"true\",\n \"JSON_db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n \"JSON_table\": \"sample\",\n \"JSON_fragment_column\": \"fragment\",\n \"JSON_sequence_column\": \"sequence\",\n \"JSON_annotation_column\": \"annotation\"\n}", + "stdout": "DEBG\n{\n \"execution\": \"true\",\n \"JSON_db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n \"JSON_table\": \"sample\",\n \"JSON_fragment_column\": \"fragment\",\n \"JSON_sequence_column\": \"sequence\",\n \"JSON_annotation_column\": \"annotation\"\n}", "tool_id": "json_db_config_generating", "tool_stderr": "", - "tool_stdout": "DEBUG\n{\n \"execution\": \"true\",\n \"JSON_db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n \"JSON_table\": \"sample\",\n \"JSON_fragment_column\": \"fragment\",\n \"JSON_sequence_column\": \"sequence\",\n \"JSON_annotation_column\": \"annotation\"\n}", - "update_time": "2025-06-02T13:36:51.468608", + "tool_stdout": "DEBG\n{\n \"execution\": \"true\",\n \"JSON_db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n \"JSON_table\": \"sample\",\n \"JSON_fragment_column\": \"fragment\",\n \"JSON_sequence_column\": \"sequence\",\n \"JSON_annotation_column\": \"annotation\"\n}", + "update_time": "2025-06-02T14:52:24.970443", "user_email": "planemo@galaxyproject.org", - "user_id": "abb9783f010dde16" + "user_id": "a0c0127196534838" }, "status": "success", "test_index": 0, - "time_seconds": 6.098992109298706, + "time_seconds": 6.417675256729126, "tool_id": "json_db_config_generating", "tool_version": "0.1.0+galaxy1" }, @@ -76,25 +71,20 @@ { "data": { "inputs": { - "annotation_column": "annotation", - "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db", - "execution": false, - "fragment_column": "fragment", - "sequence_column": "sequence", - "table_name": "sample" + "db_request|execution": "false" }, "job": { - "command_line": "python3 -c \"import json; params = { 'execution': 'false', 'JSON_db_uri': 'postgresql://postgres:RK17__at__localhost:5432/test_fragments_db', 'JSON_table': 'sample', 'JSON_fragment_column': 'fragment', 'JSON_sequence_column': 'sequence', 'JSON_annotation_column': 'annotation' }; f = open('/tmp/tmphuox1me_/job_working_directory/000/2/outputs/dataset_b4d39c19-882f-4805-90ee-dbfd2dc51c44.dat', 'w'); json.dump(params, f, indent=4); f.close()\" && echo DEBUG && cat '/tmp/tmphuox1me_/job_working_directory/000/2/outputs/dataset_b4d39c19-882f-4805-90ee-dbfd2dc51c44.dat'", + "command_line": "python3 -c \"import json; params = { 'execution': 'false', 'JSON_db_uri': '', 'JSON_table': '', 'JSON_fragment_column': '', 'JSON_sequence_column': '', 'JSON_annotation_column': '' }; f = open('/tmp/tmp91u1vmdr/job_working_directory/000/2/outputs/dataset_fea0778f-fc84-4194-a37e-bc74bbe239b9.dat', 'w'); json.dump(params, f, indent=4); f.close()\" && echo DEBG && cat '/tmp/tmp91u1vmdr/job_working_directory/000/2/outputs/dataset_fea0778f-fc84-4194-a37e-bc74bbe239b9.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-06-02T13:36:51.893406", + "create_time": "2025-06-02T14:52:25.368237", "dependencies": [], "exit_code": 0, - "external_id": "240333", + "external_id": "274120", "galaxy_version": "24.2", "handler": null, - "history_id": "e20768301a38397d", - "id": "e20768301a38397d", + "history_id": "819c904f5882870a", + "id": "819c904f5882870a", "inputs": {}, "job_messages": [], "job_metrics": [], @@ -105,35 +95,30 @@ "output_collections": {}, "outputs": { "output_json": { - "id": "e20768301a38397d", + "id": "819c904f5882870a", "src": "hda", - "uuid": "b4d39c19-882f-4805-90ee-dbfd2dc51c44" + "uuid": "fea0778f-fc84-4194-a37e-bc74bbe239b9" } }, "params": { "__input_ext": "\"input\"", - "annotation_column": "\"annotation\"", - "chromInfo": "\"/tmp/tmphuox1me_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", - "db_uri": "\"postgresql://postgres:RK17@localhost:5432/test_fragments_db\"", - "dbkey": "\"?\"", - "execution": "false", - "fragment_column": "\"fragment\"", - "sequence_column": "\"sequence\"", - "table_name": "\"sample\"" + "chromInfo": "\"/tmp/tmp91u1vmdr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "db_request": "{\"__current_case__\": 1, \"db_config\": {\"annotation_column\": null, \"db_uri\": null, \"fragment_column\": null, \"sequence_column\": null, \"table_name\": null}, \"execution\": \"false\"}", + "dbkey": "\"?\"" }, "state": "ok", "stderr": "", - "stdout": "DEBUG\n{\n \"execution\": \"false\",\n \"JSON_db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n \"JSON_table\": \"sample\",\n \"JSON_fragment_column\": \"fragment\",\n \"JSON_sequence_column\": \"sequence\",\n \"JSON_annotation_column\": \"annotation\"\n}", + "stdout": "DEBG\n{\n \"execution\": \"false\",\n \"JSON_db_uri\": \"\",\n \"JSON_table\": \"\",\n \"JSON_fragment_column\": \"\",\n \"JSON_sequence_column\": \"\",\n \"JSON_annotation_column\": \"\"\n}", "tool_id": "json_db_config_generating", "tool_stderr": "", - "tool_stdout": "DEBUG\n{\n \"execution\": \"false\",\n \"JSON_db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n \"JSON_table\": \"sample\",\n \"JSON_fragment_column\": \"fragment\",\n \"JSON_sequence_column\": \"sequence\",\n \"JSON_annotation_column\": \"annotation\"\n}", - "update_time": "2025-06-02T13:36:57.648501", + "tool_stdout": "DEBG\n{\n \"execution\": \"false\",\n \"JSON_db_uri\": \"\",\n \"JSON_table\": \"\",\n \"JSON_fragment_column\": \"\",\n \"JSON_sequence_column\": \"\",\n \"JSON_annotation_column\": \"\"\n}", + "update_time": "2025-06-02T14:52:31.112726", "user_email": "planemo@galaxyproject.org", - "user_id": "abb9783f010dde16" + "user_id": "a0c0127196534838" }, "status": "success", "test_index": 1, - "time_seconds": 6.048913240432739, + "time_seconds": 6.040508270263672, "tool_id": "json_db_config_generating", "tool_version": "0.1.0+galaxy1" },