Mercurial > repos > tduigou > json_db_config_generating

diff output.json @ 5:40aa268ce07f draft default tip

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planemo upload for repository https://github.com/brsynth commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
author tduigou
date Wed, 11 Jun 2025 16:00:37 +0000
parents 8eb6c417d4f5
children
line wrap: on
line diff
--- a/output.json	Wed Jun 11 15:25:55 2025 +0000
+++ b/output.json	Wed Jun 11 16:00:37 2025 +0000
@@ -9,25 +9,25 @@
         {
             "data": {
                 "inputs": {
-                    "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
+                    "db|db_request|db_config|annotation_column": "annotation",
+                    "db|db_request|db_config|db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",
+                    "db|db_request|db_config|fragment_column": "fragment",
+                    "db|db_request|db_config|sequence_column": "sequence",
+                    "db|db_request|db_config|table_name": "sample",
+                    "db|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/tmpexzs2_xe/job_working_directory/000/1/outputs/dataset_0349192e-9e75-4498-b48a-0a53dbf83783.dat', 'w'); json.dump(params, f, indent=4); f.close()\" && echo DEBG && cat '/tmp/tmpexzs2_xe/job_working_directory/000/1/outputs/dataset_0349192e-9e75-4498-b48a-0a53dbf83783.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/tmpetlap50a/job_working_directory/000/1/outputs/dataset_adbe4688-ac5a-4157-9d00-bd44d8e5925a.dat', 'w'); json.dump(params, f, indent=4); f.close()\" && echo DEBUG && cat '/tmp/tmpetlap50a/job_working_directory/000/1/outputs/dataset_adbe4688-ac5a-4157-9d00-bd44d8e5925a.dat'",
                     "command_version": "",
                     "copied_from_job_id": null,
-                    "create_time": "2025-06-02T15:09:13.299180",
+                    "create_time": "2025-06-11T15:59:58.065310",
                     "dependencies": [],
                     "exit_code": 0,
-                    "external_id": "282809",
+                    "external_id": "75561",
                     "galaxy_version": "24.2",
                     "handler": null,
-                    "history_id": "a5a635de282655c8",
-                    "id": "a5a635de282655c8",
+                    "history_id": "6ee26cd2a9b017f6",
+                    "id": "6ee26cd2a9b017f6",
                     "inputs": {},
                     "job_messages": [],
                     "job_metrics": [],
@@ -38,30 +38,30 @@
                     "output_collections": {},
                     "outputs": {
                         "output_json": {
-                            "id": "a5a635de282655c8",
+                            "id": "6ee26cd2a9b017f6",
                             "src": "hda",
-                            "uuid": "0349192e-9e75-4498-b48a-0a53dbf83783"
+                            "uuid": "adbe4688-ac5a-4157-9d00-bd44d8e5925a"
                         }
                     },
                     "params": {
                         "__input_ext": "\"input\"",
-                        "chromInfo": "\"/tmp/tmpexzs2_xe/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}",
+                        "chromInfo": "\"/tmp/tmpetlap50a/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+                        "db": "{\"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": "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}",
+                    "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}",
                     "tool_id": "json_db_config_generating",
                     "tool_stderr": "",
-                    "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": "2025-06-02T15:09:19.180152",
+                    "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": "2025-06-11T16:00:13.304790",
                     "user_email": "planemo@galaxyproject.org",
-                    "user_id": "a5a635de282655c8"
+                    "user_id": "6ee26cd2a9b017f6"
                 },
                 "status": "success",
                 "test_index": 0,
-                "time_seconds": 6.056678056716919,
+                "time_seconds": 15.370232105255127,
                 "tool_id": "json_db_config_generating",
                 "tool_version": "0.1.0+galaxy2"
             },
@@ -70,21 +70,19 @@
         },
         {
             "data": {
-                "inputs": {
-                    "db_request|execution": false
-                },
+                "inputs": {},
                 "job": {
-                    "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/tmpexzs2_xe/job_working_directory/000/2/outputs/dataset_1d7dac23-dc24-4747-901c-6441a3b1807a.dat', 'w'); json.dump(params, f, indent=4); f.close()\" && echo DEBG && cat '/tmp/tmpexzs2_xe/job_working_directory/000/2/outputs/dataset_1d7dac23-dc24-4747-901c-6441a3b1807a.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/tmpetlap50a/job_working_directory/000/2/outputs/dataset_c331c972-0356-4042-917b-f63fe99f938d.dat', 'w'); json.dump(params, f, indent=4); f.close()\" && echo DEBUG && cat '/tmp/tmpetlap50a/job_working_directory/000/2/outputs/dataset_c331c972-0356-4042-917b-f63fe99f938d.dat'",
                     "command_version": "",
                     "copied_from_job_id": null,
-                    "create_time": "2025-06-02T15:09:19.474779",
+                    "create_time": "2025-06-11T16:00:13.510772",
                     "dependencies": [],
                     "exit_code": 0,
-                    "external_id": "282881",
+                    "external_id": "75631",
                     "galaxy_version": "24.2",
                     "handler": null,
-                    "history_id": "1d721e33ec06790c",
-                    "id": "1d721e33ec06790c",
+                    "history_id": "39ef7b54816acc5a",
+                    "id": "39ef7b54816acc5a",
                     "inputs": {},
                     "job_messages": [],
                     "job_metrics": [],
@@ -95,30 +93,30 @@
                     "output_collections": {},
                     "outputs": {
                         "output_json": {
-                            "id": "1d721e33ec06790c",
+                            "id": "39ef7b54816acc5a",
                             "src": "hda",
-                            "uuid": "1d7dac23-dc24-4747-901c-6441a3b1807a"
+                            "uuid": "c331c972-0356-4042-917b-f63fe99f938d"
                         }
                     },
                     "params": {
                         "__input_ext": "\"input\"",
-                        "chromInfo": "\"/tmp/tmpexzs2_xe/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}",
+                        "chromInfo": "\"/tmp/tmpetlap50a/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+                        "db": "{\"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": "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}",
+                    "stdout": "DEBUG\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": "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": "2025-06-02T15:09:25.155850",
+                    "tool_stdout": "DEBUG\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": "2025-06-11T16:00:19.478490",
                     "user_email": "planemo@galaxyproject.org",
-                    "user_id": "a5a635de282655c8"
+                    "user_id": "6ee26cd2a9b017f6"
                 },
                 "status": "success",
                 "test_index": 1,
-                "time_seconds": 6.073927402496338,
+                "time_seconds": 6.3762428760528564,
                 "tool_id": "json_db_config_generating",
                 "tool_version": "0.1.0+galaxy2"
             },