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comparison output.json @ 3:8eb6c417d4f5 draft

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planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
author tduigou
date Mon, 02 Jun 2025 15:10:45 +0000
parents 2909e53fac5b
children 40aa268ce07f
comparison
equal deleted inserted replaced
2:33ebf3ea3eb6 3:8eb6c417d4f5
12 "db_request|db_config|annotation_column": "annotation", 12 "db_request|db_config|annotation_column": "annotation",
13 "db_request|db_config|db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db", 13 "db_request|db_config|db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",
14 "db_request|db_config|fragment_column": "fragment", 14 "db_request|db_config|fragment_column": "fragment",
15 "db_request|db_config|sequence_column": "sequence", 15 "db_request|db_config|sequence_column": "sequence",
16 "db_request|db_config|table_name": "sample", 16 "db_request|db_config|table_name": "sample",
17 "db_request|execution": "true" 17 "db_request|execution": true
18 }, 18 },
19 "job": { 19 "job": {
20 "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'", 20 "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'",
21 "command_version": "", 21 "command_version": "",
22 "copied_from_job_id": null, 22 "copied_from_job_id": null,
23 "create_time": "2025-06-02T14:52:18.811266", 23 "create_time": "2025-06-02T15:09:13.299180",
24 "dependencies": [], 24 "dependencies": [],
25 "exit_code": 0, 25 "exit_code": 0,
26 "external_id": "274048", 26 "external_id": "282809",
27 "galaxy_version": "24.2", 27 "galaxy_version": "24.2",
28 "handler": null, 28 "handler": null,
29 "history_id": "a0c0127196534838", 29 "history_id": "a5a635de282655c8",
30 "id": "a0c0127196534838", 30 "id": "a5a635de282655c8",
31 "inputs": {}, 31 "inputs": {},
32 "job_messages": [], 32 "job_messages": [],
33 "job_metrics": [], 33 "job_metrics": [],
34 "job_runner_name": null, 34 "job_runner_name": null,
35 "job_stderr": "", 35 "job_stderr": "",
36 "job_stdout": "", 36 "job_stdout": "",
37 "model_class": "Job", 37 "model_class": "Job",
38 "output_collections": {}, 38 "output_collections": {},
39 "outputs": { 39 "outputs": {
40 "output_json": { 40 "output_json": {
41 "id": "a0c0127196534838", 41 "id": "a5a635de282655c8",
42 "src": "hda", 42 "src": "hda",
43 "uuid": "b781e9dc-83b4-4c3f-99ef-6c1eb6078f62" 43 "uuid": "0349192e-9e75-4498-b48a-0a53dbf83783"
44 } 44 }
45 }, 45 },
46 "params": { 46 "params": {
47 "__input_ext": "\"input\"", 47 "__input_ext": "\"input\"",
48 "chromInfo": "\"/tmp/tmp91u1vmdr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 48 "chromInfo": "\"/tmp/tmpexzs2_xe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
49 "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\"}", 49 "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}",
50 "dbkey": "\"?\"" 50 "dbkey": "\"?\""
51 }, 51 },
52 "state": "ok", 52 "state": "ok",
53 "stderr": "", 53 "stderr": "",
54 "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}", 54 "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}",
55 "tool_id": "json_db_config_generating", 55 "tool_id": "json_db_config_generating",
56 "tool_stderr": "", 56 "tool_stderr": "",
57 "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}", 57 "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}",
58 "update_time": "2025-06-02T14:52:24.970443", 58 "update_time": "2025-06-02T15:09:19.180152",
59 "user_email": "planemo@galaxyproject.org", 59 "user_email": "planemo@galaxyproject.org",
60 "user_id": "a0c0127196534838" 60 "user_id": "a5a635de282655c8"
61 }, 61 },
62 "status": "success", 62 "status": "success",
63 "test_index": 0, 63 "test_index": 0,
64 "time_seconds": 6.417675256729126, 64 "time_seconds": 6.056678056716919,
65 "tool_id": "json_db_config_generating", 65 "tool_id": "json_db_config_generating",
66 "tool_version": "0.1.0+galaxy1" 66 "tool_version": "0.1.0+galaxy2"
67 }, 67 },
68 "has_data": true, 68 "has_data": true,
69 "id": "json_db_config_generating-0" 69 "id": "json_db_config_generating-0"
70 }, 70 },
71 { 71 {
72 "data": { 72 "data": {
73 "inputs": { 73 "inputs": {
74 "db_request|execution": "false" 74 "db_request|execution": false
75 }, 75 },
76 "job": { 76 "job": {
77 "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'", 77 "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'",
78 "command_version": "", 78 "command_version": "",
79 "copied_from_job_id": null, 79 "copied_from_job_id": null,
80 "create_time": "2025-06-02T14:52:25.368237", 80 "create_time": "2025-06-02T15:09:19.474779",
81 "dependencies": [], 81 "dependencies": [],
82 "exit_code": 0, 82 "exit_code": 0,
83 "external_id": "274120", 83 "external_id": "282881",
84 "galaxy_version": "24.2", 84 "galaxy_version": "24.2",
85 "handler": null, 85 "handler": null,
86 "history_id": "819c904f5882870a", 86 "history_id": "1d721e33ec06790c",
87 "id": "819c904f5882870a", 87 "id": "1d721e33ec06790c",
88 "inputs": {}, 88 "inputs": {},
89 "job_messages": [], 89 "job_messages": [],
90 "job_metrics": [], 90 "job_metrics": [],
91 "job_runner_name": null, 91 "job_runner_name": null,
92 "job_stderr": "", 92 "job_stderr": "",
93 "job_stdout": "", 93 "job_stdout": "",
94 "model_class": "Job", 94 "model_class": "Job",
95 "output_collections": {}, 95 "output_collections": {},
96 "outputs": { 96 "outputs": {
97 "output_json": { 97 "output_json": {
98 "id": "819c904f5882870a", 98 "id": "1d721e33ec06790c",
99 "src": "hda", 99 "src": "hda",
100 "uuid": "fea0778f-fc84-4194-a37e-bc74bbe239b9" 100 "uuid": "1d7dac23-dc24-4747-901c-6441a3b1807a"
101 } 101 }
102 }, 102 },
103 "params": { 103 "params": {
104 "__input_ext": "\"input\"", 104 "__input_ext": "\"input\"",
105 "chromInfo": "\"/tmp/tmp91u1vmdr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 105 "chromInfo": "\"/tmp/tmpexzs2_xe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
106 "db_request": "{\"__current_case__\": 1, \"db_config\": {\"annotation_column\": null, \"db_uri\": null, \"fragment_column\": null, \"sequence_column\": null, \"table_name\": null}, \"execution\": \"false\"}", 106 "db_request": "{\"__current_case__\": 1, \"db_config\": {\"annotation_column\": null, \"db_uri\": null, \"fragment_column\": null, \"sequence_column\": null, \"table_name\": null}, \"execution\": false}",
107 "dbkey": "\"?\"" 107 "dbkey": "\"?\""
108 }, 108 },
109 "state": "ok", 109 "state": "ok",
110 "stderr": "", 110 "stderr": "",
111 "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}", 111 "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}",
112 "tool_id": "json_db_config_generating", 112 "tool_id": "json_db_config_generating",
113 "tool_stderr": "", 113 "tool_stderr": "",
114 "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}", 114 "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}",
115 "update_time": "2025-06-02T14:52:31.112726", 115 "update_time": "2025-06-02T15:09:25.155850",
116 "user_email": "planemo@galaxyproject.org", 116 "user_email": "planemo@galaxyproject.org",
117 "user_id": "a0c0127196534838" 117 "user_id": "a5a635de282655c8"
118 }, 118 },
119 "status": "success", 119 "status": "success",
120 "test_index": 1, 120 "test_index": 1,
121 "time_seconds": 6.040508270263672, 121 "time_seconds": 6.073927402496338,
122 "tool_id": "json_db_config_generating", 122 "tool_id": "json_db_config_generating",
123 "tool_version": "0.1.0+galaxy1" 123 "tool_version": "0.1.0+galaxy2"
124 }, 124 },
125 "has_data": true, 125 "has_data": true,
126 "id": "json_db_config_generating-1" 126 "id": "json_db_config_generating-1"
127 } 127 }
128 ], 128 ],