Mercurial > repos > tduigou > json_db_config_generating

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
comparison
equal deleted inserted replaced
4:f103f5253a93 5:40aa268ce07f
7 }, 7 },
8 "tests": [ 8 "tests": [
9 { 9 {
10 "data": { 10 "data": {
11 "inputs": { 11 "inputs": {
12 "db_request|db_config|annotation_column": "annotation", 12 "db|db_request|db_config|annotation_column": "annotation",
13 "db_request|db_config|db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db", 13 "db|db_request|db_config|db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",
14 "db_request|db_config|fragment_column": "fragment", 14 "db|db_request|db_config|fragment_column": "fragment",
15 "db_request|db_config|sequence_column": "sequence", 15 "db|db_request|db_config|sequence_column": "sequence",
16 "db_request|db_config|table_name": "sample", 16 "db|db_request|db_config|table_name": "sample",
17 "db_request|execution": true 17 "db|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/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'", 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/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'",
21 "command_version": "", 21 "command_version": "",
22 "copied_from_job_id": null, 22 "copied_from_job_id": null,
23 "create_time": "2025-06-02T15:09:13.299180", 23 "create_time": "2025-06-11T15:59:58.065310",
24 "dependencies": [], 24 "dependencies": [],
25 "exit_code": 0, 25 "exit_code": 0,
26 "external_id": "282809", 26 "external_id": "75561",
27 "galaxy_version": "24.2", 27 "galaxy_version": "24.2",
28 "handler": null, 28 "handler": null,
29 "history_id": "a5a635de282655c8", 29 "history_id": "6ee26cd2a9b017f6",
30 "id": "a5a635de282655c8", 30 "id": "6ee26cd2a9b017f6",
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": "a5a635de282655c8", 41 "id": "6ee26cd2a9b017f6",
42 "src": "hda", 42 "src": "hda",
43 "uuid": "0349192e-9e75-4498-b48a-0a53dbf83783" 43 "uuid": "adbe4688-ac5a-4157-9d00-bd44d8e5925a"
44 } 44 }
45 }, 45 },
46 "params": { 46 "params": {
47 "__input_ext": "\"input\"", 47 "__input_ext": "\"input\"",
48 "chromInfo": "\"/tmp/tmpexzs2_xe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 48 "chromInfo": "\"/tmp/tmpetlap50a/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": "{\"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": "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}",
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": "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}",
58 "update_time": "2025-06-02T15:09:19.180152", 58 "update_time": "2025-06-11T16:00:13.304790",
59 "user_email": "planemo@galaxyproject.org", 59 "user_email": "planemo@galaxyproject.org",
60 "user_id": "a5a635de282655c8" 60 "user_id": "6ee26cd2a9b017f6"
61 }, 61 },
62 "status": "success", 62 "status": "success",
63 "test_index": 0, 63 "test_index": 0,
64 "time_seconds": 6.056678056716919, 64 "time_seconds": 15.370232105255127,
65 "tool_id": "json_db_config_generating", 65 "tool_id": "json_db_config_generating",
66 "tool_version": "0.1.0+galaxy2" 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
75 },
76 "job": { 74 "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/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'", 75 "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'",
78 "command_version": "", 76 "command_version": "",
79 "copied_from_job_id": null, 77 "copied_from_job_id": null,
80 "create_time": "2025-06-02T15:09:19.474779", 78 "create_time": "2025-06-11T16:00:13.510772",
81 "dependencies": [], 79 "dependencies": [],
82 "exit_code": 0, 80 "exit_code": 0,
83 "external_id": "282881", 81 "external_id": "75631",
84 "galaxy_version": "24.2", 82 "galaxy_version": "24.2",
85 "handler": null, 83 "handler": null,
86 "history_id": "1d721e33ec06790c", 84 "history_id": "39ef7b54816acc5a",
87 "id": "1d721e33ec06790c", 85 "id": "39ef7b54816acc5a",
88 "inputs": {}, 86 "inputs": {},
89 "job_messages": [], 87 "job_messages": [],
90 "job_metrics": [], 88 "job_metrics": [],
91 "job_runner_name": null, 89 "job_runner_name": null,
92 "job_stderr": "", 90 "job_stderr": "",
93 "job_stdout": "", 91 "job_stdout": "",
94 "model_class": "Job", 92 "model_class": "Job",
95 "output_collections": {}, 93 "output_collections": {},
96 "outputs": { 94 "outputs": {
97 "output_json": { 95 "output_json": {
98 "id": "1d721e33ec06790c", 96 "id": "39ef7b54816acc5a",
99 "src": "hda", 97 "src": "hda",
100 "uuid": "1d7dac23-dc24-4747-901c-6441a3b1807a" 98 "uuid": "c331c972-0356-4042-917b-f63fe99f938d"
101 } 99 }
102 }, 100 },
103 "params": { 101 "params": {
104 "__input_ext": "\"input\"", 102 "__input_ext": "\"input\"",
105 "chromInfo": "\"/tmp/tmpexzs2_xe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 103 "chromInfo": "\"/tmp/tmpetlap50a/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}", 104 "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}}",
107 "dbkey": "\"?\"" 105 "dbkey": "\"?\""
108 }, 106 },
109 "state": "ok", 107 "state": "ok",
110 "stderr": "", 108 "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}", 109 "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}",
112 "tool_id": "json_db_config_generating", 110 "tool_id": "json_db_config_generating",
113 "tool_stderr": "", 111 "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}", 112 "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}",
115 "update_time": "2025-06-02T15:09:25.155850", 113 "update_time": "2025-06-11T16:00:19.478490",
116 "user_email": "planemo@galaxyproject.org", 114 "user_email": "planemo@galaxyproject.org",
117 "user_id": "a5a635de282655c8" 115 "user_id": "6ee26cd2a9b017f6"
118 }, 116 },
119 "status": "success", 117 "status": "success",
120 "test_index": 1, 118 "test_index": 1,
121 "time_seconds": 6.073927402496338, 119 "time_seconds": 6.3762428760528564,
122 "tool_id": "json_db_config_generating", 120 "tool_id": "json_db_config_generating",
123 "tool_version": "0.1.0+galaxy2" 121 "tool_version": "0.1.0+galaxy2"
124 }, 122 },
125 "has_data": true, 123 "has_data": true,
126 "id": "json_db_config_generating-1" 124 "id": "json_db_config_generating-1"