Mercurial > repos > tduigou > json_db_config_generating

comparison output.json @ 0:95757ea6c333 draft

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planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
author tduigou
date Mon, 02 Jun 2025 13:39:41 +0000
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children 2909e53fac5b
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-1:000000000000 0:95757ea6c333
1 {
2 "summary": {
3 "num_errors": 0,
4 "num_failures": 0,
5 "num_skips": 0,
6 "num_tests": 2
7 },
8 "tests": [
9 {
10 "data": {
11 "inputs": {
12 "annotation_column": "annotation",
13 "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",
14 "execution": true,
15 "fragment_column": "fragment",
16 "sequence_column": "sequence",
17 "table_name": "sample"
18 },
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/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'",
21 "command_version": "",
22 "copied_from_job_id": null,
23 "create_time": "2025-06-02T13:36:45.666819",
24 "dependencies": [],
25 "exit_code": 0,
26 "external_id": "240263",
27 "galaxy_version": "24.2",
28 "handler": null,
29 "history_id": "abb9783f010dde16",
30 "id": "abb9783f010dde16",
31 "inputs": {},
32 "job_messages": [],
33 "job_metrics": [],
34 "job_runner_name": null,
35 "job_stderr": "",
36 "job_stdout": "",
37 "model_class": "Job",
38 "output_collections": {},
39 "outputs": {
40 "output_json": {
41 "id": "abb9783f010dde16",
42 "src": "hda",
43 "uuid": "a57d4381-ba51-4c7e-8409-1ec0f85d3ba2"
44 }
45 },
46 "params": {
47 "__input_ext": "\"input\"",
48 "annotation_column": "\"annotation\"",
49 "chromInfo": "\"/tmp/tmphuox1me_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
50 "db_uri": "\"postgresql://postgres:RK17@localhost:5432/test_fragments_db\"",
51 "dbkey": "\"?\"",
52 "execution": "true",
53 "fragment_column": "\"fragment\"",
54 "sequence_column": "\"sequence\"",
55 "table_name": "\"sample\""
56 },
57 "state": "ok",
58 "stderr": "",
59 "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}",
60 "tool_id": "json_db_config_generating",
61 "tool_stderr": "",
62 "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}",
63 "update_time": "2025-06-02T13:36:51.468608",
64 "user_email": "planemo@galaxyproject.org",
65 "user_id": "abb9783f010dde16"
66 },
67 "status": "success",
68 "test_index": 0,
69 "time_seconds": 6.098992109298706,
70 "tool_id": "json_db_config_generating",
71 "tool_version": "0.1.0+galaxy1"
72 },
73 "has_data": true,
74 "id": "json_db_config_generating-0"
75 },
76 {
77 "data": {
78 "inputs": {
79 "annotation_column": "annotation",
80 "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",
81 "execution": false,
82 "fragment_column": "fragment",
83 "sequence_column": "sequence",
84 "table_name": "sample"
85 },
86 "job": {
87 "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'",
88 "command_version": "",
89 "copied_from_job_id": null,
90 "create_time": "2025-06-02T13:36:51.893406",
91 "dependencies": [],
92 "exit_code": 0,
93 "external_id": "240333",
94 "galaxy_version": "24.2",
95 "handler": null,
96 "history_id": "e20768301a38397d",
97 "id": "e20768301a38397d",
98 "inputs": {},
99 "job_messages": [],
100 "job_metrics": [],
101 "job_runner_name": null,
102 "job_stderr": "",
103 "job_stdout": "",
104 "model_class": "Job",
105 "output_collections": {},
106 "outputs": {
107 "output_json": {
108 "id": "e20768301a38397d",
109 "src": "hda",
110 "uuid": "b4d39c19-882f-4805-90ee-dbfd2dc51c44"
111 }
112 },
113 "params": {
114 "__input_ext": "\"input\"",
115 "annotation_column": "\"annotation\"",
116 "chromInfo": "\"/tmp/tmphuox1me_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
117 "db_uri": "\"postgresql://postgres:RK17@localhost:5432/test_fragments_db\"",
118 "dbkey": "\"?\"",
119 "execution": "false",
120 "fragment_column": "\"fragment\"",
121 "sequence_column": "\"sequence\"",
122 "table_name": "\"sample\""
123 },
124 "state": "ok",
125 "stderr": "",
126 "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}",
127 "tool_id": "json_db_config_generating",
128 "tool_stderr": "",
129 "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}",
130 "update_time": "2025-06-02T13:36:57.648501",
131 "user_email": "planemo@galaxyproject.org",
132 "user_id": "abb9783f010dde16"
133 },
134 "status": "success",
135 "test_index": 1,
136 "time_seconds": 6.048913240432739,
137 "tool_id": "json_db_config_generating",
138 "tool_version": "0.1.0+galaxy1"
139 },
140 "has_data": true,
141 "id": "json_db_config_generating-1"
142 }
143 ],
144 "version": "0.1"
145 }