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comparison output.json @ 1:2909e53fac5b draft

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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
comparison
equal deleted inserted replaced
0:95757ea6c333 1:2909e53fac5b
7 }, 7 },
8 "tests": [ 8 "tests": [
9 { 9 {
10 "data": { 10 "data": {
11 "inputs": { 11 "inputs": {
12 "annotation_column": "annotation", 12 "db_request|db_config|annotation_column": "annotation",
13 "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 "execution": true, 14 "db_request|db_config|fragment_column": "fragment",
15 "fragment_column": "fragment", 15 "db_request|db_config|sequence_column": "sequence",
16 "sequence_column": "sequence", 16 "db_request|db_config|table_name": "sample",
17 "table_name": "sample" 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/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'", 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'",
21 "command_version": "", 21 "command_version": "",
22 "copied_from_job_id": null, 22 "copied_from_job_id": null,
23 "create_time": "2025-06-02T13:36:45.666819", 23 "create_time": "2025-06-02T14:52:18.811266",
24 "dependencies": [], 24 "dependencies": [],
25 "exit_code": 0, 25 "exit_code": 0,
26 "external_id": "240263", 26 "external_id": "274048",
27 "galaxy_version": "24.2", 27 "galaxy_version": "24.2",
28 "handler": null, 28 "handler": null,
29 "history_id": "abb9783f010dde16", 29 "history_id": "a0c0127196534838",
30 "id": "abb9783f010dde16", 30 "id": "a0c0127196534838",
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": "abb9783f010dde16", 41 "id": "a0c0127196534838",
42 "src": "hda", 42 "src": "hda",
43 "uuid": "a57d4381-ba51-4c7e-8409-1ec0f85d3ba2" 43 "uuid": "b781e9dc-83b4-4c3f-99ef-6c1eb6078f62"
44 } 44 }
45 }, 45 },
46 "params": { 46 "params": {
47 "__input_ext": "\"input\"", 47 "__input_ext": "\"input\"",
48 "annotation_column": "\"annotation\"", 48 "chromInfo": "\"/tmp/tmp91u1vmdr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
49 "chromInfo": "\"/tmp/tmphuox1me_/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\"}",
50 "db_uri": "\"postgresql://postgres:RK17@localhost:5432/test_fragments_db\"", 50 "dbkey": "\"?\""
51 "dbkey": "\"?\"",
52 "execution": "true",
53 "fragment_column": "\"fragment\"",
54 "sequence_column": "\"sequence\"",
55 "table_name": "\"sample\""
56 }, 51 },
57 "state": "ok", 52 "state": "ok",
58 "stderr": "", 53 "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}", 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}",
60 "tool_id": "json_db_config_generating", 55 "tool_id": "json_db_config_generating",
61 "tool_stderr": "", 56 "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}", 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}",
63 "update_time": "2025-06-02T13:36:51.468608", 58 "update_time": "2025-06-02T14:52:24.970443",
64 "user_email": "planemo@galaxyproject.org", 59 "user_email": "planemo@galaxyproject.org",
65 "user_id": "abb9783f010dde16" 60 "user_id": "a0c0127196534838"
66 }, 61 },
67 "status": "success", 62 "status": "success",
68 "test_index": 0, 63 "test_index": 0,
69 "time_seconds": 6.098992109298706, 64 "time_seconds": 6.417675256729126,
70 "tool_id": "json_db_config_generating", 65 "tool_id": "json_db_config_generating",
71 "tool_version": "0.1.0+galaxy1" 66 "tool_version": "0.1.0+galaxy1"
72 }, 67 },
73 "has_data": true, 68 "has_data": true,
74 "id": "json_db_config_generating-0" 69 "id": "json_db_config_generating-0"
75 }, 70 },
76 { 71 {
77 "data": { 72 "data": {
78 "inputs": { 73 "inputs": {
79 "annotation_column": "annotation", 74 "db_request|execution": "false"
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 }, 75 },
86 "job": { 76 "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'", 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'",
88 "command_version": "", 78 "command_version": "",
89 "copied_from_job_id": null, 79 "copied_from_job_id": null,
90 "create_time": "2025-06-02T13:36:51.893406", 80 "create_time": "2025-06-02T14:52:25.368237",
91 "dependencies": [], 81 "dependencies": [],
92 "exit_code": 0, 82 "exit_code": 0,
93 "external_id": "240333", 83 "external_id": "274120",
94 "galaxy_version": "24.2", 84 "galaxy_version": "24.2",
95 "handler": null, 85 "handler": null,
96 "history_id": "e20768301a38397d", 86 "history_id": "819c904f5882870a",
97 "id": "e20768301a38397d", 87 "id": "819c904f5882870a",
98 "inputs": {}, 88 "inputs": {},
99 "job_messages": [], 89 "job_messages": [],
100 "job_metrics": [], 90 "job_metrics": [],
101 "job_runner_name": null, 91 "job_runner_name": null,
102 "job_stderr": "", 92 "job_stderr": "",
103 "job_stdout": "", 93 "job_stdout": "",
104 "model_class": "Job", 94 "model_class": "Job",
105 "output_collections": {}, 95 "output_collections": {},
106 "outputs": { 96 "outputs": {
107 "output_json": { 97 "output_json": {
108 "id": "e20768301a38397d", 98 "id": "819c904f5882870a",
109 "src": "hda", 99 "src": "hda",
110 "uuid": "b4d39c19-882f-4805-90ee-dbfd2dc51c44" 100 "uuid": "fea0778f-fc84-4194-a37e-bc74bbe239b9"
111 } 101 }
112 }, 102 },
113 "params": { 103 "params": {
114 "__input_ext": "\"input\"", 104 "__input_ext": "\"input\"",
115 "annotation_column": "\"annotation\"", 105 "chromInfo": "\"/tmp/tmp91u1vmdr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
116 "chromInfo": "\"/tmp/tmphuox1me_/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\"}",
117 "db_uri": "\"postgresql://postgres:RK17@localhost:5432/test_fragments_db\"", 107 "dbkey": "\"?\""
118 "dbkey": "\"?\"",
119 "execution": "false",
120 "fragment_column": "\"fragment\"",
121 "sequence_column": "\"sequence\"",
122 "table_name": "\"sample\""
123 }, 108 },
124 "state": "ok", 109 "state": "ok",
125 "stderr": "", 110 "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}", 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}",
127 "tool_id": "json_db_config_generating", 112 "tool_id": "json_db_config_generating",
128 "tool_stderr": "", 113 "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}", 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}",
130 "update_time": "2025-06-02T13:36:57.648501", 115 "update_time": "2025-06-02T14:52:31.112726",
131 "user_email": "planemo@galaxyproject.org", 116 "user_email": "planemo@galaxyproject.org",
132 "user_id": "abb9783f010dde16" 117 "user_id": "a0c0127196534838"
133 }, 118 },
134 "status": "success", 119 "status": "success",
135 "test_index": 1, 120 "test_index": 1,
136 "time_seconds": 6.048913240432739, 121 "time_seconds": 6.040508270263672,
137 "tool_id": "json_db_config_generating", 122 "tool_id": "json_db_config_generating",
138 "tool_version": "0.1.0+galaxy1" 123 "tool_version": "0.1.0+galaxy1"
139 }, 124 },
140 "has_data": true, 125 "has_data": true,
141 "id": "json_db_config_generating-1" 126 "id": "json_db_config_generating-1"