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comparison output.json @ 0:034686b5bc15 draft

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planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
author tduigou
date Thu, 24 Apr 2025 09:56:36 +0000
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children eca0d710bbe9
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-1:000000000000 0:034686b5bc15
1 {
2 "summary": {
3 "num_errors": 0,
4 "num_failures": 0,
5 "num_skips": 0,
6 "num_tests": 1
7 },
8 "tests": [
9 {
10 "data": {
11 "inputs": {
12 "annotation_column": "annotation",
13 "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",
14 "fragment_column": "fragment",
15 "genbank_files": [
16 {
17 "id": "0ed824750a9f5374",
18 "src": "hda"
19 },
20 {
21 "id": "93c5e169024bda92",
22 "src": "hda"
23 },
24 {
25 "id": "7e79446a5abd8b5f",
26 "src": "hda"
27 },
28 {
29 "id": "81603bca0e110055",
30 "src": "hda"
31 },
32 {
33 "id": "f1c08c8102faa4bc",
34 "src": "hda"
35 }
36 ],
37 "sequence_column": "sequence",
38 "table": "sample"
39 },
40 "job": {
41 "command_line": "python '/home/rkhaled/galaxytools/tools/save_to_db/save_to_db.py' --input '/tmp/tmp_mv7gt3c/files/5/2/2/dataset_5228856a-39be-4f27-afa9-d1f613dea185.dat,/tmp/tmp_mv7gt3c/files/f/a/a/dataset_faa1d0aa-2bb0-47c0-bc3e-949253dd5c3c.dat,/tmp/tmp_mv7gt3c/files/9/6/1/dataset_961fe859-a187-4b45-98ac-bc9c8bd29463.dat,/tmp/tmp_mv7gt3c/files/a/5/c/dataset_a5c56d98-0435-435b-ad8a-01906b2ab961.dat,/tmp/tmp_mv7gt3c/files/2/a/7/dataset_2a788c0d-f89d-4961-95c4-423fd51249f0.dat' --sequence_column 'sequence' --annotation_column 'annotation' --db_uri 'postgresql://postgres:RK17__at__localhost:5432/test_fragments_db' --table 'sample' --fragment_column 'fragment' --output '/tmp/tmp_mv7gt3c/job_working_directory/000/6/outputs/dataset_c2d55cf8-9c51-42f9-84da-9aa06323c7ce.dat' --file_name_mapping '/tmp/tmp_mv7gt3c/files/5/2/2/dataset_5228856a-39be-4f27-afa9-d1f613dea185.dat:p7_L7Ae-Weiss.gb,/tmp/tmp_mv7gt3c/files/f/a/a/dataset_faa1d0aa-2bb0-47c0-bc3e-949253dd5c3c.dat:p6_Nt-IgKLsequence.gb,/tmp/tmp_mv7gt3c/files/9/6/1/dataset_961fe859-a187-4b45-98ac-bc9c8bd29463.dat:p6_Kozak-ATG.gb,/tmp/tmp_mv7gt3c/files/a/5/c/dataset_a5c56d98-0435-435b-ad8a-01906b2ab961.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmp_mv7gt3c/files/2/a/7/dataset_2a788c0d-f89d-4961-95c4-423fd51249f0.dat:HC_Amp_ccdB.gb'",
42 "command_version": "",
43 "copied_from_job_id": null,
44 "create_time": "2025-04-24T09:49:34.459208",
45 "dependencies": [],
46 "exit_code": 0,
47 "external_id": "84720",
48 "galaxy_version": "24.2",
49 "handler": null,
50 "history_id": "0ed824750a9f5374",
51 "id": "016b212ed10ed695",
52 "inputs": {
53 "genbank_files": {
54 "id": "0ed824750a9f5374",
55 "src": "hda",
56 "uuid": "5228856a-39be-4f27-afa9-d1f613dea185"
57 },
58 "genbank_files1": {
59 "id": "0ed824750a9f5374",
60 "src": "hda",
61 "uuid": "5228856a-39be-4f27-afa9-d1f613dea185"
62 },
63 "genbank_files2": {
64 "id": "93c5e169024bda92",
65 "src": "hda",
66 "uuid": "faa1d0aa-2bb0-47c0-bc3e-949253dd5c3c"
67 },
68 "genbank_files3": {
69 "id": "7e79446a5abd8b5f",
70 "src": "hda",
71 "uuid": "961fe859-a187-4b45-98ac-bc9c8bd29463"
72 },
73 "genbank_files4": {
74 "id": "81603bca0e110055",
75 "src": "hda",
76 "uuid": "a5c56d98-0435-435b-ad8a-01906b2ab961"
77 },
78 "genbank_files5": {
79 "id": "f1c08c8102faa4bc",
80 "src": "hda",
81 "uuid": "2a788c0d-f89d-4961-95c4-423fd51249f0"
82 }
83 },
84 "job_messages": [],
85 "job_metrics": [],
86 "job_runner_name": null,
87 "job_stderr": "",
88 "job_stdout": "",
89 "model_class": "Job",
90 "output_collections": {},
91 "outputs": {
92 "output": {
93 "id": "016b212ed10ed695",
94 "src": "hda",
95 "uuid": "c2d55cf8-9c51-42f9-84da-9aa06323c7ce"
96 }
97 },
98 "params": {
99 "__input_ext": "\"input\"",
100 "annotation_column": "\"annotation\"",
101 "chromInfo": "\"/tmp/tmp_mv7gt3c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
102 "db_uri": "\"postgresql://postgres:RK17@localhost:5432/test_fragments_db\"",
103 "dbkey": "\"?\"",
104 "fragment_column": "\"fragment\"",
105 "sequence_column": "\"sequence\"",
106 "table": "\"sample\""
107 },
108 "state": "ok",
109 "stderr": "",
110 "stdout": "Container 'test_fragments_db' is already running.\nConnected to database.\nProcessing file: dataset_5228856a-39be-4f27-afa9-d1f613dea185.dat\nProcessing file: dataset_faa1d0aa-2bb0-47c0-bc3e-949253dd5c3c.dat\nProcessing file: dataset_961fe859-a187-4b45-98ac-bc9c8bd29463.dat\nProcessing file: dataset_a5c56d98-0435-435b-ad8a-01906b2ab961.dat\nProcessing file: dataset_2a788c0d-f89d-4961-95c4-423fd51249f0.dat\nInserted 5 fragments.\nFragment names written to '/tmp/tmp_mv7gt3c/job_working_directory/000/6/outputs/dataset_c2d55cf8-9c51-42f9-84da-9aa06323c7ce.dat'.\n",
111 "tool_id": "save_to_db",
112 "tool_stderr": "",
113 "tool_stdout": "Container 'test_fragments_db' is already running.\nConnected to database.\nProcessing file: dataset_5228856a-39be-4f27-afa9-d1f613dea185.dat\nProcessing file: dataset_faa1d0aa-2bb0-47c0-bc3e-949253dd5c3c.dat\nProcessing file: dataset_961fe859-a187-4b45-98ac-bc9c8bd29463.dat\nProcessing file: dataset_a5c56d98-0435-435b-ad8a-01906b2ab961.dat\nProcessing file: dataset_2a788c0d-f89d-4961-95c4-423fd51249f0.dat\nInserted 5 fragments.\nFragment names written to '/tmp/tmp_mv7gt3c/job_working_directory/000/6/outputs/dataset_c2d55cf8-9c51-42f9-84da-9aa06323c7ce.dat'.\n",
114 "update_time": "2025-04-24T09:49:41.678113",
115 "user_email": "planemo@galaxyproject.org",
116 "user_id": "0ed824750a9f5374"
117 },
118 "status": "success",
119 "test_index": 0,
120 "time_seconds": 26.82854700088501,
121 "tool_id": "save_to_db",
122 "tool_version": "0.1.0+galaxy0"
123 },
124 "has_data": true,
125 "id": "save_to_db-0"
126 }
127 ],
128 "version": "0.1"
129 }