Mercurial > repos > tduigou > json_db_config_generating

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