Mercurial > repos > tduigou > json_db_config_generating

annotate 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
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95757ea6c333 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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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
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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": {
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11 "inputs": {
1
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12 "db_request|db_config|annotation_column": "annotation",
2909e53fac5b planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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parents: 0
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13 "db_request|db_config|db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",
2909e53fac5b planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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14 "db_request|db_config|fragment_column": "fragment",
2909e53fac5b planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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15 "db_request|db_config|sequence_column": "sequence",
2909e53fac5b planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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16 "db_request|db_config|table_name": "sample",
2909e53fac5b planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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17 "db_request|execution": "true"
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18 },
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19 "job": {
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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/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'",
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21 "command_version": "",
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22 "copied_from_job_id": null,
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23 "create_time": "2025-06-02T14:52:18.811266",
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24 "dependencies": [],
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25 "exit_code": 0,
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26 "external_id": "274048",
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27 "galaxy_version": "24.2",
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28 "handler": null,
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29 "history_id": "a0c0127196534838",
2909e53fac5b planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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30 "id": "a0c0127196534838",
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95757ea6c333 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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31 "inputs": {},
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32 "job_messages": [],
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33 "job_metrics": [],
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34 "job_runner_name": null,
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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",
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38 "output_collections": {},
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39 "outputs": {
95757ea6c333 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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40 "output_json": {
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41 "id": "a0c0127196534838",
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42 "src": "hda",
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43 "uuid": "b781e9dc-83b4-4c3f-99ef-6c1eb6078f62"
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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": {
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47 "__input_ext": "\"input\"",
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48 "chromInfo": "\"/tmp/tmp91u1vmdr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
2909e53fac5b planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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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\"}",
2909e53fac5b planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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50 "dbkey": "\"?\""
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51 },
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52 "state": "ok",
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53 "stderr": "",
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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}",
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95757ea6c333 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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55 "tool_id": "json_db_config_generating",
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56 "tool_stderr": "",
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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}",
2909e53fac5b planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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58 "update_time": "2025-06-02T14:52:24.970443",
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59 "user_email": "planemo@galaxyproject.org",
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60 "user_id": "a0c0127196534838"
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61 },
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62 "status": "success",
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63 "test_index": 0,
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64 "time_seconds": 6.417675256729126,
0
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65 "tool_id": "json_db_config_generating",
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66 "tool_version": "0.1.0+galaxy1"
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67 },
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68 "has_data": true,
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69 "id": "json_db_config_generating-0"
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70 },
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71 {
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72 "data": {
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73 "inputs": {
1
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74 "db_request|execution": "false"
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75 },
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76 "job": {
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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'",
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78 "command_version": "",
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79 "copied_from_job_id": null,
1
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80 "create_time": "2025-06-02T14:52:25.368237",
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81 "dependencies": [],
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82 "exit_code": 0,
1
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83 "external_id": "274120",
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84 "galaxy_version": "24.2",
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85 "handler": null,
1
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86 "history_id": "819c904f5882870a",
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87 "id": "819c904f5882870a",
0
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88 "inputs": {},
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89 "job_messages": [],
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90 "job_metrics": [],
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91 "job_runner_name": null,
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92 "job_stderr": "",
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93 "job_stdout": "",
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94 "model_class": "Job",
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95 "output_collections": {},
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96 "outputs": {
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97 "output_json": {
1
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98 "id": "819c904f5882870a",
0
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99 "src": "hda",
1
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100 "uuid": "fea0778f-fc84-4194-a37e-bc74bbe239b9"
0
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101 }
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102 },
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103 "params": {
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104 "__input_ext": "\"input\"",
1
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105 "chromInfo": "\"/tmp/tmp91u1vmdr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
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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\"}",
2909e53fac5b planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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107 "dbkey": "\"?\""
0
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108 },
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109 "state": "ok",
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110 "stderr": "",
1
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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}",
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112 "tool_id": "json_db_config_generating",
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113 "tool_stderr": "",
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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}",
2909e53fac5b planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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115 "update_time": "2025-06-02T14:52:31.112726",
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116 "user_email": "planemo@galaxyproject.org",
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117 "user_id": "a0c0127196534838"
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118 },
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119 "status": "success",
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120 "test_index": 1,
1
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121 "time_seconds": 6.040508270263672,
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122 "tool_id": "json_db_config_generating",
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123 "tool_version": "0.1.0+galaxy1"
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124 },
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125 "has_data": true,
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126 "id": "json_db_config_generating-1"
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127 }
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128 ],
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129 "version": "0.1"
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130 }