Mercurial > repos > tduigou > save_to_db

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