Mercurial > repos > tduigou > save_to_db

annotate output.json @ 3:eca0d710bbe9 draft

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planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
author tduigou
date Fri, 23 May 2025 08:51:50 +0000
parents 034686b5bc15
children c7a7520afb4b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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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
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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": {
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11 "inputs": {
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12 "annotation_column": "annotation",
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13 "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",
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14 "fragment_column": "fragment",
3
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15 "genbank_files": {
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16 "id": "aaa4852d508c750d",
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17 "src": "hdca"
eca0d710bbe9 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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18 },
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034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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19 "sequence_column": "sequence",
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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20 "table": "sample"
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21 },
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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22 "job": {
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23 "command_line": "python '/home/rkhaled/galaxytools/tools/save_to_db/save_to_db.py' --input '/tmp/tmp4fafueqc/files/c/4/e/dataset_c4ecd213-c62a-48fe-bfd4-f2eb1c1c6439.dat,/tmp/tmp4fafueqc/files/d/2/d/dataset_d2d9d592-9f6a-488b-b911-e2c122dc898f.dat,/tmp/tmp4fafueqc/files/3/7/a/dataset_37a5bcbb-3cf1-45ae-a439-588268402c0b.dat,/tmp/tmp4fafueqc/files/9/d/d/dataset_9dd9b73e-eb2c-460a-b612-86cc1f86f9b6.dat,/tmp/tmp4fafueqc/files/e/7/e/dataset_e7e7bd21-36d3-4e84-9177-2451bfcc09e7.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/tmp4fafueqc/job_working_directory/000/6/outputs/dataset_fdf114e7-4317-491d-8e29-85accf371db7.dat' --file_name_mapping '/tmp/tmp4fafueqc/files/c/4/e/dataset_c4ecd213-c62a-48fe-bfd4-f2eb1c1c6439.dat:p7_L7Ae-Weiss.gb,/tmp/tmp4fafueqc/files/d/2/d/dataset_d2d9d592-9f6a-488b-b911-e2c122dc898f.dat:p6_Nt-IgKLsequence.gb,/tmp/tmp4fafueqc/files/3/7/a/dataset_37a5bcbb-3cf1-45ae-a439-588268402c0b.dat:p6_Kozak-ATG.gb,/tmp/tmp4fafueqc/files/9/d/d/dataset_9dd9b73e-eb2c-460a-b612-86cc1f86f9b6.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmp4fafueqc/files/e/7/e/dataset_e7e7bd21-36d3-4e84-9177-2451bfcc09e7.dat:HC_Amp_ccdB.gb'",
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034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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24 "command_version": "",
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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25 "copied_from_job_id": null,
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26 "create_time": "2025-05-23T08:51:13.261313",
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034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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27 "dependencies": [],
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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28 "exit_code": 0,
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29 "external_id": "53981",
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034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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30 "galaxy_version": "24.2",
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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31 "handler": null,
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32 "history_id": "aaa4852d508c750d",
eca0d710bbe9 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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33 "id": "42220a2e87c70ae5",
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34 "inputs": {
3
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35 "genbank_files1": {
eca0d710bbe9 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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36 "id": "aaa4852d508c750d",
0
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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37 "src": "hda",
3
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38 "uuid": "c4ecd213-c62a-48fe-bfd4-f2eb1c1c6439"
0
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 "genbank_files2": {
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41 "id": "6139eb08ad8af00a",
0
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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42 "src": "hda",
3
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43 "uuid": "d2d9d592-9f6a-488b-b911-e2c122dc898f"
0
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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44 },
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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45 "genbank_files3": {
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46 "id": "cda565c89999ccf5",
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47 "src": "hda",
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48 "uuid": "37a5bcbb-3cf1-45ae-a439-588268402c0b"
0
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49 },
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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50 "genbank_files4": {
3
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51 "id": "f072bab19666d9bc",
0
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52 "src": "hda",
3
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53 "uuid": "9dd9b73e-eb2c-460a-b612-86cc1f86f9b6"
0
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54 },
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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55 "genbank_files5": {
3
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56 "id": "ede1fe394bce0b73",
0
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57 "src": "hda",
3
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58 "uuid": "e7e7bd21-36d3-4e84-9177-2451bfcc09e7"
0
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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59 }
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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60 },
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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61 "job_messages": [],
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62 "job_metrics": [],
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63 "job_runner_name": null,
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64 "job_stderr": "",
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65 "job_stdout": "",
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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66 "model_class": "Job",
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67 "output_collections": {},
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68 "outputs": {
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69 "output": {
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70 "id": "42220a2e87c70ae5",
0
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71 "src": "hda",
3
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72 "uuid": "fdf114e7-4317-491d-8e29-85accf371db7"
0
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73 }
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74 },
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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75 "params": {
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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76 "__input_ext": "\"input\"",
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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77 "annotation_column": "\"annotation\"",
3
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78 "chromInfo": "\"/tmp/tmp4fafueqc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
0
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79 "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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80 "dbkey": "\"?\"",
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81 "fragment_column": "\"fragment\"",
3
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82 "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}",
0
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83 "sequence_column": "\"sequence\"",
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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84 "table": "\"sample\""
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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85 },
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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86 "state": "ok",
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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87 "stderr": "",
3
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88 "stdout": "Container 'test_fragments_db' is already running.\nConnected to database.\nProcessing file: dataset_c4ecd213-c62a-48fe-bfd4-f2eb1c1c6439.dat\nProcessing file: dataset_d2d9d592-9f6a-488b-b911-e2c122dc898f.dat\nProcessing file: dataset_37a5bcbb-3cf1-45ae-a439-588268402c0b.dat\nProcessing file: dataset_9dd9b73e-eb2c-460a-b612-86cc1f86f9b6.dat\nProcessing file: dataset_e7e7bd21-36d3-4e84-9177-2451bfcc09e7.dat\nInserted 5 fragments.\nFragment names written to '/tmp/tmp4fafueqc/job_working_directory/000/6/outputs/dataset_fdf114e7-4317-491d-8e29-85accf371db7.dat'.\n",
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89 "tool_id": "save_to_db",
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90 "tool_stderr": "",
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91 "tool_stdout": "Container 'test_fragments_db' is already running.\nConnected to database.\nProcessing file: dataset_c4ecd213-c62a-48fe-bfd4-f2eb1c1c6439.dat\nProcessing file: dataset_d2d9d592-9f6a-488b-b911-e2c122dc898f.dat\nProcessing file: dataset_37a5bcbb-3cf1-45ae-a439-588268402c0b.dat\nProcessing file: dataset_9dd9b73e-eb2c-460a-b612-86cc1f86f9b6.dat\nProcessing file: dataset_e7e7bd21-36d3-4e84-9177-2451bfcc09e7.dat\nInserted 5 fragments.\nFragment names written to '/tmp/tmp4fafueqc/job_working_directory/000/6/outputs/dataset_fdf114e7-4317-491d-8e29-85accf371db7.dat'.\n",
eca0d710bbe9 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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92 "update_time": "2025-05-23T08:51:20.615309",
0
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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93 "user_email": "planemo@galaxyproject.org",
3
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94 "user_id": "aaa4852d508c750d"
0
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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95 },
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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96 "status": "success",
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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97 "test_index": 0,
3
eca0d710bbe9 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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98 "time_seconds": 28.753373384475708,
0
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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99 "tool_id": "save_to_db",
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100 "tool_version": "0.1.0+galaxy1"
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034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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101 },
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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102 "has_data": true,
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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103 "id": "save_to_db-0"
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104 }
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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105 ],
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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106 "version": "0.1"
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107 }