Mercurial > repos > tduigou > seq_to_db

annotate output.json @ 2:d77ff06f5dc9 draft default tip

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planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit d8cc8b87fdb0374745b5420f2da7f08ae905c222-dirty
author tduigou
date Wed, 16 Jul 2025 14:51:52 +0000
parents 5db1c2b9edb8
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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1 {
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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2 "summary": {
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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3 "num_errors": 0,
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4 "num_failures": 0,
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5 "num_skips": 0,
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6 "num_tests": 1
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7 },
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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8 "tests": [
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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9 {
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10 "data": {
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11 "inputs": {
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12 "genbank_files": {
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13 "id": "c483dc6e4815613d",
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14 "src": "hdca"
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15 },
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16 "json_generating": false,
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17 "json_use|json_conf": {
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18 "id": "aa2843b1b277b7a7",
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19 "src": "hda"
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20 },
5db1c2b9edb8 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
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21 "json_use|use_json_paramers": true
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22 },
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23 "job": {
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24 "command_line": "python '/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py' --input '/tmp/tmpac_768cd/files/d/4/1/dataset_d41458b9-ed0a-4b73-83bd-c0b05e03f3ca.dat,/tmp/tmpac_768cd/files/3/2/3/dataset_3234dfd4-c4b6-42fb-b254-e23532f04d7a.dat,/tmp/tmpac_768cd/files/5/c/3/dataset_5c34ee15-4ade-4ee7-9068-607cee72ba4f.dat,/tmp/tmpac_768cd/files/7/9/7/dataset_7970a203-ec8d-40ea-845f-eaa66f55ac7b.dat,/tmp/tmpac_768cd/files/b/c/5/dataset_bc5a286c-1a56-4506-90e2-1687f93f24d0.dat' --use_json_paramers 'true' --json_conf '/tmp/tmpac_768cd/files/5/7/3/dataset_57302268-f98c-4e9d-9812-c2e5bda507f5.dat' --output '/tmp/tmpac_768cd/job_working_directory/000/7/outputs/dataset_8bb5f859-22ca-4d7f-bb07-cfbb3ca3a04f.dat' --file_name_mapping '/tmp/tmpac_768cd/files/d/4/1/dataset_d41458b9-ed0a-4b73-83bd-c0b05e03f3ca.dat:p7_L7Ae-Weiss.gb,/tmp/tmpac_768cd/files/3/2/3/dataset_3234dfd4-c4b6-42fb-b254-e23532f04d7a.dat:p6_Nt-IgKLsequence.gb,/tmp/tmpac_768cd/files/5/c/3/dataset_5c34ee15-4ade-4ee7-9068-607cee72ba4f.dat:p6_Kozak-ATG.gb,/tmp/tmpac_768cd/files/7/9/7/dataset_7970a203-ec8d-40ea-845f-eaa66f55ac7b.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmpac_768cd/files/b/c/5/dataset_bc5a286c-1a56-4506-90e2-1687f93f24d0.dat:HC_Amp_ccdB.gb' --json_generating 'false' --json_output 'XXXX'",
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25 "command_version": "",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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26 "copied_from_job_id": null,
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27 "create_time": "2025-07-16T14:50:01.488998",
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28 "dependencies": [],
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29 "exit_code": 0,
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30 "external_id": "166724",
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31 "galaxy_version": "25.0",
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32 "handler": null,
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33 "history_id": "c483dc6e4815613d",
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34 "id": "bcb3b45a1cc4a671",
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35 "inputs": {
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36 "genbank_files1": {
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37 "id": "c483dc6e4815613d",
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178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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38 "src": "hda",
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39 "uuid": "d41458b9-ed0a-4b73-83bd-c0b05e03f3ca"
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40 },
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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41 "genbank_files2": {
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42 "id": "c4d3b2f0c36d8241",
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43 "src": "hda",
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44 "uuid": "3234dfd4-c4b6-42fb-b254-e23532f04d7a"
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45 },
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46 "genbank_files3": {
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47 "id": "69de8fd4747f3c3b",
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48 "src": "hda",
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49 "uuid": "5c34ee15-4ade-4ee7-9068-607cee72ba4f"
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50 },
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51 "genbank_files4": {
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52 "id": "941f1e1f3cfa391c",
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53 "src": "hda",
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54 "uuid": "7970a203-ec8d-40ea-845f-eaa66f55ac7b"
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55 },
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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56 "genbank_files5": {
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57 "id": "3a97944c68e74177",
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58 "src": "hda",
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59 "uuid": "bc5a286c-1a56-4506-90e2-1687f93f24d0"
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60 },
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61 "json_use|json_conf": {
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62 "id": "aa2843b1b277b7a7",
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63 "src": "hda",
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64 "uuid": "57302268-f98c-4e9d-9812-c2e5bda507f5"
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65 }
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66 },
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67 "job_messages": [],
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68 "job_metrics": [],
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69 "job_runner_name": null,
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70 "job_stderr": "",
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71 "job_stdout": "",
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72 "model_class": "Job",
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73 "output_collections": {},
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74 "outputs": {
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75 "output": {
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76 "id": "bcb3b45a1cc4a671",
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77 "src": "hda",
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78 "uuid": "8bb5f859-22ca-4d7f-bb07-cfbb3ca3a04f"
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79 }
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80 },
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81 "params": {
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82 "__input_ext": "\"input\"",
2
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83 "chromInfo": "\"/tmp/tmpac_768cd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
0
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84 "dbkey": "\"?\"",
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85 "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}",
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86 "json_generating": "false",
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87 "json_use": "{\"__current_case__\": 1, \"json_conf\": {\"values\": [{\"id\": 6, \"src\": \"hda\"}]}, \"use_json_paramers\": true}"
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88 },
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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89 "state": "ok",
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90 "stderr": "",
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91 "stdout": "Connected to database.\nProcessing file: dataset_d41458b9-ed0a-4b73-83bd-c0b05e03f3ca.dat(p7_L7Ae-Weiss)\nProcessing file: dataset_3234dfd4-c4b6-42fb-b254-e23532f04d7a.dat(p6_Nt-IgKLsequence)\nProcessing file: dataset_5c34ee15-4ade-4ee7-9068-607cee72ba4f.dat(p6_Kozak-ATG)\nProcessing file: dataset_7970a203-ec8d-40ea-845f-eaa66f55ac7b.dat(p4_Kt-L7Ae-Weiss)\nProcessing file: dataset_bc5a286c-1a56-4506-90e2-1687f93f24d0.dat(HC_Amp_ccdB)\nInserted 5 fragments.\nFragment names written to '/tmp/tmpac_768cd/job_working_directory/000/7/outputs/dataset_8bb5f859-22ca-4d7f-bb07-cfbb3ca3a04f.dat'.\n",
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92 "tool_id": "seq_to_db",
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93 "tool_stderr": "",
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94 "tool_stdout": "Connected to database.\nProcessing file: dataset_d41458b9-ed0a-4b73-83bd-c0b05e03f3ca.dat(p7_L7Ae-Weiss)\nProcessing file: dataset_3234dfd4-c4b6-42fb-b254-e23532f04d7a.dat(p6_Nt-IgKLsequence)\nProcessing file: dataset_5c34ee15-4ade-4ee7-9068-607cee72ba4f.dat(p6_Kozak-ATG)\nProcessing file: dataset_7970a203-ec8d-40ea-845f-eaa66f55ac7b.dat(p4_Kt-L7Ae-Weiss)\nProcessing file: dataset_bc5a286c-1a56-4506-90e2-1687f93f24d0.dat(HC_Amp_ccdB)\nInserted 5 fragments.\nFragment names written to '/tmp/tmpac_768cd/job_working_directory/000/7/outputs/dataset_8bb5f859-22ca-4d7f-bb07-cfbb3ca3a04f.dat'.\n",
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95 "update_time": "2025-07-16T14:50:07.342567",
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96 "user_email": "planemo@galaxyproject.org",
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97 "user_id": "c483dc6e4815613d"
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98 },
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99 "status": "success",
2
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100 "test_index": 0,
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101 "time_seconds": 35.08016586303711,
0
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102 "tool_id": "seq_to_db",
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103 "tool_version": "0.3.0+galaxy2"
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104 },
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105 "has_data": true,
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106 "id": "seq_to_db-0"
0
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107 }
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108 ],
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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109 "version": "0.1"
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110 }