Mercurial > repos > tduigou > seq_to_db

annotate output.json @ 1:5db1c2b9edb8 draft

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planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
author tduigou
date Fri, 11 Jul 2025 14:16:33 +0000
parents 178d068648f4
children d77ff06f5dc9
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": 1,
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5 "num_skips": 0,
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6 "num_tests": 2
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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": [
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9 {
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10 "data": {
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11 "inputs": {
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12 "genbank_files": {
1
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13 "id": "5035e3bab9835d6e",
0
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14 "src": "hdca"
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15 },
1
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16 "json_generating": false,
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17 "json_use|json_conf": {
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18 "id": "48861e2bb98fa8f3",
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19 "src": "hda"
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20 },
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21 "json_use|use_json_paramers": true
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22 },
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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23 "job": {
1
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24 "command_line": "python '/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py' --input '/tmp/tmp_qydb9xn/files/8/c/6/dataset_8c6c4607-b545-411e-8565-3c6ca3472443.dat,/tmp/tmp_qydb9xn/files/e/b/6/dataset_eb604a05-357c-45df-ae5a-81ddb65244e3.dat,/tmp/tmp_qydb9xn/files/3/6/6/dataset_366741cf-94b2-42de-8d64-7f00e58563e0.dat,/tmp/tmp_qydb9xn/files/f/f/1/dataset_ff11bb17-ed2d-415e-96cf-e5ed35c7d997.dat,/tmp/tmp_qydb9xn/files/5/8/6/dataset_5861c673-e009-436c-9020-a23df5356851.dat' --use_json_paramers 'true' --json_conf '/tmp/tmp_qydb9xn/files/8/c/a/dataset_8ca49aab-9732-422b-bd76-9975c97f5f2a.dat' --output '/tmp/tmp_qydb9xn/job_working_directory/000/7/outputs/dataset_b5f885e2-68c2-4441-9ade-922799b2cfd6.dat' --file_name_mapping '/tmp/tmp_qydb9xn/files/8/c/6/dataset_8c6c4607-b545-411e-8565-3c6ca3472443.dat:p7_L7Ae-Weiss.gb,/tmp/tmp_qydb9xn/files/e/b/6/dataset_eb604a05-357c-45df-ae5a-81ddb65244e3.dat:p6_Nt-IgKLsequence.gb,/tmp/tmp_qydb9xn/files/3/6/6/dataset_366741cf-94b2-42de-8d64-7f00e58563e0.dat:p6_Kozak-ATG.gb,/tmp/tmp_qydb9xn/files/f/f/1/dataset_ff11bb17-ed2d-415e-96cf-e5ed35c7d997.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmp_qydb9xn/files/5/8/6/dataset_5861c673-e009-436c-9020-a23df5356851.dat:HC_Amp_ccdB.gb' --json_generating 'false' --json_output 'XXXX' && echo \"DEBUG\" && cat \"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": "2025-07-11T14:13:47.541606",
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28 "dependencies": [],
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29 "exit_code": 1,
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30 "external_id": "133184",
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31 "galaxy_version": "25.0",
0
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32 "handler": null,
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33 "history_id": "5035e3bab9835d6e",
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34 "id": "cf8d16af14dc294f",
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35 "inputs": {
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36 "genbank_files1": {
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37 "id": "5035e3bab9835d6e",
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38 "src": "hda",
1
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39 "uuid": "8c6c4607-b545-411e-8565-3c6ca3472443"
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40 },
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41 "genbank_files2": {
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42 "id": "6a141869249298e9",
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43 "src": "hda",
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44 "uuid": "eb604a05-357c-45df-ae5a-81ddb65244e3"
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45 },
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46 "genbank_files3": {
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47 "id": "8ca00df555c44d56",
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48 "src": "hda",
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49 "uuid": "366741cf-94b2-42de-8d64-7f00e58563e0"
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50 },
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51 "genbank_files4": {
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52 "id": "be795001aeb7b4a0",
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53 "src": "hda",
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54 "uuid": "ff11bb17-ed2d-415e-96cf-e5ed35c7d997"
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55 },
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56 "genbank_files5": {
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57 "id": "8fbddce2c6d1629d",
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58 "src": "hda",
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59 "uuid": "5861c673-e009-436c-9020-a23df5356851"
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60 },
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61 "json_use|json_conf": {
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62 "id": "48861e2bb98fa8f3",
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63 "src": "hda",
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64 "uuid": "8ca49aab-9732-422b-bd76-9975c97f5f2a"
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65 }
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66 },
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67 "job_messages": [
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68 {
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69 "code_desc": "",
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70 "desc": "Fatal error: Exit code 1 ()",
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71 "error_level": 3.0,
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72 "exit_code": 1,
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73 "type": "exit_code"
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74 }
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75 ],
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76 "job_metrics": [],
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77 "job_runner_name": null,
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78 "job_stderr": "",
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79 "job_stdout": "",
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80 "model_class": "Job",
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81 "output_collections": {},
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82 "outputs": {
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83 "output": {
1
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84 "id": "cf8d16af14dc294f",
0
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85 "src": "hda",
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86 "uuid": "b5f885e2-68c2-4441-9ade-922799b2cfd6"
0
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87 }
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88 },
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89 "params": {
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90 "__input_ext": "\"input\"",
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91 "chromInfo": "\"/tmp/tmp_qydb9xn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
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92 "dbkey": "\"?\"",
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93 "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}",
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94 "json_generating": "false",
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95 "json_use": "{\"__current_case__\": 1, \"json_conf\": {\"values\": [{\"id\": 6, \"src\": \"hda\"}]}, \"use_json_paramers\": true}"
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96 },
1
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97 "state": "error",
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98 "stderr": "cat: XXXX: No such file or directory\n",
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99 "stdout": "Execution blocked by config (execution = false)\nDEBUG\n",
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100 "tool_id": "seq_to_db",
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101 "tool_stderr": "cat: XXXX: No such file or directory\n",
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102 "tool_stdout": "Execution blocked by config (execution = false)\nDEBUG\n",
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103 "update_time": "2025-07-11T14:13:54.198241",
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104 "user_email": "planemo@galaxyproject.org",
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105 "user_id": "5035e3bab9835d6e"
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106 },
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107 "output_problems": [
1
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108 "Job in error state.. tool_id: seq_to_db, exit_code: 1, stderr: cat: XXXX: No such file or directory\n.",
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109 "Job in error state.. tool_id: seq_to_db, exit_code: 1, stderr: cat: XXXX: No such file or directory\n."
0
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110 ],
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111 "status": "failure",
1
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112 "test_index": 1,
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113 "time_seconds": 28.040581941604614,
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114 "tool_id": "seq_to_db",
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115 "tool_version": "0.2.0+galaxy1"
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116 },
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117 "has_data": true,
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118 "id": "seq_to_db-1"
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119 },
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120 {
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121 "data": {
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122 "inputs": {
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123 "genbank_files": {
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124 "id": "6a141869249298e9",
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125 "src": "hdca"
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126 },
1
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127 "json_use|annotation_column": "annotation",
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128 "json_use|db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",
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129 "json_use|execution_enable": true,
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130 "json_use|fragment_column": "fragment",
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131 "json_use|sequence_column": "sequence",
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132 "json_use|table": "sample",
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133 "json_use|use_json_paramers": false
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134 },
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135 "job": {
1
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136 "command_line": "python '/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py' --input '/tmp/tmp_qydb9xn/files/e/2/4/dataset_e2429fd0-5082-415d-869b-2f7c67516829.dat,/tmp/tmp_qydb9xn/files/8/5/2/dataset_85256206-1030-4b72-bc8d-786951caba8a.dat,/tmp/tmp_qydb9xn/files/d/d/a/dataset_ddae9a40-9b20-4439-8022-532bb18a89a9.dat,/tmp/tmp_qydb9xn/files/1/b/2/dataset_1b2fd1a2-9b4f-42f0-a66c-6d7f5b6d935f.dat,/tmp/tmp_qydb9xn/files/3/a/9/dataset_3a93ffcc-6958-4761-a4c3-1f6e5b64bbb6.dat' --use_json_paramers 'false' --sequence_column 'sequence' --annotation_column 'annotation' --db_uri 'postgresql://postgres:RK17__at__localhost:5432/test_fragments_db' --table 'sample' --fragment_column 'fragment' --execution_enable 'true' --output '/tmp/tmp_qydb9xn/job_working_directory/000/13/outputs/dataset_c78df7ec-701b-4f3e-8081-d63aa4a4ba90.dat' --file_name_mapping '/tmp/tmp_qydb9xn/files/e/2/4/dataset_e2429fd0-5082-415d-869b-2f7c67516829.dat:p7_L7Ae-Weiss.gb,/tmp/tmp_qydb9xn/files/8/5/2/dataset_85256206-1030-4b72-bc8d-786951caba8a.dat:p6_Nt-IgKLsequence.gb,/tmp/tmp_qydb9xn/files/d/d/a/dataset_ddae9a40-9b20-4439-8022-532bb18a89a9.dat:p6_Kozak-ATG.gb,/tmp/tmp_qydb9xn/files/1/b/2/dataset_1b2fd1a2-9b4f-42f0-a66c-6d7f5b6d935f.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmp_qydb9xn/files/3/a/9/dataset_3a93ffcc-6958-4761-a4c3-1f6e5b64bbb6.dat:HC_Amp_ccdB.gb' --json_generating 'true' --json_output '/tmp/tmp_qydb9xn/job_working_directory/000/13/outputs/dataset_705e4a52-0582-42c5-afba-22b1cbe3eb9f.dat' && echo \"DEBUG\" && cat \"/tmp/tmp_qydb9xn/job_working_directory/000/13/outputs/dataset_705e4a52-0582-42c5-afba-22b1cbe3eb9f.dat\"",
0
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137 "command_version": "",
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138 "copied_from_job_id": null,
1
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139 "create_time": "2025-07-11T14:14:15.037467",
0
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140 "dependencies": [
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141 {
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142 "cacheable": false,
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143 "dependency_resolver": {
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144 "auto_init": true,
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145 "auto_install": true,
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146 "can_uninstall_dependencies": true,
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147 "ensure_channels": "conda-forge,bioconda",
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148 "model_class": "CondaDependencyResolver",
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149 "prefix": "/home/rkhaled/miniconda3",
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150 "read_only": false,
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151 "resolver_type": "conda",
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152 "resolves_simple_dependencies": true,
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153 "use_local": false,
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154 "versionless": false
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155 },
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156 "dependency_type": "conda",
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157 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966",
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158 "exact": true,
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159 "model_class": "MergedCondaDependency",
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160 "name": "pandas",
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161 "version": "2.2.3"
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162 },
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163 {
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164 "cacheable": false,
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165 "dependency_resolver": {
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166 "auto_init": true,
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167 "auto_install": true,
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168 "can_uninstall_dependencies": true,
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169 "ensure_channels": "conda-forge,bioconda",
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170 "model_class": "CondaDependencyResolver",
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171 "prefix": "/home/rkhaled/miniconda3",
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172 "read_only": false,
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173 "resolver_type": "conda",
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174 "resolves_simple_dependencies": true,
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175 "use_local": false,
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176 "versionless": false
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177 },
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178 "dependency_type": "conda",
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179 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966",
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180 "exact": true,
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181 "model_class": "MergedCondaDependency",
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182 "name": "sqlalchemy",
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183 "version": "2.0.40"
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184 },
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185 {
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186 "cacheable": false,
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187 "dependency_resolver": {
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188 "auto_init": true,
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189 "auto_install": true,
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190 "can_uninstall_dependencies": true,
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191 "ensure_channels": "conda-forge,bioconda",
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192 "model_class": "CondaDependencyResolver",
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193 "prefix": "/home/rkhaled/miniconda3",
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194 "read_only": false,
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195 "resolver_type": "conda",
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196 "resolves_simple_dependencies": true,
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197 "use_local": false,
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198 "versionless": false
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199 },
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200 "dependency_type": "conda",
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201 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966",
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202 "exact": true,
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203 "model_class": "MergedCondaDependency",
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204 "name": "psycopg2",
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205 "version": "2.9.9"
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206 }
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207 ],
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208 "exit_code": 0,
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209 "external_id": "133675",
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210 "galaxy_version": "25.0",
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211 "handler": null,
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212 "history_id": "6a141869249298e9",
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213 "id": "179da9a21af79ae5",
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214 "inputs": {
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215 "genbank_files1": {
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216 "id": "e058757b81e0ebed",
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217 "src": "hda",
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218 "uuid": "e2429fd0-5082-415d-869b-2f7c67516829"
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219 },
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220 "genbank_files2": {
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221 "id": "10993b807f8c1a73",
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222 "src": "hda",
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223 "uuid": "85256206-1030-4b72-bc8d-786951caba8a"
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224 },
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225 "genbank_files3": {
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226 "id": "d964653210776bae",
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227 "src": "hda",
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228 "uuid": "ddae9a40-9b20-4439-8022-532bb18a89a9"
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229 },
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230 "genbank_files4": {
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231 "id": "1187622ddb220809",
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232 "src": "hda",
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233 "uuid": "1b2fd1a2-9b4f-42f0-a66c-6d7f5b6d935f"
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234 },
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235 "genbank_files5": {
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236 "id": "0ec72b924a1ee71e",
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237 "src": "hda",
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238 "uuid": "3a93ffcc-6958-4761-a4c3-1f6e5b64bbb6"
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239 }
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240 },
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241 "job_messages": [],
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242 "job_metrics": [],
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243 "job_runner_name": null,
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244 "job_stderr": "",
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245 "job_stdout": "",
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246 "model_class": "Job",
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247 "output_collections": {},
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248 "outputs": {
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249 "json_output": {
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250 "id": "8d85a3e6aa2938f6",
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251 "src": "hda",
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252 "uuid": "705e4a52-0582-42c5-afba-22b1cbe3eb9f"
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253 },
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254 "output": {
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255 "id": "179da9a21af79ae5",
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256 "src": "hda",
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257 "uuid": "c78df7ec-701b-4f3e-8081-d63aa4a4ba90"
0
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258 }
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259 },
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260 "params": {
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261 "__input_ext": "\"input\"",
1
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262 "chromInfo": "\"/tmp/tmp_qydb9xn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
0
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263 "dbkey": "\"?\"",
1
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264 "genbank_files": "{\"values\": [{\"id\": 2, \"src\": \"hdca\"}]}",
5db1c2b9edb8 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
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265 "json_generating": "true",
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266 "json_use": "{\"__current_case__\": 0, \"annotation_column\": \"annotation\", \"db_uri\": \"postgresql://postgres:RK17@localhost:5432/test_fragments_db\", \"execution_enable\": true, \"fragment_column\": \"fragment\", \"sequence_column\": \"sequence\", \"table\": \"sample\", \"use_json_paramers\": false}"
0
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267 },
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268 "state": "ok",
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269 "stderr": "",
1
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270 "stdout": "JSON configuration written to: /tmp/tmp_qydb9xn/job_working_directory/000/13/outputs/dataset_705e4a52-0582-42c5-afba-22b1cbe3eb9f.dat\nConnected to database.\nProcessing file: dataset_e2429fd0-5082-415d-869b-2f7c67516829.dat(p7_L7Ae-Weiss)\nProcessing file: dataset_85256206-1030-4b72-bc8d-786951caba8a.dat(p6_Nt-IgKLsequence)\nProcessing file: dataset_ddae9a40-9b20-4439-8022-532bb18a89a9.dat(p6_Kozak-ATG)\nProcessing file: dataset_1b2fd1a2-9b4f-42f0-a66c-6d7f5b6d935f.dat(p4_Kt-L7Ae-Weiss)\nProcessing file: dataset_3a93ffcc-6958-4761-a4c3-1f6e5b64bbb6.dat(HC_Amp_ccdB)\nInserted 5 fragments.\nFragment names written to '/tmp/tmp_qydb9xn/job_working_directory/000/13/outputs/dataset_c78df7ec-701b-4f3e-8081-d63aa4a4ba90.dat'.\nDEBUG\n{\n \"table\": \"sample\",\n \"sequence_column\": \"sequence\",\n \"annotation_column\": \"annotation\",\n \"fragment_column\": \"fragment\",\n \"db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n \"execution\": \"true\"\n}",
0
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271 "tool_id": "seq_to_db",
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272 "tool_stderr": "",
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273 "tool_stdout": "JSON configuration written to: /tmp/tmp_qydb9xn/job_working_directory/000/13/outputs/dataset_705e4a52-0582-42c5-afba-22b1cbe3eb9f.dat\nConnected to database.\nProcessing file: dataset_e2429fd0-5082-415d-869b-2f7c67516829.dat(p7_L7Ae-Weiss)\nProcessing file: dataset_85256206-1030-4b72-bc8d-786951caba8a.dat(p6_Nt-IgKLsequence)\nProcessing file: dataset_ddae9a40-9b20-4439-8022-532bb18a89a9.dat(p6_Kozak-ATG)\nProcessing file: dataset_1b2fd1a2-9b4f-42f0-a66c-6d7f5b6d935f.dat(p4_Kt-L7Ae-Weiss)\nProcessing file: dataset_3a93ffcc-6958-4761-a4c3-1f6e5b64bbb6.dat(HC_Amp_ccdB)\nInserted 5 fragments.\nFragment names written to '/tmp/tmp_qydb9xn/job_working_directory/000/13/outputs/dataset_c78df7ec-701b-4f3e-8081-d63aa4a4ba90.dat'.\nDEBUG\n{\n \"table\": \"sample\",\n \"sequence_column\": \"sequence\",\n \"annotation_column\": \"annotation\",\n \"fragment_column\": \"fragment\",\n \"db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n \"execution\": \"true\"\n}",
5db1c2b9edb8 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
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274 "update_time": "2025-07-11T14:14:21.313512",
0
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275 "user_email": "planemo@galaxyproject.org",
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276 "user_id": "5035e3bab9835d6e"
0
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277 },
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278 "status": "success",
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279 "test_index": 2,
1
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280 "time_seconds": 26.91756534576416,
0
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281 "tool_id": "seq_to_db",
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282 "tool_version": "0.2.0+galaxy1"
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283 },
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284 "has_data": true,
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285 "id": "seq_to_db-2"
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286 }
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287 ],
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288 "version": "0.1"
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289 }