Mercurial > repos > tduigou > seq_to_db

annotate output.json @ 0:178d068648f4 draft

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planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
author tduigou
date Thu, 12 Jun 2025 08:27:18 +0000
parents
children 5db1c2b9edb8
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178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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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": 3,
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5 "num_skips": 0,
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6 "num_tests": 4
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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 "adv|execution_enable": false,
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13 "annotation_column": "annotation",
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14 "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",
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15 "fragment_column": "fragment",
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16 "genbank_files": {
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17 "id": "d1dc40ebed860870",
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18 "src": "hdca"
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19 },
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20 "sequence_column": "sequence",
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21 "table": "sample"
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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": {
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24 "command_line": "python '/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py' --input '/tmp/tmphs5lamwi/files/8/6/d/dataset_86d5129f-932a-4577-895e-245fe4d628fc.dat,/tmp/tmphs5lamwi/files/5/d/a/dataset_5dae2e32-d3f9-4f9b-9732-e6e2d297c2a7.dat,/tmp/tmphs5lamwi/files/0/9/a/dataset_09a835e8-673b-43e3-9bb3-f51c3a727f59.dat,/tmp/tmphs5lamwi/files/3/3/7/dataset_337d084d-9ace-4611-ac83-5ad372068c7f.dat,/tmp/tmphs5lamwi/files/6/f/2/dataset_6f2d701c-7b19-4604-a1ee-a74bd2a57870.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/tmphs5lamwi/job_working_directory/000/6/outputs/dataset_18f1dadc-56f5-4df2-beeb-04c270bb1b29.dat' --file_name_mapping '/tmp/tmphs5lamwi/files/8/6/d/dataset_86d5129f-932a-4577-895e-245fe4d628fc.dat:p7_L7Ae-Weiss.gb,/tmp/tmphs5lamwi/files/5/d/a/dataset_5dae2e32-d3f9-4f9b-9732-e6e2d297c2a7.dat:p6_Nt-IgKLsequence.gb,/tmp/tmphs5lamwi/files/0/9/a/dataset_09a835e8-673b-43e3-9bb3-f51c3a727f59.dat:p6_Kozak-ATG.gb,/tmp/tmphs5lamwi/files/3/3/7/dataset_337d084d-9ace-4611-ac83-5ad372068c7f.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmphs5lamwi/files/6/f/2/dataset_6f2d701c-7b19-4604-a1ee-a74bd2a57870.dat:HC_Amp_ccdB.gb' --json_conf 'None' --execution_enable 'false'",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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25 "command_version": "",
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26 "copied_from_job_id": null,
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27 "create_time": "2025-06-12T08:11:40.445752",
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28 "dependencies": [],
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29 "exit_code": 0,
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30 "external_id": "126337",
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31 "galaxy_version": "24.2",
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32 "handler": null,
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33 "history_id": "d1dc40ebed860870",
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34 "id": "9b05862cf50a24d4",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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35 "inputs": {
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36 "genbank_files1": {
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37 "id": "d1dc40ebed860870",
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38 "src": "hda",
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39 "uuid": "86d5129f-932a-4577-895e-245fe4d628fc"
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40 },
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41 "genbank_files2": {
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42 "id": "8a8d0bbb0c3dafa4",
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43 "src": "hda",
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44 "uuid": "5dae2e32-d3f9-4f9b-9732-e6e2d297c2a7"
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45 },
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46 "genbank_files3": {
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47 "id": "bf0fa404613c4f02",
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48 "src": "hda",
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49 "uuid": "09a835e8-673b-43e3-9bb3-f51c3a727f59"
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50 },
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51 "genbank_files4": {
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52 "id": "f71740853e0eea8f",
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53 "src": "hda",
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54 "uuid": "337d084d-9ace-4611-ac83-5ad372068c7f"
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55 },
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56 "genbank_files5": {
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57 "id": "5f099fbe1e7e1218",
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58 "src": "hda",
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59 "uuid": "6f2d701c-7b19-4604-a1ee-a74bd2a57870"
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60 }
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61 },
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62 "job_messages": [],
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63 "job_metrics": [],
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64 "job_runner_name": null,
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65 "job_stderr": "",
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66 "job_stdout": "",
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67 "model_class": "Job",
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68 "output_collections": {},
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69 "outputs": {
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70 "output": {
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71 "id": "9b05862cf50a24d4",
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72 "src": "hda",
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73 "uuid": "18f1dadc-56f5-4df2-beeb-04c270bb1b29"
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74 }
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75 },
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76 "params": {
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77 "__input_ext": "\"input\"",
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78 "adv": "{\"execution_enable\": false, \"json_conf\": null}",
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79 "annotation_column": "\"annotation\"",
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80 "chromInfo": "\"/tmp/tmphs5lamwi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
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81 "db_uri": "\"postgresql://postgres:RK17@localhost:5432/test_fragments_db\"",
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82 "dbkey": "\"?\"",
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83 "fragment_column": "\"fragment\"",
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84 "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}",
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85 "sequence_column": "\"sequence\"",
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86 "table": "\"sample\""
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87 },
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88 "state": "ok",
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89 "stderr": "",
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90 "stdout": "Execution disabled because sequence_column is set to 'false'.\n",
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91 "tool_id": "seq_to_db",
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92 "tool_stderr": "",
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93 "tool_stdout": "Execution disabled because sequence_column is set to 'false'.\n",
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94 "update_time": "2025-06-12T08:11:46.862307",
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95 "user_email": "planemo@galaxyproject.org",
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96 "user_id": "d1dc40ebed860870"
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97 },
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98 "output_problems": [
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99 "Output output: different than expected\nExpected 5+-0 lines in the output found 0"
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100 ],
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101 "status": "failure",
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102 "test_index": 0,
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103 "time_seconds": 26.20578122138977,
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104 "tool_id": "seq_to_db",
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105 "tool_version": "0.1.0+galaxy0"
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106 },
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107 "has_data": true,
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108 "id": "seq_to_db-0"
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109 },
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110 {
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111 "data": {
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112 "inputs": {
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113 "adv|json_conf": {
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114 "id": "faf36c8bb3bbf1fc",
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115 "src": "hda"
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116 },
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117 "genbank_files": {
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118 "id": "8a8d0bbb0c3dafa4",
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119 "src": "hdca"
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120 }
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121 },
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122 "job": {
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123 "command_line": "python '/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py' --input '/tmp/tmphs5lamwi/files/2/b/e/dataset_2be2db07-173c-45ff-94a0-3461122df268.dat,/tmp/tmphs5lamwi/files/f/1/5/dataset_f1590ccd-1d12-4f95-98b0-fcc4b2cbc80e.dat,/tmp/tmphs5lamwi/files/8/c/2/dataset_8c22a014-8cf2-4575-ae96-c85556a689fb.dat,/tmp/tmphs5lamwi/files/7/f/b/dataset_7fb30eee-10c8-4d84-932e-28f674b1dfc4.dat,/tmp/tmphs5lamwi/files/4/f/b/dataset_4fb6ab60-c194-420f-b10f-de2aa2086638.dat' --sequence_column '' --annotation_column '' --db_uri '' --table '' --fragment_column '' --output '/tmp/tmphs5lamwi/job_working_directory/000/13/outputs/dataset_1370843e-a97d-4de9-84c1-8965359a1401.dat' --file_name_mapping '/tmp/tmphs5lamwi/files/2/b/e/dataset_2be2db07-173c-45ff-94a0-3461122df268.dat:p7_L7Ae-Weiss.gb,/tmp/tmphs5lamwi/files/f/1/5/dataset_f1590ccd-1d12-4f95-98b0-fcc4b2cbc80e.dat:p6_Nt-IgKLsequence.gb,/tmp/tmphs5lamwi/files/8/c/2/dataset_8c22a014-8cf2-4575-ae96-c85556a689fb.dat:p6_Kozak-ATG.gb,/tmp/tmphs5lamwi/files/7/f/b/dataset_7fb30eee-10c8-4d84-932e-28f674b1dfc4.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmphs5lamwi/files/4/f/b/dataset_4fb6ab60-c194-420f-b10f-de2aa2086638.dat:HC_Amp_ccdB.gb' --json_conf '/tmp/tmphs5lamwi/files/d/0/0/dataset_d00d7320-cfff-4799-af9d-476da677e0c1.dat' --execution_enable 'true'",
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124 "command_version": "",
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125 "copied_from_job_id": null,
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126 "create_time": "2025-06-12T08:12:07.955341",
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127 "dependencies": [
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128 {
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129 "cacheable": false,
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130 "dependency_resolver": {
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131 "auto_init": true,
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132 "auto_install": true,
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133 "can_uninstall_dependencies": true,
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134 "ensure_channels": "conda-forge,bioconda",
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135 "model_class": "CondaDependencyResolver",
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136 "prefix": "/home/rkhaled/miniconda3",
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137 "read_only": false,
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138 "resolver_type": "conda",
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139 "resolves_simple_dependencies": true,
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140 "use_local": false,
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141 "versionless": false
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142 },
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143 "dependency_type": "conda",
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144 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966",
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145 "exact": true,
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146 "model_class": "MergedCondaDependency",
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147 "name": "pandas",
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148 "version": "2.2.3"
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149 },
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150 {
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151 "cacheable": false,
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152 "dependency_resolver": {
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153 "auto_init": true,
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154 "auto_install": true,
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155 "can_uninstall_dependencies": true,
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156 "ensure_channels": "conda-forge,bioconda",
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157 "model_class": "CondaDependencyResolver",
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158 "prefix": "/home/rkhaled/miniconda3",
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159 "read_only": false,
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160 "resolver_type": "conda",
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161 "resolves_simple_dependencies": true,
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162 "use_local": false,
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163 "versionless": false
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164 },
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165 "dependency_type": "conda",
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166 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966",
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167 "exact": true,
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168 "model_class": "MergedCondaDependency",
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169 "name": "sqlalchemy",
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170 "version": "2.0.40"
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171 },
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172 {
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173 "cacheable": false,
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174 "dependency_resolver": {
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175 "auto_init": true,
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176 "auto_install": true,
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177 "can_uninstall_dependencies": true,
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178 "ensure_channels": "conda-forge,bioconda",
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179 "model_class": "CondaDependencyResolver",
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180 "prefix": "/home/rkhaled/miniconda3",
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181 "read_only": false,
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182 "resolver_type": "conda",
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183 "resolves_simple_dependencies": true,
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184 "use_local": false,
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185 "versionless": false
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186 },
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187 "dependency_type": "conda",
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188 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966",
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189 "exact": true,
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190 "model_class": "MergedCondaDependency",
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191 "name": "psycopg2",
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192 "version": "2.9.9"
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193 }
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194 ],
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195 "exit_code": 0,
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196 "external_id": "126847",
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197 "galaxy_version": "24.2",
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198 "handler": null,
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199 "history_id": "8a8d0bbb0c3dafa4",
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200 "id": "e932b28e673f61fd",
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201 "inputs": {
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202 "adv|json_conf": {
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203 "id": "faf36c8bb3bbf1fc",
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204 "src": "hda",
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205 "uuid": "d00d7320-cfff-4799-af9d-476da677e0c1"
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206 },
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207 "genbank_files1": {
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208 "id": "17b31bc27bcedfbf",
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209 "src": "hda",
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210 "uuid": "2be2db07-173c-45ff-94a0-3461122df268"
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211 },
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212 "genbank_files2": {
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213 "id": "5a37da6eaa46c4f4",
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214 "src": "hda",
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215 "uuid": "f1590ccd-1d12-4f95-98b0-fcc4b2cbc80e"
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216 },
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217 "genbank_files3": {
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218 "id": "8d24f24cec97882b",
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219 "src": "hda",
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220 "uuid": "8c22a014-8cf2-4575-ae96-c85556a689fb"
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221 },
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222 "genbank_files4": {
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223 "id": "07e58d3b99df4277",
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224 "src": "hda",
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225 "uuid": "7fb30eee-10c8-4d84-932e-28f674b1dfc4"
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226 },
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227 "genbank_files5": {
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228 "id": "80d24c12e045669e",
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229 "src": "hda",
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230 "uuid": "4fb6ab60-c194-420f-b10f-de2aa2086638"
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231 }
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232 },
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233 "job_messages": [],
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234 "job_metrics": [],
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235 "job_runner_name": null,
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236 "job_stderr": "",
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237 "job_stdout": "",
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238 "model_class": "Job",
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239 "output_collections": {},
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240 "outputs": {
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241 "output": {
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242 "id": "e932b28e673f61fd",
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243 "src": "hda",
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244 "uuid": "1370843e-a97d-4de9-84c1-8965359a1401"
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245 }
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246 },
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247 "params": {
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248 "__input_ext": "\"input\"",
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249 "adv": "{\"execution_enable\": true, \"json_conf\": {\"values\": [{\"id\": 12, \"src\": \"hda\"}]}}",
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250 "annotation_column": null,
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251 "chromInfo": "\"/tmp/tmphs5lamwi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
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252 "db_uri": null,
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253 "dbkey": "\"?\"",
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254 "fragment_column": null,
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255 "genbank_files": "{\"values\": [{\"id\": 2, \"src\": \"hdca\"}]}",
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256 "sequence_column": null,
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257 "table": null
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258 },
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259 "state": "ok",
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260 "stderr": "",
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261 "stdout": "Execution was blocked by config (execution = false)\n",
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262 "tool_id": "seq_to_db",
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263 "tool_stderr": "",
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264 "tool_stdout": "Execution was blocked by config (execution = false)\n",
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265 "update_time": "2025-06-12T08:12:14.967090",
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266 "user_email": "planemo@galaxyproject.org",
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267 "user_id": "d1dc40ebed860870"
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268 },
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269 "output_problems": [
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270 "Output output: different than expected\nExpected 5+-0 lines in the output found 0"
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271 ],
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272 "status": "failure",
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273 "test_index": 1,
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274 "time_seconds": 28.067287921905518,
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275 "tool_id": "seq_to_db",
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276 "tool_version": "0.1.0+galaxy0"
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277 },
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278 "has_data": true,
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279 "id": "seq_to_db-1"
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280 },
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281 {
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282 "data": {
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283 "inputs": {
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284 "annotation_column": "annotation",
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285 "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",
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286 "fragment_column": "fragment",
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287 "genbank_files": {
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288 "id": "bf0fa404613c4f02",
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289 "src": "hdca"
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290 },
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291 "sequence_column": "sequence",
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292 "table": "sample"
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293 },
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294 "job": {
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295 "command_line": "python '/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py' --input '/tmp/tmphs5lamwi/files/1/5/a/dataset_15a3a402-8761-43db-81ae-e4bb3f2d41d8.dat,/tmp/tmphs5lamwi/files/0/2/6/dataset_02636863-d06d-46bb-bcd3-c22b162ad92c.dat,/tmp/tmphs5lamwi/files/0/6/a/dataset_06a85205-3621-425b-8eca-56f44a3ceaed.dat,/tmp/tmphs5lamwi/files/5/7/a/dataset_57afe769-fe76-4890-9c62-c2014ecf8529.dat,/tmp/tmphs5lamwi/files/2/a/a/dataset_2aaaf350-bb2f-4390-81e3-6eeeaae0481e.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/tmphs5lamwi/job_working_directory/000/19/outputs/dataset_168a000a-8805-4f1d-918e-4ebbd60fd654.dat' --file_name_mapping '/tmp/tmphs5lamwi/files/1/5/a/dataset_15a3a402-8761-43db-81ae-e4bb3f2d41d8.dat:p7_L7Ae-Weiss.gb,/tmp/tmphs5lamwi/files/0/2/6/dataset_02636863-d06d-46bb-bcd3-c22b162ad92c.dat:p6_Nt-IgKLsequence.gb,/tmp/tmphs5lamwi/files/0/6/a/dataset_06a85205-3621-425b-8eca-56f44a3ceaed.dat:p6_Kozak-ATG.gb,/tmp/tmphs5lamwi/files/5/7/a/dataset_57afe769-fe76-4890-9c62-c2014ecf8529.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmphs5lamwi/files/2/a/a/dataset_2aaaf350-bb2f-4390-81e3-6eeeaae0481e.dat:HC_Amp_ccdB.gb' --json_conf 'None' --execution_enable 'true'",
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296 "command_version": "",
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297 "copied_from_job_id": null,
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298 "create_time": "2025-06-12T08:12:35.708354",
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299 "dependencies": [
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300 {
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301 "cacheable": false,
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302 "dependency_resolver": {
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303 "auto_init": true,
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304 "auto_install": true,
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305 "can_uninstall_dependencies": true,
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306 "ensure_channels": "conda-forge,bioconda",
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307 "model_class": "CondaDependencyResolver",
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308 "prefix": "/home/rkhaled/miniconda3",
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309 "read_only": false,
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310 "resolver_type": "conda",
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311 "resolves_simple_dependencies": true,
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312 "use_local": false,
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313 "versionless": false
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314 },
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315 "dependency_type": "conda",
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316 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966",
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317 "exact": true,
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318 "model_class": "MergedCondaDependency",
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319 "name": "pandas",
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320 "version": "2.2.3"
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321 },
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322 {
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323 "cacheable": false,
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324 "dependency_resolver": {
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325 "auto_init": true,
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326 "auto_install": true,
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327 "can_uninstall_dependencies": true,
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328 "ensure_channels": "conda-forge,bioconda",
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329 "model_class": "CondaDependencyResolver",
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330 "prefix": "/home/rkhaled/miniconda3",
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331 "read_only": false,
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332 "resolver_type": "conda",
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333 "resolves_simple_dependencies": true,
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334 "use_local": false,
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335 "versionless": false
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336 },
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337 "dependency_type": "conda",
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338 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966",
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339 "exact": true,
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340 "model_class": "MergedCondaDependency",
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341 "name": "sqlalchemy",
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342 "version": "2.0.40"
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343 },
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344 {
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345 "cacheable": false,
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346 "dependency_resolver": {
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347 "auto_init": true,
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348 "auto_install": true,
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349 "can_uninstall_dependencies": true,
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350 "ensure_channels": "conda-forge,bioconda",
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351 "model_class": "CondaDependencyResolver",
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352 "prefix": "/home/rkhaled/miniconda3",
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353 "read_only": false,
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354 "resolver_type": "conda",
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355 "resolves_simple_dependencies": true,
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diff changeset
356 "use_local": false,
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diff changeset
357 "versionless": false
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358 },
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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359 "dependency_type": "conda",
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diff changeset
360 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
361 "exact": true,
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diff changeset
362 "model_class": "MergedCondaDependency",
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diff changeset
363 "name": "psycopg2",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
364 "version": "2.9.9"
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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365 }
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
366 ],
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
367 "exit_code": 0,
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diff changeset
368 "external_id": "127455",
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369 "galaxy_version": "24.2",
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diff changeset
370 "handler": null,
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diff changeset
371 "history_id": "bf0fa404613c4f02",
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diff changeset
372 "id": "48ac62a10b51b648",
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diff changeset
373 "inputs": {
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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374 "genbank_files1": {
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
375 "id": "9863db5e96bd9ae2",
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diff changeset
376 "src": "hda",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
377 "uuid": "15a3a402-8761-43db-81ae-e4bb3f2d41d8"
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diff changeset
378 },
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
379 "genbank_files2": {
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
380 "id": "c55450b682f38454",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
381 "src": "hda",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
382 "uuid": "02636863-d06d-46bb-bcd3-c22b162ad92c"
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
383 },
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
384 "genbank_files3": {
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
385 "id": "b2f6887fdac0a65b",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
386 "src": "hda",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
387 "uuid": "06a85205-3621-425b-8eca-56f44a3ceaed"
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
388 },
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
389 "genbank_files4": {
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
390 "id": "f5829ca36951d902",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
391 "src": "hda",
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diff changeset
392 "uuid": "57afe769-fe76-4890-9c62-c2014ecf8529"
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
393 },
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
394 "genbank_files5": {
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
395 "id": "baef710e55d31add",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
396 "src": "hda",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
397 "uuid": "2aaaf350-bb2f-4390-81e3-6eeeaae0481e"
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
398 }
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
399 },
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
400 "job_messages": [],
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diff changeset
401 "job_metrics": [],
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
402 "job_runner_name": null,
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
403 "job_stderr": "",
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diff changeset
404 "job_stdout": "",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
405 "model_class": "Job",
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diff changeset
406 "output_collections": {},
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diff changeset
407 "outputs": {
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diff changeset
408 "output": {
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diff changeset
409 "id": "48ac62a10b51b648",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
410 "src": "hda",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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411 "uuid": "168a000a-8805-4f1d-918e-4ebbd60fd654"
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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412 }
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
413 },
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
414 "params": {
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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415 "__input_ext": "\"input\"",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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416 "adv": "{\"execution_enable\": true, \"json_conf\": null}",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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417 "annotation_column": "\"annotation\"",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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418 "chromInfo": "\"/tmp/tmphs5lamwi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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419 "db_uri": "\"postgresql://postgres:RK17@localhost:5432/test_fragments_db\"",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
420 "dbkey": "\"?\"",
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421 "fragment_column": "\"fragment\"",
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422 "genbank_files": "{\"values\": [{\"id\": 3, \"src\": \"hdca\"}]}",
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423 "sequence_column": "\"sequence\"",
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424 "table": "\"sample\""
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diff changeset
425 },
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
426 "state": "ok",
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diff changeset
427 "stderr": "",
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428 "stdout": "Connected to database.\nProcessing file: dataset_15a3a402-8761-43db-81ae-e4bb3f2d41d8.dat(p7_L7Ae-Weiss)\nProcessing file: dataset_02636863-d06d-46bb-bcd3-c22b162ad92c.dat(p6_Nt-IgKLsequence)\nProcessing file: dataset_06a85205-3621-425b-8eca-56f44a3ceaed.dat(p6_Kozak-ATG)\nProcessing file: dataset_57afe769-fe76-4890-9c62-c2014ecf8529.dat(p4_Kt-L7Ae-Weiss)\nProcessing file: dataset_2aaaf350-bb2f-4390-81e3-6eeeaae0481e.dat(HC_Amp_ccdB)\nInserted 5 fragments.\nFragment names written to '/tmp/tmphs5lamwi/job_working_directory/000/19/outputs/dataset_168a000a-8805-4f1d-918e-4ebbd60fd654.dat'.\n",
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429 "tool_id": "seq_to_db",
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diff changeset
430 "tool_stderr": "",
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431 "tool_stdout": "Connected to database.\nProcessing file: dataset_15a3a402-8761-43db-81ae-e4bb3f2d41d8.dat(p7_L7Ae-Weiss)\nProcessing file: dataset_02636863-d06d-46bb-bcd3-c22b162ad92c.dat(p6_Nt-IgKLsequence)\nProcessing file: dataset_06a85205-3621-425b-8eca-56f44a3ceaed.dat(p6_Kozak-ATG)\nProcessing file: dataset_57afe769-fe76-4890-9c62-c2014ecf8529.dat(p4_Kt-L7Ae-Weiss)\nProcessing file: dataset_2aaaf350-bb2f-4390-81e3-6eeeaae0481e.dat(HC_Amp_ccdB)\nInserted 5 fragments.\nFragment names written to '/tmp/tmphs5lamwi/job_working_directory/000/19/outputs/dataset_168a000a-8805-4f1d-918e-4ebbd60fd654.dat'.\n",
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432 "update_time": "2025-06-12T08:12:41.972140",
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433 "user_email": "planemo@galaxyproject.org",
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diff changeset
434 "user_id": "d1dc40ebed860870"
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diff changeset
435 },
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
436 "status": "success",
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437 "test_index": 2,
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diff changeset
438 "time_seconds": 27.17548680305481,
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diff changeset
439 "tool_id": "seq_to_db",
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diff changeset
440 "tool_version": "0.1.0+galaxy0"
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441 },
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diff changeset
442 "has_data": true,
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443 "id": "seq_to_db-2"
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444 },
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
445 {
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446 "data": {
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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447 "inputs": {
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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448 "adv|json_conf": {
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449 "id": "81096e298c6cd33b",
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450 "src": "hda"
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451 },
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452 "genbank_files": {
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453 "id": "f71740853e0eea8f",
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diff changeset
454 "src": "hdca"
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455 }
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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456 },
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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457 "job": {
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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458 "command_line": "python '/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py' --input '/tmp/tmphs5lamwi/files/7/7/d/dataset_77d5679d-4fb4-4b27-afe7-930f4b3d6076.dat,/tmp/tmphs5lamwi/files/5/1/a/dataset_51ae04ed-e634-4f46-ae13-0ce31dbacc37.dat,/tmp/tmphs5lamwi/files/c/6/4/dataset_c64f9b84-cf82-4b1b-96cb-3f98f0fda7a9.dat,/tmp/tmphs5lamwi/files/e/f/7/dataset_ef7a853c-dc0e-47dc-bf52-6f45291358b1.dat,/tmp/tmphs5lamwi/files/1/3/a/dataset_13a4680c-d654-45d9-bdab-75dca91c36da.dat' --sequence_column '' --annotation_column '' --db_uri '' --table '' --fragment_column '' --output '/tmp/tmphs5lamwi/job_working_directory/000/26/outputs/dataset_431acc98-f2ee-4e32-876a-33ef788c7eeb.dat' --file_name_mapping '/tmp/tmphs5lamwi/files/7/7/d/dataset_77d5679d-4fb4-4b27-afe7-930f4b3d6076.dat:p7_L7Ae-Weiss.gb,/tmp/tmphs5lamwi/files/5/1/a/dataset_51ae04ed-e634-4f46-ae13-0ce31dbacc37.dat:p6_Nt-IgKLsequence.gb,/tmp/tmphs5lamwi/files/c/6/4/dataset_c64f9b84-cf82-4b1b-96cb-3f98f0fda7a9.dat:p6_Kozak-ATG.gb,/tmp/tmphs5lamwi/files/e/f/7/dataset_ef7a853c-dc0e-47dc-bf52-6f45291358b1.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmphs5lamwi/files/1/3/a/dataset_13a4680c-d654-45d9-bdab-75dca91c36da.dat:HC_Amp_ccdB.gb' --json_conf '/tmp/tmphs5lamwi/files/1/6/8/dataset_1681d2f4-591b-48a4-a469-0b6d9d29897b.dat' --execution_enable 'true'",
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459 "command_version": "",
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460 "copied_from_job_id": null,
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461 "create_time": "2025-06-12T08:13:02.907605",
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462 "dependencies": [
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463 {
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464 "cacheable": false,
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465 "dependency_resolver": {
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466 "auto_init": true,
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diff changeset
467 "auto_install": true,
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468 "can_uninstall_dependencies": true,
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469 "ensure_channels": "conda-forge,bioconda",
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470 "model_class": "CondaDependencyResolver",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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471 "prefix": "/home/rkhaled/miniconda3",
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472 "read_only": false,
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diff changeset
473 "resolver_type": "conda",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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474 "resolves_simple_dependencies": true,
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diff changeset
475 "use_local": false,
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diff changeset
476 "versionless": false
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477 },
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
478 "dependency_type": "conda",
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diff changeset
479 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
480 "exact": true,
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481 "model_class": "MergedCondaDependency",
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482 "name": "pandas",
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483 "version": "2.2.3"
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484 },
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diff changeset
485 {
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diff changeset
486 "cacheable": false,
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diff changeset
487 "dependency_resolver": {
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diff changeset
488 "auto_init": true,
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489 "auto_install": true,
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490 "can_uninstall_dependencies": true,
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491 "ensure_channels": "conda-forge,bioconda",
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492 "model_class": "CondaDependencyResolver",
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493 "prefix": "/home/rkhaled/miniconda3",
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494 "read_only": false,
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diff changeset
495 "resolver_type": "conda",
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496 "resolves_simple_dependencies": true,
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497 "use_local": false,
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498 "versionless": false
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499 },
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500 "dependency_type": "conda",
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501 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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502 "exact": true,
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diff changeset
503 "model_class": "MergedCondaDependency",
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504 "name": "sqlalchemy",
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diff changeset
505 "version": "2.0.40"
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diff changeset
506 },
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diff changeset
507 {
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diff changeset
508 "cacheable": false,
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509 "dependency_resolver": {
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diff changeset
510 "auto_init": true,
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511 "auto_install": true,
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512 "can_uninstall_dependencies": true,
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513 "ensure_channels": "conda-forge,bioconda",
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514 "model_class": "CondaDependencyResolver",
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515 "prefix": "/home/rkhaled/miniconda3",
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516 "read_only": false,
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diff changeset
517 "resolver_type": "conda",
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diff changeset
518 "resolves_simple_dependencies": true,
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diff changeset
519 "use_local": false,
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diff changeset
520 "versionless": false
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diff changeset
521 },
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522 "dependency_type": "conda",
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523 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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diff changeset
524 "exact": true,
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525 "model_class": "MergedCondaDependency",
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526 "name": "psycopg2",
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527 "version": "2.9.9"
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diff changeset
528 }
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
529 ],
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
530 "exit_code": 1,
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
531 "external_id": "127952",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
532 "galaxy_version": "24.2",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
533 "handler": null,
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
534 "history_id": "f71740853e0eea8f",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
535 "id": "ae7479dd630bf125",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
536 "inputs": {
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
537 "adv|json_conf": {
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
538 "id": "81096e298c6cd33b",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
539 "src": "hda",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
540 "uuid": "1681d2f4-591b-48a4-a469-0b6d9d29897b"
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
541 },
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
542 "genbank_files1": {
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
543 "id": "4bb85627388cf8ba",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
544 "src": "hda",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
545 "uuid": "77d5679d-4fb4-4b27-afe7-930f4b3d6076"
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
546 },
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
547 "genbank_files2": {
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
548 "id": "00078d50fa80d7bb",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
549 "src": "hda",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
550 "uuid": "51ae04ed-e634-4f46-ae13-0ce31dbacc37"
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
551 },
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
552 "genbank_files3": {
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
553 "id": "221d11c5cc4eab13",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
554 "src": "hda",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
555 "uuid": "c64f9b84-cf82-4b1b-96cb-3f98f0fda7a9"
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
556 },
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
557 "genbank_files4": {
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
558 "id": "bc838ca4b455c7c4",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
559 "src": "hda",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
560 "uuid": "ef7a853c-dc0e-47dc-bf52-6f45291358b1"
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
561 },
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
562 "genbank_files5": {
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
563 "id": "04052285d124af02",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
564 "src": "hda",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
565 "uuid": "13a4680c-d654-45d9-bdab-75dca91c36da"
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
566 }
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
567 },
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
568 "job_messages": [
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
569 {
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
570 "code_desc": "",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
571 "desc": "Fatal error: Exit code 1 ()",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
572 "error_level": 3,
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
573 "exit_code": 1,
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
574 "type": "exit_code"
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
575 }
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
576 ],
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
577 "job_metrics": [],
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
578 "job_runner_name": null,
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
579 "job_stderr": "",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
580 "job_stdout": "",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
581 "model_class": "Job",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
582 "output_collections": {},
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
583 "outputs": {
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
584 "output": {
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
585 "id": "ae7479dd630bf125",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
586 "src": "hda",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
587 "uuid": "431acc98-f2ee-4e32-876a-33ef788c7eeb"
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
588 }
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
589 },
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
590 "params": {
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
591 "__input_ext": "\"input\"",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
592 "adv": "{\"execution_enable\": true, \"json_conf\": {\"values\": [{\"id\": 25, \"src\": \"hda\"}]}}",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
593 "annotation_column": null,
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
594 "chromInfo": "\"/tmp/tmphs5lamwi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
595 "db_uri": null,
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
596 "dbkey": "\"?\"",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
597 "fragment_column": null,
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
598 "genbank_files": "{\"values\": [{\"id\": 4, \"src\": \"hdca\"}]}",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
599 "sequence_column": null,
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
600 "table": null
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
601 },
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
602 "state": "error",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
603 "stderr": "Traceback (most recent call last):\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 273, in <module>\n main()\n ~~~~^^\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 260, in main\n push_gb_annotations(\n ~~~~~~~~~~~~~~~~~~~^\n gb_file_list,\n ^^^^^^^^^^^^^\n ...<6 lines>...\n args.file_name_mapping\n ^^^^^^^^^^^^^^^^^^^^^^\n )\n ^\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 148, in push_gb_annotations\n raise RuntimeError(f\"Fatal Error: Fragment '{fragment_name}' already exists in DB. Stopping the process.\")\nRuntimeError: Fatal Error: Fragment 'p7_L7Ae-Weiss' already exists in DB. Stopping the process.\n",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
604 "stdout": "Connected to database.\nProcessing file: dataset_77d5679d-4fb4-4b27-afe7-930f4b3d6076.dat(p7_L7Ae-Weiss)\nError during GB file insertion: Fatal Error: Fragment 'p7_L7Ae-Weiss' already exists in DB. Stopping the process.\n",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
605 "tool_id": "seq_to_db",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
606 "tool_stderr": "Traceback (most recent call last):\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 273, in <module>\n main()\n ~~~~^^\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 260, in main\n push_gb_annotations(\n ~~~~~~~~~~~~~~~~~~~^\n gb_file_list,\n ^^^^^^^^^^^^^\n ...<6 lines>...\n args.file_name_mapping\n ^^^^^^^^^^^^^^^^^^^^^^\n )\n ^\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 148, in push_gb_annotations\n raise RuntimeError(f\"Fatal Error: Fragment '{fragment_name}' already exists in DB. Stopping the process.\")\nRuntimeError: Fatal Error: Fragment 'p7_L7Ae-Weiss' already exists in DB. Stopping the process.\n",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
607 "tool_stdout": "Connected to database.\nProcessing file: dataset_77d5679d-4fb4-4b27-afe7-930f4b3d6076.dat(p7_L7Ae-Weiss)\nError during GB file insertion: Fatal Error: Fragment 'p7_L7Ae-Weiss' already exists in DB. Stopping the process.\n",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
608 "update_time": "2025-06-12T08:13:09.078361",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
609 "user_email": "planemo@galaxyproject.org",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
610 "user_id": "d1dc40ebed860870"
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
611 },
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
612 "output_problems": [
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
613 "Job in error state.. tool_id: seq_to_db, exit_code: 1, stderr: Traceback (most recent call last):\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 273, in <module>\n main()\n ~~~~^^\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 260, in main\n push_gb_annotations(\n ~~~~~~~~~~~~~~~~~~~^\n gb_file_list,\n ^^^^^^^^^^^^^\n ...<6 lines>...\n args.file_name_mapping\n ^^^^^^^^^^^^^^^^^^^^^^\n )\n ^\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 148, in push_gb_annotations\n raise RuntimeError(f\"Fatal Error: Fragment '{fragment_name}' already exists in DB. Stopping the process.\")\nRuntimeError: Fatal Error: Fragment 'p7_L7Ae-Weiss' already exists in DB. Stopping the process.\n.",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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614 "Job in error state.. tool_id: seq_to_db, exit_code: 1, stderr: Traceback (most recent call last):\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 273, in <module>\n main()\n ~~~~^^\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 260, in main\n push_gb_annotations(\n ~~~~~~~~~~~~~~~~~~~^\n gb_file_list,\n ^^^^^^^^^^^^^\n ...<6 lines>...\n args.file_name_mapping\n ^^^^^^^^^^^^^^^^^^^^^^\n )\n ^\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 148, in push_gb_annotations\n raise RuntimeError(f\"Fatal Error: Fragment '{fragment_name}' already exists in DB. Stopping the process.\")\nRuntimeError: Fatal Error: Fragment 'p7_L7Ae-Weiss' already exists in DB. Stopping the process.\n."
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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615 ],
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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616 "status": "failure",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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617 "test_index": 3,
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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618 "time_seconds": 26.706940174102783,
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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619 "tool_id": "seq_to_db",
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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620 "tool_version": "0.1.0+galaxy0"
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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621 },
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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622 "has_data": true,
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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623 "id": "seq_to_db-3"
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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624 }
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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625 ],
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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626 "version": "0.1"
178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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627 }