# HG changeset patch
# User tduigou
# Date 1749719054 0
# Node ID 3daf04425ea16fe78918514271b4a50eda0693bb
# Parent 9f845ccb1a9fb1c74910623f8e3480b1c801be2c
planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
diff -r 9f845ccb1a9f -r 3daf04425ea1 output.html
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+++ b/output.html Thu Jun 12 09:04:14 2025 +0000
@@ -0,0 +1,291 @@
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+ Test Results (powered by Planemo)
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\ No newline at end of file
diff -r 9f845ccb1a9f -r 3daf04425ea1 output.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/output.json Thu Jun 12 09:04:14 2025 +0000
@@ -0,0 +1,627 @@
+{
+ "summary": {
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+ "num_failures": 3,
+ "num_skips": 0,
+ "num_tests": 4
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+ "tests": [
+ {
+ "data": {
+ "inputs": {
+ "adv|execution_enable": false,
+ "annotation_column": "annotation",
+ "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",
+ "fragment_column": "fragment",
+ "genbank_files": {
+ "id": "d1dc40ebed860870",
+ "src": "hdca"
+ },
+ "sequence_column": "sequence",
+ "table": "sample"
+ },
+ "job": {
+ "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'",
+ "command_version": "",
+ "copied_from_job_id": null,
+ "create_time": "2025-06-12T08:11:40.445752",
+ "dependencies": [],
+ "exit_code": 0,
+ "external_id": "126337",
+ "galaxy_version": "24.2",
+ "handler": null,
+ "history_id": "d1dc40ebed860870",
+ "id": "9b05862cf50a24d4",
+ "inputs": {
+ "genbank_files1": {
+ "id": "d1dc40ebed860870",
+ "src": "hda",
+ "uuid": "86d5129f-932a-4577-895e-245fe4d628fc"
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+ "src": "hda",
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+ "genbank_files": {
+ "id": "8a8d0bbb0c3dafa4",
+ "src": "hdca"
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+ "job": {
+ "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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+ "exact": true,
+ "model_class": "MergedCondaDependency",
+ "name": "pandas",
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+ "ensure_channels": "conda-forge,bioconda",
+ "model_class": "CondaDependencyResolver",
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+ "exact": true,
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+ "history_id": "8a8d0bbb0c3dafa4",
+ "id": "e932b28e673f61fd",
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+ "genbank_files5": {
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+ "adv": "{\"execution_enable\": true, \"json_conf\": {\"values\": [{\"id\": 12, \"src\": \"hda\"}]}}",
+ "annotation_column": null,
+ "chromInfo": "\"/tmp/tmphs5lamwi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+ "db_uri": null,
+ "dbkey": "\"?\"",
+ "fragment_column": null,
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+ "table": null
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+ "stdout": "Execution was blocked by config (execution = false)\n",
+ "tool_id": "seq_to_db",
+ "tool_stderr": "",
+ "tool_stdout": "Execution was blocked by config (execution = false)\n",
+ "update_time": "2025-06-12T08:12:14.967090",
+ "user_email": "planemo@galaxyproject.org",
+ "user_id": "d1dc40ebed860870"
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+ "output_problems": [
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+ "status": "failure",
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+ "time_seconds": 28.067287921905518,
+ "tool_id": "seq_to_db",
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+ "has_data": true,
+ "id": "seq_to_db-1"
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+ {
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+ "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",
+ "fragment_column": "fragment",
+ "genbank_files": {
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+ "src": "hdca"
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+ "job": {
+ "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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+ "uuid": "02636863-d06d-46bb-bcd3-c22b162ad92c"
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+ "src": "hda",
+ "uuid": "06a85205-3621-425b-8eca-56f44a3ceaed"
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+ "src": "hda",
+ "uuid": "57afe769-fe76-4890-9c62-c2014ecf8529"
+ },
+ "genbank_files5": {
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+ "genbank_files": "{\"values\": [{\"id\": 3, \"src\": \"hdca\"}]}",
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+ "state": "ok",
+ "stderr": "",
+ "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",
+ "tool_id": "seq_to_db",
+ "tool_stderr": "",
+ "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",
+ "update_time": "2025-06-12T08:12:41.972140",
+ "user_email": "planemo@galaxyproject.org",
+ "user_id": "d1dc40ebed860870"
+ },
+ "status": "success",
+ "test_index": 2,
+ "time_seconds": 27.17548680305481,
+ "tool_id": "seq_to_db",
+ "tool_version": "0.1.0+galaxy0"
+ },
+ "has_data": true,
+ "id": "seq_to_db-2"
+ },
+ {
+ "data": {
+ "inputs": {
+ "adv|json_conf": {
+ "id": "81096e298c6cd33b",
+ "src": "hda"
+ },
+ "genbank_files": {
+ "id": "f71740853e0eea8f",
+ "src": "hdca"
+ }
+ },
+ "job": {
+ "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'",
+ "command_version": "",
+ "copied_from_job_id": null,
+ "create_time": "2025-06-12T08:13:02.907605",
+ "dependencies": [
+ {
+ "cacheable": false,
+ "dependency_resolver": {
+ "auto_init": true,
+ "auto_install": true,
+ "can_uninstall_dependencies": true,
+ "ensure_channels": "conda-forge,bioconda",
+ "model_class": "CondaDependencyResolver",
+ "prefix": "/home/rkhaled/miniconda3",
+ "read_only": false,
+ "resolver_type": "conda",
+ "resolves_simple_dependencies": true,
+ "use_local": false,
+ "versionless": false
+ },
+ "dependency_type": "conda",
+ "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966",
+ "exact": true,
+ "model_class": "MergedCondaDependency",
+ "name": "pandas",
+ "version": "2.2.3"
+ },
+ {
+ "cacheable": false,
+ "dependency_resolver": {
+ "auto_init": true,
+ "auto_install": true,
+ "can_uninstall_dependencies": true,
+ "ensure_channels": "conda-forge,bioconda",
+ "model_class": "CondaDependencyResolver",
+ "prefix": "/home/rkhaled/miniconda3",
+ "read_only": false,
+ "resolver_type": "conda",
+ "resolves_simple_dependencies": true,
+ "use_local": false,
+ "versionless": false
+ },
+ "dependency_type": "conda",
+ "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966",
+ "exact": true,
+ "model_class": "MergedCondaDependency",
+ "name": "sqlalchemy",
+ "version": "2.0.40"
+ },
+ {
+ "cacheable": false,
+ "dependency_resolver": {
+ "auto_init": true,
+ "auto_install": true,
+ "can_uninstall_dependencies": true,
+ "ensure_channels": "conda-forge,bioconda",
+ "model_class": "CondaDependencyResolver",
+ "prefix": "/home/rkhaled/miniconda3",
+ "read_only": false,
+ "resolver_type": "conda",
+ "resolves_simple_dependencies": true,
+ "use_local": false,
+ "versionless": false
+ },
+ "dependency_type": "conda",
+ "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966",
+ "exact": true,
+ "model_class": "MergedCondaDependency",
+ "name": "psycopg2",
+ "version": "2.9.9"
+ }
+ ],
+ "exit_code": 1,
+ "external_id": "127952",
+ "galaxy_version": "24.2",
+ "handler": null,
+ "history_id": "f71740853e0eea8f",
+ "id": "ae7479dd630bf125",
+ "inputs": {
+ "adv|json_conf": {
+ "id": "81096e298c6cd33b",
+ "src": "hda",
+ "uuid": "1681d2f4-591b-48a4-a469-0b6d9d29897b"
+ },
+ "genbank_files1": {
+ "id": "4bb85627388cf8ba",
+ "src": "hda",
+ "uuid": "77d5679d-4fb4-4b27-afe7-930f4b3d6076"
+ },
+ "genbank_files2": {
+ "id": "00078d50fa80d7bb",
+ "src": "hda",
+ "uuid": "51ae04ed-e634-4f46-ae13-0ce31dbacc37"
+ },
+ "genbank_files3": {
+ "id": "221d11c5cc4eab13",
+ "src": "hda",
+ "uuid": "c64f9b84-cf82-4b1b-96cb-3f98f0fda7a9"
+ },
+ "genbank_files4": {
+ "id": "bc838ca4b455c7c4",
+ "src": "hda",
+ "uuid": "ef7a853c-dc0e-47dc-bf52-6f45291358b1"
+ },
+ "genbank_files5": {
+ "id": "04052285d124af02",
+ "src": "hda",
+ "uuid": "13a4680c-d654-45d9-bdab-75dca91c36da"
+ }
+ },
+ "job_messages": [
+ {
+ "code_desc": "",
+ "desc": "Fatal error: Exit code 1 ()",
+ "error_level": 3,
+ "exit_code": 1,
+ "type": "exit_code"
+ }
+ ],
+ "job_metrics": [],
+ "job_runner_name": null,
+ "job_stderr": "",
+ "job_stdout": "",
+ "model_class": "Job",
+ "output_collections": {},
+ "outputs": {
+ "output": {
+ "id": "ae7479dd630bf125",
+ "src": "hda",
+ "uuid": "431acc98-f2ee-4e32-876a-33ef788c7eeb"
+ }
+ },
+ "params": {
+ "__input_ext": "\"input\"",
+ "adv": "{\"execution_enable\": true, \"json_conf\": {\"values\": [{\"id\": 25, \"src\": \"hda\"}]}}",
+ "annotation_column": null,
+ "chromInfo": "\"/tmp/tmphs5lamwi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+ "db_uri": null,
+ "dbkey": "\"?\"",
+ "fragment_column": null,
+ "genbank_files": "{\"values\": [{\"id\": 4, \"src\": \"hdca\"}]}",
+ "sequence_column": null,
+ "table": null
+ },
+ "state": "error",
+ "stderr": "Traceback (most recent call last):\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 273, in \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",
+ "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",
+ "tool_id": "seq_to_db",
+ "tool_stderr": "Traceback (most recent call last):\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 273, in \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",
+ "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",
+ "update_time": "2025-06-12T08:13:09.078361",
+ "user_email": "planemo@galaxyproject.org",
+ "user_id": "d1dc40ebed860870"
+ },
+ "output_problems": [
+ "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 \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.",
+ "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 \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."
+ ],
+ "status": "failure",
+ "test_index": 3,
+ "time_seconds": 26.706940174102783,
+ "tool_id": "seq_to_db",
+ "tool_version": "0.1.0+galaxy0"
+ },
+ "has_data": true,
+ "id": "seq_to_db-3"
+ }
+ ],
+ "version": "0.1"
+}
\ No newline at end of file
diff -r 9f845ccb1a9f -r 3daf04425ea1 save_to_db.py
--- a/save_to_db.py Wed Jun 11 13:36:44 2025 +0000
+++ b/save_to_db.py Thu Jun 12 09:04:14 2025 +0000
@@ -201,8 +201,15 @@
parser.add_argument("--output", required=True, help="Text report")
parser.add_argument("--file_name_mapping", required=True, help="real fragments names")
parser.add_argument("--json_conf", required=False, help="JSON config file with DB parameters")
+ parser.add_argument("--execution_enable", required=True, help="enabbe or desable execution directly from the tool option")
args = parser.parse_args()
+ # enabbe or desable execution based on galaxy param (execution_enable)
+
+ if args.execution_enable == 'false':
+ print("Execution disabled. 'Send Requenst to DB' is set to 'false'")
+ return
+
# Load JSON config if provided
json_config = {}
if args.json_conf != 'None' or '':
diff -r 9f845ccb1a9f -r 3daf04425ea1 seq_to_db.xml
--- a/seq_to_db.xml Wed Jun 11 13:36:44 2025 +0000
+++ b/seq_to_db.xml Thu Jun 12 09:04:14 2025 +0000
@@ -1,8 +1,8 @@
Save fragment's sequence in an accessible database and import it from .gb files
- 0
- 0.1.0
+ 1
+ 0.2.0
pandas
@@ -22,6 +22,7 @@
--output '$output'
--file_name_mapping '$file_name_mapping'
--json_conf '$json_conf'
+ --execution_enable '$execution_enable'
]]>
@@ -29,8 +30,9 @@
-
+
@@ -38,7 +40,34 @@
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -62,6 +91,7 @@
+
@@ -128,6 +158,7 @@
* **DB Column Contains Annotation For Ganbank File**: Column containing annotation data, to save al part before "ORIGIN" in the .gb file.
* **DB IDs Column Name**: Column holding the unique fragment IDs.
* **DB Connection URI**: URI used to connect to the database (e.g., postgresql://postgres:pass@localhost:5432/test_fragments_db).
+* **Send Requenst to DB**: Enable or Desable the interaction with the DB (can be usefull in workflows).
* **DB config as a json file**: JSON file contains the DB configuration:
- "JSON_table": will be the key to the table name.
- "JSON_sequence_column": will be the key to the sequence column.