# HG changeset patch
# User tduigou
# Date 1748871581 0
# Node ID 95757ea6c3338e1b2dc1185ac28d5e51a4032df6
planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
diff -r 000000000000 -r 95757ea6c333 json_db_config_generating.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/json_db_config_generating.xml Mon Jun 02 13:39:41 2025 +0000
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+ Genarate a JSON file used as DB config
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+ @unpublished{json_db_config_generating
+ author = {Ramiz Khaled},
+ title = {{json_db_config_generating}},
+ url = {https://github.com/brsynth/},
+ }
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\ No newline at end of file
diff -r 000000000000 -r 95757ea6c333 output.html
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+++ b/output.html Mon Jun 02 13:39:41 2025 +0000
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+ Test Results (powered by Planemo)
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diff -r 000000000000 -r 95757ea6c333 output.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/output.json Mon Jun 02 13:39:41 2025 +0000
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+{
+ "summary": {
+ "num_errors": 0,
+ "num_failures": 0,
+ "num_skips": 0,
+ "num_tests": 2
+ },
+ "tests": [
+ {
+ "data": {
+ "inputs": {
+ "annotation_column": "annotation",
+ "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",
+ "execution": true,
+ "fragment_column": "fragment",
+ "sequence_column": "sequence",
+ "table_name": "sample"
+ },
+ "job": {
+ "command_line": "python3 -c \"import json; params = { 'execution': 'true', 'JSON_db_uri': 'postgresql://postgres:RK17__at__localhost:5432/test_fragments_db', 'JSON_table': 'sample', 'JSON_fragment_column': 'fragment', 'JSON_sequence_column': 'sequence', 'JSON_annotation_column': 'annotation' }; f = open('/tmp/tmphuox1me_/job_working_directory/000/1/outputs/dataset_a57d4381-ba51-4c7e-8409-1ec0f85d3ba2.dat', 'w'); json.dump(params, f, indent=4); f.close()\" && echo DEBUG && cat '/tmp/tmphuox1me_/job_working_directory/000/1/outputs/dataset_a57d4381-ba51-4c7e-8409-1ec0f85d3ba2.dat'",
+ "command_version": "",
+ "copied_from_job_id": null,
+ "create_time": "2025-06-02T13:36:45.666819",
+ "dependencies": [],
+ "exit_code": 0,
+ "external_id": "240263",
+ "galaxy_version": "24.2",
+ "handler": null,
+ "history_id": "abb9783f010dde16",
+ "id": "abb9783f010dde16",
+ "inputs": {},
+ "job_messages": [],
+ "job_metrics": [],
+ "job_runner_name": null,
+ "job_stderr": "",
+ "job_stdout": "",
+ "model_class": "Job",
+ "output_collections": {},
+ "outputs": {
+ "output_json": {
+ "id": "abb9783f010dde16",
+ "src": "hda",
+ "uuid": "a57d4381-ba51-4c7e-8409-1ec0f85d3ba2"
+ }
+ },
+ "params": {
+ "__input_ext": "\"input\"",
+ "annotation_column": "\"annotation\"",
+ "chromInfo": "\"/tmp/tmphuox1me_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+ "db_uri": "\"postgresql://postgres:RK17@localhost:5432/test_fragments_db\"",
+ "dbkey": "\"?\"",
+ "execution": "true",
+ "fragment_column": "\"fragment\"",
+ "sequence_column": "\"sequence\"",
+ "table_name": "\"sample\""
+ },
+ "state": "ok",
+ "stderr": "",
+ "stdout": "DEBUG\n{\n \"execution\": \"true\",\n \"JSON_db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n \"JSON_table\": \"sample\",\n \"JSON_fragment_column\": \"fragment\",\n \"JSON_sequence_column\": \"sequence\",\n \"JSON_annotation_column\": \"annotation\"\n}",
+ "tool_id": "json_db_config_generating",
+ "tool_stderr": "",
+ "tool_stdout": "DEBUG\n{\n \"execution\": \"true\",\n \"JSON_db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n \"JSON_table\": \"sample\",\n \"JSON_fragment_column\": \"fragment\",\n \"JSON_sequence_column\": \"sequence\",\n \"JSON_annotation_column\": \"annotation\"\n}",
+ "update_time": "2025-06-02T13:36:51.468608",
+ "user_email": "planemo@galaxyproject.org",
+ "user_id": "abb9783f010dde16"
+ },
+ "status": "success",
+ "test_index": 0,
+ "time_seconds": 6.098992109298706,
+ "tool_id": "json_db_config_generating",
+ "tool_version": "0.1.0+galaxy1"
+ },
+ "has_data": true,
+ "id": "json_db_config_generating-0"
+ },
+ {
+ "data": {
+ "inputs": {
+ "annotation_column": "annotation",
+ "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",
+ "execution": false,
+ "fragment_column": "fragment",
+ "sequence_column": "sequence",
+ "table_name": "sample"
+ },
+ "job": {
+ "command_line": "python3 -c \"import json; params = { 'execution': 'false', 'JSON_db_uri': 'postgresql://postgres:RK17__at__localhost:5432/test_fragments_db', 'JSON_table': 'sample', 'JSON_fragment_column': 'fragment', 'JSON_sequence_column': 'sequence', 'JSON_annotation_column': 'annotation' }; f = open('/tmp/tmphuox1me_/job_working_directory/000/2/outputs/dataset_b4d39c19-882f-4805-90ee-dbfd2dc51c44.dat', 'w'); json.dump(params, f, indent=4); f.close()\" && echo DEBUG && cat '/tmp/tmphuox1me_/job_working_directory/000/2/outputs/dataset_b4d39c19-882f-4805-90ee-dbfd2dc51c44.dat'",
+ "command_version": "",
+ "copied_from_job_id": null,
+ "create_time": "2025-06-02T13:36:51.893406",
+ "dependencies": [],
+ "exit_code": 0,
+ "external_id": "240333",
+ "galaxy_version": "24.2",
+ "handler": null,
+ "history_id": "e20768301a38397d",
+ "id": "e20768301a38397d",
+ "inputs": {},
+ "job_messages": [],
+ "job_metrics": [],
+ "job_runner_name": null,
+ "job_stderr": "",
+ "job_stdout": "",
+ "model_class": "Job",
+ "output_collections": {},
+ "outputs": {
+ "output_json": {
+ "id": "e20768301a38397d",
+ "src": "hda",
+ "uuid": "b4d39c19-882f-4805-90ee-dbfd2dc51c44"
+ }
+ },
+ "params": {
+ "__input_ext": "\"input\"",
+ "annotation_column": "\"annotation\"",
+ "chromInfo": "\"/tmp/tmphuox1me_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+ "db_uri": "\"postgresql://postgres:RK17@localhost:5432/test_fragments_db\"",
+ "dbkey": "\"?\"",
+ "execution": "false",
+ "fragment_column": "\"fragment\"",
+ "sequence_column": "\"sequence\"",
+ "table_name": "\"sample\""
+ },
+ "state": "ok",
+ "stderr": "",
+ "stdout": "DEBUG\n{\n \"execution\": \"false\",\n \"JSON_db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n \"JSON_table\": \"sample\",\n \"JSON_fragment_column\": \"fragment\",\n \"JSON_sequence_column\": \"sequence\",\n \"JSON_annotation_column\": \"annotation\"\n}",
+ "tool_id": "json_db_config_generating",
+ "tool_stderr": "",
+ "tool_stdout": "DEBUG\n{\n \"execution\": \"false\",\n \"JSON_db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n \"JSON_table\": \"sample\",\n \"JSON_fragment_column\": \"fragment\",\n \"JSON_sequence_column\": \"sequence\",\n \"JSON_annotation_column\": \"annotation\"\n}",
+ "update_time": "2025-06-02T13:36:57.648501",
+ "user_email": "planemo@galaxyproject.org",
+ "user_id": "abb9783f010dde16"
+ },
+ "status": "success",
+ "test_index": 1,
+ "time_seconds": 6.048913240432739,
+ "tool_id": "json_db_config_generating",
+ "tool_version": "0.1.0+galaxy1"
+ },
+ "has_data": true,
+ "id": "json_db_config_generating-1"
+ }
+ ],
+ "version": "0.1"
+}
\ No newline at end of file