| Previous changeset 0:41ac63b5d221 (2025-04-10) Next changeset 2:0443378b44e5 (2025-04-11) |
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Commit message:
planemo upload for repository https://github.com/brsynth commit 15dbdd1f0a222a8e1b0fb5c16b36885520a3d005 |
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modified:
output.html output.json test-data/output_annotations.json test-data/test_input.csv |
| b |
| diff -r 41ac63b5d221 -r fecc90231d86 output.html --- a/output.html Thu Apr 10 08:45:18 2025 +0000 +++ b/output.html Thu Apr 10 09:50:23 2025 +0000 |
| b |
| b"@@ -285,7 +285,7 @@\n var md = window.markdownit({\n html: true,\n });\n- target.innerHTML = 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| b |
| diff -r 41ac63b5d221 -r fecc90231d86 output.json --- a/output.json Thu Apr 10 08:45:18 2025 +0000 +++ b/output.json Thu Apr 10 09:50:23 2025 +0000 |
| [ |
| b'@@ -12,28 +12,28 @@\n "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",\n "fragment_column": "fragment",\n "input": {\n- "id": "2956404b1302731f",\n+ "id": "e534d9c0c1dff50b",\n "src": "hda"\n },\n "table": "sample"\n },\n "job": {\n- "command_line": "python \'/home/rkhaled/galaxytools/tools/get_db_data/get_DB_info.py\' --input \'/tmp/tmp48sxixl1/files/7/5/d/dataset_75daf398-093d-46eb-8cf7-3f75df4101e4.dat\' --db_uri \'postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\' --table \'sample\' --fragment_column \'fragment\' --output \'/tmp/tmp48sxixl1/job_working_directory/000/2/outputs/dataset_7ada1e0a-429a-4d22-84f4-03ee16dbb01a.dat\'&& echo \'debug\' && cat \'/tmp/tmp48sxixl1/job_working_directory/000/2/outputs/dataset_7ada1e0a-429a-4d22-84f4-03ee16dbb01a.dat\'",\n+ "command_line": "python \'/home/rkhaled/galaxytools/tools/get_db_data/get_db_info.py\' --input \'/tmp/tmppfe65grz/files/b/c/f/dataset_bcf0f14f-54dc-4538-a68b-4811231bf7ea.dat\' --db_uri \'postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\' --table \'sample\' --fragment_column \'fragment\' --output \'/tmp/tmppfe65grz/job_working_directory/000/2/outputs/dataset_934f430f-d65f-4121-87ba-77fcbfc51860.dat\'",\n "command_version": "",\n "copied_from_job_id": null,\n- "create_time": "2025-04-10T08:35:13.763882",\n+ "create_time": "2025-04-10T09:49:38.004865",\n "dependencies": [],\n "exit_code": 0,\n- "external_id": "49355",\n+ "external_id": "81074",\n "galaxy_version": "24.2",\n "handler": null,\n- "history_id": "2956404b1302731f",\n- "id": "d5b5fa41022deb44",\n+ "history_id": "e534d9c0c1dff50b",\n+ "id": "b82b82861f770b56",\n "inputs": {\n "input": {\n- "id": "2956404b1302731f",\n+ "id": "e534d9c0c1dff50b",\n "src": "hda",\n- "uuid": "75daf398-093d-46eb-8cf7-3f75df4101e4"\n+ "uuid": "bcf0f14f-54dc-4538-a68b-4811231bf7ea"\n }\n },\n "job_messages": [],\n@@ -45,14 +45,14 @@\n "output_collections": {},\n "outputs": {\n "output": {\n- "id": "d5b5fa41022deb44",\n+ "id": "b82b82861f770b56",\n "src": "hda",\n- "uuid": "7ada1e0a-429a-4d22-84f4-03ee16dbb01a"\n+ "uuid": "934f430f-d65f-4121-87ba-77fcbfc51860"\n }\n },\n "params": {\n "__input_ext": "\\"input\\"",\n- "chromInfo": "\\"/tmp/tmp48sxixl1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\\"",\n+ "chromInfo": "\\"/tmp/tmppfe65grz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\\"",\n "db_uri": "\\"postgresql://postgres:RK17@localhost:5432/test_fragments_db\\"",\n "dbkey": "\\"?\\"",\n "fragment_column": "\\"fragment\\"",\n@@ -60,17 +60,17 @@\n },\n "state": "ok",\n "stderr": "",\n- "stdout": "Container \'test_fragments_db\' is already running.\\nConnected to database.\\nAnnotation saved to /tmp/tmp48sxixl1/job_working_directory/000/2/outputs/dataset_7ada1e0a-429a-4d22-84f4-03ee16dbb01a.dat\\ndebug\\n[\\n {\\n \\"Backbone\\": \\"ACP10001AaCbbBS\\",\\n \\"F'..b' \\"metadata_1\\": \\"Metadata1 for CFP10002AaCbbBS\\",\\n \\"metadata_2\\": \\"Metadata2 for CFP10002AaCbbBS\\"\\n },\\n {\\n \\"id\\": \\"XYZ10003AaCbbBS\\",\\n \\"sequence\\": \\"seq for XYZ10003AaCbbBS\\",\\n \\"metadata_1\\": \\"Metadata1 for XYZ10003AaCbbBS\\",\\n \\"metadata_2\\": \\"Metadata2 for XYZ10003AaCbbBS\\"\\n }\\n ]\\n },\\n {\\n \\"Backbone\\": \\"CFP10002AaCbbBS\\",\\n \\"Fragments\\": [\\n {\\n \\"id\\": \\"CFP10002AaCbbBS\\",\\n \\"sequence\\": \\"seq for CFP10002AaCbbBS\\",\\n \\"metadata_1\\": \\"Metadata1 for CFP10002AaCbbBS\\",\\n \\"metadata_2\\": \\"Metadata2 for CFP10002AaCbbBS\\"\\n },\\n {\\n \\"id\\": \\"ACP10001AaCbbBS\\",\\n \\"sequence\\": \\"seq for ACP10001AaCbbBS\\",\\n \\"metadata_1\\": \\"Metadata1 for ACP10001AaCbbBS\\",\\n \\"metadata_2\\": \\"Metadata2 for ACP10001AaCbbBS\\"\\n },\\n {\\n \\"id\\": \\"QWE10004AaCbbBS\\",\\n \\"sequence\\": \\"seq for QWE10004AaCbbBS\\",\\n \\"metadata_1\\": \\"Metadata1 for QWE10004AaCbbBS\\",\\n \\"metadata_2\\": \\"Metadata2 for QWE10004AaCbbBS\\"\\n }\\n ]\\n },\\n {\\n \\"Backbone\\": \\"XYZ10003AaCbbBS\\",\\n \\"Fragments\\": [\\n {\\n \\"id\\": \\"XYZ10003AaCbbBS\\",\\n \\"sequence\\": \\"seq for XYZ10003AaCbbBS\\",\\n \\"metadata_1\\": \\"Metadata1 for XYZ10003AaCbbBS\\",\\n \\"metadata_2\\": \\"Metadata2 for XYZ10003AaCbbBS\\"\\n },\\n {\\n \\"id\\": \\"QWE10004AaCbbBS\\",\\n \\"sequence\\": \\"seq for QWE10004AaCbbBS\\",\\n \\"metadata_1\\": \\"Metadata1 for QWE10004AaCbbBS\\",\\n \\"metadata_2\\": \\"Metadata2 for QWE10004AaCbbBS\\"\\n },\\n {\\n \\"id\\": \\"ACP10001AaCbbBS\\",\\n \\"sequence\\": \\"seq for ACP10001AaCbbBS\\",\\n \\"metadata_1\\": \\"Metadata1 for ACP10001AaCbbBS\\",\\n \\"metadata_2\\": \\"Metadata2 for ACP10001AaCbbBS\\"\\n }\\n ]\\n },\\n {\\n \\"Backbone\\": \\"QWE10004AaCbbBS\\",\\n \\"Fragments\\": [\\n {\\n \\"id\\": \\"QWE10004AaCbbBS\\",\\n \\"sequence\\": \\"seq for QWE10004AaCbbBS\\",\\n \\"metadata_1\\": \\"Metadata1 for QWE10004AaCbbBS\\",\\n \\"metadata_2\\": \\"Metadata2 for QWE10004AaCbbBS\\"\\n },\\n {\\n \\"id\\": \\"XYZ10003AaCbbBS\\",\\n \\"sequence\\": \\"seq for XYZ10003AaCbbBS\\",\\n \\"metadata_1\\": \\"Metadata1 for XYZ10003AaCbbBS\\",\\n \\"metadata_2\\": \\"Metadata2 for XYZ10003AaCbbBS\\"\\n },\\n {\\n \\"id\\": \\"CFP10002AaCbbBS\\",\\n \\"sequence\\": \\"seq for CFP10002AaCbbBS\\",\\n \\"metadata_1\\": \\"Metadata1 for CFP10002AaCbbBS\\",\\n \\"metadata_2\\": \\"Metadata2 for CFP10002AaCbbBS\\"\\n }\\n ]\\n }\\n]",\n- "update_time": "2025-04-10T08:35:21.268906",\n+ "tool_stdout": "Container \'test_fragments_db\' is already running.\\nConnected to database.\\nAnnotation saved to /tmp/tmppfe65grz/job_working_directory/000/2/outputs/dataset_934f430f-d65f-4121-87ba-77fcbfc51860.dat\\n",\n+ "update_time": "2025-04-10T09:49:44.552746",\n "user_email": "planemo@galaxyproject.org",\n- "user_id": "2956404b1302731f"\n+ "user_id": "e534d9c0c1dff50b"\n },\n "status": "success",\n "test_index": 0,\n- "time_seconds": 18.426533937454224,\n+ "time_seconds": 16.582475662231445,\n "tool_id": "get_DB_data",\n "tool_version": "0.1.0"\n },\n' |
| b |
| diff -r 41ac63b5d221 -r fecc90231d86 test-data/output_annotations.json --- a/test-data/output_annotations.json Thu Apr 10 08:45:18 2025 +0000 +++ b/test-data/output_annotations.json Thu Apr 10 09:50:23 2025 +0000 |
| [ |
| @@ -1,6 +1,6 @@ [ { - "Backbone": "ACP10001AaCbbBS", + "Backbone": "Sample-1", "Fragments": [ { "id": "ACP10001AaCbbBS", @@ -23,7 +23,7 @@ ] }, { - "Backbone": "CFP10002AaCbbBS", + "Backbone": "Sample-2", "Fragments": [ { "id": "CFP10002AaCbbBS", @@ -46,7 +46,7 @@ ] }, { - "Backbone": "XYZ10003AaCbbBS", + "Backbone": "Sample-3", "Fragments": [ { "id": "XYZ10003AaCbbBS", @@ -69,7 +69,7 @@ ] }, { - "Backbone": "QWE10004AaCbbBS", + "Backbone": "Sample-4", "Fragments": [ { "id": "QWE10004AaCbbBS", |
| b |
| diff -r 41ac63b5d221 -r fecc90231d86 test-data/test_input.csv --- a/test-data/test_input.csv Thu Apr 10 08:45:18 2025 +0000 +++ b/test-data/test_input.csv Thu Apr 10 09:50:23 2025 +0000 |
| b |
| @@ -1,6 +1,5 @@ ID,Frag1,Frag2,Frag3 -ACP10001AaCbbBS,ACP10001AaCbbBS,CFP10002AaCbbBS,XYZ10003AaCbbBS -CFP10002AaCbbBS,CFP10002AaCbbBS,ACP10001AaCbbBS,QWE10004AaCbbBS -XYZ10003AaCbbBS,XYZ10003AaCbbBS,QWE10004AaCbbBS,ACP10001AaCbbBS -QWE10004AaCbbBS,QWE10004AaCbbBS,XYZ10003AaCbbBS,CFP10002AaCbbBS - +Sample-1,ACP10001AaCbbBS,CFP10002AaCbbBS,XYZ10003AaCbbBS +Sample-2,CFP10002AaCbbBS,ACP10001AaCbbBS,QWE10004AaCbbBS +Sample-3,XYZ10003AaCbbBS,QWE10004AaCbbBS,ACP10001AaCbbBS +Sample-4,QWE10004AaCbbBS,XYZ10003AaCbbBS,CFP10002AaCbbBS |