| Previous changeset 1:fecc90231d86 (2025-04-10) Next changeset 3:72e99f02308e (2025-04-11) |
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Commit message:
planemo upload for repository https://github.com/brsynth commit 15dbdd1f0a222a8e1b0fb5c16b36885520a3d005 |
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modified:
get_db_info.py output.html output.json |
| b |
| diff -r fecc90231d86 -r 0443378b44e5 get_db_info.py --- a/get_db_info.py Thu Apr 10 09:50:23 2025 +0000 +++ b/get_db_info.py Fri Apr 11 13:20:22 2025 +0000 |
| [ |
| @@ -95,8 +95,12 @@ columns = [column['name'] for column in inspector.get_columns(table_name)] # Fetch all fragments from the table once + if fragment_column_name not in columns: + raise ValueError(f"Fragment column '{fragment_column_name}' not found in table '{table_name}'.") + + fragment_column_index = columns.index(fragment_column_name) all_rows = connection.execute(text(f"SELECT * FROM {table_name}")).fetchall() - fragment_map = {row[0]: row for row in all_rows} # Assuming the first column is fragment ID + fragment_map = {row[fragment_column_index]: row for row in all_rows} for _, row in df.iterrows(): annotated_row = {"Backbone": row["ID"], "Fragments": []} |
| b |
| diff -r fecc90231d86 -r 0443378b44e5 output.html --- a/output.html Thu Apr 10 09:50:23 2025 +0000 +++ b/output.html Fri Apr 11 13:20:22 2025 +0000 |
| b |
| @@ -285,7 +285,7 @@ var md = window.markdownit({ html: true, }); - target.innerHTML = md.render(atob('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')); + target.innerHTML = md.render(atob('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')); </script> </body> </html> \ No newline at end of file |
| b |
| diff -r fecc90231d86 -r 0443378b44e5 output.json --- a/output.json Thu Apr 10 09:50:23 2025 +0000 +++ b/output.json Fri Apr 11 13:20:22 2025 +0000 |
| [ |
| @@ -12,28 +12,28 @@ "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db", "fragment_column": "fragment", "input": { - "id": "e534d9c0c1dff50b", + "id": "3536ad1aa76135cc", "src": "hda" }, "table": "sample" }, "job": { - "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'", + "command_line": "python '/home/rkhaled/galaxytools/tools/get_db_data/get_db_info.py' --input '/tmp/tmpkidxewga/files/0/0/9/dataset_00944c3e-fd0d-44a4-a8ee-70df67c52925.dat' --db_uri 'postgresql://postgres:RK17__at__localhost:5432/test_fragments_db' --table 'sample' --fragment_column 'fragment' --output '/tmp/tmpkidxewga/job_working_directory/000/2/outputs/dataset_4e7ca8d3-50bd-4a9b-bdd6-00e4f0c85456.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-04-10T09:49:38.004865", + "create_time": "2025-04-11T13:19:06.203241", "dependencies": [], "exit_code": 0, - "external_id": "81074", + "external_id": "164114", "galaxy_version": "24.2", "handler": null, - "history_id": "e534d9c0c1dff50b", - "id": "b82b82861f770b56", + "history_id": "3536ad1aa76135cc", + "id": "9b5d036db8df9326", "inputs": { "input": { - "id": "e534d9c0c1dff50b", + "id": "3536ad1aa76135cc", "src": "hda", - "uuid": "bcf0f14f-54dc-4538-a68b-4811231bf7ea" + "uuid": "00944c3e-fd0d-44a4-a8ee-70df67c52925" } }, "job_messages": [], @@ -45,14 +45,14 @@ "output_collections": {}, "outputs": { "output": { - "id": "b82b82861f770b56", + "id": "9b5d036db8df9326", "src": "hda", - "uuid": "934f430f-d65f-4121-87ba-77fcbfc51860" + "uuid": "4e7ca8d3-50bd-4a9b-bdd6-00e4f0c85456" } }, "params": { "__input_ext": "\"input\"", - "chromInfo": "\"/tmp/tmppfe65grz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmpkidxewga/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "db_uri": "\"postgresql://postgres:RK17@localhost:5432/test_fragments_db\"", "dbkey": "\"?\"", "fragment_column": "\"fragment\"", @@ -60,17 +60,17 @@ }, "state": "ok", "stderr": "", - "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", + "stdout": "Container 'test_fragments_db' is already running.\nConnected to database.\nAnnotation saved to /tmp/tmpkidxewga/job_working_directory/000/2/outputs/dataset_4e7ca8d3-50bd-4a9b-bdd6-00e4f0c85456.dat\n", "tool_id": "get_DB_data", "tool_stderr": "", - "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", - "update_time": "2025-04-10T09:49:44.552746", + "tool_stdout": "Container 'test_fragments_db' is already running.\nConnected to database.\nAnnotation saved to /tmp/tmpkidxewga/job_working_directory/000/2/outputs/dataset_4e7ca8d3-50bd-4a9b-bdd6-00e4f0c85456.dat\n", + "update_time": "2025-04-11T13:19:13.057635", "user_email": "planemo@galaxyproject.org", - "user_id": "e534d9c0c1dff50b" + "user_id": "3536ad1aa76135cc" }, "status": "success", "test_index": 0, - "time_seconds": 16.582475662231445, + "time_seconds": 16.42380690574646, "tool_id": "get_DB_data", "tool_version": "0.1.0" }, |