| Previous changeset 8:87585c392228 (2025-04-18) Next changeset 10:703fda6c48c5 (2025-05-23) |
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Commit message:
planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae |
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modified:
get_DB_data.xml get_db_info.py output.html output.json |
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added:
test-data/test_input.csv |
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removed:
test-data/test_input.tsv |
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| diff -r 87585c392228 -r 6401a277ee72 get_DB_data.xml --- a/get_DB_data.xml Fri Apr 18 13:07:58 2025 +0000 +++ b/get_DB_data.xml Fri Apr 18 13:36:40 2025 +0000 |
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| @@ -22,7 +22,7 @@ --output 'outdir' ]]></command> <inputs> - <param name="input" type="data" format="tabular" label="Input TSV file" /> + <param name="input" type="data" format="csv" label="Input CSV file" /> <param name="table" type="text" label="Database Table Name" optional="false" /> <param name="sequence_column" type="text" label="DB column contains sequence for ganbank file" optional="false" /> <param name="annotation_columns" type="text" label="DB column contains annotation for ganbank file" optional="false" /> @@ -37,7 +37,7 @@ <tests> <!--python get_db_info.py -input 'test-data/test_input.tsv' -sequence_column 'sequence' -annotation_column 'annotation' -db_uri 'postgresql://postgres:RK17@localhost:5432/test_fragments_db' -table 'sample' -fragment_column 'fragment' -output 'test-data/output'--> <test> - <param name="input" value="test_input.tsv" /> + <param name="input" value="test_input.csv" /> <param name="table" value="sample" /> <param name="sequence_column" value="sequence" /> <param name="annotation_columns" value="annotation" /> @@ -72,7 +72,7 @@ Pick Data From DB =================== -generate GanDank files from tsv file based on SQL DB. +generate GanDank files from csv file based on SQL DB. ]]></help> <citations> <citation type="bibtex"> |
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| diff -r 87585c392228 -r 6401a277ee72 get_db_info.py --- a/get_db_info.py Fri Apr 18 13:07:58 2025 +0000 +++ b/get_db_info.py Fri Apr 18 13:36:40 2025 +0000 |
| b |
| @@ -81,10 +81,10 @@ time.sleep(2) raise Exception("Database connection failed after timeout.") -def fetch_annotations(tsv_file, sequence_column, annotation_columns, db_uri, table_name, fragment_column_name, output): +def fetch_annotations(csv_file, sequence_column, annotation_columns, db_uri, table_name, fragment_column_name, output): """Fetch annotations from the database and save the result as GenBank files.""" db_uri = fix_db_uri(db_uri) - df = pd.read_csv(tsv_file, sep='\t') + df = pd.read_csv(csv_file, sep=',') engine = create_engine(db_uri) connection = engine.connect() @@ -216,7 +216,7 @@ def main(): parser = argparse.ArgumentParser(description="Fetch annotations from PostgreSQL database and save as JSON.") - parser.add_argument("--input", required=True, help="Input TSV file") + parser.add_argument("--input", required=True, help="Input CSV file") parser.add_argument("--sequence_column", required=True, help="DB column contains sequence for ganbank file") parser.add_argument("--annotation_columns", required=True, help="DB column contains head for ganbank file") parser.add_argument("--db_uri", required=True, help="Database URI connection string") |
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| diff -r 87585c392228 -r 6401a277ee72 output.html --- a/output.html Fri Apr 18 13:07:58 2025 +0000 +++ b/output.html Fri Apr 18 13:36:40 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 87585c392228 -r 6401a277ee72 output.json --- a/output.json Fri Apr 18 13:07:58 2025 +0000 +++ b/output.json Fri Apr 18 13:36:40 2025 +0000 |
| [ |
| @@ -13,29 +13,29 @@ "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db", "fragment_column": "fragment", "input": { - "id": "706ba6c84a03098c", + "id": "dc3c012b3492f2da", "src": "hda" }, "sequence_column": "sequence", "table": "sample" }, "job": { - "command_line": "mkdir 'outdir' && python '/home/rkhaled/galaxytools/tools/get_db_data/get_db_info.py' --input '/tmp/tmp42w72yto/files/3/6/2/dataset_3622642b-aec9-4602-bb27-170ce5daff6d.dat' --sequence_column 'sequence' --annotation_columns 'annotation' --db_uri 'postgresql://postgres:RK17__at__localhost:5432/test_fragments_db' --table 'sample' --fragment_column 'fragment' --output 'outdir'", + "command_line": "mkdir 'outdir' && python '/home/rkhaled/galaxytools/tools/get_db_data/get_db_info.py' --input '/tmp/tmpteq_uiar/files/9/0/2/dataset_90283960-be8f-4d26-82d8-ff96600131ea.dat' --sequence_column 'sequence' --annotation_columns 'annotation' --db_uri 'postgresql://postgres:RK17__at__localhost:5432/test_fragments_db' --table 'sample' --fragment_column 'fragment' --output 'outdir'", "command_version": null, "copied_from_job_id": null, - "create_time": "2025-04-18T12:52:15.493942", + "create_time": "2025-04-18T13:27:46.888469", "dependencies": [], "exit_code": 0, - "external_id": "157761", + "external_id": "173646", "galaxy_version": "24.2", "handler": null, - "history_id": "706ba6c84a03098c", - "id": "cc02f40f5df38cc6", + "history_id": "dc3c012b3492f2da", + "id": "59227df095fccb36", "inputs": { "input": { - "id": "706ba6c84a03098c", + "id": "dc3c012b3492f2da", "src": "hda", - "uuid": "3622642b-aec9-4602-bb27-170ce5daff6d" + "uuid": "90283960-be8f-4d26-82d8-ff96600131ea" } }, "job_messages": [], @@ -46,36 +46,36 @@ "model_class": "Job", "output_collections": { "output_gb": { - "id": "706ba6c84a03098c", + "id": "dc3c012b3492f2da", "src": "hdca" } }, "outputs": { "__new_primary_file_output_gb|ACP10001AaCbbBS__": { - "id": "cc02f40f5df38cc6", + "id": "59227df095fccb36", "src": "hda", - "uuid": "808dfb23-fd8a-4bd8-a8b1-c1cb9f569537" + "uuid": "2e35873d-c887-4bfe-b52f-0785b50f80e1" }, "__new_primary_file_output_gb|CFP10002AaCbbBS__": { - "id": "c817ad70fa00c136", + "id": "38eb154a8cd15a5b", "src": "hda", - "uuid": "33a35584-db32-4cf5-9f97-29e32956b76a" + "uuid": "eb1948b5-5d9f-4019-b2df-970f182182bf" }, "__new_primary_file_output_gb|QWE10004AaCbbBS__": { - "id": "ecde0ca67d20406e", + "id": "5a84ee5dbe848008", "src": "hda", - "uuid": "50ef4259-8c5c-48f3-b6d8-77b478bff207" + "uuid": "6522b4e8-2ddf-4109-b798-aa68d5cbce10" }, "__new_primary_file_output_gb|XYZ10003AaCbbBS__": { - "id": "5dd74542a4c0f825", + "id": "0f080313538f12a9", "src": "hda", - "uuid": "65a4517c-ed95-4894-9846-73d8d8f4b3ec" + "uuid": "233ac826-87d2-4106-b9ed-1e518202e552" } }, "params": { "__input_ext": "\"input\"", "annotation_columns": "\"annotation\"", - "chromInfo": "\"/tmp/tmp42w72yto/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmpteq_uiar/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "db_uri": "\"postgresql://postgres:RK17@localhost:5432/test_fragments_db\"", "dbkey": "\"?\"", "fragment_column": "\"fragment\"", @@ -88,13 +88,13 @@ "tool_id": "get_DB_data", "tool_stderr": "", "tool_stdout": "Container 'test_fragments_db' is already running.\nConnected to database.\n", - "update_time": "2025-04-18T12:52:21.995313", + "update_time": "2025-04-18T13:27:53.640966", "user_email": "planemo@galaxyproject.org", - "user_id": "706ba6c84a03098c" + "user_id": "dc3c012b3492f2da" }, "status": "success", "test_index": 0, - "time_seconds": 16.213179349899292, + "time_seconds": 16.462403059005737, "tool_id": "get_DB_data", "tool_version": "0.1.0+galaxy0" }, |
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| diff -r 87585c392228 -r 6401a277ee72 test-data/test_input.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_input.csv Fri Apr 18 13:36:40 2025 +0000 |
| b |
| @@ -0,0 +1,5 @@ +ID,Frag1,Frag2,Frag3 +Sample-1,ACP10001AaCbbBS,CFP10002AaCbbBS,XYZ10003AaCbbBS +Sample-2,CFP10002AaCbbBS,ACP10001AaCbbBS,QWE10004AaCbbBS +Sample-3,XYZ10003AaCbbBS,QWE10004AaCbbBS,ACP10001AaCbbBS +Sample-4,QWE10004AaCbbBS,XYZ10003AaCbbBS,CFP10002AaCbbBS |
| b |
| diff -r 87585c392228 -r 6401a277ee72 test-data/test_input.tsv --- a/test-data/test_input.tsv Fri Apr 18 13:07:58 2025 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,5 +0,0 @@ -ID Frag1 Frag2 Frag3 -Sample-1 ACP10001AaCbbBS CFP10002AaCbbBS XYZ10003AaCbbBS -Sample-2 CFP10002AaCbbBS ACP10001AaCbbBS QWE10004AaCbbBS -Sample-3 XYZ10003AaCbbBS QWE10004AaCbbBS ACP10001AaCbbBS -Sample-4 QWE10004AaCbbBS XYZ10003AaCbbBS CFP10002AaCbbBS |