Mercurial > repos > tduigou > save_to_db

--- a/output.html	Fri May 16 09:34:35 2025 +0000
+++ b/output.html	Fri May 23 08:51:50 2025 +0000
@@ -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
--- a/output.json	Fri May 16 09:34:35 2025 +0000
+++ b/output.json	Fri May 23 08:51:50 2025 +0000
@@ -12,73 +12,50 @@
                     "annotation_column": "annotation",
                     "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",
                     "fragment_column": "fragment",
-                    "genbank_files": [
-                        {
-                            "id": "0ed824750a9f5374",
-                            "src": "hda"
-                        },
-                        {
-                            "id": "93c5e169024bda92",
-                            "src": "hda"
-                        },
-                        {
-                            "id": "7e79446a5abd8b5f",
-                            "src": "hda"
-                        },
-                        {
-                            "id": "81603bca0e110055",
-                            "src": "hda"
-                        },
-                        {
-                            "id": "f1c08c8102faa4bc",
-                            "src": "hda"
-                        }
-                    ],
+                    "genbank_files": {
+                        "id": "aaa4852d508c750d",
+                        "src": "hdca"
+                    },
                     "sequence_column": "sequence",
                     "table": "sample"
                 },
                 "job": {
-                    "command_line": "python '/home/rkhaled/galaxytools/tools/save_to_db/save_to_db.py' --input '/tmp/tmp_mv7gt3c/files/5/2/2/dataset_5228856a-39be-4f27-afa9-d1f613dea185.dat,/tmp/tmp_mv7gt3c/files/f/a/a/dataset_faa1d0aa-2bb0-47c0-bc3e-949253dd5c3c.dat,/tmp/tmp_mv7gt3c/files/9/6/1/dataset_961fe859-a187-4b45-98ac-bc9c8bd29463.dat,/tmp/tmp_mv7gt3c/files/a/5/c/dataset_a5c56d98-0435-435b-ad8a-01906b2ab961.dat,/tmp/tmp_mv7gt3c/files/2/a/7/dataset_2a788c0d-f89d-4961-95c4-423fd51249f0.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/tmp_mv7gt3c/job_working_directory/000/6/outputs/dataset_c2d55cf8-9c51-42f9-84da-9aa06323c7ce.dat' --file_name_mapping '/tmp/tmp_mv7gt3c/files/5/2/2/dataset_5228856a-39be-4f27-afa9-d1f613dea185.dat:p7_L7Ae-Weiss.gb,/tmp/tmp_mv7gt3c/files/f/a/a/dataset_faa1d0aa-2bb0-47c0-bc3e-949253dd5c3c.dat:p6_Nt-IgKLsequence.gb,/tmp/tmp_mv7gt3c/files/9/6/1/dataset_961fe859-a187-4b45-98ac-bc9c8bd29463.dat:p6_Kozak-ATG.gb,/tmp/tmp_mv7gt3c/files/a/5/c/dataset_a5c56d98-0435-435b-ad8a-01906b2ab961.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmp_mv7gt3c/files/2/a/7/dataset_2a788c0d-f89d-4961-95c4-423fd51249f0.dat:HC_Amp_ccdB.gb'",
+                    "command_line": "python '/home/rkhaled/galaxytools/tools/save_to_db/save_to_db.py' --input '/tmp/tmp4fafueqc/files/c/4/e/dataset_c4ecd213-c62a-48fe-bfd4-f2eb1c1c6439.dat,/tmp/tmp4fafueqc/files/d/2/d/dataset_d2d9d592-9f6a-488b-b911-e2c122dc898f.dat,/tmp/tmp4fafueqc/files/3/7/a/dataset_37a5bcbb-3cf1-45ae-a439-588268402c0b.dat,/tmp/tmp4fafueqc/files/9/d/d/dataset_9dd9b73e-eb2c-460a-b612-86cc1f86f9b6.dat,/tmp/tmp4fafueqc/files/e/7/e/dataset_e7e7bd21-36d3-4e84-9177-2451bfcc09e7.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/tmp4fafueqc/job_working_directory/000/6/outputs/dataset_fdf114e7-4317-491d-8e29-85accf371db7.dat' --file_name_mapping '/tmp/tmp4fafueqc/files/c/4/e/dataset_c4ecd213-c62a-48fe-bfd4-f2eb1c1c6439.dat:p7_L7Ae-Weiss.gb,/tmp/tmp4fafueqc/files/d/2/d/dataset_d2d9d592-9f6a-488b-b911-e2c122dc898f.dat:p6_Nt-IgKLsequence.gb,/tmp/tmp4fafueqc/files/3/7/a/dataset_37a5bcbb-3cf1-45ae-a439-588268402c0b.dat:p6_Kozak-ATG.gb,/tmp/tmp4fafueqc/files/9/d/d/dataset_9dd9b73e-eb2c-460a-b612-86cc1f86f9b6.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmp4fafueqc/files/e/7/e/dataset_e7e7bd21-36d3-4e84-9177-2451bfcc09e7.dat:HC_Amp_ccdB.gb'",
                     "command_version": "",
                     "copied_from_job_id": null,
-                    "create_time": "2025-04-24T09:49:34.459208",
+                    "create_time": "2025-05-23T08:51:13.261313",
                     "dependencies": [],
                     "exit_code": 0,
-                    "external_id": "84720",
+                    "external_id": "53981",
                     "galaxy_version": "24.2",
                     "handler": null,
-                    "history_id": "0ed824750a9f5374",
-                    "id": "016b212ed10ed695",
+                    "history_id": "aaa4852d508c750d",
+                    "id": "42220a2e87c70ae5",
                     "inputs": {
-                        "genbank_files": {
-                            "id": "0ed824750a9f5374",
+                        "genbank_files1": {
+                            "id": "aaa4852d508c750d",
                             "src": "hda",
-                            "uuid": "5228856a-39be-4f27-afa9-d1f613dea185"
-                        },
-                        "genbank_files1": {
-                            "id": "0ed824750a9f5374",
-                            "src": "hda",
-                            "uuid": "5228856a-39be-4f27-afa9-d1f613dea185"
+                            "uuid": "c4ecd213-c62a-48fe-bfd4-f2eb1c1c6439"
                         },
                         "genbank_files2": {
-                            "id": "93c5e169024bda92",
+                            "id": "6139eb08ad8af00a",
                             "src": "hda",
-                            "uuid": "faa1d0aa-2bb0-47c0-bc3e-949253dd5c3c"
+                            "uuid": "d2d9d592-9f6a-488b-b911-e2c122dc898f"
                         },
                         "genbank_files3": {
-                            "id": "7e79446a5abd8b5f",
+                            "id": "cda565c89999ccf5",
                             "src": "hda",
-                            "uuid": "961fe859-a187-4b45-98ac-bc9c8bd29463"
+                            "uuid": "37a5bcbb-3cf1-45ae-a439-588268402c0b"
                         },
                         "genbank_files4": {
-                            "id": "81603bca0e110055",
+                            "id": "f072bab19666d9bc",
                             "src": "hda",
-                            "uuid": "a5c56d98-0435-435b-ad8a-01906b2ab961"
+                            "uuid": "9dd9b73e-eb2c-460a-b612-86cc1f86f9b6"
                         },
                         "genbank_files5": {
-                            "id": "f1c08c8102faa4bc",
+                            "id": "ede1fe394bce0b73",
                             "src": "hda",
-                            "uuid": "2a788c0d-f89d-4961-95c4-423fd51249f0"
+                            "uuid": "e7e7bd21-36d3-4e84-9177-2451bfcc09e7"
                         }
                     },
                     "job_messages": [],
@@ -90,36 +67,37 @@
                     "output_collections": {},
                     "outputs": {
                         "output": {
-                            "id": "016b212ed10ed695",
+                            "id": "42220a2e87c70ae5",
                             "src": "hda",
-                            "uuid": "c2d55cf8-9c51-42f9-84da-9aa06323c7ce"
+                            "uuid": "fdf114e7-4317-491d-8e29-85accf371db7"
                         }
                     },
                     "params": {
                         "__input_ext": "\"input\"",
                         "annotation_column": "\"annotation\"",
-                        "chromInfo": "\"/tmp/tmp_mv7gt3c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+                        "chromInfo": "\"/tmp/tmp4fafueqc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
                         "db_uri": "\"postgresql://postgres:RK17@localhost:5432/test_fragments_db\"",
                         "dbkey": "\"?\"",
                         "fragment_column": "\"fragment\"",
+                        "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}",
                         "sequence_column": "\"sequence\"",
                         "table": "\"sample\""
                     },
                     "state": "ok",
                     "stderr": "",
-                    "stdout": "Container 'test_fragments_db' is already running.\nConnected to database.\nProcessing file: dataset_5228856a-39be-4f27-afa9-d1f613dea185.dat\nProcessing file: dataset_faa1d0aa-2bb0-47c0-bc3e-949253dd5c3c.dat\nProcessing file: dataset_961fe859-a187-4b45-98ac-bc9c8bd29463.dat\nProcessing file: dataset_a5c56d98-0435-435b-ad8a-01906b2ab961.dat\nProcessing file: dataset_2a788c0d-f89d-4961-95c4-423fd51249f0.dat\nInserted 5 fragments.\nFragment names written to '/tmp/tmp_mv7gt3c/job_working_directory/000/6/outputs/dataset_c2d55cf8-9c51-42f9-84da-9aa06323c7ce.dat'.\n",
+                    "stdout": "Container 'test_fragments_db' is already running.\nConnected to database.\nProcessing file: dataset_c4ecd213-c62a-48fe-bfd4-f2eb1c1c6439.dat\nProcessing file: dataset_d2d9d592-9f6a-488b-b911-e2c122dc898f.dat\nProcessing file: dataset_37a5bcbb-3cf1-45ae-a439-588268402c0b.dat\nProcessing file: dataset_9dd9b73e-eb2c-460a-b612-86cc1f86f9b6.dat\nProcessing file: dataset_e7e7bd21-36d3-4e84-9177-2451bfcc09e7.dat\nInserted 5 fragments.\nFragment names written to '/tmp/tmp4fafueqc/job_working_directory/000/6/outputs/dataset_fdf114e7-4317-491d-8e29-85accf371db7.dat'.\n",
                     "tool_id": "save_to_db",
                     "tool_stderr": "",
-                    "tool_stdout": "Container 'test_fragments_db' is already running.\nConnected to database.\nProcessing file: dataset_5228856a-39be-4f27-afa9-d1f613dea185.dat\nProcessing file: dataset_faa1d0aa-2bb0-47c0-bc3e-949253dd5c3c.dat\nProcessing file: dataset_961fe859-a187-4b45-98ac-bc9c8bd29463.dat\nProcessing file: dataset_a5c56d98-0435-435b-ad8a-01906b2ab961.dat\nProcessing file: dataset_2a788c0d-f89d-4961-95c4-423fd51249f0.dat\nInserted 5 fragments.\nFragment names written to '/tmp/tmp_mv7gt3c/job_working_directory/000/6/outputs/dataset_c2d55cf8-9c51-42f9-84da-9aa06323c7ce.dat'.\n",
-                    "update_time": "2025-04-24T09:49:41.678113",
+                    "tool_stdout": "Container 'test_fragments_db' is already running.\nConnected to database.\nProcessing file: dataset_c4ecd213-c62a-48fe-bfd4-f2eb1c1c6439.dat\nProcessing file: dataset_d2d9d592-9f6a-488b-b911-e2c122dc898f.dat\nProcessing file: dataset_37a5bcbb-3cf1-45ae-a439-588268402c0b.dat\nProcessing file: dataset_9dd9b73e-eb2c-460a-b612-86cc1f86f9b6.dat\nProcessing file: dataset_e7e7bd21-36d3-4e84-9177-2451bfcc09e7.dat\nInserted 5 fragments.\nFragment names written to '/tmp/tmp4fafueqc/job_working_directory/000/6/outputs/dataset_fdf114e7-4317-491d-8e29-85accf371db7.dat'.\n",
+                    "update_time": "2025-05-23T08:51:20.615309",
                     "user_email": "planemo@galaxyproject.org",
-                    "user_id": "0ed824750a9f5374"
+                    "user_id": "aaa4852d508c750d"
                 },
                 "status": "success",
                 "test_index": 0,
-                "time_seconds": 26.82854700088501,
+                "time_seconds": 28.753373384475708,
                 "tool_id": "save_to_db",
-                "tool_version": "0.1.0+galaxy0"
+                "tool_version": "0.1.0+galaxy1"
             },
             "has_data": true,
             "id": "save_to_db-0"
--- a/save_to_db.xml	Fri May 16 09:34:35 2025 +0000
+++ b/save_to_db.xml	Fri May 23 08:51:50 2025 +0000
@@ -24,11 +24,11 @@
     ]]></command>
     <inputs>
         <param name="genbank_files" type="data_collection" collection_type="list" format="genbank" label="GenBank File(s)"/>
-        <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_column" type="text" label="DB column contains annotation for ganbank file" optional="false" />
-        <param name="fragment_column" type="text" label="Database Fragments Column Name" optional="false" />
-        <param name="db_uri" type="text" label="Database Connection URI" help="postgresql+psycopg2://username:password@db_container_name:port/database" optional="false" />
+        <param name="table" type="text" label="DB Table Name" optional="false" />
+        <param name="sequence_column" type="text" label="DB Column Contains Sequence For ganbank File" optional="false" />
+        <param name="annotation_column" type="text" label="DB Column Contains Annotation For Ganbank File" optional="false" />
+        <param name="fragment_column" type="text" label="DB IDs Column Name" optional="false" />
+        <param name="db_uri" type="text" label="DB Connection URI" help="postgresql+psycopg2://username:password@db_container_name:port/database" optional="false" />
     </inputs>
     <outputs>
         <data name="output" format="txt" label="saving report" />
@@ -68,7 +68,17 @@
 Save Data To DB
 ===================

-Save GanDank data in SQL DB.
+Implemented a system to save GenBank (.gb) files in SQL DB, based on a connection via URI requests.
+The tool is tested on a locally hosted PostgreSQL database running in a Docker container.
+
+**Parameters**:
+---------------
+* **GenBank File(s)**: List of GenBaks files.
+* **DB Table Name**: Name of the target table in the PostgreSQL database.
+* **DB Column Contains Sequence For ganbank File**: Column storing sequence data, expected to start with "ORIGIN".
+* **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://user:password@host:port/DB_name).
     ]]></help>
     <citations>
         <citation type="bibtex">