diff output.json @ 0:034686b5bc15 draft

planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
author tduigou
date Thu, 24 Apr 2025 09:56:36 +0000
parents
children eca0d710bbe9
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/output.json	Thu Apr 24 09:56:36 2025 +0000
@@ -0,0 +1,129 @@
+{
+    "summary": {
+        "num_errors": 0,
+        "num_failures": 0,
+        "num_skips": 0,
+        "num_tests": 1
+    },
+    "tests": [
+        {
+            "data": {
+                "inputs": {
+                    "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"
+                        }
+                    ],
+                    "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_version": "",
+                    "copied_from_job_id": null,
+                    "create_time": "2025-04-24T09:49:34.459208",
+                    "dependencies": [],
+                    "exit_code": 0,
+                    "external_id": "84720",
+                    "galaxy_version": "24.2",
+                    "handler": null,
+                    "history_id": "0ed824750a9f5374",
+                    "id": "016b212ed10ed695",
+                    "inputs": {
+                        "genbank_files": {
+                            "id": "0ed824750a9f5374",
+                            "src": "hda",
+                            "uuid": "5228856a-39be-4f27-afa9-d1f613dea185"
+                        },
+                        "genbank_files1": {
+                            "id": "0ed824750a9f5374",
+                            "src": "hda",
+                            "uuid": "5228856a-39be-4f27-afa9-d1f613dea185"
+                        },
+                        "genbank_files2": {
+                            "id": "93c5e169024bda92",
+                            "src": "hda",
+                            "uuid": "faa1d0aa-2bb0-47c0-bc3e-949253dd5c3c"
+                        },
+                        "genbank_files3": {
+                            "id": "7e79446a5abd8b5f",
+                            "src": "hda",
+                            "uuid": "961fe859-a187-4b45-98ac-bc9c8bd29463"
+                        },
+                        "genbank_files4": {
+                            "id": "81603bca0e110055",
+                            "src": "hda",
+                            "uuid": "a5c56d98-0435-435b-ad8a-01906b2ab961"
+                        },
+                        "genbank_files5": {
+                            "id": "f1c08c8102faa4bc",
+                            "src": "hda",
+                            "uuid": "2a788c0d-f89d-4961-95c4-423fd51249f0"
+                        }
+                    },
+                    "job_messages": [],
+                    "job_metrics": [],
+                    "job_runner_name": null,
+                    "job_stderr": "",
+                    "job_stdout": "",
+                    "model_class": "Job",
+                    "output_collections": {},
+                    "outputs": {
+                        "output": {
+                            "id": "016b212ed10ed695",
+                            "src": "hda",
+                            "uuid": "c2d55cf8-9c51-42f9-84da-9aa06323c7ce"
+                        }
+                    },
+                    "params": {
+                        "__input_ext": "\"input\"",
+                        "annotation_column": "\"annotation\"",
+                        "chromInfo": "\"/tmp/tmp_mv7gt3c/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+                        "db_uri": "\"postgresql://postgres:RK17@localhost:5432/test_fragments_db\"",
+                        "dbkey": "\"?\"",
+                        "fragment_column": "\"fragment\"",
+                        "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",
+                    "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",
+                    "user_email": "planemo@galaxyproject.org",
+                    "user_id": "0ed824750a9f5374"
+                },
+                "status": "success",
+                "test_index": 0,
+                "time_seconds": 26.82854700088501,
+                "tool_id": "save_to_db",
+                "tool_version": "0.1.0+galaxy0"
+            },
+            "has_data": true,
+            "id": "save_to_db-0"
+        }
+    ],
+    "version": "0.1"
+}
\ No newline at end of file