Mercurial > repos > tduigou > save_to_db

view output.json @ 5:f934215bdb78 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
author tduigou
date Mon, 02 Jun 2025 10:29:28 +0000
parents c7a7520afb4b
children
line wrap: on
line source

{
    "summary": {
        "num_errors": 0,
        "num_failures": 1,
        "num_skips": 0,
        "num_tests": 2
    },
    "tests": [
        {
            "data": {
                "inputs": {
                    "adv|json_conf": {
                        "id": "c9e99bc7539b08e5",
                        "src": "hda"
                    },
                    "genbank_files": {
                        "id": "c804608f95de6282",
                        "src": "hdca"
                    }
                },
                "job": {
                    "command_line": "python '/home/rkhaled/galaxytools/tools/save_to_db/save_to_db.py' --input '/tmp/tmpgfe8mdmw/files/a/5/a/dataset_a5a56a5c-573a-4b34-8c98-27b2edff54f3.dat,/tmp/tmpgfe8mdmw/files/1/7/7/dataset_1779bfb3-ff31-4b6d-8c6f-82172c987fee.dat,/tmp/tmpgfe8mdmw/files/4/c/c/dataset_4cc83056-e7b7-4dcd-9360-cde2bc1978f1.dat,/tmp/tmpgfe8mdmw/files/9/6/9/dataset_969b7b35-4f05-48bc-92f5-4e2f5ce375ca.dat,/tmp/tmpgfe8mdmw/files/7/b/4/dataset_7b47f46b-3e00-4a65-9c9a-6a25e3c30b04.dat' --sequence_column '' --annotation_column '' --db_uri '' --table '' --fragment_column '' --output '/tmp/tmpgfe8mdmw/job_working_directory/000/7/outputs/dataset_89f2f3f4-04a0-4998-a3f6-d065b9e1f365.dat' --file_name_mapping '/tmp/tmpgfe8mdmw/files/a/5/a/dataset_a5a56a5c-573a-4b34-8c98-27b2edff54f3.dat:p7_L7Ae-Weiss.gb,/tmp/tmpgfe8mdmw/files/1/7/7/dataset_1779bfb3-ff31-4b6d-8c6f-82172c987fee.dat:p6_Nt-IgKLsequence.gb,/tmp/tmpgfe8mdmw/files/4/c/c/dataset_4cc83056-e7b7-4dcd-9360-cde2bc1978f1.dat:p6_Kozak-ATG.gb,/tmp/tmpgfe8mdmw/files/9/6/9/dataset_969b7b35-4f05-48bc-92f5-4e2f5ce375ca.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmpgfe8mdmw/files/7/b/4/dataset_7b47f46b-3e00-4a65-9c9a-6a25e3c30b04.dat:HC_Amp_ccdB.gb' --json_conf '/tmp/tmpgfe8mdmw/files/b/3/e/dataset_b3e3a95b-dd84-41de-b53b-ea44d034e11b.dat'",
                    "command_version": "",
                    "copied_from_job_id": null,
                    "create_time": "2025-06-02T10:25:46.744304",
                    "dependencies": [],
                    "exit_code": 0,
                    "external_id": "148807",
                    "galaxy_version": "24.2",
                    "handler": null,
                    "history_id": "c804608f95de6282",
                    "id": "91a273dde5f46de6",
                    "inputs": {
                        "adv|json_conf": {
                            "id": "c9e99bc7539b08e5",
                            "src": "hda",
                            "uuid": "b3e3a95b-dd84-41de-b53b-ea44d034e11b"
                        },
                        "genbank_files1": {
                            "id": "c804608f95de6282",
                            "src": "hda",
                            "uuid": "a5a56a5c-573a-4b34-8c98-27b2edff54f3"
                        },
                        "genbank_files2": {
                            "id": "dc78a71e9d46a610",
                            "src": "hda",
                            "uuid": "1779bfb3-ff31-4b6d-8c6f-82172c987fee"
                        },
                        "genbank_files3": {
                            "id": "32d06e9182be9fe5",
                            "src": "hda",
                            "uuid": "4cc83056-e7b7-4dcd-9360-cde2bc1978f1"
                        },
                        "genbank_files4": {
                            "id": "a50e356be1f2db6f",
                            "src": "hda",
                            "uuid": "969b7b35-4f05-48bc-92f5-4e2f5ce375ca"
                        },
                        "genbank_files5": {
                            "id": "64d80998680b05e1",
                            "src": "hda",
                            "uuid": "7b47f46b-3e00-4a65-9c9a-6a25e3c30b04"
                        }
                    },
                    "job_messages": [],
                    "job_metrics": [],
                    "job_runner_name": null,
                    "job_stderr": "",
                    "job_stdout": "",
                    "model_class": "Job",
                    "output_collections": {},
                    "outputs": {
                        "output": {
                            "id": "91a273dde5f46de6",
                            "src": "hda",
                            "uuid": "89f2f3f4-04a0-4998-a3f6-d065b9e1f365"
                        }
                    },
                    "params": {
                        "__input_ext": "\"input\"",
                        "adv": "{\"json_conf\": {\"values\": [{\"id\": 6, \"src\": \"hda\"}]}}",
                        "annotation_column": null,
                        "chromInfo": "\"/tmp/tmpgfe8mdmw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
                        "db_uri": null,
                        "dbkey": "\"?\"",
                        "fragment_column": null,
                        "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}",
                        "sequence_column": null,
                        "table": null
                    },
                    "state": "ok",
                    "stderr": "",
                    "stdout": "Execution was blocked by config (execution = false)\n",
                    "tool_id": "save_to_db",
                    "tool_stderr": "",
                    "tool_stdout": "Execution was blocked by config (execution = false)\n",
                    "update_time": "2025-06-02T10:25:54.228017",
                    "user_email": "planemo@galaxyproject.org",
                    "user_id": "c804608f95de6282"
                },
                "output_problems": [
                    "Output output:  different than expected\nExpected 5+-0 lines in the output found 0"
                ],
                "status": "failure",
                "test_index": 0,
                "time_seconds": 28.49768567085266,
                "tool_id": "save_to_db",
                "tool_version": "0.2.0+galaxy2"
            },
            "has_data": true,
            "id": "save_to_db-0"
        },
        {
            "data": {
                "inputs": {
                    "adv|json_conf": {
                        "id": "ba5e0bd88cc3030c",
                        "src": "hda"
                    },
                    "genbank_files": {
                        "id": "dc78a71e9d46a610",
                        "src": "hdca"
                    }
                },
                "job": {
                    "command_line": "python '/home/rkhaled/galaxytools/tools/save_to_db/save_to_db.py' --input '/tmp/tmpgfe8mdmw/files/3/6/2/dataset_362bcc57-3b7e-4089-b9c7-33155498d352.dat,/tmp/tmpgfe8mdmw/files/4/e/0/dataset_4e03baea-fd7c-45b3-b808-4443adc60f91.dat,/tmp/tmpgfe8mdmw/files/6/d/a/dataset_6da90158-c02d-457e-8908-56b532b4b3c2.dat,/tmp/tmpgfe8mdmw/files/8/0/b/dataset_80b64d26-b0b2-40df-ad9b-41446c172705.dat,/tmp/tmpgfe8mdmw/files/3/8/7/dataset_38751000-4953-44bb-b142-81b4bc41ad97.dat' --sequence_column '' --annotation_column '' --db_uri '' --table '' --fragment_column '' --output '/tmp/tmpgfe8mdmw/job_working_directory/000/14/outputs/dataset_ee43072f-661d-47e0-b30f-d905aac37a4a.dat' --file_name_mapping '/tmp/tmpgfe8mdmw/files/3/6/2/dataset_362bcc57-3b7e-4089-b9c7-33155498d352.dat:p7_L7Ae-Weiss.gb,/tmp/tmpgfe8mdmw/files/4/e/0/dataset_4e03baea-fd7c-45b3-b808-4443adc60f91.dat:p6_Nt-IgKLsequence.gb,/tmp/tmpgfe8mdmw/files/6/d/a/dataset_6da90158-c02d-457e-8908-56b532b4b3c2.dat:p6_Kozak-ATG.gb,/tmp/tmpgfe8mdmw/files/8/0/b/dataset_80b64d26-b0b2-40df-ad9b-41446c172705.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmpgfe8mdmw/files/3/8/7/dataset_38751000-4953-44bb-b142-81b4bc41ad97.dat:HC_Amp_ccdB.gb' --json_conf '/tmp/tmpgfe8mdmw/files/8/3/d/dataset_83ddd986-5a07-406e-91f8-fcc403a6e927.dat'",
                    "command_version": "",
                    "copied_from_job_id": null,
                    "create_time": "2025-06-02T10:26:14.771419",
                    "dependencies": [
                        {
                            "cacheable": false,
                            "dependency_resolver": {
                                "auto_init": true,
                                "auto_install": true,
                                "can_uninstall_dependencies": true,
                                "ensure_channels": "conda-forge,bioconda",
                                "model_class": "CondaDependencyResolver",
                                "prefix": "/home/rkhaled/miniconda3",
                                "read_only": false,
                                "resolver_type": "conda",
                                "resolves_simple_dependencies": true,
                                "use_local": false,
                                "versionless": false
                            },
                            "dependency_type": "conda",
                            "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966",
                            "exact": true,
                            "model_class": "MergedCondaDependency",
                            "name": "pandas",
                            "version": "2.2.3"
                        },
                        {
                            "cacheable": false,
                            "dependency_resolver": {
                                "auto_init": true,
                                "auto_install": true,
                                "can_uninstall_dependencies": true,
                                "ensure_channels": "conda-forge,bioconda",
                                "model_class": "CondaDependencyResolver",
                                "prefix": "/home/rkhaled/miniconda3",
                                "read_only": false,
                                "resolver_type": "conda",
                                "resolves_simple_dependencies": true,
                                "use_local": false,
                                "versionless": false
                            },
                            "dependency_type": "conda",
                            "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966",
                            "exact": true,
                            "model_class": "MergedCondaDependency",
                            "name": "sqlalchemy",
                            "version": "2.0.40"
                        },
                        {
                            "cacheable": false,
                            "dependency_resolver": {
                                "auto_init": true,
                                "auto_install": true,
                                "can_uninstall_dependencies": true,
                                "ensure_channels": "conda-forge,bioconda",
                                "model_class": "CondaDependencyResolver",
                                "prefix": "/home/rkhaled/miniconda3",
                                "read_only": false,
                                "resolver_type": "conda",
                                "resolves_simple_dependencies": true,
                                "use_local": false,
                                "versionless": false
                            },
                            "dependency_type": "conda",
                            "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966",
                            "exact": true,
                            "model_class": "MergedCondaDependency",
                            "name": "psycopg2",
                            "version": "2.9.9"
                        }
                    ],
                    "exit_code": 0,
                    "external_id": "149308",
                    "galaxy_version": "24.2",
                    "handler": null,
                    "history_id": "dc78a71e9d46a610",
                    "id": "c6ad8bbeb64086ff",
                    "inputs": {
                        "adv|json_conf": {
                            "id": "ba5e0bd88cc3030c",
                            "src": "hda",
                            "uuid": "83ddd986-5a07-406e-91f8-fcc403a6e927"
                        },
                        "genbank_files1": {
                            "id": "4da6c37b755c621f",
                            "src": "hda",
                            "uuid": "362bcc57-3b7e-4089-b9c7-33155498d352"
                        },
                        "genbank_files2": {
                            "id": "83933cf19817c19f",
                            "src": "hda",
                            "uuid": "4e03baea-fd7c-45b3-b808-4443adc60f91"
                        },
                        "genbank_files3": {
                            "id": "33ff3c6dc742881e",
                            "src": "hda",
                            "uuid": "6da90158-c02d-457e-8908-56b532b4b3c2"
                        },
                        "genbank_files4": {
                            "id": "8187d0d2b67e72bf",
                            "src": "hda",
                            "uuid": "80b64d26-b0b2-40df-ad9b-41446c172705"
                        },
                        "genbank_files5": {
                            "id": "a744ea399046e427",
                            "src": "hda",
                            "uuid": "38751000-4953-44bb-b142-81b4bc41ad97"
                        }
                    },
                    "job_messages": [],
                    "job_metrics": [],
                    "job_runner_name": null,
                    "job_stderr": "",
                    "job_stdout": "",
                    "model_class": "Job",
                    "output_collections": {},
                    "outputs": {
                        "output": {
                            "id": "c6ad8bbeb64086ff",
                            "src": "hda",
                            "uuid": "ee43072f-661d-47e0-b30f-d905aac37a4a"
                        }
                    },
                    "params": {
                        "__input_ext": "\"input\"",
                        "adv": "{\"json_conf\": {\"values\": [{\"id\": 13, \"src\": \"hda\"}]}}",
                        "annotation_column": null,
                        "chromInfo": "\"/tmp/tmpgfe8mdmw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
                        "db_uri": null,
                        "dbkey": "\"?\"",
                        "fragment_column": null,
                        "genbank_files": "{\"values\": [{\"id\": 2, \"src\": \"hdca\"}]}",
                        "sequence_column": null,
                        "table": null
                    },
                    "state": "ok",
                    "stderr": "",
                    "stdout": "Container 'test_fragments_db' is already running.\nConnected to database.\nProcessing file: dataset_362bcc57-3b7e-4089-b9c7-33155498d352.dat(p7_L7Ae-Weiss)\nProcessing file: dataset_4e03baea-fd7c-45b3-b808-4443adc60f91.dat(p6_Nt-IgKLsequence)\nProcessing file: dataset_6da90158-c02d-457e-8908-56b532b4b3c2.dat(p6_Kozak-ATG)\nProcessing file: dataset_80b64d26-b0b2-40df-ad9b-41446c172705.dat(p4_Kt-L7Ae-Weiss)\nProcessing file: dataset_38751000-4953-44bb-b142-81b4bc41ad97.dat(HC_Amp_ccdB)\nInserted 5 fragments.\nFragment names written to '/tmp/tmpgfe8mdmw/job_working_directory/000/14/outputs/dataset_ee43072f-661d-47e0-b30f-d905aac37a4a.dat'.\n",
                    "tool_id": "save_to_db",
                    "tool_stderr": "",
                    "tool_stdout": "Container 'test_fragments_db' is already running.\nConnected to database.\nProcessing file: dataset_362bcc57-3b7e-4089-b9c7-33155498d352.dat(p7_L7Ae-Weiss)\nProcessing file: dataset_4e03baea-fd7c-45b3-b808-4443adc60f91.dat(p6_Nt-IgKLsequence)\nProcessing file: dataset_6da90158-c02d-457e-8908-56b532b4b3c2.dat(p6_Kozak-ATG)\nProcessing file: dataset_80b64d26-b0b2-40df-ad9b-41446c172705.dat(p4_Kt-L7Ae-Weiss)\nProcessing file: dataset_38751000-4953-44bb-b142-81b4bc41ad97.dat(HC_Amp_ccdB)\nInserted 5 fragments.\nFragment names written to '/tmp/tmpgfe8mdmw/job_working_directory/000/14/outputs/dataset_ee43072f-661d-47e0-b30f-d905aac37a4a.dat'.\n",
                    "update_time": "2025-06-02T10:26:21.180586",
                    "user_email": "planemo@galaxyproject.org",
                    "user_id": "c804608f95de6282"
                },
                "status": "success",
                "test_index": 1,
                "time_seconds": 26.70093870162964,
                "tool_id": "save_to_db",
                "tool_version": "0.2.0+galaxy2"
            },
            "has_data": true,
            "id": "save_to_db-1"
        }
    ],
    "version": "0.1"
}