Mercurial > repos > tduigou > save_to_db
diff output.json @ 5:f934215bdb78 draft default tip
planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
| author | tduigou |
|---|---|
| date | Mon, 02 Jun 2025 10:29:28 +0000 |
| parents | c7a7520afb4b |
| children |
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--- a/output.json Mon Jun 02 09:48:14 2025 +0000 +++ b/output.json Mon Jun 02 10:29:28 2025 +0000 @@ -1,65 +1,65 @@ { "summary": { "num_errors": 0, - "num_failures": 0, + "num_failures": 1, "num_skips": 0, - "num_tests": 1 + "num_tests": 2 }, "tests": [ { "data": { "inputs": { "adv|json_conf": { - "id": "1895a93fdf3c72e9", + "id": "c9e99bc7539b08e5", "src": "hda" }, "genbank_files": { - "id": "c0d7a43ba58f94b5", + "id": "c804608f95de6282", "src": "hdca" } }, "job": { - "command_line": "python '/home/rkhaled/galaxytools/tools/save_to_db/save_to_db.py' --input '/tmp/tmpxct9x70x/files/3/0/f/dataset_30fc2017-6620-4a80-a60e-0c795c89f106.dat,/tmp/tmpxct9x70x/files/b/f/b/dataset_bfb54321-8ad0-4e42-b307-f32e47e0618a.dat,/tmp/tmpxct9x70x/files/1/e/5/dataset_1e5a0d80-dc9e-42d0-b0e1-c2e78aff18d3.dat,/tmp/tmpxct9x70x/files/a/b/a/dataset_aba8d5b4-a4f3-4487-803c-be5dee1445cd.dat,/tmp/tmpxct9x70x/files/7/b/7/dataset_7b7fb70f-da0c-45e7-ba4e-0e8cb8d31968.dat' --sequence_column '' --annotation_column '' --db_uri '' --table '' --fragment_column '' --output '/tmp/tmpxct9x70x/job_working_directory/000/7/outputs/dataset_41b844ab-5a85-46cd-8367-7ad1fbee7d3c.dat' --file_name_mapping '/tmp/tmpxct9x70x/files/3/0/f/dataset_30fc2017-6620-4a80-a60e-0c795c89f106.dat:p7_L7Ae-Weiss.gb,/tmp/tmpxct9x70x/files/b/f/b/dataset_bfb54321-8ad0-4e42-b307-f32e47e0618a.dat:p6_Nt-IgKLsequence.gb,/tmp/tmpxct9x70x/files/1/e/5/dataset_1e5a0d80-dc9e-42d0-b0e1-c2e78aff18d3.dat:p6_Kozak-ATG.gb,/tmp/tmpxct9x70x/files/a/b/a/dataset_aba8d5b4-a4f3-4487-803c-be5dee1445cd.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmpxct9x70x/files/7/b/7/dataset_7b7fb70f-da0c-45e7-ba4e-0e8cb8d31968.dat:HC_Amp_ccdB.gb' --json_conf '/tmp/tmpxct9x70x/files/f/4/f/dataset_f4fd59e8-f8d6-4be2-8b00-9e12ca8319ef.dat'", + "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": "2025-06-02T09:46:35.368351", + "create_time": "2025-06-02T10:25:46.744304", "dependencies": [], "exit_code": 0, - "external_id": "129989", + "external_id": "148807", "galaxy_version": "24.2", "handler": null, - "history_id": "c0d7a43ba58f94b5", - "id": "92e9df4c7abf24ab", + "history_id": "c804608f95de6282", + "id": "91a273dde5f46de6", "inputs": { "adv|json_conf": { - "id": "1895a93fdf3c72e9", + "id": "c9e99bc7539b08e5", "src": "hda", - "uuid": "f4fd59e8-f8d6-4be2-8b00-9e12ca8319ef" + "uuid": "b3e3a95b-dd84-41de-b53b-ea44d034e11b" }, "genbank_files1": { - "id": "c0d7a43ba58f94b5", + "id": "c804608f95de6282", "src": "hda", - "uuid": "30fc2017-6620-4a80-a60e-0c795c89f106" + "uuid": "a5a56a5c-573a-4b34-8c98-27b2edff54f3" }, "genbank_files2": { - "id": "1e3e46a5cbeec338", + "id": "dc78a71e9d46a610", "src": "hda", - "uuid": "bfb54321-8ad0-4e42-b307-f32e47e0618a" + "uuid": "1779bfb3-ff31-4b6d-8c6f-82172c987fee" }, "genbank_files3": { - "id": "81fab13a93a3da95", + "id": "32d06e9182be9fe5", "src": "hda", - "uuid": "1e5a0d80-dc9e-42d0-b0e1-c2e78aff18d3" + "uuid": "4cc83056-e7b7-4dcd-9360-cde2bc1978f1" }, "genbank_files4": { - "id": "a9ff23755d49e4b6", + "id": "a50e356be1f2db6f", "src": "hda", - "uuid": "aba8d5b4-a4f3-4487-803c-be5dee1445cd" + "uuid": "969b7b35-4f05-48bc-92f5-4e2f5ce375ca" }, "genbank_files5": { - "id": "2ca788c708559c16", + "id": "64d80998680b05e1", "src": "hda", - "uuid": "7b7fb70f-da0c-45e7-ba4e-0e8cb8d31968" + "uuid": "7b47f46b-3e00-4a65-9c9a-6a25e3c30b04" } }, "job_messages": [], @@ -71,16 +71,16 @@ "output_collections": {}, "outputs": { "output": { - "id": "92e9df4c7abf24ab", + "id": "91a273dde5f46de6", "src": "hda", - "uuid": "41b844ab-5a85-46cd-8367-7ad1fbee7d3c" + "uuid": "89f2f3f4-04a0-4998-a3f6-d065b9e1f365" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"json_conf\": {\"values\": [{\"id\": 6, \"src\": \"hda\"}]}}", "annotation_column": null, - "chromInfo": "\"/tmp/tmpxct9x70x/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmpgfe8mdmw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "db_uri": null, "dbkey": "\"?\"", "fragment_column": null, @@ -90,22 +90,193 @@ }, "state": "ok", "stderr": "", - "stdout": "Container 'test_fragments_db' is already running.\nConnected to database.\nProcessing file: dataset_30fc2017-6620-4a80-a60e-0c795c89f106.dat\nProcessing file: dataset_bfb54321-8ad0-4e42-b307-f32e47e0618a.dat\nProcessing file: dataset_1e5a0d80-dc9e-42d0-b0e1-c2e78aff18d3.dat\nProcessing file: dataset_aba8d5b4-a4f3-4487-803c-be5dee1445cd.dat\nProcessing file: dataset_7b7fb70f-da0c-45e7-ba4e-0e8cb8d31968.dat\nInserted 5 fragments.\nFragment names written to '/tmp/tmpxct9x70x/job_working_directory/000/7/outputs/dataset_41b844ab-5a85-46cd-8367-7ad1fbee7d3c.dat'.\n", + "stdout": "Execution was blocked by config (execution = false)\n", "tool_id": "save_to_db", "tool_stderr": "", - "tool_stdout": "Container 'test_fragments_db' is already running.\nConnected to database.\nProcessing file: dataset_30fc2017-6620-4a80-a60e-0c795c89f106.dat\nProcessing file: dataset_bfb54321-8ad0-4e42-b307-f32e47e0618a.dat\nProcessing file: dataset_1e5a0d80-dc9e-42d0-b0e1-c2e78aff18d3.dat\nProcessing file: dataset_aba8d5b4-a4f3-4487-803c-be5dee1445cd.dat\nProcessing file: dataset_7b7fb70f-da0c-45e7-ba4e-0e8cb8d31968.dat\nInserted 5 fragments.\nFragment names written to '/tmp/tmpxct9x70x/job_working_directory/000/7/outputs/dataset_41b844ab-5a85-46cd-8367-7ad1fbee7d3c.dat'.\n", - "update_time": "2025-06-02T09:46:41.929779", + "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": "c0d7a43ba58f94b5" + "user_id": "c804608f95de6282" }, - "status": "success", + "output_problems": [ + "Output output: different than expected\nExpected 5+-0 lines in the output found 0" + ], + "status": "failure", "test_index": 0, - "time_seconds": 29.02011752128601, + "time_seconds": 28.49768567085266, "tool_id": "save_to_db", - "tool_version": "0.1.0+galaxy1" + "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"