Skip to content

GitLab

Closed
Created by Romain Therville@rtherville🐭Contributor

The DownloadSymlink workflow bugs when an analysis is an ONT Demultiplex

When does it happen?

From the "download" page, when selecting an entire project that contains a demultiplex ONT analysis. 2019-12-16_172314

It's okay when the run and analyzes are deployed and selected: 2019-12-16_172422

Why?

In utils.py:

12-16 13:19 Utils DEBUG get_directories_structure_and_content. src_directories = /save/ng6///data/run/fb3cdcb00, /save/ng6///data/analyze/e3df5acbb, /save/ng6///data/analyze/2753b0457, /save/ng6///data/run/b2e7de531, /save/ng6///data/analyze/ae6d2ec97, /save/ng6///data/analyze/cfec28f91 12-16 13:19 Utils DEBUG get_directories_structure_and_content. dest_directories = /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT3_Climares_mtplx6_2_PAD92409.16250/RawData, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT3_Climares_mtplx6_2_PAD92409.16250/Analyse_RUNStats.64606, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT3_Climares_mtplx6_2_PAD92409.16250/Analyse_DemultiplexONT.64608, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT2_Climares_mtplx6_PAD92409.16245/RawData, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT2_Climares_mtplx6_PAD92409.16245/Analyse_DemultiplexONT.64568, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT2_Climares_mtplx6_PAD92409.16245/Analyse_RUNStats.64567, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT3-Climares-mtplx6-2-PAD92409.16250/Analyse_DemultiplexONT.64608, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT3-Climares-mtplx6-2-PAD92409.16250/Analyse_RUNStats.64606, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT2-Climares-mtplx6-PAD92409.16245/Analyse_DemultiplexONT.64568, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT2-Climares-mtplx6-PAD92409.16245/Analyse_RUNStats.64567

(The destination tab contains 2 versions of the same runs and analyzes, one with '-' separatores, one with '_'.)

This may be fixed with an update to the download page's javascript call:

http://ng6-test.toulouse.inra.fr:8080//run_workflow?username=ng6-test&password=aCYLKVdYzI8AaTcB%25C2%25A4%25C3%2596%25C3%25B3i%2540%25C3%2598%2515%25C3%25B6%2522&user_directory=/work/ng6-test/jflow_rtherville/&admin_login=CTD&data_id=15032&run_id=15032&analysis_id=57729::-::57730&workflow_class=DownloadSymlink&callback=jQuery111105034437105204775_1576513683378&_=1576513683383

(By removing the analyzes that have no directory.)

The workflow tries the following treatment:

ln -s /save/ng6/data/run/fb3cdcb00 /work/ng6/Project_CLIMARES.482/Run_ONT3_Climares_mtplx6_2_PAD92409.16250/RawData ln -s /save/ng6/data/analyze/e3df5acbb /work/ng6/Project_CLIMARES.482/Run_ONT3_Climares_mtplx6_2_PAD92409.16250/Analyse_RUNStats.64606 ln -s /save/ng6/data/analyze/2753b0457 /work/ng6/Project_CLIMARES.482/Run_ONT3_Climares_mtplx6_2_PAD92409.16250/Analyse_DemultiplexONT.64608 ln -s /save/ng6/data/run/b2e7de531 /work/ng6/Project_CLIMARES.482/Run_ONT2_Climares_mtplx6_PAD92409.16245/RawData ln -s /save/ng6/data/analyze/ae6d2ec97 /work/ng6/Project_CLIMARES.482/Run_ONT2_Climares_mtplx6_PAD92409.16245/Analyse_DemultiplexONT.64568 ln -s /save/ng6/data/analyze/cfec28f91 /work/ng6/Project_CLIMARES.482/Run_ONT2_Climares_mtplx6_PAD92409.16245/Analyse_RUNStats.64567

But fails, BECAUSE /save/ng6/data/analyze/2753b0457 AND /save/ng6/data/analyze/ae6d2ec97 DO NOT EXIST!