35254 Add Metagenomic Workflow #1473
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johnphan96
commented
Nov 27, 2024
johnphan96
commented
- Aded MetagenomicsBatch and MetagenomicsBatchItem interfaces
- Added metagenomics-workflow/list page
- Added links to main page and navbar to metagenomics-workflow/list
- Added metagenomics-workflow/run page
- Added required tabs for run page with MetagenomicsBatchDetailsStep and a few stub tabs
- Aded MetagenomicsBatch and MetagenomicsBatchItem interfaces - Added metagenomics-workflow/list page - Added links to main page and navbar to metagenomics-workflow/list - Added metagenomics-workflow/run page - Added required tabs for run page with MetagenomicsBatchDetailsStep and a few stub tabs
- Revised tabs in metagenomics-workflow - Added PCR Batch tab, can save and load PCR batch - Added Select Material Samples tab, can select and create pcr-batch-items - Added Select Coordinates tab, can choose coordinates and save storageUnitUsages - Addded PCR Reaction Results tab, can save result of pcr-batch-items - Fixed Metagenomics Batch tab, can save and load metagenomics batch by reverse look up from PcrBatch uuid
- Added Index Assignment tab - Implemented Assign by table to fit usage of MetagenimicsBatchItem and PcrBatchItem - Assign by table correctly loads Well Coordinates and Material Sample Name - Can assign, save, and load Index i5 and Index i7
- Implemented Index Assignment Assign by grid that works with metagenomics batch item - Can select index, save, and load
- Added MolecularAnalysisRunItem relationship to MetagenomicsBatchItem - Implemented Run tab to create MoleclarAnalysisRun + RunItem and link to MetagenomicsBatchItem - Can save and load MolecularAnalysisRun TODO: - Need to modify SelectMaterialSamples step to create MolecularAnalysisRunItems for new select samples if MolecularAnalysisRun exists - Handle deleting MetagenomicsBatchItems, MetagenomicsBatch, MolecularAnalysisRunItems, MolecularAnalysisRun when samples are deselected
- Fixed bug where data was not being loaded in Index Assignment tab on MetadatagenomicsBatch first creation - Fixed bug where workflow was not redirected to Run tab from Index Assignment tab on save - Selecting new material samples from the Select Material Samples tab when there's a MetagenomicsBatch should create MetagenomicsBatchItems - Selecting new material samples from the Select Material Samples tab when there's a MolecularAnalysisRun should create MolecularAnalysisRunItems - Removing material samples from Select Material Samples tab should delete MetagenomicsBatchItem, MolecularAnalysisRunItem, and PcrBatchItem
- Now automatically selects Illumina Metagenomics for Batch Type and disables dropdown - molecular-analysis-run/view page now supports usageType "metagenomics-batch-item" - I wasn't able to replicate the Index Assignment tab not loading. The rendering of the tab should be dictated by presence of Metagenomics Batch and Pcr Batch
brandonandre
approved these changes
Dec 4, 2024
brandonandre
approved these changes
Dec 4, 2024
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