Merge discvr 21.3 #109
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Merge discvr 21.3 #109
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Added demo plugin to demo config
Base demo plugin added to demo config
labkey-jeckels
approved these changes
Jun 26, 2021
| var config = { | ||
| containerID: "GenomeBrowser", | ||
| baseUrl: "<%=h(base)%>", |
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This should be q() as well, though the base URL is unlikely to have quotes in it so very low risk.
bbimber
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Nov 7, 2021
* Refactor JBrowse search component into a separate package/app, and move the Ajax call into RefNameAutocompleteWrapper
bbimber
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Dec 16, 2021
* Implement RefNameAutocomplete view of the current session * Add correct navigation URL * Remove unneeded imports * Use session id instead of track id * Use unique key in all tables to stop devtools warning (#98) * Upgrade to jbrowse 1.5.0 * Fix location navigation on search submit * Use correct container when updating replaced readsets * Fix console error on submit with no input * Add Search test -- no session provided * Test stub * Add navigate check * Test search box autocomplete * Fix JBrowseTest typo * Fix final JBrowseTest compilation error * Add option to run DietSeurat prior to merge * Fix timing issue on test * Wait for search autocomplete dropdown * Handle case where expected result is not the first elem * Correct values for expected and optionText in SequenceTest * Use external /tmp directory when running seurat docker jobs * Allow saturation calculation to run on merged objects, and to run on ADT/HTO data * Bugfix filepath in AppendSaturation * Bugfix fieldname in AppendSaturation * Variant Filtering and UI (#105) * Hardcoded filtering * check adapterConfig.filters exists before setting filters * Read filters from FilterWidget/filters.js * Removed logging * filter config try/catch blocks * expandedFilter syntax * Handle when no filters added in config * Tidied up some comments and leftover code * Switched from raw string eval to jexl (#102) * base filter ui functionality * Cleaned up FilterWidget.js * Update filter syntax in mGAPsession * Filter UI tests * Updated styling to table format and updated tests * removed some unneeded comments and code * Removed more comments * Merge tidying and invalid config filter handling * Invalid config filter test * Tidied up filterUtil * Updated testAddingNumericFilter() for TC debug * Attempt to fix TeamCity-specific JBrowseTest failure * Removed extra comma Co-authored-by: bbimber <bbimber@gmail.com> * Bugfix to AppendSaturation * Fix Title Mapping (#108) * Fixed title mapping * Updated testTitleMapping() * Allow cell hashing to pass molInfo file to calculate saturation * Correctly copy molInfo file locally to cluster * Allow hashing to be run retroactively * Allow nextclade AA import to skip complex indels * Change default value for hashing param * Bugfix to SubsetSeurat when a downstream filter returns zero cells * Fix R syntax * Enable seurat merge to include extra validation * Allow GenotypeGVCFHandler to leave a memory buffer for C layer * Refactor JBrowse search component into a separate package/app (#109) * Refactor JBrowse search component into a separate package/app, and move the Ajax call into RefNameAutocompleteWrapper * Fix for blank filter bug (#111) * Improved logging on slurm execution errors * Reduced the number of times we load seurat objects into memory * Fix typo * Attempt to fix test intermittent failures (#112) * Attempt to fix test intermittent failures * Bugfix seurat merge * Allow TagPcrSummaryStep to run when Blast module not enabled * Change default for GenotypeGVCFs --max-alternate-alleles * Support --include-reverse-reads for IntegrationSiteMapper * Add hook to enable more verbose cluster logging * Color Widget (#114) * Base color widget functionality * Color widget tests * Tidied up leftover dev comments * Updated icon, removed unused comments * Removed unneeded imports, tidied up logs * Patches to fix warnings * setColor cleanup, Filter key * Tidied some JSX whitespace Co-authored-by: hextraza <sebastiancbenjamin@gmail.com> Co-authored-by: James Trotter <43728787+jctrotter@users.noreply.github.com>
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