Mobile Site Development #533
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…oints should be publicly accessible.
…into mobile-dev
* Rsvg workflow main (#420) * Created input files and files for rsv * Ready for testing * Successful dry run * Successfully ran snakemake * Accept partial genomes from GenBank * Documented availbale genbank fields * Updated vvsearch2 documentation * Added complete list of response fields * Updated workflow, allows multiple sequences in reference.fasta * Finalized workflow_rsv_main, ready to move on to server * RSVG and CG run on different dbs * Server and postgres working for RSVG * Changed config from SARS-CoV-2 to sars2 * Frontend loads for rsvg * Added exampleStore to dynamically import examples according to config.virus * Updated examples.rsv.js to work with new exampleStore * Initial values for stores now defined in initialValueStore, allowing different values for different viruses * plotSettingsStore now reads initialValues from initialvalueStore * Moved intialValueStore to App to ensure intial values are set before stores are initialized * Removed a console.log * Added defs.json imports to rsv intialValues * hotfix: mutation extractions for insertions * CORS fix (#421) * Converted logo from svg to png * Added AY.4 as a defualt group to the lineage report tab. * CORS fix. Blanket CORS on all routes, can be changed if some API endpoints should be publicly accessible. * Added covidcg.org default url to CORS for safety * Tooltip Fix - Rebased (#423) * Converted logo from svg to png * Added AY.4 as a defualt group to the lineage report tab. * CORS fix. Blanket CORS on all routes, can be changed if some API endpoints should be publicly accessible. * Added covidcg.org default url to CORS for safety * Fixed tooltip rebuilds on mode switches. * Tree Line Width Fix (#424) * CORS fix. Blanket CORS on all routes, can be changed if some API endpoints should be publicly accessible. * Added covidcg.org default url to CORS for safety * Fixed tooltip rebuilds on mode switches. * Set line width of Vega tree to fixed width of 1to improve readability. * Sequences from before 1996 are not chunked into the fasta files (#425) * Question Button Fix (#427) * CORS fix. Blanket CORS on all routes, can be changed if some API endpoints should be publicly accessible. * Added covidcg.org default url to CORS for safety * Fixed tooltip rebuilds on mode switches. * Set line width of Vega tree to fixed width of 1to improve readability. * Refactored Tooltip fix * Albert the all-knowing * Fixes (v2.2.4) (#400) * Fix #398, along with other UI persistence issues in surveillance plot * Adjust axis labels for sequencing effort plot, change case axis from log to linear * Fix paths in database push script * Limit cores for final analysis tasks to limit RAM consumption * Ignore AA extraction errors for now - need to address large insertions in some genomes * rename strain to virus_name, for phylotree analyses * Update pangolin deps * Bump to v2.2.4 * Rsolved conflict * Resolved conflict * Resolved conflict * Resolved examples.js conflict * Resolved conflict * Resolved conflicts * RSV Workflow Main updated to work with new database structure * RSVG works with new db schema * Adding genotype to list of surveillance mode Co-authored-by: Albert Tian Chen <[email protected]> Co-authored-by: Alex Klementovich <[email protected]> * Updated to work with new server layout * Plots load for RSVG * Added separate MIN_DATES for RSV and SARS2 * dateRangeStart set by signal for GroupStack and LocationDate plots * Updated selection main_query * Loading surveillance plot data in jsons * Removed typo that prevented init * Surveillance Plot loads form surveillanceDataStore * RSV data displays on Surveillance Plot * Added surv_start_date to config * RSV Genotype can be filtered from Select Sequences Modal * Fixed bug undefined group_id * Fixed bug undefined group_id * Only filtering by genotype in mutation mode * Displays Subtypes instead of Genotypes * Added temp RSVCG logos * Different tabs added based on config.virus * SurveillancePlot correctly displays RSV data * SurveillancePlot correctly displays RSV data * Updated version 2.4.5-rsvdev0 * String-replace-loader specifies static_data dir * Copied new string-replace-loader options to webpack prod * Pushed to Cloud Run * Pushed to Cloud Run * VOC Overflow Fix (#477) * Added VOCTable * VOCTable hides and shows variants on click * VOCToogle flips when clicked * Tweaked toggle button color * Workflow fixes (#476) * update example data * Ignore rclone filter list * upgrade pangolin, add pysam * Capture more 'original' isolate terms * cleanup, run minimap on a single core * Resolving conflicts * Resolved conflicts * Resolved conflict * Resolved conflicts * Mutation formatting - stop codons as *, deletions with delta, and insertions without missing char * group mutations follow same general mutation format * Resolved conflicts * Add dev VM to cors_domains (#505) * Fix #398, along with other UI persistence issues in surveillance plot * Adjust axis labels for sequencing effort plot, change case axis from log to linear * Fix paths in database push script * Limit cores for final analysis tasks to limit RAM consumption * Ignore AA extraction errors for now - need to address large insertions in some genomes * rename strain to virus_name, for phylotree analyses * Update pangolin deps * CORS fix. Blanket CORS on all routes, can be changed if some API endpoints should be publicly accessible. * Added covidcg.org default url to CORS for safety * Fixed tooltip rebuilds on mode switches. * Set line width of Vega tree to fixed width of 1to improve readability. * bigtable test * New bigtable wrapper stuff * Mapping of gene data and family creation. * Fixed mutations binarization * Added sklearn to env for data processing * Upload testing * Vega counts per location work * Hover tooltip on line chart. * Added hover to line charts * Removed unused dependencies * Added tooltip on hover for bargraphs. * Updated vega to use configStore, still not done * Fixing issue with MobX ObservableObjectAdmin * Fixed colors in bar and line chart to use cat10 * Vega stuff * Fixed location bar and line charts to sync with store * Delete bigtable_upload.py * Delete bigtable_test.py * Delete BigTable.md * Added bar and line charts to group page * gitignore with cors config file * VM added to cors_domains * Deleted bigtable stuff * Fix git issues Co-authored-by: Albert Chen <[email protected]> * Resolved conflicts * Resolved conflicts * Reversed arrow direction (#506) * Dynamic Group Mutation Frequencies (#507) * Add query and route * update API * Fix URL * Added Paul Tol light scheme to mutation color palette (#508) * Updated version * Fix TOC in API docs * Resolving conflicts * Resolving conflicts * Resolving conflicts * Resolving conflicts * Updated selection main_query * Loading surveillance plot data in jsons * Removed typo that prevented init * Resolving conflicts * Resolving conflicts * Only filtering by genotype in mutation mode * Resolving conflicts * SurveillancePlot correctly displays RSV data * Resolving conflicts * Refactored RSV * Reran workflow * Fixed bug where insert sequences would not return * Temporarily removed Reports from RSV; updated About Tab name * Updated reference.js to work with multiple entries in reference.json * Updates xLabel depending on config.virus * Surveillance Plot downloads data from surveillanceDataStore * Reference Sequence option in top bar now has same formatting as other options * Migrating prod url to rsv.pathmut.org * Updated push to database script for rsv * MutationList displaying rsv data * Genotype List and Structural Viewer working * RSV reference can be set in the Lineage Reports Tab * Adding login to rsv.pathmut.org * v2.5.0-rsvdev2 * Lineage Reports does not display GroupTree for RSV * RSV displays all data by default * Fixed bug in workflow which threw out sequences * Fixed bug where VOCContainer changed with between RSVA and RSVB selection * Up to date with local * Subtype assignment in ingest - split sequences by subtype * RSV mutation processing by subtype * RSV main workflow - generalized * Fix gene/protein defs (use CDS instead of mRNA bounds) * Fix ingest, basic mutation fetching * generalize report API * Add variant table API method * Bump RSV version * RSV copy * RSV build script, dont send example data to docker context * Fix linter errors/warnings * Remove default selected D614G group * Fix overpruning of variant table rows (from location metadata), keep rows without mutations to first table * Bump to rsvdev6 * Add example data as LFS tarball * shorten hint text to prevent overflows on smaller screens Co-authored-by: Albert Tian Chen <[email protected]> Co-authored-by: Alex Klementovich <[email protected]>
Fixed dev_hostname in config
Reverted to genbank config
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A couple of requests:
Thanks! |
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Closing in favor of #535 |
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Available for viewing on the development server in mobile mode or on a mobile device.
It's important to not that the performance on Chrome "mobile mode" is significantly worse than the phone I tried the site on.