| 9de6ebe | Albert Chen | 02 August 2020, 17:44:15 UTC | bump version | 02 August 2020, 17:44:15 UTC |
| dd7b5b6 | Albert Tian Chen | 02 August 2020, 17:03:19 UTC | Plot settings in store (#143) * add store, consts and plug into VegaStackedBars * change component name * add plotsettings to locationdate plot * change defaults for locationdate plot * add table color modes to plotsettings store * add table sort settings to plotsettingsstore | 02 August 2020, 17:03:19 UTC |
| 1a45f03 | kevin altschuler | 01 August 2020, 23:26:22 UTC | Other grouping + Perf Improvements (#121) * other grouping wip * legend works too * remove some prints * other selection working for table * try not to overrun memory in bowtie2 * add task for calculating global counts per group * change inputs from sliders to just normal number inputs * store the low freq filter type in configstore * fix grouping logic with new filter type in store * filter by global counts * add tooltips * gray out unselected options * add vega-like transform aggregate function, and use it to make the 'other' groupings work in the location tab * adjust copy, hide low freq grouping by default * fix prop error * performance improvements * legend: use one listener on the parent, instead of listeners for every child * table: replace listeners for each row with one listener on the table wrapper * use hooks in rowrenderer to try to re-render less often * increase spacing on legend items Co-authored-by: Albert Chen <chena@broadinstitute.org> | 01 August 2020, 23:26:22 UTC |
| 461e837 | Albert Tian Chen | 31 July 2020, 00:08:50 UTC | Separate stores (#140) * rename covid -> datastore * refactor uiStore * move tab state into UIStore * separate settings * change capitalization * remove print | 31 July 2020, 00:08:50 UTC |
| fdebb4d | Albert Tian Chen | 30 July 2020, 20:22:54 UTC | UI fixes (#139) * Rename, clean up TabBar * add short logo, favicon, adjust title (Closes #118) * Sorting on position columns (Closes #115) * fix location counts in select tree (Closes #125) * Fix select all locations (Closes #126) * change copy from 'SNP' to 'SNV' (Closes #124) * Update metadata selector from store, unset selected metadata fields on location change (Closes #127) * Updates to custom coordinate select (Closes #130) * add stylized keyboard button component * Add question button component, change copy for metadata filtering (Closes #128) * move help text out of tooltips and above plots. Closes #133 * add color utilities from kevin * nevermind use a package * prettier legend items * group colors in table. Closes #116 * fix typo * try to make the groupby/mutation format pop out more (Closes #131) * enable scrolling on the whole geo tree select component -- not just the infinite scroll component. Closes #135 * rename vega -> vega_specs * better copy when nothing is selected. Closes #134 * Add link to lineage descriptions. Closes #129 | 30 July 2020, 20:22:54 UTC |
| 65e44ac | Albert Tian Chen | 29 July 2020, 01:34:30 UTC | Snakemake (#136) * wip * remove pycache * working pipeline * fix typo * updates for new genes format and new filenames | 29 July 2020, 01:34:30 UTC |
| 6d8d848 | Albert Chen | 27 July 2020, 17:02:44 UTC | bump version | 27 July 2020, 17:02:44 UTC |
| 4cf3830 | Albert Chen | 27 July 2020, 17:02:14 UTC | fix linter errors | 27 July 2020, 17:02:14 UTC |
| 3f44181 | Albert Chen | 27 July 2020, 17:00:26 UTC | fix date selection error | 27 July 2020, 17:00:26 UTC |
| bc4e8d9 | Albert Chen | 27 July 2020, 16:52:01 UTC | bump version to v0.5.0 | 27 July 2020, 16:52:01 UTC |
| a6a6621 | Albert Chen | 27 July 2020, 16:51:11 UTC | disable default group selections | 27 July 2020, 16:51:11 UTC |
| b6e9be3 | Albert Chen | 27 July 2020, 16:45:24 UTC | move warning to separate component, add to main view as well | 27 July 2020, 16:45:24 UTC |
| c4ff347 | Albert Chen | 27 July 2020, 16:39:09 UTC | change copy on splash screen (closes #104) | 27 July 2020, 16:39:09 UTC |
| 55074d7 | Albert Tian Chen | 27 July 2020, 16:17:56 UTC | Location tab (#117) * move header component to sidebar folder * tabbed navigation * add github link to header * package location_id into the geo select tree * wip - process aggregate location data * More fixes to the vega wrapper, dimensions issues worked out * define width once in bar stack spec * move data/signal listeners into state * working location group barplot * working location date lineplot * re-run vega view on new signals * pass vega configuration through signals instead of rewriting the spec * add list of signals to trigger data reload * set prop signals on view creation * remove redundant vega import * flags for recreating view on certain dataset changes * update plots, cross-interactions between plots * fix location node selection * try to draw text over everything * move some components around * make accordion title component * add annotations, warnings * xlabel for location group plot * increase max height for location date plot * clear selected groups on change in groupings * fix filtering out of reference group in snp mode * show all groups if none selected * rename tab * adaptive status bar status widths | 27 July 2020, 16:17:56 UTC |
| 3e20a2b | Albert Chen | 25 July 2020, 15:29:01 UTC | bump version to v0.4.4 | 25 July 2020, 15:29:01 UTC |
| d44e95f | Albert Chen | 25 July 2020, 15:28:31 UTC | merge color definitions | 25 July 2020, 15:28:31 UTC |
| 85c9d63 | Albert Chen | 25 July 2020, 15:20:46 UTC | incorporate logo | 25 July 2020, 15:20:46 UTC |
| 08165b9 | Albert Chen | 25 July 2020, 15:01:28 UTC | compress filter sidebar layouts, fix copy | 25 July 2020, 15:01:28 UTC |
| 007b317 | Albert Chen | 24 July 2020, 15:12:41 UTC | Add plot download options back (Closes #110) | 24 July 2020, 15:12:45 UTC |
| ba4424c | Albert Chen | 24 July 2020, 14:21:51 UTC | don't squish the header | 24 July 2020, 14:21:51 UTC |
| 2dd5e54 | Albert Chen | 24 July 2020, 13:55:36 UTC | fix the initial date range for file names of downloads | 24 July 2020, 13:55:36 UTC |
| 1000400 | Albert Tian Chen | 24 July 2020, 13:50:50 UTC | Accession ID decryption (#111) * google cloud function * fix typo * add documentation for the google cloud function * add CORS handling * add decryption request and plug into download acknowledgements * use static hidden download link, instead of creating a new one each time * rename downloadAcknowledgements -> downloadAcknowledgementsData in download worker to avoid confusion between it and the action * Add basic download accession IDs option, and simplify the selection string generation... need a better way to serialize the genomic coordinate selection in a compact way | 24 July 2020, 13:50:50 UTC |
| 14e2dc8 | Albert Chen | 24 July 2020, 10:50:04 UTC | add comments to the vega spec | 24 July 2020, 10:50:04 UTC |
| f108bc8 | Albert Tian Chen | 23 July 2020, 21:50:48 UTC | Vega fixes (#108) * stop highlighting bars with zero cases * snap date selection to the nearest day * add date selection to status bar | 23 July 2020, 21:50:48 UTC |
| e660d12 | Albert Chen | 23 July 2020, 21:21:00 UTC | fix DOM issue in splash screen | 23 July 2020, 21:21:00 UTC |
| de5b1c6 | Albert Tian Chen | 23 July 2020, 21:19:50 UTC | Splash screen (#107) * add react-modal package * move pages into own folder * move filter sidebar components into own folder * move litemol components into own folder * add splash screen content | 23 July 2020, 21:19:50 UTC |
| 5897e8a | Albert Chen | 23 July 2020, 16:55:14 UTC | Reset table coloring settings when dnaOrAa changes (Closes #66) | 23 July 2020, 16:55:14 UTC |
| da4d756 | Albert Chen | 23 July 2020, 16:15:49 UTC | Process sequences from 07-20 -- 07-22 | 23 July 2020, 16:15:49 UTC |
| 18cbc2f | Albert Chen | 23 July 2020, 15:54:12 UTC | bump version to v0.4.3 | 23 July 2020, 15:54:12 UTC |
| 7211d51 | Albert Tian Chen | 23 July 2020, 15:53:22 UTC | Grouping by GISAID Clade (#105) * get consensus snps for clades too * add clade grouping * add link to releases page | 23 July 2020, 15:53:22 UTC |
| 17878e8 | Albert Chen | 23 July 2020, 14:27:43 UTC | extend ssl to alpha subdomain | 23 July 2020, 14:27:43 UTC |
| 1847dcd | Albert Chen | 23 July 2020, 01:28:19 UTC | add alpha subdomain to server configuration | 23 July 2020, 01:28:19 UTC |
| 3e4d82c | Albert Chen | 23 July 2020, 01:08:51 UTC | bump version | 23 July 2020, 01:08:51 UTC |
| 5cca4e8 | Albert Chen | 23 July 2020, 01:07:52 UTC | filter out sequences before 2019-12-15 | 23 July 2020, 01:07:52 UTC |
| 0fbbcce | Albert Chen | 23 July 2020, 01:07:42 UTC | remove sequences with very unspecific collection dates | 23 July 2020, 01:07:42 UTC |
| 56acc59 | kevinaltschuler | 22 July 2020, 22:51:53 UTC | clean packagejson | 22 July 2020, 22:51:53 UTC |
| ea8fb3d | Albert Tian Chen | 22 July 2020, 19:01:07 UTC | Cumulative Counts (#99) * cumulative counts and date binning * hide actions for now -- will reconstruct in UI later * fix width for overview -- should stop the date selection from not working on the right end * allow drag events on overview to start on the bars as well * compute group counts in store * rewrite a lot of the react_vega code. it still needs some work, but it's functional for now * merge both spec modifiers into one effect hook * impute missing group-date values, for cumulative viz * add tooltip package and tooltip help for legend, plot, and table | 22 July 2020, 19:01:07 UTC |
| c73ace4 | Albert Chen | 21 July 2020, 19:17:01 UTC | bump version to v0.4.1 | 21 July 2020, 19:17:01 UTC |
| 8b0d126 | Albert Tian Chen | 21 July 2020, 19:15:06 UTC | Metadata filtering (#98) * add react-multi-select-component package * metadata filtering working, mostly * geneselect -> coordinateselect * sidebar accordions * remove extra maxheight prop * wrap location selector in accordion, fix clipping of selected locations * adjust copy * move location selector out of accordion due to scrolling issues, add back maxheight for primer selection * basic statusbar | 21 July 2020, 19:15:06 UTC |
| 77a26f2 | Albert Tian Chen | 21 July 2020, 09:44:25 UTC | About page (#95) * add SSL instructions * add configuration with certbot additions * flesh out about page, add attributions | 21 July 2020, 09:44:25 UTC |
| a20cb65 | Albert Chen | 20 July 2020, 16:30:19 UTC | processing code for sequences 2020-07-07 -- 2020-07-19 | 20 July 2020, 16:30:19 UTC |
| 4878859 | Albert Chen | 20 July 2020, 16:30:04 UTC | fix processing bug - stop returning list of genes since its defined separately | 20 July 2020, 16:30:04 UTC |
| 0691bd6 | Albert Chen | 20 July 2020, 16:28:03 UTC | add flag for north macedonia | 20 July 2020, 16:28:03 UTC |
| e2c7823 | Albert Chen | 20 July 2020, 15:54:32 UTC | downgrade pysam | 20 July 2020, 15:54:32 UTC |
| aa65cbe | Albert Tian Chen | 20 July 2020, 11:11:02 UTC | Stacked barplots (#94) * initial stacked barplot * integrate plot options, move plot options into plot wrapper * move vega components into own folder * sort legend items by group name * plot -> legend cross-highlighting * rewrite react-vega with hooks * update license * simplify signalListeners logic * move width/height changes to separate hook, simplify signalListener logic * move signalListener code to separate hook * simplify function calls * honestly not sure how this works but im running with it * handling selected groups -- the data update code is now super jenky and this will probably result in some frustrating bugs in the future. but that's for future me * shift-select on legend * more compact dates on x-axis * simplify datatable prop passing * hover/select for table, using custom rowrenderer * allow deselecting groups from legend * row selection in table * move rowrenderer to own file, add hover listener * add bgcolor for hovered items in legend * render header row over selected rows * remove vega webgl import * bump version * don't track old app versions | 20 July 2020, 11:11:02 UTC |
| 6042637 | Albert Chen | 18 July 2020, 05:17:38 UTC | unset the public path in the webpack config so it uses the webpack-public-path.js file on runtime instead | 18 July 2020, 05:17:38 UTC |
| 9750409 | Albert Chen | 18 July 2020, 05:17:03 UTC | define publicPath once | 18 July 2020, 05:17:03 UTC |
| b9f2be0 | Albert Chen | 18 July 2020, 05:16:48 UTC | fix skeleton elements | 18 July 2020, 05:16:48 UTC |
| 05665e1 | Albert Chen | 18 July 2020, 02:40:56 UTC | fix prop-types | 18 July 2020, 02:40:56 UTC |
| a7ab45d | Albert Chen | 18 July 2020, 02:36:30 UTC | simplify initialization process, remove debug code | 18 July 2020, 02:36:30 UTC |
| 01ec382 | Albert Chen | 18 July 2020, 02:28:37 UTC | disable VegaTree for now | 18 July 2020, 02:28:37 UTC |
| 61d0cbb | Albert Tian Chen | 18 July 2020, 02:17:45 UTC | New ranges (#88) * formatting, move reference data files to static_data, clean up imports * fix json paths * move genes object out of store as an observable * simplify gene options further * update metadata maps * Change strategy or AA SNP discovery, generate for both gene and protein ORFs * add protein selection add protein selection in UI * fix linter errors * fix download logic -- we'll need to filter by selected gene/protein later * add custom coordinate mode, change GroupBySelect to be its own controlled component * add processing code and data for primers * start tracking changes in csv/tsv files * primer selection in UI * disable AA mode for All Genes/All Proteins * fix DNA SNPs for All Proteins selection | 18 July 2020, 02:17:45 UTC |
| 8ee35bf | Albert Chen | 08 July 2020, 22:40:33 UTC | bump version | 08 July 2020, 22:40:33 UTC |
| a783ca3 | Albert Chen | 08 July 2020, 22:28:14 UTC | hide structural viewer for now | 08 July 2020, 22:28:14 UTC |
| 8da093a | Albert Chen | 08 July 2020, 22:22:34 UTC | Fix off-by-one for AA SNPs | 08 July 2020, 22:22:34 UTC |
| 6277108 | Albert Chen | 08 July 2020, 22:15:52 UTC | pass in raw int arrays instead of semicolon-delimited strings, for SNP IDs | 08 July 2020, 22:15:52 UTC |
| 56f2ca4 | Albert Chen | 08 July 2020, 21:56:46 UTC | fix prop type | 08 July 2020, 21:56:46 UTC |
| 242af82 | Albert Chen | 08 July 2020, 21:50:28 UTC | fix typo | 08 July 2020, 21:50:28 UTC |
| 4f0c592 | Albert Chen | 08 July 2020, 21:49:02 UTC | remove debug prints, fix linter errors | 08 July 2020, 21:49:02 UTC |
| ff4075c | Albert Chen | 08 July 2020, 21:43:36 UTC | Fixes for empty acknowledgements | 08 July 2020, 21:43:36 UTC |
| c771a20 | Albert Chen | 08 July 2020, 21:28:20 UTC | add location processing for sequences up to 2020-07-06, bump sequences date | 08 July 2020, 21:28:20 UTC |
| fedca76 | Albert Chen | 08 July 2020, 21:27:40 UTC | updates for new metadata formatting | 08 July 2020, 21:27:40 UTC |
| 3920e60 | Albert Chen | 08 July 2020, 21:27:28 UTC | update package lock | 08 July 2020, 21:27:28 UTC |
| 2e55b5b | Albert Chen | 08 July 2020, 21:27:22 UTC | remove pangolin, again | 08 July 2020, 21:27:22 UTC |
| 840f84d | kevin altschuler | 08 July 2020, 15:47:31 UTC | treeview (#84) * fix conflicts * conflict * delete sample data * updates | 08 July 2020, 15:47:31 UTC |
| 0164b48 | Albert Chen | 07 July 2020, 23:33:06 UTC | Default to original authors entry if abbreviation failed | 07 July 2020, 23:33:06 UTC |
| e270f0c | Albert Chen | 07 July 2020, 22:11:08 UTC | clean up, rename main function | 07 July 2020, 22:11:08 UTC |
| b8721e3 | Albert Chen | 07 July 2020, 22:07:52 UTC | Merge branch 'master' of https://github.com/vector-engineering/COVID19-CG | 07 July 2020, 22:07:52 UTC |
| 3b0162e | Albert Tian Chen | 07 July 2020, 22:06:17 UTC | GISAID Requests (#85) * Location fixes for 2020-06-19 * Increase size of GISAID logo (slightly bigger than on Nextstrain) * Add link to DAA * remove sequences + metadata download option * stop tracking notebooks * Reorganize case data processing * Add more metadata fields, for future filtering * Try to put as much data as possible into one dataframe * Hash Accession IDs to semi-anonymize data. Will have to write a backend to convert these into GISAID Accession IDs * Simplify lineage consensus SNP code - SNP IDs will have to be mapped in the frontend * remove pangolin ref * fix off-by-one error for lineage AA SNPs * Adapt front-end to new data source * Logging, add Accession ID to JSON case data * Fix acknowledgement download * Fix linter errors * Basic acknowledgements table * Try to shorten author names, by pulling last name and adding 'et al' * prettier acknowledgements table | 07 July 2020, 22:06:17 UTC |
| 2eeb4c3 | kevin altschuler | 07 July 2020, 02:43:01 UTC | Legend (#82) * legendv1; * legendv2 | 07 July 2020, 02:43:01 UTC |
| 7333252 | Albert Chen | 07 July 2020, 00:31:26 UTC | Merge branch 'master' of https://github.com/vector-engineering/COVID19-CG | 07 July 2020, 00:31:26 UTC |
| 825c484 | kevin altschuler | 07 July 2020, 00:25:08 UTC | Explicit colors (#81) * add infra for colors * colors * other category | 07 July 2020, 00:25:08 UTC |
| dde4c39 | kevin altschuler | 29 June 2020, 23:28:36 UTC | Colorsv1 (#80) * add infra for colors * colors | 29 June 2020, 23:28:36 UTC |
| 45a8d64 | kevin altschuler | 23 June 2020, 03:14:30 UTC | add all selector (#76) * add all selector * style fixes * fixes * Sidebar loading (#78) * clicking box now works during load * remove prints Co-authored-by: Albert Tian Chen <chena@broadinstitute.org> | 23 June 2020, 03:14:30 UTC |
| bb8a098 | kevin altschuler | 23 June 2020, 03:04:11 UTC | fix sorting and default to seq (#77) | 23 June 2020, 03:04:11 UTC |
| 25d569b | kevinaltschuler | 20 June 2020, 21:00:21 UTC | fix scroll bar | 20 June 2020, 21:00:21 UTC |
| 3233422 | Albert Chen | 20 June 2020, 20:07:13 UTC | Merge branch 'master' of https://github.com/vector-engineering/COVID19-CG | 20 June 2020, 20:07:13 UTC |
| fff5372 | kevin altschuler | 20 June 2020, 20:06:32 UTC | Locked scroll (#74) * not select all but formatting dif * lock main page scroll and let sections scroll seperately * fix conflicts | 20 June 2020, 20:06:32 UTC |
| 3caa5d3 | Albert Chen | 20 June 2020, 19:55:08 UTC | Location fixes for 2020-06-19 | 20 June 2020, 19:55:08 UTC |
| 0fae6f5 | Albert Chen | 20 June 2020, 19:25:14 UTC | Add country flag emojis to location tree (#75) Thanks to https://github.com/matiassingers/emoji-flags for the data | 20 June 2020, 19:26:19 UTC |
| e422e75 | Albert Chen | 20 June 2020, 18:49:49 UTC | update notebooks | 20 June 2020, 18:49:49 UTC |
| dd5fa06 | Albert Chen | 20 June 2020, 18:49:40 UTC | Fallback to pangolin lineage assignments from GISAID | 20 June 2020, 18:49:40 UTC |
| 8a5f0b8 | Albert Chen | 17 June 2020, 17:13:07 UTC | add location processing code for 2020-06-16, bump data date | 17 June 2020, 17:13:07 UTC |
| 9b4355e | Albert Chen | 17 June 2020, 14:34:11 UTC | link figures folder | 17 June 2020, 14:34:11 UTC |
| a0c78ec | Albert Chen | 16 June 2020, 18:37:14 UTC | Update pymol scripts for Fig 2 | 16 June 2020, 18:37:14 UTC |
| b756e16 | Albert Chen | 16 June 2020, 18:37:02 UTC | add collection date --> submission date analysis | 16 June 2020, 18:37:02 UTC |
| 546e6f9 | Albert Chen | 16 June 2020, 18:36:43 UTC | Update README | 16 June 2020, 18:36:43 UTC |
| e4f8fb3 | Albert Chen | 16 June 2020, 11:00:21 UTC | location processing up to 2020-06-15, update data date | 16 June 2020, 18:36:26 UTC |
| 8305530 | Albert Chen | 16 June 2020, 09:37:14 UTC | update server to NGINX | 16 June 2020, 09:37:14 UTC |
| 8c5a995 | Albert Chen | 13 June 2020, 11:30:03 UTC | bump version | 13 June 2020, 11:30:03 UTC |
| 3d0f8e4 | Albert Chen | 13 June 2020, 06:32:21 UTC | update data and location processing for 2020-06-12 | 13 June 2020, 06:32:21 UTC |
| e2c45e7 | Albert Chen | 13 June 2020, 05:28:02 UTC | remove old redux file | 13 June 2020, 05:28:02 UTC |
| 4916f5d | Albert Chen | 13 June 2020, 05:27:21 UTC | Location processing, 2020-06-11 | 13 June 2020, 05:27:21 UTC |
| 761a3cd | Albert Chen | 12 June 2020, 14:38:08 UTC | consistent border radiuses (#38) | 12 June 2020, 14:38:08 UTC |
| 5728e0c | Albert Chen | 12 June 2020, 14:30:40 UTC | remove old redux constants | 12 June 2020, 14:30:40 UTC |
| 3d6babe | Albert Chen | 12 June 2020, 14:26:39 UTC | add plot title, fix main css grid | 12 June 2020, 14:26:39 UTC |
| 7a56f87 | kevin altschuler | 12 June 2020, 14:13:17 UTC | not select all but formatting dif (#60) * not select all but formatting dif * style adjustments Co-authored-by: Albert Chen <chena@broadinstitute.org> | 12 June 2020, 14:13:17 UTC |
| 6062e4b | Albert Chen | 12 June 2020, 13:33:14 UTC | In DataTable dots mode, don't mask the reference letters with dots (fixes #61) | 12 June 2020, 13:33:14 UTC |
| ceb4319 | Albert Chen | 12 June 2020, 13:30:31 UTC | Update README | 12 June 2020, 13:30:31 UTC |
| 87fd3b6 | Albert Tian Chen | 12 June 2020, 12:34:09 UTC | Download Sequences, Aggregated Sequences (#62) * Download aggregate data * refactor, selectedAccessionIds -> selectedRows * refactor snpData functions to camelCase * download sequences and metadata | 12 June 2020, 12:34:09 UTC |
