| 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 |
| 71ee455 | Albert Chen | 12 June 2020, 03:16:57 UTC | fix linter errors | 12 June 2020, 03:16:57 UTC |
| 9e4b98a | Albert Chen | 12 June 2020, 03:11:07 UTC | fix clipping issues with dropdownbutton menu | 12 June 2020, 03:11:07 UTC |
| b18e245 | Albert Chen | 12 June 2020, 02:53:00 UTC | add server documentation | 12 June 2020, 02:56:59 UTC |
| 960158f | kevinaltschuler | 12 June 2020, 02:16:34 UTC | laoding anim | 12 June 2020, 02:16:34 UTC |
| 305ae49 | kevinaltschuler | 12 June 2020, 01:13:18 UTC | wip | 12 June 2020, 01:13:18 UTC |
| f479ffe | Albert Chen | 11 June 2020, 22:16:18 UTC | bump version and sequence date | 11 June 2020, 22:16:18 UTC |
| 95a53da | kevin altschuler | 11 June 2020, 22:07:32 UTC | new table (#50) * new table * remove lines * remove example * new table fixes * styling to match old table * update package-lock * dropdown button component for downloads * fix linter errors * decouple plot and table loading states - so that the plot doesn't re-render on a date-range change * remove old component * Display custom element when no rows passed to NewLineageDataTable * remove old datatable package, rename new component * Add more color options, and dot letter option * update package-lock * add initial sort column, depending on grouping mode Co-authored-by: Albert Chen <chena@broadinstitute.org> | 11 June 2020, 22:07:32 UTC |
| 0f8ffaf | Albert Chen | 11 June 2020, 21:56:04 UTC | formatting | 11 June 2020, 21:56:04 UTC |
| c429176 | Albert Chen | 11 June 2020, 21:55:57 UTC | Update location processing code (2020-06-10) | 11 June 2020, 21:55:57 UTC |
| 2e72373 | Albert Chen | 11 June 2020, 18:32:31 UTC | Merge branch 'loading-anim' | 11 June 2020, 18:32:31 UTC |
| 433dde5 | Albert Chen | 11 June 2020, 18:32:16 UTC | Merge branch 'master' into loading-anim | 11 June 2020, 18:32:16 UTC |
| b9e8236 | Albert Chen | 11 June 2020, 14:38:47 UTC | Update page title | 11 June 2020, 14:38:47 UTC |
| 38085e5 | Albert Chen | 11 June 2020, 14:37:06 UTC | add analytics add analytics (#42) | 11 June 2020, 14:37:10 UTC |
| f14fb88 | kevinaltschuler | 11 June 2020, 04:44:34 UTC | remove console | 11 June 2020, 04:44:34 UTC |
| c0432c3 | kevinaltschuler | 11 June 2020, 04:41:29 UTC | loading anim | 11 June 2020, 04:41:29 UTC |
| 492c940 | Albert Tian Chen | 11 June 2020, 04:41:13 UTC | Acknowledgements (#51) * Scripts for generating acknowledgement IDs and mapping back to taxons * restructure acknowledgements output for better indexing in JS * download acknowledgements | 11 June 2020, 04:41:13 UTC |
| d1a14e5 | kevinaltschuler | 10 June 2020, 23:22:42 UTC | fix lint err | 10 June 2020, 23:22:42 UTC |
| 8d4d0a5 | kevin altschuler | 10 June 2020, 23:21:15 UTC | add worker for scripts, improve runtime of scripts and add async states (#43) * add worker for scripts, improve runtime of scripts and add async states * add example * fix some linter errors * Don't display null values in HeatmapCell The missing values checked here initially were NaN values, but now since the worker code is stringifying/parsing objects I think these NaNs got changed to nulls, so now I'm checking for both * clean up debug prints * update package-lock * console remova Co-authored-by: Albert Chen <chena@broadinstitute.org> | 10 June 2020, 23:21:15 UTC |
| 0e7c8a7 | Albert Chen | 10 June 2020, 08:35:55 UTC | move version variables to separate file, bump version for now | 10 June 2020, 08:35:55 UTC |
| f1ab07c | Albert Chen | 10 June 2020, 08:35:34 UTC | add new location rules, 2020-06-08 | 10 June 2020, 08:35:34 UTC |
| 6bd0f29 | Albert Chen | 09 June 2020, 23:25:25 UTC | notebook: framework for sequence clustering and plotting whole genes | 09 June 2020, 23:25:25 UTC |
| bc8437d | Albert Chen | 09 June 2020, 23:24:59 UTC | ignore generated figures from notebooks | 09 June 2020, 23:24:59 UTC |
| 7c41a89 | Albert Chen | 09 June 2020, 15:51:56 UTC | Add location filtering optimization, cherry-picked from Kevin's commit 0ae89ee in the worker branch | 09 June 2020, 15:51:56 UTC |
| d80dfd8 | Albert Chen | 09 June 2020, 05:42:53 UTC | remove old scripts | 09 June 2020, 05:42:53 UTC |
| 23b0ca8 | Albert Chen | 09 June 2020, 05:42:17 UTC | move pymol scripts | 09 June 2020, 05:42:17 UTC |
| e0082fd | Albert Chen | 09 June 2020, 05:37:09 UTC | Merge branch 'master' of github.com:vector-engineering/covid_ui | 09 June 2020, 05:37:09 UTC |
| fa71227 | Albert Chen | 09 June 2020, 05:37:01 UTC | Add custom colormap limits, fix float -> hex conversion, set low or 0 SNP counts to gray | 09 June 2020, 05:37:01 UTC |
| eabe3a8 | Albert Tian Chen | 09 June 2020, 05:35:23 UTC | Add simple HTTP server with authorization (#44) * use 6X2A model as example * add simple server server files | 09 June 2020, 05:35:23 UTC |
| 926bbfc | Albert Chen | 09 June 2020, 04:30:25 UTC | catch direct file path in dist build | 09 June 2020, 04:30:25 UTC |
| 71fd810 | Albert Chen | 08 June 2020, 17:56:57 UTC | add version and sequence analysis date to header | 08 June 2020, 17:56:57 UTC |
| 6794a0b | Albert Chen | 08 June 2020, 17:28:08 UTC | Make separate columns for each chunk of SNPs, when grouping by SNPs | 08 June 2020, 17:28:08 UTC |
| 6a8ef91 | Albert Chen | 08 June 2020, 17:02:45 UTC | change nomenclature from cases -> sequences | 08 June 2020, 17:02:45 UTC |
| 7d747be | Albert Tian Chen | 08 June 2020, 16:26:04 UTC | Vega Adjustments (#40) * vega plot adaptive to container width, and remove legend * add standalone vega plot for development * Fix conditionalRowStyles style object * functionalize HomePage * move static location tree props into container * Make a deep copy of the vega spec on render to allow for dynamic spec editing * clean up spec, give a little more padding * clean up console output * more descriptive tooltips | 08 June 2020, 16:26:04 UTC |
| fff1b03 | Albert Chen | 08 June 2020, 14:42:04 UTC | Sidebar adjustments | 08 June 2020, 14:43:23 UTC |
| 9c1e357 | Albert Chen | 08 June 2020, 14:37:26 UTC | restore group key column name in data table | 08 June 2020, 14:37:26 UTC |
| ad305b0 | Albert Chen | 08 June 2020, 14:09:20 UTC | update package-lock | 08 June 2020, 14:09:20 UTC |
| a40b3ba | Albert Chen | 08 June 2020, 14:09:01 UTC | Update title, squash linter errors | 08 June 2020, 14:09:01 UTC |
| 166b952 | Albert Tian Chen | 08 June 2020, 14:04:09 UTC | Data table (#35) * hide NaNs in HeatmapCell * remove testing code * rotate position labels 45 degrees, more compact cells * Adaptive group key column name * clean up caseData * merge 'Reference' and 'None' rows when in SNP mode * Fix: ignore Reference with collecting changingPositions * Make LineageDataTable an observer, so it can get new data when the date range changes * snapgene-like base/aa highlighting * Annotation for position column headers | 08 June 2020, 14:04:09 UTC |
| 2440b3c | Albert Chen | 08 June 2020, 05:01:03 UTC | location fixes for sequences up to 2020-06-06 | 08 June 2020, 05:01:03 UTC |
| fb9279e | Albert Chen | 08 June 2020, 04:17:01 UTC | generate select tree with the rest of the case_data | 08 June 2020, 05:00:37 UTC |
| 4b5edee | Albert Chen | 08 June 2020, 04:05:46 UTC | CSS touchups on sidebar | 08 June 2020, 04:05:46 UTC |
| d7e338e | kevinaltschuler | 08 June 2020, 01:12:27 UTC | fix stuff | 08 June 2020, 01:12:27 UTC |
| 50bc3ea | kevinaltschuler | 08 June 2020, 00:51:52 UTC | fix litemol | 08 June 2020, 00:51:52 UTC |
| 25afed1 | Albert Chen | 08 June 2020, 00:45:07 UTC | update README | 08 June 2020, 00:45:07 UTC |
| fe295c1 | Albert Chen | 08 June 2020, 00:21:03 UTC | remove some boilerplate code, and remove test libraries and tasks | 08 June 2020, 00:21:03 UTC |
| a47e7c1 | Albert Chen | 08 June 2020, 00:19:43 UTC | Add sequence counts to the location tree | 08 June 2020, 00:19:43 UTC |
| 693d26a | Albert Chen | 07 June 2020, 23:04:59 UTC | Fix more location typos | 07 June 2020, 23:04:59 UTC |
| 3a63e11 | Albert Chen | 07 June 2020, 10:10:45 UTC | more compact location cleaning code, add more cleaning rules for newly included sequences | 07 June 2020, 10:10:45 UTC |
| 7b6426c | Albert Tian Chen | 07 June 2020, 07:19:43 UTC | get rid of all css/scss in favor of styled-components (#28) | 07 June 2020, 07:19:43 UTC |
| 98dd071 | Albert Chen | 07 June 2020, 05:24:15 UTC | update case data path and fix linter errors | 07 June 2020, 05:24:15 UTC |
| d02011a | Albert Chen | 07 June 2020, 05:16:13 UTC | ignore data files generated from notebooks | 07 June 2020, 05:16:13 UTC |
| 557c656 | Albert Chen | 07 June 2020, 05:13:21 UTC | Merge branch 'new-dataframe' | 07 June 2020, 05:13:21 UTC |
| 6730c95 | Albert Chen | 07 June 2020, 05:13:11 UTC | Merge branch 'master' into new-dataframe | 07 June 2020, 05:13:11 UTC |
| 62cb2de | Albert Chen | 07 June 2020, 05:09:01 UTC | update package lock | 07 June 2020, 05:09:01 UTC |
| fb76607 | Albert Chen | 07 June 2020, 05:02:12 UTC | This is a big one. Main changes: - Adapt app to work with the new dataframe, where it is not pre-grouped by lineage, location_id, and sample_date. This let's us do the grouping in JS - Allow grouping by lineage or SNP - Allow display of mutations by NT (DNA) or AA - Remove some redundant observables from the covidStore - Generally clean up the data processing. Prioritizing filtering tasks before aggregation tasks to speed up the computations | 07 June 2020, 05:02:12 UTC |
| 52cf5f1 | kevin altschuler | 07 June 2020, 01:16:12 UTC | sidebar mvp with higlighting sample (#25) * unstyled mvp * sidebar wip * add highlighting sample to the viewer * hihglight sample | 07 June 2020, 01:16:12 UTC |
| 2621cb0 | Albert Chen | 06 June 2020, 21:12:26 UTC | Merge branch 'master' into new-dataframe | 06 June 2020, 21:12:26 UTC |
| a0e291e | kevin altschuler | 06 June 2020, 21:10:43 UTC | Merge pull request #20 from vector-engineering/componentize-stuff move stuff out to components | 06 June 2020, 21:10:43 UTC |
| fe0be97 | kevinaltschuler | 06 June 2020, 21:09:19 UTC | move stuff out to components | 06 June 2020, 21:09:19 UTC |
| 7d89762 | Albert Chen | 06 June 2020, 18:56:31 UTC | bundle case data with SNPs | 06 June 2020, 18:56:31 UTC |
| 5ff61c7 | kevin altschuler | 06 June 2020, 06:22:20 UTC | Mobxrouter (#18) * switch to mobx router * switch over to mobx router * fixes * fixes | 06 June 2020, 06:22:20 UTC |
| 86696ed | Albert Chen | 06 June 2020, 03:31:44 UTC | Merge branch 'master' of github.com:vector-engineering/covid_ui | 06 June 2020, 03:31:44 UTC |
| 292ada3 | Albert Chen | 06 June 2020, 03:31:39 UTC | select regions of interest on spike structure | 06 June 2020, 03:31:39 UTC |
| f089d0b | kevinaltschuler | 06 June 2020, 03:29:18 UTC | fix lint | 06 June 2020, 03:29:18 UTC |
| 3e576ef | kevin altschuler | 06 June 2020, 03:08:35 UTC | Merge pull request #11 from vector-engineering/mobx Mobx | 06 June 2020, 03:08:35 UTC |
| eee4fe3 | kevinaltschuler | 06 June 2020, 03:05:28 UTC | fix provider / consumer | 06 June 2020, 03:05:28 UTC |
| 1c648dd | kevinaltschuler | 06 June 2020, 02:30:24 UTC | mob x | 06 June 2020, 02:30:24 UTC |
| 6f100f1 | kevin altschuler | 06 June 2020, 00:51:10 UTC | Merge pull request #9 from vector-engineering/sidepanel placeholder checkbox ui and file move | 06 June 2020, 00:51:10 UTC |
| 9a1d2e8 | kevinaltschuler | 06 June 2020, 00:50:09 UTC | light ui and file move | 06 June 2020, 00:50:09 UTC |
| 585d2e8 | kevin altschuler | 06 June 2020, 00:18:45 UTC | Merge pull request #4 from vector-engineering/litemol Litemol mvp with open/close in each cell, no data passed in yet | 06 June 2020, 00:18:45 UTC |
| 70c8e66 | kevinaltschuler | 06 June 2020, 00:13:02 UTC | add basic mvp | 06 June 2020, 00:13:02 UTC |
| 35cfe3e | Albert Chen | 05 June 2020, 04:41:48 UTC | add data requirements | 05 June 2020, 04:44:08 UTC |
| 7276fa4 | Albert Chen | 05 June 2020, 04:30:40 UTC | update license holders | 05 June 2020, 04:30:40 UTC |
| 84b99e2 | kevinaltschuler | 05 June 2020, 03:37:48 UTC | wip | 05 June 2020, 03:37:48 UTC |
| d06f8c8 | Albert Chen | 05 June 2020, 02:39:27 UTC | add PyMOL analysis scripts - will organize later | 05 June 2020, 02:39:27 UTC |
| 46485a9 | Albert Chen | 04 June 2020, 03:36:57 UTC | add new SNP analysis | 04 June 2020, 03:36:57 UTC |
| 35b6963 | Albert Chen | 04 June 2020, 03:36:31 UTC | update data source, percentage view by default | 04 June 2020, 03:36:31 UTC |
| 967af5e | Albert Chen | 29 May 2020, 16:15:57 UTC | remove redundant vega spec | 29 May 2020, 16:15:57 UTC |
| cf1d71c | Albert Chen | 29 May 2020, 16:15:18 UTC | location cleaning | 29 May 2020, 16:15:18 UTC |
| b30e5d8 | Albert Chen | 29 May 2020, 16:14:57 UTC | get aa snps, consensus AA snps | 29 May 2020, 16:14:57 UTC |
| 26af164 | Albert Chen | 28 May 2020, 13:17:19 UTC | switch between absolute counts/percentages for lineages, add tooltip and hover opacity | 28 May 2020, 13:17:19 UTC |
| 0b198f1 | Albert Chen | 28 May 2020, 12:39:18 UTC | Adapt to real data, change terminology from clades --> lineages | 28 May 2020, 12:39:18 UTC |
| a61f938 | Albert Chen | 28 May 2020, 12:38:13 UTC | add license | 28 May 2020, 12:38:13 UTC |
| 54054a2 | Albert Chen | 27 May 2020, 09:34:56 UTC | improve alignment procedures, remove offsets, preserve entry names | 27 May 2020, 09:34:56 UTC |
| 4cd23d7 | Albert Chen | 26 May 2020, 20:09:23 UTC | update pangolin | 26 May 2020, 20:09:23 UTC |
| 0c50005 | Albert Chen | 26 May 2020, 20:08:47 UTC | remove old assignment function | 26 May 2020, 20:08:47 UTC |
| 78fde22 | Albert Chen | 26 May 2020, 20:08:19 UTC | create folders before processing files | 26 May 2020, 20:08:19 UTC |
| aeb64dc | Albert Chen | 26 May 2020, 20:08:01 UTC | add notebook for clade SNP definitions | 26 May 2020, 20:08:01 UTC |
| 29be7aa | Albert Chen | 26 May 2020, 20:07:33 UTC | remove old data | 26 May 2020, 20:07:33 UTC |
