| e9558dc | Albert Tian Chen | 24 January 2021, 10:43:42 UTC | Fix location typos | 24 January 2021, 10:43:42 UTC |
| 86cf54a | Albert Tian Chen | 19 January 2021, 15:45:57 UTC | Metadata Downloads (#264) * remove old download code - move download code in worker to util file (we don't need async for this) * Use existing intToIso function * Build location_id -> [region, country, division, location] map * Add download for selected sequence metadata * Fix height bug on metadata filter block * Fix missing metadata field selects * Add additional observable for number of sequences, since status box was observing a non-observable dataset * Add loading element for status box * Add download options to status box * Add configuration option for allowing metadata downloads * Fix typo | 19 January 2021, 15:45:57 UTC |
| 421dda3 | Albert Tian Chen | 19 January 2021, 14:28:10 UTC | GISAID ingest updates (#262) * working rclone exclusions * Rework GISAID ingest - split files based on existing Accession IDs and MD5 hashed sequences, instead of by submission date. Should reduce the burden of daily updates/alignment processes * Process host metadata * For duplicate sequences, only process the SNVs from the latest one * Helper script for migrating after preprocessing change * Add back temp flags for intermediate files * Update data endpoint * Stop tracking more deployment stuff * Fix bug when removing duplicate sequences on SNV level * Add private site config file, and config option for hashing Accession IDs * Ignore GISAID update script | 19 January 2021, 14:28:10 UTC |
| 89a8d05 | Albert Tian Chen | 19 January 2021, 08:54:18 UTC | Status box (dynamic footnote) (#263) * Let tabs calculate their own width - closes #261 * Fix typo in tooltip ref * revert dev changes to package caching * Add status box | 19 January 2021, 08:54:18 UTC |
| 0d4da11 | Albert Chen | 19 January 2021, 03:16:25 UTC | Add build for private pw-protected site | 19 January 2021, 03:16:25 UTC |
| 57bf799 | Albert Chen | 19 January 2021, 02:55:44 UTC | Merge branch 'master' of https://github.com/vector-engineering/covidcg | 19 January 2021, 02:56:18 UTC |
| 0132e22 | Albert Chen | 19 January 2021, 02:55:35 UTC | Stop tracking site deployment script | 19 January 2021, 02:55:35 UTC |
| febe381 | Albert Tian Chen | 09 January 2021, 22:24:48 UTC | Merge branch 'master' of github.com:vector-engineering/covidcg | 09 January 2021, 22:24:48 UTC |
| 2b53b30 | Albert Tian Chen | 09 January 2021, 22:24:35 UTC | update location corrections | 09 January 2021, 22:24:35 UTC |
| a736631 | Albert Tian Chen | 08 January 2021, 07:35:49 UTC | Bugfixes (#260) * Fix warning text * refactor to LegendSidebar * simplify grid layout * Remove code for old legend, clean up lint warnings * Add tooltip for legend - replacing old help text * Bump the max date range... we'll check back in 2099 * bump version to v1.4.6 | 08 January 2021, 07:35:49 UTC |
| 7d8576b | Albert Tian Chen | 08 January 2021, 06:49:39 UTC | Fix missing geographical annotations for Czechia and Palestine (West Bank and Gaza) | 08 January 2021, 06:49:39 UTC |
| 2c35a7c | Aaron Petkau | 07 January 2021, 21:22:05 UTC | Ingestion of custom/in-house data (#259) * Added workflow_custom * Fixed snakefile to work with custom data * Removed unneeded code * Adding test data derived from genbank * Removing some unneeded metadata * Removed more unneeded metadata columns * Updated pangolin from master * Fixed up import/added samtools dependency * Modify to default to local data package * Added instructions in readme * Fixing typos in readme * Automatically replace location n/a with -1 * Updated main README file * Updated readme with additional instructions * Added text describing where to look for an example | 07 January 2021, 21:22:05 UTC |
| f90939c | kevin altschuler | 05 January 2021, 04:37:46 UTC | lineage sidebar (#254) * lineage sidebar * wip * wip * fully working sidebar * works now * sort by pos * dont show on loading * Add sorting condition - for proteins and NT SNVs * Change legend column titles * fix bug - last item in legend list cut off * Fix wrapping in legend list for long protein names * change default date bin to week - trying to increase performance * Add heatmap code to table cells Co-authored-by: Albert Chen <chena@broadinstitute.org> | 05 January 2021, 04:37:46 UTC |
| 2f261d6 | dependabot[bot] | 05 January 2021, 03:31:32 UTC | Bump vega from 5.12.3 to 5.17.3 (#257) Bumps [vega](https://github.com/vega/vega) from 5.12.3 to 5.17.3. - [Release notes](https://github.com/vega/vega/releases) - [Commits](https://github.com/vega/vega/compare/v5.12.3...v5.17.3) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> | 05 January 2021, 03:31:32 UTC |
| 131d61a | Albert Chen | 05 January 2021, 03:27:27 UTC | Merge branch 'master' of https://github.com/vector-engineering/covidcg | 05 January 2021, 03:27:27 UTC |
| 0c08b4f | Aaron Petkau | 05 January 2021, 03:26:41 UTC | Fixed up import/added samtools dependency (#258) | 05 January 2021, 03:26:41 UTC |
| 419c94f | Albert Chen | 05 January 2021, 03:25:48 UTC | Add SNV bias warning | 05 January 2021, 03:25:48 UTC |
| 36ed383 | Albert Chen | 05 January 2021, 03:25:26 UTC | Add config file env arg to server start command | 05 January 2021, 03:25:26 UTC |
| 093512e | Albert Tian Chen | 02 January 2021, 20:22:47 UTC | fix typo | 02 January 2021, 20:22:47 UTC |
| 2e32938 | Albert Tian Chen | 02 January 2021, 20:22:36 UTC | bump pangolin version | 02 January 2021, 20:22:36 UTC |
| ddabbd0 | Aaron Petkau | 30 December 2020, 18:53:48 UTC | Added gzip library (#256) | 30 December 2020, 18:54:35 UTC |
| a469aa3 | Albert Tian Chen | 30 December 2020, 18:51:51 UTC | Add metadata fixes for GISAID ingest | 30 December 2020, 18:52:08 UTC |
| a6db3ba | Albert Tian Chen | 30 December 2020, 18:51:43 UTC | Fix missing import | 30 December 2020, 18:51:43 UTC |
| 2b97691 | Albert Chen | 29 December 2020, 13:02:06 UTC | Update workflow figure | 29 December 2020, 13:02:06 UTC |
| 394f23a | Albert Chen | 28 December 2020, 20:59:29 UTC | fix duplicate link | 28 December 2020, 20:59:29 UTC |
| 5510c5e | Albert Chen | 28 December 2020, 14:13:07 UTC | Bump version to v1.4.2 | 28 December 2020, 14:13:07 UTC |
| 2830755 | Albert Chen | 28 December 2020, 14:11:24 UTC | Add links to UCSC genome browser and WUSTL virus gateway | 28 December 2020, 14:11:24 UTC |
| 5dc34c8 | Albert Tian Chen | 25 December 2020, 09:31:11 UTC | Fix typos/bugs | 25 December 2020, 09:31:11 UTC |
| 155c839 | Albert Chen | 23 December 2020, 15:51:03 UTC | bump pangolin version | 23 December 2020, 15:51:03 UTC |
| cb119fb | Albert Chen | 23 December 2020, 15:50:39 UTC | remove dev script | 23 December 2020, 15:50:39 UTC |
| 2694141 | Albert Chen | 23 December 2020, 10:39:14 UTC | Bump version to v1.4.1 | 23 December 2020, 10:39:14 UTC |
| 7319106 | Albert Tian Chen | 23 December 2020, 10:38:30 UTC | New Pipeline (#255) * Switch to compressed formats (gzipped fasta and bam) to save disk space * Fix bug when calling two in/dels with no mutations in between * fix AA deletion numbering * Refactor snakemake pipeline into ingest and main steps * Refactor snakemake pipeline into ingest and main steps * Remove redundant gisaid IDs * Combine group consensus counts (in preparation for greater modularization), remove location map from data package * remove dependence on location map * Generalize group consensus data handling * Consolidate steps, process SNPs inside combine_all_data rule * Load SNP maps from the new consolidated metadata map * More robust GISAID ingestion, start to parametrize some of the workflow into config files to prepare for GenBank ingest option * Add GenBank ingestion workflow * update dotfiles * Update documentation * Unify config files * Unify config files * Fix bugs in ingest workflows * More robust fasta file comparisons * Fix vulnerabilities, add yaml loader * Refactor to generalize sequence groupings, adapt to new data package format * generalize over sequence groupings/metadata in workflow * re-flag feed as temporary in genbank ingest * refactor * Refactor configuration files - now one for each ingestion method/data type. Inject configuration file as JSON into front-end files via. webpack, to make config fields immediately accessible * Fix download of global sequencing data * Add build scripts | 23 December 2020, 10:38:30 UTC |
| e2fde69 | Albert Chen | 15 December 2020, 18:11:55 UTC | bump version to v1.3.0 | 15 December 2020, 18:11:55 UTC |
| f5d7109 | Albert Chen | 15 December 2020, 17:54:38 UTC | fetch new data package every hour | 15 December 2020, 17:55:07 UTC |
| 5ec918c | Albert Chen | 15 December 2020, 17:53:26 UTC | fix missing column for reference/other rows in AA table downloads | 15 December 2020, 17:53:26 UTC |
| 27a3dc3 | Albert Chen | 15 December 2020, 17:47:20 UTC | Merge branch 'master' of https://github.com/vector-engineering/covidcg | 15 December 2020, 17:52:10 UTC |
| 18a0af4 | Albert Tian Chen | 15 December 2020, 17:47:08 UTC | fix bug where dna_snps were being skipped from the group consensus count | 15 December 2020, 17:47:08 UTC |
| 1572b2d | Albert Chen | 15 December 2020, 17:16:05 UTC | Fix broken download of lineages - account for 'Other' group | 15 December 2020, 17:16:05 UTC |
| 6cc1b6f | Albert Tian Chen | 08 December 2020, 13:56:44 UTC | Fix bug where last chunk wasn't being flushed to disk | 08 December 2020, 13:56:44 UTC |
| 1fd25e0 | Albert Tian Chen | 06 December 2020, 09:03:40 UTC | Define chunks by submission date, improve readability and DRY a bit | 06 December 2020, 09:03:40 UTC |
| bb4bbae | Albert Tian Chen | 06 December 2020, 09:02:50 UTC | Update passage metadata cleaner | 06 December 2020, 09:02:50 UTC |
| 1b924ed | Albert Tian Chen | 06 December 2020, 09:02:28 UTC | faster version of consensus SNV counting | 06 December 2020, 09:02:28 UTC |
| b5bdb75 | Albert Tian Chen | 04 December 2020, 13:07:51 UTC | fix typo | 04 December 2020, 13:07:51 UTC |
| 8ace6c6 | Albert Tian Chen | 04 December 2020, 13:07:44 UTC | Push map vega spec on site update | 04 December 2020, 13:07:44 UTC |
| e7caed2 | Albert Tian Chen | 04 December 2020, 13:05:34 UTC | remove references to data feed | 04 December 2020, 13:05:34 UTC |
| 3fef9d9 | Albert Tian Chen | 30 November 2020, 08:49:11 UTC | location metadata fixes | 30 November 2020, 08:49:11 UTC |
| cf9a108 | Albert Tian Chen | 30 November 2020, 08:49:01 UTC | remove some metadata collapsing to better preserve original intent | 30 November 2020, 08:49:01 UTC |
| c23146e | Albert Tian Chen | 30 November 2020, 08:48:48 UTC | Capture more age metadata strings | 30 November 2020, 08:48:48 UTC |
| 23c0f7b | Albert Tian Chen | 30 November 2020, 08:48:28 UTC | Add curl, node requirements | 30 November 2020, 08:48:28 UTC |
| bd45e5a | Albert Tian Chen | 28 November 2020, 23:01:32 UTC | exclude some files from upload | 28 November 2020, 23:01:32 UTC |
| 6052b9c | Albert Tian Chen | 28 November 2020, 23:01:21 UTC | location data fixes | 28 November 2020, 23:01:21 UTC |
| 858da62 | Albert Tian Chen | 24 November 2020, 17:21:11 UTC | location metadata fixes | 24 November 2020, 17:21:11 UTC |
| 5597174 | Albert Tian Chen | 24 November 2020, 07:47:05 UTC | Data feed (#250) * first working version * add documentation * Add updated data documentation in the README | 24 November 2020, 07:47:05 UTC |
| a1ec327 | Albert Chen | 05 November 2020, 15:51:52 UTC | Update data section in README | 05 November 2020, 15:51:52 UTC |
| 854a4e2 | Albert Tian Chen | 05 November 2020, 02:59:18 UTC | Update README.md | 05 November 2020, 02:59:18 UTC |
| b2b304d | dependabot[bot] | 30 October 2020, 00:59:29 UTC | Bump node-fetch from 2.6.0 to 2.6.1 (#240) Bumps [node-fetch](https://github.com/bitinn/node-fetch) from 2.6.0 to 2.6.1. - [Release notes](https://github.com/bitinn/node-fetch/releases) - [Changelog](https://github.com/node-fetch/node-fetch/blob/master/docs/CHANGELOG.md) - [Commits](https://github.com/bitinn/node-fetch/compare/v2.6.0...v2.6.1) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> | 30 October 2020, 00:59:29 UTC |
| cac96f8 | Albert Chen | 17 October 2020, 20:20:04 UTC | Add link to preprint in README (closes #249) | 17 October 2020, 20:20:04 UTC |
| 07172ab | Albert Chen | 13 October 2020, 20:50:24 UTC | Add documentation about new data package system | 13 October 2020, 20:50:24 UTC |
| c1b7085 | Albert Chen | 13 October 2020, 20:44:22 UTC | Add text showing number of sequences analyzed | 13 October 2020, 20:44:27 UTC |
| 36450b7 | Albert Chen | 13 October 2020, 17:05:46 UTC | bump version | 13 October 2020, 17:05:46 UTC |
| 5d1e986 | Albert Chen | 13 October 2020, 17:05:30 UTC | remove build dependencies on data | 13 October 2020, 17:05:30 UTC |
| 00b6e0b | Albert Chen | 13 October 2020, 17:05:09 UTC | Hotfix - don't show initial loading screen after the first initialization | 13 October 2020, 17:05:09 UTC |
| e6e55a4 | Albert Chen | 13 October 2020, 02:14:33 UTC | bump version to 1.2.0 | 13 October 2020, 02:14:33 UTC |
| 887ef3f | kevin altschuler | 13 October 2020, 02:12:46 UTC | fade in on the splash screen (#247) | 13 October 2020, 02:12:46 UTC |
| 093c683 | Albert Chen | 13 October 2020, 02:12:16 UTC | Use data date in package contents | 13 October 2020, 02:12:16 UTC |
| 70bd7cf | Albert Chen | 13 October 2020, 02:11:47 UTC | Merge branch 'master' of https://github.com/vector-engineering/covidcg | 13 October 2020, 02:11:47 UTC |
| 0a84616 | Albert Tian Chen | 13 October 2020, 02:11:26 UTC | Merge branch 'master' of github.com:vector-engineering/covidcg | 13 October 2020, 02:11:26 UTC |
| 3469fa1 | Albert Tian Chen | 13 October 2020, 02:10:51 UTC | Add data date to package contents, add push script | 13 October 2020, 02:10:51 UTC |
| 2329446 | Albert Chen | 13 October 2020, 01:12:13 UTC | add back australia S477N example | 13 October 2020, 01:12:13 UTC |
| b22929b | Albert Chen | 13 October 2020, 01:10:42 UTC | Global Sequencing data now uses all available data | 13 October 2020, 01:10:42 UTC |
| 076f379 | Albert Chen | 13 October 2020, 00:56:22 UTC | Merge branch 'master' of https://github.com/vector-engineering/covidcg | 13 October 2020, 00:56:22 UTC |
| 752d319 | kevin altschuler | 13 October 2020, 00:56:09 UTC | Async data loading (#243) * wip, better than before * moved over one thing * move rootstore to a class * just barely working * snp data store * snp should be fully working now * lineage good * more * bump version and data date * bump version and data date * middle of refactoring, prepare to merge with master * mostly working * fetch gzipped data package and decompress client-side * Fix crash when gettings SNVs from 'other' or 'reference' groups * loading screen Co-authored-by: Albert Chen <chena@broadinstitute.org> | 13 October 2020, 00:56:09 UTC |
| e11985a | Albert Chen | 12 October 2020, 07:04:41 UTC | bump version and data date | 12 October 2020, 07:04:41 UTC |
| 893f37d | Albert Chen | 05 October 2020, 16:42:06 UTC | bump version and data date | 05 October 2020, 16:42:06 UTC |
| 572a01d | Albert Chen | 05 October 2020, 15:36:41 UTC | Merge branch 'master' of https://github.com/vector-engineering/covidcg | 05 October 2020, 15:36:41 UTC |
| ee23da3 | Albert Tian Chen | 05 October 2020, 15:36:30 UTC | Build fixes for sparse data (#245) * Add link to preprint, bump version and data date * Allow builds without acknowledgements files * Add documentation for the nextmeta file * Add more descriptive warning when nextmeta file is not found * Fixing pipeline crashes on sparse metadata * Remove underscore calls, return no data when no locations are selected * Remove initially selected location nodes if they don't exist in the data | 05 October 2020, 15:36:30 UTC |
| 123f803 | Albert Chen | 29 September 2020, 19:46:59 UTC | Add link to preprint, bump version and data date | 29 September 2020, 19:46:59 UTC |
| 591eed4 | Albert Chen | 25 September 2020, 00:54:20 UTC | bump version, clean location metadata | 25 September 2020, 00:54:20 UTC |
| 368c01f | Albert Chen | 19 September 2020, 16:41:03 UTC | bump version and data date | 19 September 2020, 16:41:03 UTC |
| 0a0f238 | Albert Chen | 18 September 2020, 06:02:03 UTC | bump version and data date | 18 September 2020, 06:02:03 UTC |
| e789dc4 | Albert Chen | 16 September 2020, 06:01:36 UTC | bump version and data date | 16 September 2020, 06:01:36 UTC |
| ee43241 | Albert Chen | 15 September 2020, 19:03:46 UTC | update country_score data package, bump version | 15 September 2020, 19:03:46 UTC |
| 036dd36 | Albert Chen | 15 September 2020, 18:50:04 UTC | adjust copy, bump version | 15 September 2020, 18:50:04 UTC |
| 0db04f3 | Albert Chen | 15 September 2020, 15:18:13 UTC | Merge branch 'master' of https://github.com/vector-engineering/covidcg | 15 September 2020, 15:18:13 UTC |
| 5d5be1f | Albert Tian Chen | 15 September 2020, 15:17:34 UTC | Getting Started Page (#241) * bump version and data date * Bump version and data date * bump version and data date * simplify constants - prep for query string feature * Hide filter sidebar for text pages * fix typo * Add tutorial sections * temporarily bump version * Use all data for the global sequencing coverage plot * Move splash screen content to getting started page * Hide tutorial 1, for now * UI Adjustments | 15 September 2020, 15:17:34 UTC |
| 6c37389 | Albert Chen | 14 September 2020, 00:46:22 UTC | simplify constants - prep for query string feature | 14 September 2020, 00:46:22 UTC |
| 022fda9 | Albert Chen | 13 September 2020, 04:02:30 UTC | bump version and data date | 13 September 2020, 04:02:30 UTC |
| 8179590 | Albert Chen | 11 September 2020, 16:05:05 UTC | Bump version and data date | 11 September 2020, 16:05:05 UTC |
| a26adba | Albert Chen | 10 September 2020, 15:39:23 UTC | bump version and data date | 10 September 2020, 15:39:23 UTC |
| 4237da7 | Albert Chen | 10 September 2020, 00:49:02 UTC | Bump version to v1.0.17 | 10 September 2020, 00:49:02 UTC |
| 9ee1333 | Albert Chen | 10 September 2020, 00:48:44 UTC | Sort co-occurrence SNVs by gene/protein (if applicable), then position as integer, not text (Closes #237) | 10 September 2020, 00:48:44 UTC |
| ac17722 | Albert Chen | 10 September 2020, 00:48:19 UTC | When in AA SNV mode, filter on gene/protein name as well as on residue indices | 10 September 2020, 00:48:19 UTC |
| bd30217 | Albert Chen | 09 September 2020, 20:23:39 UTC | bump version to v1.0.16 | 09 September 2020, 20:23:39 UTC |
| 0170052 | Albert Chen | 09 September 2020, 20:23:14 UTC | Ignore more folders, organize gcloudignore | 09 September 2020, 20:23:14 UTC |
| 5741dfb | Albert Chen | 09 September 2020, 20:22:58 UTC | Fix ID of Turkmenistan | 09 September 2020, 20:22:58 UTC |
| b1b5ac4 | Albert Chen | 09 September 2020, 20:13:09 UTC | bump version and data date | 09 September 2020, 20:13:09 UTC |
| 08a8046 | Albert Chen | 09 September 2020, 20:09:23 UTC | Fix geographic inconsistencies in the global sequencing plot. Increase data range to 2020-01-01 -- 2020-07-01, and include countries with >100 confirmed cases in the bar plots below | 09 September 2020, 20:10:06 UTC |
| 017e397 | Albert Chen | 09 September 2020, 20:00:00 UTC | Taken from: https://github.com/vega/vega-datasets/blob/master/data/world-110m.json Modified to: * Recover unique ID for Kosovo * Recover unique ID for Eritrea * Recover unique ID for Northern Cyprus * Separate France and French Guiana | 09 September 2020, 20:00:00 UTC |
| baba26f | Albert Chen | 07 September 2020, 03:09:19 UTC | bump version and data date | 07 September 2020, 03:09:19 UTC |
| 02af263 | Albert Chen | 03 September 2020, 19:19:20 UTC | Adjust copy, bump version | 03 September 2020, 19:27:15 UTC |
