Changes in OurDNA Browser #97
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This PR contains required minimal changes to setup OurDNA Browser as custom version of gnomAD. * Lower resources for dev/testing. * Change hardcoded docker location to more dynamic one, temp customise to deploye first version of production system. * Making cluster_name as custom string, removing hardcoded gnomad. * ES user always starts with gnomad prefix. * Keep gnomad name in ES LB. * Fixed formatting. * Lower dataproc cluster idle time. * Removed links from navbar not used by OurDNA Browser. * Removed user banner. * Updated Menu App Name. * Add info log regarding found variant in gnomad-v4-variant-queries. * Fix for gnomad-v4-variant-queries, we would not have hgdp & tgp in OurDNA Browser. * Added extra checks into gnomad-v4-variant-queries so it won't crash if joint ot exome fields are not present. * Prevent crashing on missing in_silico_predictors for gnomad-v4-variant-queries. * One more check for in_silico_predictors attribute in gnomad-v4-variant-queries. * ES table LOCAL_ANCESTRY_INDICES should be an alias and not index itself. * Added logs to investigate missing fields. * Check for attribute colocated_variants in gnomad-v4-variant-queries. * Add empty coverage if missing for fetchVariantById. * Fixing coverage in variant condition. * Disable temporarily LiftoverTarget for gnomad_r4. * Fix linting and action/cache upgrade. * Disable Jest tests for the time being. * Add deploy to dev github action. * First attempt to implement CI. * Updating github action to use the right WIP. * Added deploy action for production.
* Testing CI - development version. * Testing CI - production deployment. * Cleanup github actions.
* First version of website content, removed headshots related to gnomAd browser team. * Fixing missing federation page. * More content changes, introducing gnomad_r4_ourdna dataset. * Fixing building APi issue. * Added gnomad_r4_ourdna dataset to API. * Add more logs to API. * Fix hasExomeVariant in fetchVariantById API function. * Fix hasExomeVariant in fetchVariantById API function. * Removing read data section and fixing link to variant example. * Added favicon and update pages title. * Fixing favicon. * Fix get_elasticsearch_password function. * Updating GraphQL-API code to use the right alias and update ourdna dataset metadata. * Make gnomad_r4_ourdna as default dataset. * Fixing API for empty exome records. * Add logs to _fetchCoverageForGene. * Ignore TS(7053). * Make blog link as relative path. * Removing main branch from CI. * Removing test branch CI. * Pass cluster name around in ES commands. * Fixing linting.
* First version of website content, removed headshots related to gnomAd browser team. * Fixing missing federation page. * More content changes, introducing gnomad_r4_ourdna dataset. * Fixing building APi issue. * Added gnomad_r4_ourdna dataset to API. * Add more logs to API. * Fix hasExomeVariant in fetchVariantById API function. * Fix hasExomeVariant in fetchVariantById API function. * Removing read data section and fixing link to variant example. * Added favicon and update pages title. * Fixing favicon. * Fix get_elasticsearch_password function. * Updating GraphQL-API code to use the right alias and update ourdna dataset metadata. * Make gnomad_r4_ourdna as default dataset. * Fixing API for empty exome records. * Add logs to _fetchCoverageForGene. * Ignore TS(7053). * Fixing OurDNA Browser ingress. * Remove test branch CI.
* Replaced ac_raw checks with ac.
* Renaming Ancestry groups for OurDNA Browser data. * Added logs. * Add temp deploy to dev. * More logs. * Update Ancestry Group names casing. * Removing console.logs. * Removing temp deploy CI. * Removing empty line.
* Updating inbreeding_coeff with InbreedingCoeff. * Keep both inbreeding_coeff and InbreedingCoeff.
* Remove url to team page * Landing: update federated link * About: remove p referring to Broad * About: update page, including funding * Contact: update text * Policies: update text, esp expectations for use * Policies: reformat * Publications: update text * Publications: format, fix linting errors * Publications: update br to self closing * Contact: Add closing tag for ExternalLink * Contact: fix linting errors * Contact: Fix linting error * Contact: address more linting issues * Fix linting errors * Add error ignore for externalLink * Replacing Link tag to fix type checks. --------- Co-authored-by: Milo Hyben <[email protected]>
* Apply formatting for gnomAD styled table * Add centred container style definition * Fixing type check issue. --------- Co-authored-by: Milo Hyben <[email protected]>
* About: add PIs to Data contributors * About: Add funding info to About md file; tidy AboutPage.tsx to remove unused elements * Remove funding md page * Policies: update text * Contact: remove rogue period * Resolve formatting error in table * About: remove PIs from Mackenzie's Mission * Fix linting issue
* Added fetchVariantsAgeDistribution to load from table_globals. * Add age_distribution to graphql schema. * Fixing query for age_distribution. * Formatting age-distribution object content. * Mockup exome/genome age distribution data. * Added Distribution graphql type. * Update to age_distribution query. * Fixing age_distribution query. * Implementing dynamic loading of global age distribution.
* Policies: add link from licence to publications page * Ethics: create table in tsx * Ethics: tidy pages and fix errors * Update table on ethics contact page with additional header and description * Ethics: update TOB description * Fix layout on contact page * Update ethics page with MCRI contact details
* Update age distribution mapping to reflect ES index structure * update OurDNA dataset name * add new population code mappings
* Removing second tab in Dataset selection on Gene page. * Removing co-occurrence box from Gene page. * Replace the 'gnomAD variants' title with 'OurDNA variants'. * Transcript page options in the dropdown should only be ‘OurDNA v1.0’ for now * Transcript page - drop Constraint box. * Fixing Dataset drop down box on variant page. * Replacing gnomad email with OurDNA support email. * Updating VEP note. * Disable Genomic Constraint of Surrounding 1kb Region.
Updating Coverage GraphQL to reflect table schema.
* fix gnomAD mention * ignore missing module warnings * correct sample counts to remove 1kgp samples * amend 'samples' -> 'variants' for disabled barplot * revert bar exome/genome colours, gnomad blue/green * comment out unused import
* add homepage msg to about page, run prettier * about OurDNA browser -> about "the" OurDNA browser
* Link reference to ethics on About page to ethics contact page * Update link to Funding header on About page * Capitalise OurDNA Browser consistently across product * Add link to LinkedIn on Contact page * Rolling back precommit config. --------- Co-authored-by: Milo Hyben <[email protected]>
* Disable performance hints, allow for larger JS file. * Make Banner depending on env. * Added offline page, controlled by ENV variable. * Preparing offline message and include GA-tagging.
Restructured the page to make data contributors more prominent, and made some other content and style tweaks. Added working URLs for several cohorts as well as Garvan, MCRI, and the Digital Futures Initiative
* Fixing fetchVariantsByRegion when genome or exome is not present.
* add footer text to ancestry groups table * fix graph legend formatting * fix stylelint error * fix lint error * left-align chart and plot
Stats page edits - fix legends, add sample counts footer (#88)
* Moving favicon to a subfolder to fix the caching issue with the old favicon.
* Making Error page change. * Change Footer background colour and font color.
Added clearer credit to the gnomAD team for the browser code-base.
Making Error page change. Change Footer background colour and font color. Update About.md
Convert the ancestry code to lowercase. (#98)
milo-hyben
temporarily deployed
to
production
GitHub Actions
Inactive
Replacing reference to gnomAD in QC Filter Tooltip.
PR includes Team list extracted from approved list of OurDNA dataset creators. PR also includes some light housekeeping: Renames md file used to display team list Uncomments Team link in nav bar Removes import of Team list on About page. * Delete data-contributors.md * Rename data-generation page to cpg-team * Add staff and contributors to md doc * Uncomment Team option in navbar * Delete contributing projects list from About page * TeamPage column width fix and precommit back. --------- Co-authored-by: Milo Hyben <[email protected]>
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This is just dummy PR to show what we have changed to get OurDNA Browser working.