-
Notifications
You must be signed in to change notification settings - Fork 48
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Augment sarscov2 community builds listing and include datasets in sequence search #266
Commits on Feb 2, 2021
-
fetch sars-cov-2 build metatdata for /sars-cov-2;
creates an augmented version of static-site/content/allSARS-CoV-2Builds.yaml by fetching the actual datasets to get information about them such as date updated and number of tips to be displayed on the build listing and map.
Configuration menu - View commit details
-
Copy full SHA for 82259cb - Browse repository at this point
Copy the full SHA 82259cbView commit details -
Configuration menu - View commit details
-
Copy full SHA for a8168aa - Browse repository at this point
Copy the full SHA a8168aaView commit details -
incl. community builds in sarscov2 search results;
building on: 081bd55633133e586a3dae86617564e1f2854418 , which fetched community datasets listed in static-site/content/allSARS-CoV-2Builds.yaml in order to augment that list with metadata. This takes the fetched community datasets and includes them in the sarscov2 search results database file. Still to-do is testing this on the front end.
Configuration menu - View commit details
-
Copy full SHA for f83c15c - Browse repository at this point
Copy the full SHA f83c15cView commit details -
Configuration menu - View commit details
-
Copy full SHA for 9c0cb06 - Browse repository at this point
Copy the full SHA 9c0cb06View commit details
Commits on Feb 5, 2021
-
fetch and parse augmented build catalogue;
scripts/collect-search-results.js reads in a list of builds in a manually maintained pathogen build catalogue yaml file such as static-site/content/allSARS-CoV-2Builds.yaml and produces an augmented version with metadata from each corresponding dataset. (see 82e072d). That augmented yaml file is stored on s3 and fetched here to populate e.g the build-map (front-end manisfestation of that pathogen build catalogue on the page) with metadata about each dataset (e.g. date updated).
Configuration menu - View commit details
-
Copy full SHA for 91c6623 - Browse repository at this point
Copy the full SHA 91c6623View commit details -
build page component: remove fixed sarscov2 text;
this makes this component more generally applicable for when we want to have similar build catalogues for other pathogens
Configuration menu - View commit details
-
Copy full SHA for 0cac621 - Browse repository at this point
Copy the full SHA 0cac621View commit details -
Configuration menu - View commit details
-
Copy full SHA for ee588ba - Browse repository at this point
Copy the full SHA ee588baView commit details -
Generalize pathogen resource scripts;
we have a couple of scripts that are utilities for creating and checking the format of data resources behind pages like nextstrain.org/sars-cov-2. This generalizes the code in those scripts so that they make sense when we apply them to other pathogens in the future
Configuration menu - View commit details
-
Copy full SHA for a3aad83 - Browse repository at this point
Copy the full SHA a3aad83View commit details -
general names for pathogen resources scripts;
also update the github action using scripts/collect-pathogen-resources.js also note that upon merging this we will need to update a link in the following doc: https://docs.nextstrain.org/en/latest/guides/share/sars-cov-2.html ; the link points to: scripts/check-sars-cov-2-builds-yaml.js which is now called: scripts/check-build-catalogue-yaml.js
Configuration menu - View commit details
-
Copy full SHA for dcf74d0 - Browse repository at this point
Copy the full SHA dcf74d0View commit details -
generalize step in collect-pathogen-resources.js;
this takes the augmenting of the build catalogue and abstracts it into a function
Configuration menu - View commit details
-
Copy full SHA for 7b14dcd - Browse repository at this point
Copy the full SHA 7b14dcdView commit details -
fix outputs collect-pathogen-resources.js;
fixes bug when running for seasonal-flu introduced by work on this script. Better logic overall for writing outputs and printing messages
Configuration menu - View commit details
-
Copy full SHA for 5764d33 - Browse repository at this point
Copy the full SHA 5764d33View commit details -
Configuration menu - View commit details
-
Copy full SHA for eab57a7 - Browse repository at this point
Copy the full SHA eab57a7View commit details
Commits on Feb 8, 2021
-
rename static-site/src/components/sars-cov-2;
this directory contains components which are now generally applicable to any page that wants to display a collection of info about any grouping of builds (e.g. flu, groups, commeunity), not just for sars-cov-2.
Configuration menu - View commit details
-
Copy full SHA for b50b224 - Browse repository at this point
Copy the full SHA b50b224View commit details