Skip to content
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

Closed
wants to merge 13 commits into from

Commits on Feb 2, 2021

  1. 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.
    eharkins committed Feb 2, 2021
    Configuration menu
    Copy the full SHA
    82259cb View commit details
    Browse the repository at this point in the history
  2. Configuration menu
    Copy the full SHA
    a8168aa View commit details
    Browse the repository at this point in the history
  3. 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.
    eharkins committed Feb 2, 2021
    Configuration menu
    Copy the full SHA
    f83c15c View commit details
    Browse the repository at this point in the history
  4. Configuration menu
    Copy the full SHA
    9c0cb06 View commit details
    Browse the repository at this point in the history

Commits on Feb 5, 2021

  1. 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).
    eharkins committed Feb 5, 2021
    Configuration menu
    Copy the full SHA
    91c6623 View commit details
    Browse the repository at this point in the history
  2. 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
    eharkins committed Feb 5, 2021
    Configuration menu
    Copy the full SHA
    0cac621 View commit details
    Browse the repository at this point in the history
  3. Configuration menu
    Copy the full SHA
    ee588ba View commit details
    Browse the repository at this point in the history
  4. 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
    eharkins committed Feb 5, 2021
    Configuration menu
    Copy the full SHA
    a3aad83 View commit details
    Browse the repository at this point in the history
  5. 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
    eharkins committed Feb 5, 2021
    Configuration menu
    Copy the full SHA
    dcf74d0 View commit details
    Browse the repository at this point in the history
  6. generalize step in collect-pathogen-resources.js;

    this takes the augmenting of the build
    catalogue and abstracts it into a function
    eharkins committed Feb 5, 2021
    Configuration menu
    Copy the full SHA
    7b14dcd View commit details
    Browse the repository at this point in the history
  7. 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
    eharkins committed Feb 5, 2021
    Configuration menu
    Copy the full SHA
    5764d33 View commit details
    Browse the repository at this point in the history
  8. Configuration menu
    Copy the full SHA
    eab57a7 View commit details
    Browse the repository at this point in the history

Commits on Feb 8, 2021

  1. 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.
    eharkins committed Feb 8, 2021
    Configuration menu
    Copy the full SHA
    b50b224 View commit details
    Browse the repository at this point in the history