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.

Sign up for GitHub

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

Jump to bottom

[GH-1221] import snapshots into a workspace #347

Merged
merged 18 commits into from
Apr 2, 2021
Merged

[GH-1221] import snapshots into a workspace #347

merged 18 commits into from
Apr 2, 2021

Commits on Mar 18, 2021

  1. update sarscov2_illumina_full_inputs dataset to match flowcell values

    @ehigham
    ehigham committed Mar 18, 2021
    Configuration menu
    Copy the full SHA
    b018685 View commit details
    Browse the repository at this point in the history

Commits on Mar 19, 2021

  1. remove trailing slash from tdr url

    @ehigham
    ehigham committed Mar 19, 2021
    Configuration menu
    Copy the full SHA
    286264b View commit details
    Browse the repository at this point in the history

Commits on Mar 25, 2021

  1. add/refactor querying for TDR dataset via BigQuery. Fix `flatten-rows… 

    …` implementation for REPEATED data types
    @ehigham
    ehigham committed Mar 25, 2021
    Configuration menu
    Copy the full SHA
    358a0a6 View commit details
    Browse the repository at this point in the history

Commits on Mar 27, 2021

  1. start implementing importing into a workspace

    @ehigham
    ehigham committed Mar 27, 2021
    Configuration menu
    Copy the full SHA
    68a3ae7 View commit details
    Browse the repository at this point in the history

  2. inline concat of firecloud route

    @ehigham
    ehigham committed Mar 27, 2021
    Configuration menu
    Copy the full SHA
    7880563 View commit details
    Browse the repository at this point in the history

  3. fix error in docstring

    @ehigham
    ehigham committed Mar 27, 2021
    Configuration menu
    Copy the full SHA
    7dd4d8d View commit details
    Browse the repository at this point in the history

Commits on Mar 30, 2021

  1. Update sarscov2_illumina_full_inputs dataset to include flowcell_id 

    and an `updated` datetime.
Add REST wrappers for getting/deleting entities in a workspace
Implement test for importing a snapshot into a workspace. Won't work
until the dataset above is rebuild.
    @ehigham
    ehigham committed Mar 30, 2021
    Configuration menu
    Copy the full SHA
    b60220b View commit details
    Browse the repository at this point in the history

  2. format

    @ehigham
    ehigham committed Mar 30, 2021
    Configuration menu
    Copy the full SHA
    bcbb75c View commit details
    Browse the repository at this point in the history

  3. use timestamps instead of datetime for timezones

    @ehigham
    ehigham committed Mar 30, 2021
    Configuration menu
    Copy the full SHA
    8fc86b1 View commit details
    Browse the repository at this point in the history

  4. update tests for new dataset + try to fix failures

    @ehigham
    ehigham committed Mar 30, 2021
    Configuration menu
    Copy the full SHA
    c5fe494 View commit details
    Browse the repository at this point in the history

  5. fix unit test

    @ehigham
    ehigham committed Mar 30, 2021
    Configuration menu
    Copy the full SHA
    a8f1cb2 View commit details
    Browse the repository at this point in the history

Commits on Mar 31, 2021

  1. use temporary workspaces. fix import test. fix bigquery table->csv.

    @ehigham
    ehigham committed Mar 31, 2021
    Configuration menu
    Copy the full SHA
    8c46330 View commit details
    Browse the repository at this point in the history

  2. fix tests again

    @ehigham
    ehigham committed Mar 31, 2021
    Configuration menu
    Copy the full SHA
    2b8d226 View commit details
    Browse the repository at this point in the history

  3. use threading instead of >>>

    @ehigham
    ehigham committed Mar 31, 2021
    Configuration menu
    Copy the full SHA
    211bccd View commit details
    Browse the repository at this point in the history

Commits on Apr 1, 2021

  1. address feedback after review

    @ehigham
    ehigham committed Apr 1, 2021
    Configuration menu
    Copy the full SHA
    a357b47 View commit details
    Browse the repository at this point in the history

  2. pass in columns to table import code

    @ehigham
    ehigham committed Apr 1, 2021
    Configuration menu
    Copy the full SHA
    0e1ee3e View commit details
    Browse the repository at this point in the history

  3. fix some docstring

    @ehigham
    ehigham committed Apr 1, 2021
    Configuration menu
    Copy the full SHA
    9485e93 View commit details
    Browse the repository at this point in the history

Commits on Apr 2, 2021

  1. reuse polling logic. remove duplicate fircloud function

    @ehigham
    ehigham committed Apr 2, 2021
    Configuration menu
    Copy the full SHA
    09984ca View commit details
    Browse the repository at this point in the history