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@shapiromatron shapiromatron released this 25 Jan 14:37
· 816 commits to main since this release
2020-Q1
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Learn about vigilant mode.

March 31st 2020

Multiple updates were added to the literature import and tagging module, as well as more flexibility in the risk of bias/study evaluation section by allowing study-level overrides to specific questions. We've also expanded the visualization libraries being used, making it easier to make new visualizations in future releases. Stability was improved by adding a database fixture for easier testing, updating all packages to recent versions, and adding full windows support to the developer environment.

We also released both a Python and R-based HAWC client. This allows for developers, data scientists, and scientists to interact with both reading and writing data to HAWC via code instead of manually in the user-interface. Expect a dramatic expansion of the API in future releases.

Full changelist below:

  • General

    • Replace chemspider with the EPA chemicals dashboard
    • Add the ability to select language for NOAEL/NOEL/NEL, LOAEL/LOEL/LEL for assessments
    • Updated all packages to latest version for stability and easier development in Windows
    • Update django to version 2.2 LTS

  • Literature

    • Fix imports from HERO using new HERO API
    • Addition validation when importing from HERO to ensure all selected references for import can be imported into HAWC
    • Allow faster querying of PubMed using the new PubMed API key
    • Customizable literature tagtrees - can change which nodes are displayed and filter references by selected tags
    • Preserve UI settings for expanded/collapsed tags when tagging literature
    • Increase maximum PubMed query size to 10,000
    • Update reference detail layout; add related searches/imports for references
    • Show full author list instead of subset; full-author list is now also searchable when finding references
    • Add new histogram for literature overview by year
    • Added new API endpoints for interacting with literature module
      • /lit/api/assessment/{id}/tags/ - view all tags for assessment
      • /lit/api/assessment/{id}/reference-ids/ - view references for assessment and related PubMed/HERO ids
      • /lit/api/assessment/{id}/reference-tags/
        • GET: view references and associated hawc tags for each reference
        • POST: append/replace existing reference-tag relationships with new relationships
      • /lit/api/search/
        • POST: added new create HERO import API for importing references from HERO

  • Risk of bias app

    • Add new risk of bias overrides feature
      • multiple scores can be selected for a single metric/study combination
      • labels can provide context to which data the score are relevant for
      • extracted bioassay or epi components can be associated with overrides
      • updated all visualizations and data views to present override results in addition to default

  • Visualization

    • Add conditional formatting to data pivot reference-bars
      • commonly used to show if a trend-test is significant
    • Wrap-text automatically for long tag-node names in literature trees

  • Client

    • Added new Python-based HAWC client for reading/writing data to HAWC
    • Added new R-based HAWC client for reading/writing data to HAWC

  • API

    • enabled token-based authorization to allow standard automated tooling to access the HAWC API
    • Created new tabular style exports - for tabular REST API, can multiple standard output formats by specifying format=xlsx, or {csv, xlsx, json, html}

  • Testing

    • Add a database test-fixture to dramatically expand unit-testing capabilities
    • Updated test to use fixture instead of creating objects in test-setup
    • Created a new test for asynchronous celery task execution in admin
    • Added tests for phantomjs (svg -> png) conversion stability

  • Developer environment

    • Support Windows as a developer environment for HAWC
    • Updated developer documentation
    • Add new commands to anonymize developer database
    • Simplified developer environment setup to make the settings/local.py file optional
    • Expanded available /admin/ views
    • Update docker deployments to use recent container versions
    • Added new API endpoints for rendering plotly visualizations
Assets 2