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@shapiromatron shapiromatron released this 25 Jan 14:37
· 692 commits to main since this release
2020-Q3
d3dc3ae

October 11, 2020.

This quarter's update has three major new features/updates:

  1. Allowing use of controlled vocabulary for in vivo bioassay endpoint data extraction in HAWC. To take advantage of this new feature, we've also released the Environmental Health Vocabulary (EHV), designed by health scientists at EPA/ORD/CHPEA, this is designed to be a living vocabulary which will be updated and curated frequently as new health assessments extract content in new biological domains (https://hawcproject.org/vocab/ehv/; login required). Controlled vocabularies in HAWC allow mapping of terms to external ontologies, including potentially mapping to adverse outcome pathways (AOP) or other ways of organizing biological causality and critical effect. Use of the vocabulary in HAWC is optional; you can still enter content without using the vocabulary as before.
  2. Integration with the US EPA Chemistry dashboard (https://comptox.epa.gov/dashboard) by using DTXSID as a preferred chemical identifier instead of name/CASRN, which allows for QA/QC of data entry by using this highly curated scientific database. Assessments, bioassay endpoints, invitro endpoints, and epidemiological exposures can now be mapped to DTXSIDs.
  3. Improving software stability by full-stack integration tests in our CI/CD pipeline, which allows for testing visualizations and rich frontend client applications

A full list of changes are available below:

  • Vocabulary

    • Create new application for controlled vocabulary and mapping to related external entities
    • Load v1 of enviro health vocabulary EHV for EPA HAWC assessments, developed by EPA/ORD/CPHEA colleagues
    • Add a display view, /vocab/ehv/ to browse the vocabulary

  • Assessment

    • Add DTXSID integration and modify dashboard to query Chemistry dashboard API
    • Migrate existing CASRN to DTXSID
    • Add assessment-level (and overall) logs
    • Add blog model for reporting HAWC updates
    • Add job-model for asynchronous reports
    • Datasets can now be published or unpublished, just like studies or visuals
    • Rewrite data-extraction cleanup using mobX instead of redux, ignoring controlled vocabulary

  • Literature

    • Added new API endpoint for replacing HERO identifiers
    • Added new API endpoint for updating all reference metadata from HERO
    • Bugfix: update API to check for unique title/slug
    • Update reference page to show all tags currently applied in all views
    • Update tagtree visualization to show/hide nodes with no references
    • Catch common RIS formatting upload errors and report to user as 400s instead of 500s

  • Risk of bias/study evaluation

    • Modify "default" score label to "overall" and only present if a label was not entered
    • Add ability to selectively filter which scores to present in an RoB heatmap

  • Animal bioassay

    • Add DTXSID integration and modify dashboard to query Chemistry Dashboard API
    • Migrate existing CASRN to DTXSID
    • Update bioassay endpoint forms for use of vocabulary, including a quick insert by ID method
    • Add mechanism (admin only) to migrate terms to use the new vocabulary
    • Update API and client to add endpoints using controlled vocabulary

  • Study

    • fixed bug for project managers locking/unlocking studies
    • Show ask_authors text details, preserving whitespace

  • Epi

    • Add DTXSID field to exposure objects in HAWC

  • Management

    • Add ability to unset users in tasks

  • Client

  • Testing

    • Add new integration tests which use a browser to test interactive javascript functionality
    • Bring in external dependencies into hawc (litter_getter and docx_utils)
    • Ensure IE11 error is still displayed on older browsers
    • Fix bugfix on /about/ page and add tests for reliability

  • Development

    • Remove eslint warnings to further standardize javascript frontend application code
    • Update d3 from v3 to v5
    • Generate lines of code report
    • Force ordered querysets in all assessments for deterministic reporting of data

  • Deployment

    • refactor to allow for kubernetes deployment in addition to docker-compose
    • added new /admin/:uuid/healthcheck/ url
Assets 2