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@jonkiky jonkiky released this 10 Jul 19:36
· 7 commits to main since this release
1.0.0
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Release Notes - Clinical and Translational Data Commons (CTDC) - Version 1.0.0 ⚕️ 🏥

This is the official first public launch for the CTDC. The CTDC is a fully functioning Data Commons that is a key component of the broader Cancer Research Data Commons (CRDC). The CTDC is equipped with authentication and authorization, faceted search capabilities, intuitive widgets and tables, a downloadable DRS-compliant file manifest and several other features to facilitate cohort building, discovery, and downstream analysis. This first production release includes data from the Cancer Moonshot Biobank (CMB) across 248 participants.

Build Details

Frontend Version: 1.0.0.259
Backend Version: 1.0.0.166
File Service Version: 1.0.0.55
Auth Version: 1.0.0.41

Supported Features

  • Global header and footer with useful links
    • Policy links align with Cancer.gov footer
  • Clinical Trial Details page inclusive of a detailed overview, diagnoses, participant-level file types and hyperlinked biospecimen counts
    • Access to study-specific image collections
    • Access to profiles of biospecimens associated with the CMB trial via thumbnail visualizations
    • Zipped file downloads of variant reports and variant call files associated with the Cancer Moonshot Biobank study with appropriate access controls
  • Explore Dashboard page inclusive of a set of informative widgets illustrating the data landscape
    • Multiple pairs of participant-level attributes via two-layer sunburst visualizations
    • Participant-level Targeted Therapy attributes via a simple donut visualization
    • Biospecimen-level attributes via a two-layer sunburst visualization
    • File-level file type attributes via a simple donut visualization
    • Informative facet-based filters and search capabilities
    • Participant records in a grid-like listing
    • Biospecimen records in a grid-like listing
    • File records in a grid-like listing
    • Buttons to easily add some or all files of interest to the Cart
    • Direct downloads of files from the Dashboard tables
  • File-centric Cart page
    • The ability to download a DRS-compliant file manifest inclusive of extended metadata
    • Reactive icons to remove unwanted files from the Cart
  • Static pages for communicating the purpose, key resources, data use agreements, data modeling, and data submission requirements
    • Purpose statement for the CTDC and contextualization within the broader CRDC
    • Cloud computing analysis options
    • Data model visualization
    • Governance of CTDC data use
    • Data access request process
    • Data harmonization efforts
    • Placeholder for CRDC data submission guidelines
    • Resources for open-source software development
    • CTDC Help Desk contact information
  • Global search across entire application with ordered and paginated results including key annotations for Participant and Biospecimen records
    • Results categorized as "All, Participants, Biospecimens, General, and Model"
    • Auto-complete functionality
    • Support for multi-word searches
  • GraphiQL interface for API-based queries
  • Dynamic Statistics Bar

Data

  • Create S3 test bucket with test data files
  • Create S3 bucket for production data files
  • Create configuration files for mock data
  • Create mock data
  • Load data into Neo4J
  • ETL data into Opensearch indices
  • Create indexing manifest for Cancer Moonshot Biobank (CMB) data and submit to DCF
  • Load CMB data into Opensearch
  • Create File Transfer Manifests for all CMB data files

Data Modeling

  • Create props, descriptions, and permissible values for CMB data
  • Include links for Common Data Elements (CDEs)
  • Add a version number to data model yaml files

Authentication & Authorization (Authn & Authz)

  • Create ECS service
  • Integration with the Data Commons Framework (DCF) Fence microservice
  • Test DCF endpoints
  • Support for login through eRA Commons ID
  • Visual indication of login status
  • Manual logout
  • Session timeout warning after 15 minutes of inactivity
  • Error messaging for downloads by unauthenticated or unauthorized users

Standup System

  • System architecture
    • authentication and authorization
  • Set up GitHub repositories
  • Set up code bases
  • Set up development infrastructure
  • Create MySQL database
  • Create infrastructure for File Service
  • Create infrastructure for auth services
  • Create S3 bucket for Opensearch snapshots
  • Create Jenkins agents and implement Jenkins pipelines and jobs
  • Implement application load balancer (ALB)
  • Set up system monitoring
  • Scan security vulnerabilities
  • Create backend API skeleton
  • Create mock APIs for application pages
  • Create development guide documentation
  • Update GraphQL schema and queries
  • Set up Opensearch and create indices
  • Create queries for page information, components, and widgets

System Design

  • Create design for the Home Page
  • Create design for the Explore Dashboard page
  • Create design for the Clinical Trial Detail Overview and Clinical Trial Details page
  • Create design for login
  • Design QA across application
  • Scan for 508 compliance

System Content

  • Create content for CRDC Cloud Resources page
  • Create content for Data Use & Governance
  • Create content for Data Submission Guidelines
  • Create content for Developer Resources page
  • Create content for Purpose page
  • Create content for CTDC Help Desk
  • Create content for Requesting Data Access

System Upgrades

  • Upgrade Neo4J to 4.4.19 or above
  • Upgrade Node.js version to 20.11.1

Bug Fixes

  • Biospecimen count value is changed based on the cursor movement within the Clinical Trial Details page
  • The Data link in the navigation bar redirects to 404 page not found
  • The Request Access link in the navigation bar redirects to 404 page not found
  • 508 compliance color contrast and label issues
  • You Tube, Instagram, and LinkedIn links don't redirect to corresponding applications
  • Limit cart files popup is missing from the Explore Dashboard page
  • The Participant tab count is not correct in the Explore Dashboard table
  • Incorrect file counts are displayed when adding files for biospecimens to the cart
  • Highlighting of widget does not appear upon mouse over within the Explore Dashboard page
  • The download cloud icon is not working for all tabs in the Explore Dashboard table
  • The biospecimen tab does not display the correct count when user selects filters
  • Incorrect file counts are added to the cart for the "Add Files for all" button in the Explore Dashboard page
  • Check box selections are not working properly within the Cart page
    -The Download File Manifest button is not functional within the Cart page
  • Single file deletion is not working within the Cart page
  • Participant File Types is not displayed within the Clinical Trial Details page
  • The "User Comments" text box is missing from the Cart page
  • Sorting of columns is not working within the Cart page
  • File ID column is missing from the downloaded File Manifest
  • The drs_uri field value is missing dg.4DFC in the downloaded File Manifest
  • The "Row(s) Selected" label is not removed clearing the cart
  • Incorrect number of Diagnoses displayed in the Stats Bar
  • Expanding facets causes text overlap within the Explore Dashboard page
  • Irrelevant instructional options are provided for downloading the file manifest below the table in the Cart page
  • System Info and Release Notes redirect to blank repo pages from the footer
  • The "Back to Top" button overlaps with the system message about the number of files added to the cart
  • The eRA commons Login page link redirects to 404 Error
  • Global search returns duplicated search results
  • Wrong cursor type when hovering over the user's name
  • State is not preserved after successful login
  • The sample query gives validation error within the GraphiQL interface
  • The focus of the Global Search page is at the bottom
  • Some terms entered into Global Search display multiple entries in the auto complete drop down
  • Data Model page - schema contains unexpected block
  • Scrollable content must accessible by keyboard for 508 compliance
  • Data Model and Data Use Policy page hyperlinks are not correct
  • Unable to login with eRa commons account
  • File counts in hero image and stats bar do not match
  • Not all content is found using Global Search
  • The Cart page table does not load after adding the files from Biospecimen tab
  • The "Add Files for Selected" button does not add files to the cart for Biospecimens
  • The Stats Bar does not update correctly with facet selection within the Explore Dashboard page
  • PDF file download throws a 404 error for authorized users
  • No content is displayed in the Studies tab within the Explore Dashboard page
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