ICDC 4.2.0

Release Notes - Integrated Canine Data Commons (ICDC) - Version 4.2.0 🐶 🧬

Build Details

FE Version: 4.2.0.475
BE Version: 14.13.0.220
FS Version: 2.3.2.87
Interop Version: 1.0.2.131

New Supported Features

• System supports free text search within table displays
• Ability to see the distribution of files loaded to the cart through an intuitive dashboard
• Ability to see the root file format of zipped files within Explore Dashboard faceted search

Tasks

• 508 Compliance for the Home, Explore Dashboard, Programs, Program Details, Studies, Data Model Navigator, and Static pages
• BE queries to support new File Distribution within Cart page
• Enable system wide banner from OCPL directive
• Improve Adobe Launch banner implementation
• Remove Twitter widget from ICDC News page

New Design

• Case Details page
• System Info page
• Cart page
• Tabs of Study Details page

New Content

• Human Relevance of Canine studies added to Study Details page
• Update checkbox language for "My Files Cart" page
• Update the primary image associated with the PRECINCT program
• Associate the appropriate primary image with the new CSU FACC program
• Re-assign the video displayed for the CMCP program to the new CSU FACC program
• Video for the CMCP program

New services

• Data Retriever Service (DRS) is a new service that was decoupled from the Interop service to exclusively handle interoperabibilty between external APIs such as the Imaging Data Commons (IDC)

Integrations

• Material UI 5

Data

• Perform a full reload of updated metadata for the OSA04 study

Data Model

• New graph node and properties to capture a study's relevance to human cancer research using words that are understandable to the lay public.

Contributions to the Bento Framework

• Contribute new Dynamic Query Bar (DQB) feature back to Bento

Bug Fixes

• Ellipses are not clickable at the end of URL
• Text link color change on Static pages and tables
• Parent Breadcrumb ,"All Studies", in the Study Details page redirects to the Programs list
• Final breadcrumb in the Study Details page redirects to the program abbreviation instead of the Study Name
• Design compliance of the breadcrumb in Study Detail page
• Design compliance of the breadcrumb in Program Detail page
• Files from the Cart page are only partially exported with a button click
• Discrepancies in histogram x-axis label within the Study Details page
• Display of histogram within Study Details page not to design specifications
• The checkboxes within the Explore Dashboard table header shifted to the right
• The search box of Global Search Results page not to design specifications
• The "Change background theme" toggle slider renders a blank page
• Breadcrumb text within Case Details page not redirecting as expected
• The NCI Integrated Canine Data Commons header is missing from JBrowse
• The counts of the study type filter are not fully visible within the Explore Dashboard
• The values of the "Additional CRDC Nodes" column of the downloaded Studies page table are not correct
• The dropdown menu options of the navigation bar are overlapping with the statistics bar
  -The Associated Samples table is missing "Download CSV" and "View Column" functionality
• Unexpected search bar appears within the Studies page
• The "View all related cases via dashboard" hyperlinks within the Study Details page renders a blank page
• The "Go To Site" hyperlink opens in the same tab
• "This study currently has no associated publications" is not displayed within the Publications tab of the Study Details page
• PDF file cannot be downloaded within Data Model Navigator page
• The property table opens and closes by clicking on button TSV/PDF download within Data Model Navigator page
• External links for the ReadMe File opens in the same tab within the Cart page
• Dynamic Query Bar URL does not open
• The Case IDs are not underlined in the Local Find feature
• Ellipsis are shown by default at the end of the given facet section within faceted search of the Explore Dashboard page

ICDC v.4.1.0

Release Notes - Integrated Canine Data Commons (ICDC) - Version 4.1.0 🐶 🧬

Build Details

FE Version: 4.1.0.361
BE Version: 14.8.1.171
FS Version: 2.3.1.83
Interop Version: 1.0.0.122

New Supported Features

• Clear selected facet values within a facet
• Expandable sample profile histograms with interactive sample distributions and legends
• Ability to copy the URL related to a query from the Explore Dashboard page
• Display abbreviated Dynamic Query Bar (DQB) URL
• Display success message when a query URL is copied
• Buttons in Local Find modal are disabled if no cases are entered or selected
• Local Find modal tooltip is updated to specify valid file types
• The Faceted Search menu on the Explore Dashboard page returns to default state upon clearing the Dynamic Query Bar (DQB)
• Clearing a facet restores default collapsed state of faceted categories within the Explore Dashboard page
• Ability to export or download a file manifest for all or only selected files
• Display a node traceback to the root node within the Data Model Navigator (DMN) when any given node is selected
• Display informative tooltips within the "My Files" Cart page for navigation

Tasks

• Update the "Cases" icon used in the statistics bar
• Implement updated design for the Supporting Data tab
• Implement updated design for the Clinical Data tab
• Bundle web fonts with ICDC application
• Replace the plural form of CASE IDS in Dynamic Query Bar (DQB)
• Achieve 508 compliance of the Dynamic Query Bar (DQB)
• Update Opensearch configuration for Global Search
• Fix downloaded CSV file for Adverse Event Node
• Refactor Button on "My Files" Cart page
• Improve FE display within the Supporting Data tab of the Study Details page
• Implement ascending sort order for each category of Global Search results
• Apply new design to navigation bar
• Update link name for ICDC Tutorial Website
• Update GraphiQL to the latest version
• Implement new design for Programs page
• Implement new design for Program Details page
• Implement new design for the "My Files" Cart page
• Upgrade version of Node on the FE
• Revise data properties and values displayed within Arms & Cohorts tab of the Study Details page
• Address 508 Compliance Scan for Design Elements on the Home page.
• Address 508 Compliance Scan for Design Elements on the Explore page
• Address 508 Compliance Scan for Design Elements on the Programs page
• Address 508 Compliance Scan for Design Elements on the Program Details page
• Address 508 Compliance Scan for Design Elements on the Studies page
• Address 508 Compliance Scan for Design Elements on the Study Details page
• Address 508 Compliance Scan for Design Elements on the File Centric Cart page
• Address 508 Compliance Scan for Design Elements on the Static pages
• Update manifest creation with new BE query
• Remove comments from the FE File Manifest

New Content

• New System Info page to inspect microservices
• New page for ICDC Working Groups

New services

None

Integrations

• New version of JBrowse (v. 2.11.0) adds capabilities https://github.com/GMOD/jbrowse-components/releases

Data Model

• None

Contributions to the Bento Framework

• Contribute new Dynamic Query Bar (DQB) feature back to Bento

Bug Fixes

• Extra whitespace within the downloadable File Manifest at EOL
• UI Styling discrepancy in Cases Tab on Dashboard
• UI Styling issue in Studies and Programs widget
• Files count mismatch between DB and UI for Biobank facet
• Text obstructed in the 'Upload Case Set' window
• "Multi-study Participant" title is cut off via Case Details view
• Incorrect label of Program category of Global Search feature
• Query strings are split across 2 lines in the Dynamic Query Bar (DQB)
• When navigating to System Info Page - focus not at the top of the page
• "sort by counts" and "sort by alphabet" move to the different lines when zoom out.
• Data in Supporting Data tab of Study Details page not per design specs
• Clinical Data download does not contain data for Adverse Event data
• Extra characters in the tooltip of csv download button
• "File Type" widget disappears when enter the case ID that does not have any files associated
• Clicking outside of the "Copy URL" modal does not close the modal
• Clinical Data - Adverse Event - download CSV file - Columns are out of order.
• Clinical Data - Adverse Event - download CSV file - Data values have been transposed across columns.
• Clinical Data - Adverse Event - download CSV file - The data export contains no identifiers.
• Clinical Data - Adverse Event - download CSV file - unexpected column title
• Clinical Data tab - incorrect column name
• Clinical Data tab - missing tooltip above column headers
• Clinical Data tab - Sort button on CSV column not working correctly
• Clinical Data tab - download CSV files - unexpected data
• Faceted Search menu does not return to default state upon clearing on the query term
• Clinical Data - Prior Surgery - download csv file - Data values have been transposed across columns.
• Content on the Studies page is upside-down
• DMN: Node modal does not close when clicking on another node icon
• The DMN node modals close by clicking on the node icon
• BE version in the footer is different from BE version in the System Page
• Versions of BE and FS are displayed incorrectly
• The number of cases for Prior Surgery for COTC007B is not correct
• System Info Page is not reachable
• Global Search Results page disappears
• Discrepancies in the design for column name "Canine Code"
• Ellipses are not clickable at the end of the Query Bar URL
• Label of the "Clear Query" button of the Query Bar is not displayed correctly
• The "Thumbnail View" of Sample Profiles is not opening the dedicated full size modal histogram bars
• Clicking on a case ID does not remove the case ID from the Query Bar
• Vertical dividers are missing within the faceted search bar within the Explore Dashboard page
• An underscore is displayed for the OFF TREATMENT node
• Incorrect colors ascribed to nodes with data vs. nodes without within the Clinical Data tab of the Study Details page
• Text is not clearly visible in Local Find feature
• Study-level file name hyperlinks within the Global Search feature do not redirect to respective Study Details page
• Programs and Studies donut disappears from the Explore Dashboard page
• Design specification errors of logos in the footer
• New version of JBrowse is missing dependencies
• Export and download of files from the "My Files" Cart page only includes the first page of files

ICDC v.4.0.0

Release Notes - Integrated Canine Data Commons (ICDC) - Version 4.0.0 🐶 🧬

Build Details

FE Version: 4.0.0.181
BE Version: 14.8.1.143
FS Version: 2.3.1.74

New Supported Features

• Button exports files directly to the Cancer Genomics Cloud (CGC)
• File manifest includes necessary field for CGC import
• Government warning banner for potential shutdown
• Download all detailed clinical observations via a single click
• Update logic for Explore Dashboard "Add All" and "Add Selected Files" buttons
• Configure Bento-table to override default paginated behavior
• Download File Manifest button is disabled if the cart is empty
• Global search for terms across the application
• Find specific case IDs within the Explore Dashboard page
• View a Dynamic Query Bar on the Explore Dashboard
• Display all selected values by clicking on ellipse in the Dynamic Query Bar
• FrontEnd error handling for the Interop Service
• Update donut widgets to display more relevant properties
• Increase the number of studies shown by default within the Studies Listing

New Content

• Updated design for "My Files" Cart page
• ICDC News page updates

New services

None

New integrations

• Bento Core Library components
• Export the ICDC File Manifest to the Cancer Genomics Cloud

Data Model

• None

Bug Fixes

• Extra whitespace within the downloadable File Manifest at EOL
• Inconsistencies across various grid-like listings in terms of pagination controls
• The "Sort" arrow that indicates which column a table is sorted by is missing
• Dynamic Query Bar should display the complete filter selection Case IDs entered by the user
• All Case Files are added to My Files cart, irrespective of the Case IDs selected by User
• The 'My Files' Cart page number of rows don't update after deleting a row
• Incorrect redirection from the "View Samples" hyperlink
• "My Files" verbiage resorted back to "My Cart" on Explore Page
• Drop-down list of the Case IDs going covers the application header on scroll
• CSV download from the Cart does not reflect the removal of single records
• Facet values in the Dynamic Query Bar do not have space in between them
• Changing the background color affects the display of Local Find
• "Upload Case Set" does not recognize IDs from GLIOMA01 and TCL01 studies
• Search results overlap Search History within Data Model Navigator page
• The "Cases" and "Associated Cases" hyperlinks improperly redirects User
• Downloaded File Manifest contains duplicate columns
• JBrowse displays BAM files as BAI
• "File Type" donut doesn't react when applying filters from "File Type" facet
• "Stage of Disease" donut is labeled improperly
• Global search throws component not found errors
• GraphQL interface is not fully visible
• Space above header logo is too small
• "Upload Case Set" does not recognize IDs from UC01 studies
• "Input Set" label does not delete the input set
• Incorrect category name on Global Search results page
• The Global Search Study category does not appear in ascending order
• Global Search displays incorrect cursor type for the text
• The Global Search "Data Model" category is missing the search term on the first line
• PDF file issue in the footer area
• The Export button on the "My Files" Cart page results in invalid redirect link

ICDC 3.59.7

Release Notes - Integrated Canine Data Commons (ICDC) - Version ICDC 3.59.7 🐶 🧬

Build Details

FE Version: 3.59.7.79
BE Version: 14.8.0.77
FS Version: 1.4.0.59

New Supported Features

• JBrowse opens in a new session window independent of application
• Load a track in JBrowse that maps gene features from the human hg38 genome onto the canine canFam3 genome
• Text search for JBrowse
• View real-time supplementary data for ICDC studies using the IDC and TCIA APIs within the Studies page
• View real-time supplementary data for ICDC studies using the IDC and TCIA APIs within the Study Details page
• View real-time supplementary data for ICDC studies using the IDC and TCIA APIs on the Program Details page
• View the availability of clinical observation data within the Studies Details page on a study by study basis
• View the availability of detailed clinical observations via a designated tab within the Study Details page
• Download detailed clinical observations on a node-by-node basis

New Content

• Privacy Policy for landing page footer
• ICDC News page updates
• README file on the "My Files" Cart page

New services

• None

New integrations

• None

Data Model

• Added new "Clinical Data Export" tag to appropriate Clinical and Clinical Trial nodes
• Added "TRIzol" as an acceptable value for the sample: sample_preservation property
• Removed unused "Color" tags from nodes
• Added the appropriate values for: stage_of_disease, sample_site, and specific_sample_pathology
• Commented out several working values for summarized_sample_type that have been superseded by the use of the terms "Tumoroid" and "Tumoroid (urine-derived)

Bug Fixes

• Download of the File Transfer Manifest is enabled regardless of the "Template" tag
• The content of one of the Data Loading File examples does not match the name of the file
• Supporting Data tab on Study Details page shows Glioma data only irrespective of study
• The Data Availability Landscape incorrectly indicates that the GLIOMA01 study has study files associated with it
• The sample profile within the Studies Detail view sometimes displays incorrect data
• An incorrect number of sample-level files are being added to the My Files cart via each of the cart action buttons within the Samples tab
• Values for Supporting Data Tab not displayed correctly
• JBrowse does not open as a new session window and still has navigation
• JBrowse button on Explore Page not consistent with approved design and function
• JBrowse button on Cart Page not consistent with approved design and function
• File manifest Download icon is blurred
• Data Model Navigator text is overlapping Filter & Search text box
• "Add All Filtered Files" button does not add all files within Case Files tab
• Clicking the PDF icon on READMe file in "My Files" Cart Page downloads as csv
• Alignment issues on the "My Files" Cart Page READMe PDF
• The footer of README PDF file doesn't display correct URL

ICDC 3.49.2

Release Notes - Integrated Canine Data Commons (ICDC) - Version ICDC 3.49.2 🐶 🧬

Build Details

FE Version: 3.49.2.21
BE Version: 14.5.1.25
FS Version: 1.4.0.59

New Supported Features

• Updated UI for the Data Model Navigator
• Data Model Navigator title bar
• Buttons for Data Model Navigator's Read Me and Available Downloads
• Node-based properties dialogue box inclusive of the node name and category in the Graph View of the Data Model Navigator
• Node-expanding property count in the Table View of the Data Model Navigator
• Download TSV versions of all controlled vocabularies via a single download action from within the Data Model Navigator
• Download JSON versions of all controlled vocabularies via a single download action from within the Data Model Navigator
• Download all data loading template files as TSV files via a single download action from within the Data Model Navigator
• Download the full data dictionary via a single download action from within the Data Model Navigator
• Download an example set of data loading files via the Data Model Navigator' Available Downloads function
• View a narrative Read Me file from within the Data Model Navigator
• Download the Data Model Navigator's Read Me file via the download drop-down menu
• Download the Data Model Navigator's Read Me file via the modal display
• Dedicated tabs for the Graph View and Table View of the Data Model Navigator
• Optimize default zoom based upon screen size and resolution
• Update footer to meet style criteria from issued NCI Digital Guidelines
• The ICDC spotlight section can redirect outside of application

New Content

• ICDC Spotlight section video
• ICDC News page updates

New services

• Interoperation Microservice

New integrations

• Data Model Navigator uses React Flow component library

Data Model

• Expanded the set of acceptable terms within several controlled vocabularies in support of new studies
• Added opt-out terms to several other controlled vocabularies
• Additional changes to the properties within the adverse_event node

Bug Fixes

• Incorrect Developer Link for Github repo
• The order in which properties are displayed within the data model explorer's Table View doesn't match the order within PDF exports
• Studies page->Data Availability Tool tip window is hiding the table headers
• Lists of Principal Investigators end with an orphaned comma
• The sample counts for sample profile histograms are difficult to read
• The tool tip for the "View in JBrowse" option is not being displayed in the correct style
• The formatting of the multi-study participation tool tip does not match that used on the Production environment
• Sort on Sample ID in the File-Centric Cart page is not working properly
• The .zip download of all data loading templates doesn't include the File Transfer Manifest template
• The dictionary download is incorrectly subject to the effects of facet-based filtering
• Files in the .zip download of all data loading templates are displayed as of Type = File
• The .zip template file download is incorrectly subject to the effects of facet-based filtering
• The two parts of the CV download combo button are misaligned for each of the two CVs within image_collection
• Displaying two File icons next to My Files
• Footer displays incorrect text and embeds incorrect link
• Multiple issues with the .zip bundle of "All Loading Templates"
• Canvas area is overlapping the footer
• The positioning of the Table View TSV and PDF download buttons has been reversed
• The number of properties displayed within the node overview table is incorrect
• "Available Downloads" button not per design spec
• Single PDF and Complete Data dictionary PDF in DMN are not working
• Within the PDF version of the Navigator's ReadMe text, the last line of text on the page is getting split between pages
• The colored icon tabs within the Graph View's node boxes have narrow lines of white above and/or below them
• The title of the Data Model Navigator's ReadMe modal is displayed too small
• The Data Model Navigator's ReadMe text is abruptly cut off by the bottom edge of the ReadMe modal
• The Properties Dialogue box is sometimes displayed behind adjacent nodes
• On Explore page blue line displays under "View in JBrowse" button
• Inconsistent display of instances of "README" text

v3.39.4

Release Notes - Integrated Canine Data Commons (ICDC) - Version ICDC 3.39.4 🐶 🧬

Build Details

FE Version: v3.39.4-992
BE Version: 14.5.1-992
FS Version: 1.4.0-992

New Supported Features

• View multiple files simultaneously in JBrowse through ICDC Explore Dashboard
• View multiple files in JBrowse through ICDC My Files Page
• Max file restriction information message for JBrowse
• Sorting of facet-based model filtering options
• Highlighting of facet-based model filtering options that have already been selected
• Download of a single controlled vocabulary in JSON format
• Download of node-specific data loading templates as TSV files
• Download of a single controlled vocabulary in TSV format
• Download of a File Transfer Manifest template
• Toggle the degree to which facet value selections already in place are displayed
• Filter the data model based upon the display of properties within the UI

New Integrations

• Elasticsearch to improve speed and scalability of queries of the database

New Content

• ICDC News page updates
• ICDC Steering Committee page updates
• ICDC DGAB page updates
• ICDC BPSC page updates

New Packages

• npm package for JBrowse2
• npm package for Data Model Explorer

Data Model

• Expanded property definitions for Adverse Event node
• Vastly augmented controlled vocabulary for Breed property
• Numerous additions, updates, and corrections to data model and property definitions
• Modified the File node's "Template" tag from no to yes

Bug Fixes

• Issue with delete records in My Files descending order on File Name
• Sort on Data landscape is not working properly
• Modals via which lengthy controlled vocabularies are displayed should be titled "Acceptable Values"
• The HTML
  code within the description of "Key" properties is being ignored
• Within the Graph View of the data model, selection of nodes filtered via the search function crashes the application
• On the DEV tier, the Dashboard fails to display any data after navigating there via hyperlinked case and sample counts
• The multi-study participant icon is being displayed in IMAX 3D on the DEV tier
• On the DEV tier, study files are being mis-represented and therefore incorrectly counted
• The legend-style tool tip for the data availability landscape is poorly placed
• Formatting error within the sample site CV when viewed via "show even more" modal
• All Hyperlinks in ICDC are displaying in Blue color
• The two parts of the newly-implemented CV download combo button are misaligned
• Unable to add Case files/Study Files of Multi Study Participant studies to My Files
• Elasticsearch: Unable to add files to cart
• JBrowse: CanFam3 reference genome is not loading properly
• The multi-study participation tool tip is poorly formatted
• Add Associated Files Button is not working as expected
• Adding "All associated files" in Samples tab displays incorrect message
• Hyperlinks are not displayed correctly
• Unified View table does not render correct data
• Unable to delete files using the "Remove Files" button in My files
• CSV download is not working in Cases, Case Files, Study File tabs
• Column-based sorting within the unified view results in data being hidden
• Toggling between Case and Study Files in the Explore page causes application to crash
• Study Files from Unified View page are not correctly added to the File Centric Cart
• CSV file downloads do not reflect faceted selections

v3.29.4

Release Notes - Integrated Canine Data Commons (ICDC) - Version ICDC 3.29.4 🐶 🧬

Build Details:
FE Version: v3.29.4-819
BE Version: 4.0.5-819
FS Version: 1.4.0

Features

• End User can access the GraphiQL query interface
• Implement ICDC static News page
• ICDC Custodian configures the display of the Data Availability Landscape
• Add feature track for Ensembl gene annotations to canFam3
• Add feature track for NCBI gene annotations to canFam3
• End User downloads csv copies of study listings inclusive of data availability metrics
• System displays a single, legend-style tool tip for the Data Availability Landscape

Task

• Disable faceted filtering from Data Model Explorer
• Apply the new design for increased visibility of ICDC's tool tip icons
• Create npm package from Gen3's latest code base
• Modify Gen3's codebase to fetch data model from yaml
• Apply ICDC changes on top of Gen3 codebase
• Refactoring of Model Explorer Side Bar Component
• Refactor styling for Data Model Explorer
• Create templates for Spotlight static content
• Set CanFam3 genome as default
• Re-implement handling of node descriptions within the Gen3 codebase
• Re-implement handling of node tags and identification of key mapping fields within the Gen3 codebase
• Re-implement the modal-based display of controlled vocabularies within the Gen3 codebase
• Re-implement the formatting of PDF outputs within the Gen3 codebase
• Re-implement PDF downloads within the Gen3 codebase
• Re-implement TSV downloads within the Gen3 codebase
• Re-implement all updates to the Graph View within the Gen3 codebase
• Disable display of the Data Model Structure visual
• Disable display of the "Open properties" button
• Disable display of the "Download templates" button
• Change URLs for ICDC Landing page, News page, and Spotlight static content
• Config for ICDC Static News Page
• Disable display of the See All versus See Only Matched option
• Address Design QA Review findings vs. Data Availability Landscape

Bug Fixes

• Excel from CSV download contains '#' as a separator between multiple lines of the same row
• Links to image collections open only a single new tab
• Property dialogue box does not display when we apply "Filter by Property"
• Property-based filtering within the data model explorer is returning overly-restricted results when multiple inclusion values are selected
• Selection of any single filtering option within the Filter by Node: Assignment and Class sections incorrectly collapses the entire facet section
• Studies View "View Columns" column label inconsistent
• The modal-based display of longer lists of acceptable values contains a formatting error
• Model Explorer displays blank page when user clicks on a node
• Opening a node via the properties dialogue from within the data model explorer's Graph View displays the node in MVP format
• Study Detail page->Unable to download (download table contents as CSV) csv file.
• Image collection identities displayed within the data availability matrix are displayed in purple
• Image collection details under additional CRDC nodes displayed within the data availability matrix are not displayed as hyperlinks
• The csv export function is no longer working for either of the two data matrix-enabled study listings
• The "Under Embargo" UI flag within study listings is no longer being applied
• Re-sorting either of the study listings via selection of any column header results in data quantitation errors
• Datamodel-Table view node description is truncating
• The blue background is bleeding into the node Category headers within the data model explorer's Table View
• Model Explorer Graph view legend displays required and optional links in legend
• Hyperlinks to external data sets as shown via the Data Availability Landscape need to be identified as external links
• Data model Explorer->Graph view->Nodes->Dialogue box-Properties counts are mismatching.
• Data Model Explorer: Properties dialog box is truncated on the Graph View for the Program node
• Data Model Explorer: Properties dialog box is not displaying for any node on Graph View
• Data Model Explorer->Graph view->Property dialogue box is displaying far away when user clicks on the nodes
• Data Model Explorer->Graph View->Search Input box->Node details are missing in the page when user clicks on the node
• Data Model Explorer->Graph View->Search Input box->Node detail->Search result is not getting highlighted in the page.
• Data model Explorer->Clear all is not clearing the selection in graph area.
• New filters selected don't result in updates across both Table and Graph Views
• Data Model Exlporer:Graph View-Nodes are not displaying in some scenarios
• Data Model Explorer->Graph View->Search is happening based on the characters entered by the user
• Highlighting of terms matching model search criteria is not consistently applied
• Node-specific Table Views invoked via the search function and the Graph View are incorrectly excluding node properties
• Gene annotation files are failing to load due to CORS policy
• Key Values were not highlighting in Table view for the proprties of Different nodes
• Total counts of Filter By Property don't match the count of properties listed near Download Dictionary button
• Data Model Explorer-> Table View-> Node name is not turning to blue when we mouse over upon the node names.
• Incorrect nomenclature applied to csv downloads from each of the data landscape-enabled study listings
• Data Model Explorer->Filter by property selection->Selection of filter by node incorrectly collapses the entire facet
• Class-based filtering of the data model breaks under certain conditions
• Search results are not reporting accurate counts
• The data model is incorrectly being read from the Develop branch by STAGE and PRODUCTION

v3.21.3.1

Release Notes - Integrated Canine Data Commons (ICDC) - Version ICDC 3.21.3 🐶 🧬

Patch

• Add Vulnerability Disclosure link to footer

v3.21.3

Release Notes - Integrated Canine Data Commons (ICDC) - Version ICDC 3.21.3 🐶 🧬

Features

• End User can access the GraphiQL query interface
• Add page for Data Use Guidelines
• Add a hyperlink for software release notes
• End User downloads node-specific data loading templates
• Data model/dictionary viewer displays the description and the "Assignment" and "Class" tags for each node
• End User searches for program-specific data sets via the dashboard's facet-driven search functionality
• System redirects End User to the Studies listing upon submission of an non-existent Accession ID
• End user can see Resources and Data in the navigation bar
• End user sees consistent verbiage for Data Model
• System supports viewing of BAM files via JBrowse, alongside direct download of small, document-like files
• End user sees expanded faceted categories
• Add new spotlight content to highlight recent data releases
• ICDC News tile temporarily redirects to "Coming Soon" page

Task

• Display the File Microservice Version in the Footer
• Update the Model Viewer to correctly handle values of "Enum:" in place of "Req:" for enumerated properties
• Research methods to improve performance of Data Model Explorer
• Apply the design/branding overlay to PDF exports from the Data Model Explorer
• Explore and/or design options for a background upon which the Data Model Explorer graph view can be displayed
• Integrate Bento code for JBrowse
• JBrowse supports all canine reference genomes
• JBrowse supports all available canine tracks
• Implement logic to exclude "map to" columns for non-relevant parents from data loading templates
• Turn off the display of the "native" node-specific tool tips within the Data Model Explorer's graph view
• Implement the modal-based display of controlled vocabularies within the Data Model Explorer's table view
• Implement the identification of "Key" properties
• Remove the "cells and dogs" theming currently shown to the right of the NIH logo/text block
• Replace the FNL text block in the footer with the corresponding NCI text block
• Disable faceted filtering from Data Model Explorer

Improvement

• Improve URL for "Unified View" page for Multi-Study Participation
• Update the way in which the Data Model Explorer's table view renders controlled vocabularies
• Modify the existing node by node PDF exports to include node descriptions and the "Assignment" and "Class" tags
• Make the default view of the Data Model Explorer the Graph View
• Update the way in which node-specific PDF downloads are named upon auto-save
• Display program acronyms within the application-wide study listing as hyperlinks
• Increase the visibility of ICDC's internal hyperlinks

Bug Fixes

• Inconsistent separation of individual filter options available within filter categories
• Blank Page when using an Identifiers.org ID
• Node-specific tool tips within the Graph View of the Data Model Explorer become disconnected after altering the zoom level
• Truncation of words on the left and right pane of GraphQL
• Files downloaded from the Data Model Explorer are not named intuitively
• The data volume indicator is no longer active when viewing certain pages
• Properties for which the value of Req: is "Preferred" are now being shown as "Optional"
• The order in which properties are displayed within the Data Model Explorer's table view doesn't match the order within PDF exports
• "Filter by Property" inclusion options never include "Optional", but selection of "Preferred" actually displays nodes with optional properties
• Display of the properties dialogue within the Data Model Explorer's graph view becomes erratic once filters are imposed
• Data Model Explorer's table view "Optional" properties are being displayed as "Preferred", and vice versa
• Case File counts are incorrectly reported by the statistics bar under certain circumstances
• OSA01 filter includes "Bull Mastiff" as breed filter when it should appear "Bullmastiff"
• "Preferred" properties are incorrectly being displayed as "Required" within the Data Model Explorer's PDF exports
• Additional navigation menu items are highlighted when user clicks on Model Explorer
• Expanding all faceted filters in Model Explorer graph view/table view blocks the NCI block in footer
• Pagination is not displaying correctly on Dashboard tabs
• Default sorting icon for Sample ID is missing in Samples tab
• The selected filter options should display together without partitions

v3.8.7

Release Notes - Integrated Canine Data Commons (ICDC) - Version ICDC 3.8.7 🐶 🧬

Features

• End user is alerted with government warning pop-up when entering ICDC
• End User is correctly re-directed to the appropriate Study Detail view via Identifiers.org
• End User can explore the data model and data dictionary
• End User views study structure and study files via designated tabs
• End User identifies study-level files of interest via facet-driven filtering
• Statistics bar displays a count of study-associated files via a designated and separate count of such files
• End User views study-level files via a designated fourth dashboard tab
• End User creates/adds to a custom list of Files via the dashboard's Study Files listing
• End User downloads "extended metadata" via the dashboard's Cases tab
• End User downloads "extended metadata" via the dashboard's Samples tab
• End User can understand the volume of data available
• End User searches for multi-study versus single-study participants via the dashboard's facet-driven search functionality
• System displays study-level files via a designated fourth tab within the Unified View
• End user sees consistent language on landing page
• End user doesn't see non-functional buttons in the dictionary viewer
• End user can download dictionary table elements by node from Table View using a button

Task

• Update Program Detail texts for the COP and CMCP programs
• Conduct comprehensive Design QA reviews across all views
• Conduct Design QA review across My Files cart view and associated cart actions
• Refactor histogram chart on Study Details page
• Identify appropriate icon(s) and verbiage for study files vs. non-study files
• Improve the rendering of the dictionary model and viewer
• Evaluate the statistics bar in terms of it including a count of Programs
• Update the way in which the Model Viewer handles values for Req:
• Update URL endpoint to match new language of "Explore" for the dashboard
• Update environment variable for dictionary and model viewer

Inquiry

• Research how to best develop the data model & dictionary viewer

Improvement

• Revise user action verbiage on home page
• FE: Refactor the footer code on the "File Cart Centric" page and create a footer component
• FE: Dashboard Tab Design Change
• Add white border to slices of donut visualizations
• Update the color palette for case dashboard donuts and sidebars
• Update the message displayed when a study has no samples associated with it
• Update the "SAMPLE PROFILE" data section header
• Update color palette for program sunburst
• Display "no files" message when a study has no case-level files
• Remove Aliquots from stats bar
• Change "Cases" to "Explore" in navigation bar
• Include "Matching Cases" in the extended metadata downloaded via the My Files cart
• Include "Matching Cases" in the extended metadata downloaded via the dashboard's Case Files tab
• Within the Table View of the model viewer, display values of "Src:" within a column labeled Source

Bug Fixes

• File uuid column is not displaying in CSV downloads of Files tab in dashboard and My Files tab
• Repeated clicks to different external sites do not open in individual tabs.
• My Files-Pagination is not working properly
• Study Detail view of pending studies include data sections deliberately hidden for studies under embargo
• Newly implemented Arms & Cohorts and Study Files tabs display redundant headers
• Resolve logic conflict for Case and Study Files count
• Table re-rendered when the user interacts with "Remove Icon" or with the comments section
• The statistics bar is not reporting the count of study-level files when viewing the Case Detail page
• Text displayed via the model viewer's Table View has the appearance of including whitespaces
• Within the model viewer's Graph View, tool-tips are incorrectly placed relative to the node being examined
• The model viewer doesn't appear to be showing all relationships
• File Manifest download name is displaying as Bento Manifest in My Files page
• Some internal hyperlinks are no longer being displayed in our standard orange typeface
• The remove icon is not working in File Centric Cart when user increases the number of rows to display
• The data model viewer lacks specific icons for certain node categories
• Relatively long lists of acceptable terms are disrupting the formatting of the Table View of the data model
• Within the Publications tab, null values for DOI and PubMed ID are incorrectly handled
• Multi-Study Participation Unified View is not rendering
• Sample Site filtering fails to resolve downstream filtering options and associated counts
• Samples tab CSV is downloading empty File without any columns
• Diagnosis filter does not display any options for specific valid filter conditions
• Minor navigation error after using the Samples hyperlink within the Study Detail view
• The dashboard's Files tab fails to display Case ID, Breed and Diagnosis values for files mapped directly to cases
• The dashboard's Files tab csv export for files mapped directly to cases is devoid of any case-based annotations
• The count displayed for the Biobank filter option of "Not Applicable" is incorrect
• The counts for Biobank filter options are getting duplicated under certain circumstances
• Node outline colors are not matching new icons
• In the Data Model Viewer, the Table view "Required" column is not displaying in the table when user enters a term in search box
• File format is missing under "Filter by Files" category in faceted filter search
• Total number of records in pagination for Case Files tab includes Study Files
• Pagination icons are not displaying properly as Dashboard tabs reset to default number when user toggles between the tabs
• The new Case Files needs to be added to My Files cart when user clicks "Add Associated Files for All" button in Cases tab
• Properties for which the value of Req: is Preferred are still being shown as Required = No
• "Cart" to "My Files" isn't consistent throughout system
• The newly-implemented Program count is incorrectly placed within the statistics bar
• PDF download does not match metadata in dictionary table
• Stats bar is obstructing the "collapse view" button on Dashboard

Test

• Test FE: Refactor the footer code on the "File Cart Centric" page and create a footer component
• Test Update the color palette for case dashboard
• Test FE: Dashboard Tab Design Change
• Test FE: Dashboard Tab Design Change
• Test End User is correctly re-directed to the appropriate Study Detail view via Identifiers.org
• Test Display "no files" message when a study has no case-level files
• Test Update the "SAMPLE PROFILE" data section header
• Test Update color palette for program sunburst
• Test Refactor Histogram Chart on Study Details page
• Test End User can explore the data model and data dictionary
• Test Revise user action verbiage on home page
• Test End user sees consistent language on landing page
• Test End User creates/adds to a custom list of Files via the dashboard's Study Files listing
• Test End User can understand the volume of data available
• Test End user doesn't see non-functional buttons in the dictionary viewer
• Test Improve the rendering of the dictionary model and viewer
• Test Update the way in which the Model Viewer handles values for Req:
• Test Within the Table View of the model viewer, display values of "Src:" within a column labeled Source