New features 🎉
Support for all Bioportal ontologies in the semantic search interface 🧠
The semantic search interface now supports all ontologies available in BioPortal, offering greater flexibility beyond the previous focus on the ECSO ontology’s MeasurementType sub-tree. As datasets increasingly incorporate annotations from a wider range of ontologies, the need for a more adaptable search experience became clear.
ontology-select-demo.mp4
Repositories can configure the set of ontologies the widget searches. The interface first identifies all classes used in datasets from the index, then cross-references BioPortal to replace class URIs with readable labels. Classes are grouped by ontology, and users can browse the list within each. Tooltips provide class descriptions and indicate the number of datasets annotated with each class.
To explore further, users can open a modal to view the full hierarchy of classes in the selected ontologies, complete with class descriptions and links to BioPortal.
This enhanced search functionality is now available in both portal searches and the main repository catalog search.
MetacatUI Helm chart ⚙️
The latest release of MetacatUI introduces support for deployment within Kubernetes using Helm charts. This feature streamlines the installation process and simplifies configuration management. For details on for deploying the Helm chart are available in the helm/README file. This feature is under active development and we welcome feedback and contributions from the community!
Fine-grained control over the Cesium map layers 🌎
The layers that show in the Cesium map are now more customizable. For each layer, users can now choose whether the opacity slider is shown in the layer details panel and what happens when a feature is clicked.
For some layers, allowing viewers to change the opacity is not useful, so the showOpacitySlider option can be set to false.
The clickFeatureAction option allows users to choose what happens when a feature is clicked. The options are "showDetails" and "zoom". With show details, a layer panel pops up with additional info about the feature. With zoom, the map zooms into the bounding sphere for that feature. If no action is set, it defaults to the map-level behavior.
Misc improvements
- Bump rexml from 3.2.8 to 3.3.6 in /docs #2503
- Move
bytesToSizemethod to Utilities module #2484 - Include links to child datasets in the parent dataset for nested data packages #2418
- Support Markdown in metadig report view #2394
- Update Formatic-UI to newest version (2.9) & improved functionality for the
SearchSelectviews #2253
Bug fixes 🛠️
- Bounding coordinates set to 0 don't display on dataset landing pages rendered from the index #2505
- Error rendering a LayerDetailsView in develop #2498
- Issues downloading single object from nested dataset #2424
- Issues rendering the response form the view service #2403
- Issues with Citation Display #2395
- Download All doesn't work for specific data package #2373
Developer notes
Note that to make use of the new ontology search interface, your repository will need to configure a bioportal API key (instructions here).
We've made the following changes to the MetacatUI codebase to improve the developer experience:
- Add recommended VS Code extensions #2504
- More flexible ES Lint rules: allow some unused variables and don't enforce import resolution #2475
New configuration options
bioportalApiBaseUrl- The base URL for the BioPortal API. This is used to fetch the list of ontologies and classes for the semantic search interface. The default value ishttps://data.bioontology.organd probably doesn't need to be changed.bioportalOntologies- An array of BioPortal ontology IDs to search, each including the ontology acronym, human-readable name, and an optional icon and sub-tree.
Deprecated configuration options
bioportalSearchUrl- Deprecated in favor of the newbioportalApiBaseUrl.