Releases: JBEI/ice
Releases · JBEI/ice
ICE 5.3.2
Bug Fixes
- Fixed issue with details of linked entries not being transferred
- Fixed permission issue when a user belongs to more than one group which have read privileges assigned to entry
- Fixed issue with enabling public access option not being shown to regular users
- Fixed issue causing plate number to not be set when using bulk sample creation
Upgrade Notes
If upgrading from a release prior to 5.3.0:
After upgrading (and before starting the server) delete the hibernate search index folder. The location is specified in hibernate.cfg.xml under the property name "hibernate.search.default.indexBase"
ICE 5.3.1
Improvements
- Traces Page improvements
Bug Fixes
- Issues in custom export
- Bulk Upload without attachments causing NPE
- ICE-79: Circular linking of entries bug sometimes causing stack overflow
Upgrade Notes
If upgrading from a release prior to 5.3.0:
After upgrading (and before starting the server) delete the hibernate search index folder. The location is specified in hibernate.cfg.xml under the property name "hibernate.search.default.indexBase"
ICE 5.3.0
New Features
- Enable annotations to be searched by name
- Auto install blast from the UI
- ICE-46: Allow download of all trace sequences
- Custom download of entries in folder
Improvements
- Upgraded storage layer to use Hibernate 5.2+ constructs
- Stronger support for SBOL2
- #55 return original sequence upload if requested download format is same as format of upload
- Display error message to user on error uploading attachments
- Show status of bulk upload processing
- Check folder entry is contained in when determining public read privileges
- More documentation
Bug Fixes
- ICE-15: Permit deletion of shared folders
- ICE-26: Allow users to move/add pending entries
- Issues with retrieving web of registries partner entries
- ICE-50: truncate study/experiment label if longer than 150 xters before attempting to store
- Issues with editing personal and administrative groups
- #44 Parsing multi-line notes in genbank
- Adding attachments to bulk upload bug
- #53 SBOL2 conversion exception when feature start is > end
- Updating visibility of folder entries
- Uploading trace sequence bug
- Verifying permissions for adding experiment bug
- Deleting samples bug
- ICE-56: NPE
- ICE-79: Circular linking of entries bug sometimes causing stack overflow
Upgrade Notes
After upgrading (and before starting the server) delete the hibernate search index folder. The location is specified in hibernate.cfg.xml under the property name "hibernate.search.default.indexBase"
ICE 5.2.2
ICE 5.2.1
Bug Fixes
- SYNBIO-1207: allow uuids (in addition to part ids) to reference parts in some resource api calls
- ICE-29: Re-trigger sequence analysis upon DNA sequence change
- De-duplicate list of entries on export
- Update label media information on admin sample page to show plate information instead of selection markers
ICE 5.2.0
New Features
- Support for Pacbio/MiSeq as simple file uploads
- ICE-30: CSV Export for admin sample request page
- ICE-38: Added list of media/selection markers to sample request
Bug Fixes
- Fixed issues updating blast search indexes on sequence upload/update
- Skip empty annotations when indexing for auto-annotation feature
- NPE fix on sequence file parsing
ICE 5.1.0
Bug Fixes
- Fixed issues with SBOL2 upload
- Fixed issues with Web of registries search
- Fixed issues with multiple records being created for parent plate
- Account for reverse complement in auto-annotation feature
- Fixed issues with retrieving sequence features
Improvements
- SYNBIO-967: restore deleted items and permanently delete functionality
- ICE-22: Accept pending and transferred entries at an individual level
- Improvements to SBOL parser
- Do not require write permissions to be able to clone entries
ICE 5.0.2
Bug Fixes
- Transfer annotations for sequence when transferring entries
- Fixed issue with bulk editing selection marker field
- Update displayed list of API keys when a new one is created
- Fixed issues with auto-complete not returning correct results
Improvements
- Added dynamic page size options to sample requests
- Added option to include the local public entries when retrieving remote entries
- Use part number for the sequence file name in CSV export to avoid ambiguity
Upgrade Notes
To upgrade from earlier versions (4.x) of ICE, some database modifications need to be made. Remember to backup your database before performing these modifications
- Delete the following columns from the sequence_feature table
- feature_start
- feature_end
- description
- Delete the following columns from the feature table
- auto_find
ICE 5.0.1
Bug Fixes
- Fixed issue with IndexOutOfBounds Exception for genbank parser
- ICE-17: Fixed issue with sorting by alias
- Fixed issues with sample creation and deletion
- Auto complete fix with bulk upload
- Admin sample requests: Fixed issue with fulfilling requests setting status to null
Improvements
- Added option to restrict annotations for the auto-annotation feature to those created by requesting user
- synbio-1359: require user id for local searches
Upgrade Notes
To upgrade from earlier versions (4.x) of ICE, some database modifications need to be made. Remember to backup your database before performing these modifications
- Delete the following columns from the sequence_feature table
- feature_start
- feature_end
- description
- Delete the following columns from the feature table
- auto_find
ICE 5.0.0
New Features
- Automatic Sequence Annotation
- Support for SBOL 2
- Sequence Annotation curation
- Feature to restrict public sharing to admins only
Bug Fixes
- ICE-6/ICE-14: Increase default limit of number of traces retrieved
- Fixed issues with retrieving remote entry sequences
- SYNBIO-1361: Handle pasted sequences when creating new entries
- Fixed history deletion feature
- Set appropriate owner when copying entries
- Fixed issues with folder sharing
- Fixed issue with web of registries search hanging when there are no results
Improvements
- BLAST search performance improvements
- Improved security
- "Select all" for search results
- More unit testing
- Site configuration improvements
- API for interacting with web of registries entries
- Improved GenBank parser to handle genbank files without feature notes
- Improvements to REST API error codes
Upgrade Notes
To upgrade from earlier versions of ICE, some database modifications need to be made. Remember to backup your database before performing these modifications
- Delete the following columns from the sequence_feature table
- feature_start
- feature_end
- description
- Delete the following columns from the feature table
- auto_find