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Change Log

All notable changes to this project will be documented in this file.

5.6.0

Added

  • GET /{path}/relationships endpoint to search SNOMED CT Relationship components
  • Namespace filter support to
  • GET /{path}/descriptions
  • GET /{path}/relationships
  • EffectiveTime filter support to
  • GET /{path}/concepts
  • GET /{path}/descriptions
  • GET /{path}/relationships
  • ECL expression support to GET /{path}/descriptions endpoint's concept and type filter
  • subclassDefinitionStatus property to SnomedConceptSearchRequest
  • referenceSet expand option to GET /{path}/concepts

Bugs

  • Fixed NPE when using only delimiter characters in termFilter query parameter
  • Server now fails to start if multiple terminology repositories have the same storageKey namespace ID assigned
  • Source and target effective time values are now indexed on module dependency reference set member index documents

5.5.0

Added

  • Support for inactive component creation. See endpoints:
  • POST /{path}/concepts
  • POST /{path}/descriptions
  • POST /{path}/relationships
  • POST /{path}/members
  • Support the complete SNOMED CT Identifier functionality via a dedicated Java API (SnomedRequests.identifiers())

Changed

  • SnomedDescription REST representation changes
  • Changed acceptabilityMap to acceptability
  • Changed descriptionInactivationIndicator to inactivationIndicator
  • SnomedRelationship REST representation changes
  • Changed sourceConcept to source
  • Changed typeConcept to type
  • Changed destinationConcept to destination
  • Removed refinability property
  • POST /{path}/concepts
  • Added support for relationship creation as part of concept creation
  • Added support for member creation as part of concept creation
  • POST /{path}/concepts/{id}/updates
  • Added support for description updates
  • Added support for relationship updates
  • Added support for member updates
  • Swagger API
  • Replaced ISnomed* types with the corresponding Snomed* type

Removed

  • The following endpoints have been completely removed from the REST API (equivalent requests can be initiated via expansion parameters, see GET /{path}/concepts endpoint)
  • GET /{path}/concepts/ancestors
  • GET /{path}/concepts/descriptions
  • GET /{path}/concepts/descendants
  • GET /{path}/concepts/outbound-relationships
  • GET /{path}/concepts/inbound-relationships
  • GET /{path}/concepts/pt
  • GET /{path}/concepts/fsn
  • Removed defaultModule configuration option (requests should specify the desired module via moduleId parameter)
  • Removed defaultNamespace configuration option (requests should specify the desired namespace via namespaceId parameter)
  • Removed enforceNamespace configuration option

5.4.0

Added

  • Support for Expression Constraint Language v1.1.1 has been added, see http://snomed.org/ecl for details
  • Support BigDecimal property mapping in index API

Changed

  • GET /{path}/concepts now supports filtering by ECL expressions via ecl query parameter
  • Deprecated escg filter on GET /concepts endpoint. Use the ecl query parameter instead
  • Snow Owl now uses sequential SNOMED CT identifier generation instead of random

Bugs

5.3.0

Changed

  • SNOMED CT Concept, Description and Relationship index schema changes
  • Added referringRefSets field to all three main SNOMED CT component documents
  • Added referringMappingRefSets field to all three main SNOMED CT component documents
  • Non-mapping reference set identifiers that reference a given component will be indexed in the referringRefSets
  • Mapping reference set identifiers that reference a given component will be indexed in the referringMappingRefSets
  • NOTE: to be able to use these fields reindex snomedStore repository using the snowowl reindex snomedStore command after dropping the index directory of it

Bugs

  • Fixed review change calculation bug, deleted components will mark their container component changed by default
  • Fixed bug with new/dirty reference set (re)indexing without concept changes
  • Handle unordered list index calculations properly during CDO revision compare

5.2.0

Added

  • New Java API to get/search commit information in a repository. See class com.b2international.snowowl.datastore.request.CommitInfoRequests. To make the new API work, you have to reindex your dataset using the snowowl reindex console command

Changed

  • SNOMED CT RF2 importer now uses the same change processing/indexing as regular commits
  • Support DOI score indexing during change processing (aka when committing changes)

Bugs

  • Fixed incorrect calculation of stated/inferred parent/ancestor information on SNOMED CT Concept documents in case of status change

5.1.0

Java 8 support

Snow Owl is now using Java 8 both compile time and runtime. Make sure your execution (and development, if you are developing custom plug-ins for Snow Owl) environment supports and uses Java 8. From 5.1.0, the minimum required Java version is 1.8.0 update 102.

5.0.0

Breaking changes

This section discusses the changes that you need to be aware of when migrating your application to Snow Owl 5.0.0.

Datasets created before 5.0.0

Snow Owl v5.0.0 no longer supports nested index directory format. The new format is flat, branches do not have their own directories under the corresponding terminology repository's root index folder. Branching and revision information are coded into each document and each terminology component has multiple documents in the index, which is called revision index and the documents are revisions. Additionally with the new index format, Snow Owl moved from Lucene v4.9.0 to v5.5.0. Indexes, that still use the old index API, but depend on the new Lucene version, should be accessible and readable by Lucene v5.5.0.

To support migration of incompatible datasets, Snow Owl v5.0.0 comes with a reindex command, which can be used to create the new index for any dataset based on the contents of the relational database. See updated Admin Console Reference Guide for details.

Java API changes

Due to index format changes, public APIs (generic and/or SNOMED CT terminology related) - that used the old format - become obsolete, and either marked with deprecated annotation or have been completely removed. See the affected public APIs in the Removed section.

Review API changes

In general the Review API still works the same way as in the 4.x versions, but the new, changed, deleted concept ID sets might contain non-Concept identifiers when a member of a Relationship/Description changes, but the corresponding Relationship/Description does not. It is recommended to fetch the container SNOMED CT Concept identifier by querying the source branch for the new or changed Relationship/Descriptions, and extracting the SNOMED CT Concept identifier from either the conceptId or sourceId properties. Querying deleted revisions from the tip of a branch is currently not supported, see next section.

With this change and limited capabilities, Snow Owl will no longer support the current version of the Review API starting from the next release (5.1.0), and it will replace it with a more generic Branch Compare API. This new API will return the new/changed/deleted document identifiers directly without trying to be smart and replace the document identifier with the corresponding container (root resource, like the SNOMED CT Concept) component identifier. API consumers will be responsible for fetching and computing the final compare result based on the actual changes between the branches, if they would like to still show the review in the scope of a SNOMED CT Concept. This enables Snow Owl to use the same Branch Compare API for different terminology implementations and the API will provide access points to query the proper revision of new/changed/deleted components (currently it only supports the latest revision, which returns HTTP 404 Not Found for deleted components).

Added

  • Maintenance commands:
  • snowowl reindex <repositoryId> <failedCommitTimestamp> - Reindexes the currently available database content from scratch, or from the specified commitTimestamp (if a previously initiated reindex process has failed at some point)
  • snowowl optimize <repositoryId> <maxSegments> - Optimizes the underlying index for the repository to have the supplied maximum number of segments (default number is 1)
  • snowowl purge <repositoryId> <branchPath> <purgeStrategy> - optimizes the underlying index by deleting unnecessary documents from the given branch using the given purge strategy (default strategy is LATEST, available strategies are ALL, LATEST, HISTORY)
  • New search options for SNOMED CT Reference Set Members:
  • acceptabilityId
  • characteristicTypeId
  • correlationId
  • descriptionFormat
  • mapCategoryId
  • operatorId
  • targetComponent
  • unitId
  • valueId
  • New revisionCache configuration option in repository section. Enables/Disables CDO revision cache based on its value (default value is true).
  • New index configuration options under repository section:
  • commitInterval - the interval in milliseconds, which specifies how often flush and sync index changes to disk (default is 15000, 15 seconds, minimum allowed value is 1000, 1 second)
  • translogSyncInterval - the interval in milliseconds, which specifies how often the transaction log flushes its changes to disk (default is 5000, 5 seconds, minimum allowed value is 1000, 1 second)
  • queryWarnThreshold - threshold in milliseconds, which specifies when to log a WARN level message in the log file about a slow query (default value is 400)
  • queryInfoThreshold - threshold in milliseconds, which specifies when to log an INFO level message in the log file about a slow query (default value is 300)
  • queryDebugThreshold - threshold in milliseconds, which specifies when to log a DEBUG level message in the log file about a slow query (default value is 100)
  • queryTraceThreshold - threshold in milliseconds, which specifies when to log a TRACE level message in the log file about a slow query (default value is 50)
  • fetchWarnThreshold - threshold in milliseconds, which specifies when to log a WARN level message in the log file about a slow fetch (default value is 200)
  • fetchInfoThreshold - threshold in milliseconds, which specifies when to log an INFO level message in the log file about a slow fetch (default value is 100)
  • fetchDebugThreshold - threshold in milliseconds, which specifies when to log a DEBUG level message in the log file about a slow fetch (default value is 50)
  • fetchTraceThreshold - threshold in milliseconds, which specifies when to log a TRACE level message in the log file about a slow fetch (default value is 10)
  • New modules:
  • com.b2international.index.api - Generic Index API module
  • com.b2international.index.lucene - Lucene based implementation of Generic Index API module
  • com.b2international.index.api.tests - Generic test cases to verify implementation modules of the Index API module
  • com.b2international.index.api.tests.tools - Useful utility classes when writing Index API based test cases
  • com.b2international.collections.jackson - Jackson ser/deser module for com.b2international.collections.api module

Changed

  • Improved change processing performance by loading only the relevant revisions from the index
  • Log entry format of requests has changed to the following
  • The logged entry is now a valid JSON object
  • Format: {"repositoryId":"string", "type":"string", "metrics": {...}, ...request specific properties}
  • Metrics
  • All values are measured in milliseconds
  • Read operations measure their execution time (responseTime)
  • Commit operations measure their execution time (responseTime) and commit subtask execution times (preCommit, preRequest, traceability, indexing, commit)

Removed

  • Deprecated public SNOMED CT APIs that have been replaced by the new Request based APIs
  • SnomedTerminologyBrowser
  • SnomedStatementBrowser
  • SnomedPredicateBrowser
  • SnomedComponentService
  • SnomedTaxonomyService
  • Configuration options:
  • indexTimeout configuration has been removed, because the new index API uses a single index and it does not require disposal of branch specific Index Readers/Writers

4.7.0

Added

  • New feature, SNOMED CT Extension support, see snomed_extension_management.adoc for details.
  • POST /codesystems - creates a new codesystem
  • PUT /codesystems - updates an existing codesystem
  • Representations
  • New branchPath property on CodeSystems (currently active path of a CodeSystem)
  • New repositoryUuid property on CodeSystems (the current repository of the CodeSystem )
  • New extensionOf property on CodeSystems (the base code system of the CodeSystem)
  • New parentBranchPath property on CodeSystemVersions (the parent branch path where the version branch is forked off)
  • effectiveTime based filtering for all components (currently members only, other components will be support on release of 4.7)
  • New module for support full javadoc of Snow Owl public APIs (com.b2international.snowowl.javadoc). The new module is part of the site Maven profile.

Changed

  • SNOMED CT Extension support
  • GET /codesystems - returns all currently known codesystems (in SNOMED CT, all releases, including extensions)
  • GET /codesystems/:id - returns a codesystem by its unique identifier, which can be its short name or its oid (both should be unique)
  • POST /codesystems/:id/versions - create a new version in a codesystem (or release in SNOMED CT)
  • SNOMED CT RF2 import
  • POST /imports - new optional property codeSystemShortName, identifies the target code system of the import, the default value is the short name of the SNOMED CT International Release
  • Revise handling of structural reference set members (language, inactivation and association members)
  • Try to reuse members where possible (reactivate if necessary)
  • Keep only one active language reference set member per description and do not create new ones when acceptability changes

Dependencies

  • Replaced custom 3.2.2 version of org.semanticweb.owl.owlapi module with a dependency to the 3.4.4 version of it.
  • Makes it possible to use ELK v0.4.2 runtime and during tests
  • Upgrade custom Protegé libraries from 4.1 to 4.3
  • Replaced the unsupported pcj library with FastUtil and also added a nice primitive collection API on top of it to support replacement of the primitive collection library underneath (and/or support multiple libraries with different capabilities, performance at the same time)
  • Migration from old terminology registry model to updated model, migration scripts are in /documentation/src/main/asciidoc/scripts/migration_4.6_to_4.7/

New modules

  • com.b2international.collections.api - primitive collections API
  • com.b2international.collections.fastutil - FastUtil implementation of primitive collections API

Bugs

  • Reduces thread usage of SNOMED CT change processing
  • Index initialization during SNOMED CT RF2 import now filters content based on the current latest system effective time, resulting in much more reliable imports and content when the import completes

Known issues

  • No RF2 import config validation when the branchPath is unrelated with the given codeSystemShortName property

4.6.0

Added

  • All references set member properties are supported (using RF2 property names)
  • Support for rebase queueing
  • GET /merges - returns all merges happened since the start of the server ()
  • GET /merges/:id - return a merge by its identifier
  • POST /merges - creates and starts a new merge between two branch points
  • DELETE /merges/:id - deletes a merge object by its identifier
  • Expansion support improvements
  • Expand targetComponent on association reference set members
  • Expand members of any SNOMED CT core component (Concept, Description, Relationship) (eq. expand=members())
  • Support stated and inferred expansion of descendants and ancestors (both Java and REST API)
  • Representations (Java and REST API)
  • New iconId property on SNOMED CT model components (not available in JSON representations)
  • New, expandable typeConcept object property on SNOMED CT Relationships (by default only id is available on the object)
  • New, expandable sourceConcept object property on SNOMED CT Relationships (by default only id is available on the object)
  • New, expandable destinationConcept object property on SNOMED CT Relationships (by default only id is available on the object)
  • New, expandable type object property on SNOMED CT Relationships (by default only id is available on the object)

Changed

  • REST API property changes
  • targetComponentId changed to targetComponent (became nested object, expandable)
  • Search improvements (Java API only, no REST support yet)
  • Support for fuzzy matching
  • Support for parsed terms
  • Support for DOI based scoring (using a default DOI file, not configurable yet)
  • Support for search profiles
  • The type of the group property changed from byte to int to support greater than 127 values
  • Using time based rolling policy with 90 days worth of history instead of fixed window with size restriction

4.5.0

Added

  • Support for simple and query type reference sets and members in RESTful API
  • GET /:path/refsets
  • GET /:path/refsets/:id
  • GET /:path/refsets/:id/history
  • POST /:path/refsets
  • POST /:path/refsets/:id/actions
  • GET /:path/members
  • GET /:path/members/:id
  • POST /:path/members
  • PUT /:path/members/:id
  • DELETE /:path/members/:id
  • POST /:path/members/:id/actions
  • Integration with Component Identifier Service (CIS), see configuration_guide.adoc for details on how to configure it
  • Indexing term, language code and acceptability values on SNOMED CT Description documents
  • Initial version of the resource expansion API is currently available (expand fsn, pt, descriptions and other nested resources within a single request)
  • numberOfWorkers configuration parameter to tweak worker threads per repository (by default it will be set to 3 x number of cores)

Changed

  • Fixed bug in Accept-Language header by introducing Extended Locales, they do support language reference set IDs properly (the original header spec. restricts the number of extension characters to 8)
  • Increased asyncTimeout in Tomcat to 60 seconds
  • Performance improvements on some endpoints by utilizing the new resource expansion API
  • Marked a bunch of old APIs as deprecated, they will be removed in upcoming releases

Removed

  • Removed label indexing from SNOMED CT component indexing (using Description term index field to find a label)

Merged pull requests

Known issues

  • CIS is currently unsupported in SNOMED CT RF2 imports (manual synchronization is required)
  • Simple type mapping reference set membership is not tracked properly if there are multiple mappings for a single referenced component

4.4.0

Added

  • Support of MRCM rules import before/after SNOMED CT import (previously was part of the SNOMED CT import)
  • Few missing SNOMED CT Inactivation Indicators have been added

Changed

  • RF2 validation in SNOMED CT import validates content based on effective times (fixes invalid errors/warnings)
  • Concept inactivation rewires immediate children to immediate parent (keeping all STATED ISA relationships and inactivating all inferred relationships)
  • Hot backup script copies entire index folder of a repository instead of just the version indexes
  • IndexService inactivity default timeout value changed to 30 minutes

Removed

  • PostProcessing support has been completely removed
  • Stopwords in index services have been completely removed

Bugs

  • Fixed stored mapTargetDescription values in SNOMED CT Simple Map Reference Set Members
  • Fixed invalid setting of released flag to false in case of already published component import (set only the effective time)
  • Removed tokenization of source field in IndexStore
  • Keep dirty indexes alive when running service inactivity checker

Merged pull requests

4.3.1

Added

  • GET /:path/descriptions - support for association targets in SNOMED CT Description representations
  • POST /:path/descriptions/:id/updates - support for inactivation indicators in SNOMED CT Description updates
  • POST /:path/descriptions/:id/updates - support for association targets in SNOMED CT Description updates

Changed

  • Renamed descriptionInactivationIndicator to inactivationIndicator in SNOMED CT Description representations
  • Changed commit notification logging to be more readable and traceable
  • Rebase across deep branches is now supported

Bugs

4.3.0

Added

  • Support for relationships with stated characteristic type
  • Importing/exporting sct2_StatedRelationship*.txt files
  • Indexing stated parentage (parent and ancestor fields) on concepts
  • Low-level Java API improvements
  • Revamped index APIs (document building, query building, fields)
  • Revamped change processing API (partial updates, parallel execution)

Changed

  • Stated relationships support changes
  • Classifier now uses the stated graph to produce changes to the DNF (inferred view)
  • Classifier now deletes any unpublished redundant inferred relationships instead of inactivating them
  • /browser/concepts/{id}/children now has a new parameter form (allowed values are stated and inferred)
  • Reference set lucene documents fields merged into their corresponding identifier concept doc

Merged pull requests

4.2.0

Added

  • Support for terminology reviews

    • POST /reviews
    • GET /reviews/:id
    • GET /reviews/:id/concept-changes
    • DELETE /reviews/:id

    Changes are computed according to existing version comparison logic in Snow Owl Server; in particular, reference set identifier concepts are marked as changed if any members are added, removed or updated in the reference set. The first modification immediately after versioning triggers an update to "Module dependency", making it appear in concept change resources.

    Inbound relationship changes do not mark the target concept as changed. Inactivating a concept marks it as changed, not deleted.

    Concept change sets and review resources are kept for a limited time, which is configurable using the snowowl_configuration.yml file.

4.1.0

Added

  • Deep branching support has been implemented
    • POST /branches endpoint
    • GET /branches endpoint
    • DELETE /branches/{path} endpoint
    • GET /branches/{path} endpoint
    • GET /branches/{path}/children endpoint
    • POST /merges endpoint

Changed

  • Added support for Unpublished component import. RF2 rows with empty effectiveTime column can be imported into Snow Owl SNOMED CT repository.
  • Breaking RESTful API changes
    • /{tag}[/tasks/{taskId}]/... URLs are replaced with URL beginning with /{path}/..., where "path" may include an arbitrary number of /-separated segments
  • Separate API documentation for each RESTful API
  • API documentation layout
    • Two column layout, one for the API docs and one for the Swagger UI
  • Deep branching support for Import/Export configuration (new branchPath)
  • API version is now included in SNOMED CT REST service URLs; the accepted media type is application/vnd.com.b2international.snowowl+json for both Administrative and SNOMED CT terminology services
  • Deployment changes: The preferred transaction isolation level is READ-COMMITTED for MySQL databases. For changing the corresponding server variable, refer to https://dev.mysql.com/doc/refman/5.6/en/set-transaction.html.

Removed

  • Breaking RESTful API changes
    • Removed /tasks API endpoints

Known issues

  • Associated index directories are not purged when a branch and any children are deleted
  • Reopening a branch can not be rolled back; if applying changes fails after reopening a branch during rebase or merge operations, previous changes will be lost
  • No additional metadata is present on version tag branches

2015-03-26

Added

  • WRP-89: both FULL and DELTA imports are now separating incoming import files into "layers" based on the effective time columns, and individual layers get imported in order. This enables importing the 20150131 INT RF2 release delta, which includes components from 20140731 as well. The import process can now create versions after importing each "layer" for all import types.

    Note that the above mentioned 20150131 release would require "re-tagging" of an already released 20140731 version, which is not supported, or placing the additional content on the existing 20140731 version branch as a patch. This, however, would make the extra 20140731 content available on that version and that version only; it would be visible neither from MAIN, nor from 20150131.

    The current implementation issues a warning when such cases are encountered; the extra content will become visible on MAIN and 20150131, but not on version 20140731, which is left untouched. A possible workaround is to import 20140731 from a delta with disabled version creation, then import the 20150131 delta with enabled version creation.

2015-03-19

Added

  • WRP-135: added properties taskId and versionId to the export configuration object to allow exporting content from task branches. URLs for exporting no longer include the version segment.
    • version/taskId is accepted, but not applicable (no tasks on versions)
    • when taskId left out, it means MAIN or head of a particular version
  • Added the transientEffectiveTime property to the export configuration object for specifying effective time values in export files, if unpublished components are present. Valid values are:
    • "" or not setting the property: uses Unpublished in exported files
    • "NOW": uses the current server date in exported files
    • dates in yyyyMMdd format, eg. "20150319": uses the specified date in exported files
    • anything else result in return code 400 bad request, date is not validated in terms of earlier/later (only proper format) Note: unpublished components are filtered out from DELTA exports if the export configuration specifies an ending effective time.

Changed

  • Changed the export service to export components from all modules if the moduleIds property of the export configuration object is not set. The previous behavior resulted in empty export files under the assumption that no modules should be exported.
  • Querying or exporting a non-existent export config returns now code 404 as opposed to 200 and an empty object.
  • After downloading the export result, the export config is cleaned up.

DEV2.1 - 2015-03-05

Changed

  • Make the Accept header mandatory for requests to "B2i" URLs, and produce application/json responses on "Browser" URLs. This means that the latter endpoints will be hit when entered in a web browser's URL bar, making testing easier.
  • Increase concept children collection performance by using a combination of low-level calls. This brings the test case of 123037004's children down from ~22 seconds to ~350 ms.
  • Sort description search results by relevance, and add offset and limit to fetch search results in smaller segments.
  • Split the API documentation into two sets: the administrative interface with the code system listing is separated from SNOMED CT services. The API viewer's own URL bar can be used to switch between generated documentation endpoints; two shortcuts were also added. The default URL is changed to http://localhost:8080/snowowl/admin/api-viewer/ .

DEV2 - 2015-02-20

Added

  • New API viewer category for URLs specific to the IHTSDO Browser:
  • GET /{tag}[/tasks/{taskId}]/concepts/{SCTID} for retrieving concepts and related details
  • GET /{tag}[/tasks/{taskId}]/concepts/{SCTID}/children for retrieving concept children
  • GET /{tag}[/tasks/{taskId}]/descriptions?query={query_string} for retrieving matching descriptions
  • GET /{tag}[/tasks/{taskId}]/constants for getting response constant FSNs and identifiers

Changed

  • effectiveDate and effectiveTime properties on SNOMED CT components and code system versions now universally follow the short yyyyMMdd format (also applies when creating new versions), other dates should use ISO8601
  • Accept-Language is required on all new endpoints which return descriptions, as Snow Owl Server stores descriptions with different language codes and acceptability side-by-side
  • Constants must be retrieved on a version/task basis, as the FSN of these enumeration values can change between versions, tasks

Removed

  • isLeafStated is not returned, as Snow Owl Server holds a mixed set of relationships which matches the inferred view only

DEV1 - 2015-02-13

Added

  • WRP-26: Support importing deltas without corresponding unchanged artefacts
  • WRP-82: Enable REST operation to support imports on branches
  • WRP-88: Add support for namespace to REST API
  • Added folder delta-import-examples which includes a set of RF2 release .zip files, containing the minimally required content for each change. A separate readme.txt file within the folder has additional instructions on how these archives can be used.

Changed

  • URLs under and including /snomed-ct/imports no longer require specifying the version to use as a path variable;
  • The input object for POST /snomed-ct/imports should now include both the version as well as the task identifier, if applicable:
{
  "version": "MAIN",
  "taskId": "SO-001",
  "type": "DELTA",
  "languageRefSetId": "900000000000508004",
  "createVersions": false
}
  • GET /snomed-ct/imports/{importId} will return information about the ongoing import and the original values from the import configuration:
{
  "type": "DELTA",
  "version": "MAIN",
  "taskId": "SO-001",
  "createVersions": false,
  "languageRefSetId": "900000000000508004",
  "id": "89feb6f4-f6a7-4652-90b9-b89b6b8587ce",
  "status": "COMPLETED",
  "startDate": "2015-02-13T15:39:56Z",
  "completionDate": "2015-02-13T15:41:05Z"
}

Removed

  • To keep the release file's size small, no indexes and SQL dumps have been attached; the ones from the previous release can be used instead. A database reload is required.