CHANGELOG.md

The LabKey Remote API Library for Java - Change Log

version 6.3.0-SNAPSHOT

Released: TBD

• Update Commons Logging, Gradle, Gradle Plugins, HttpClient, HttpCore, and JSONObject versions
• Remove defunct FileNotification API and uses

version 6.2.0

Released: 29 July 2024

• Add support for auditUserComment field for assay import
• Add support for allowPlateMetadata, plateMetadata fields for assay plate support
• Deprecate GetContainersResponse permissions methods which are incompatible with LabKey Server v24.8+
• Update Commons Codec, Commons Logging, Gradle, Gradle Plugins, HttpCore, and JSONObject versions

version 6.1.0

Released: 26 February 2024

• Issue 49238: Fix so all command responses correctly decode as UTF-8.
• Add MoveRowsCommand to query
  • Earliest compatible LabKey Server version: 24.1.0
• Remove deprecated GetDomainCommand; use GetDomainDetailsCommand instead.
• Remove deprecated method RowsResponse.getRequiredVersion().
• Deprecate GetUsersCommand methods getIncludeDeactivated() and setIncludeDeactivated(); use getIncludeInactive() and setIncludeInactive() instead.
• Remove Hamcrest references (unused)
• Update ApiKeyCredentialsProvider to respond to server auth challenges with the apikey header and use the session on subsequent requests.
• Update Commons Logging, Gradle, Gradle Plugins, HttpClient, and HttpCore versions

version 6.0.0

Released: 1 December 2023

• Encode SQL parameters passed by ExecuteSqlCommand and SqlExecuteCommand to avoid rejection by web application firewalls
  • Earliest compatible LabKey Server version: 23.9.0
  • These commands are no longer compatible with earlier versions of LabKey Server (23.8.x and before) by default. However, if targeting an older server, calling ExecuteSqlCommand.setWafEncoding(false) will restore the previous behavior.
• Update HttpCore, JSON-java, Gradle Plugins, and Gradle versions

version 5.3.0

Released: 7 September 2023

• Update to Gradle 8.3 and adjust away from deprecated syntax
• Add Ontology and Lineage filter type operators
• Add TotpManager, a simple helper that generates TOTP one-time passwords
• Update Commons Codec, HttpCore, and Gradle Plugins versions

version 5.2.0

Released: 3 May 2023

• Add RenameContainerCommand and RenameContainerResponse

version 5.1.0

Released: 3 March 2023

• Delegate first request behavior to the configured CredentialsProvider. Connection-based providers invoke login-ensureLogin.api and connection-less providers invoke login-whoAmI.api.
• Restore connection-based authentication for BasicCredentialsProvider
• Add logging to NetrcFileParser to help with debugging authentication problems
• Optional parameters to GetContainersCommand to reduce the size of the response payload
• Upgrade to most recent JSON-java, Gradle, and Gradle Plugins versions

version 5.0.1

Released: 30 January 2023

• Fix regression introduced in 5.0.0: RowsResponse.fixupParsedData() was called before _requiredVersion was set. This caused the fixup method to skip BigDecimal to Double conversions in the returned data maps.

version 5.0.0

Released: 24 January 2023

• Refactor the Command class hierarchy:
  • Add GetCommand, new abstract base class for all commands that use get
  • Make Command and PostCommand abstract
  • Add SimpleGetCommand, new concrete class used (instead of Command) to invoke GET API actions without creating a subclass
  • Add SimplePostCommand, new concrete class used (instead of PostCommand) to invoke POST API actions without creating a subclass
• Refactor parameter handling for consistency:
  • createParameterMap() is now used by subclasses to create and populate a mutable map of URL parameters
  • getParameters() now returns an immutable copy of the current URL parameter map for external use, typically logging or testing
  • Commands no longer stash and reuse the parameter map; createParameterMap() always creates a new map.
  • setParameters() is now available only on SimpleGetCommand and SimplePostCommand. Custom GetCommand and PostCommand subclasses that need to specify parameters are expected to override createParameterMap().
  • setJsonObject() is now available only on SimplePostCommand. Custom PostCommand subclasses that need to post JSON are expected to override getJsonObject().
• Stop passing command subclasses when constructing every CommandResponse. The two response classes that need this now implement it without burdening all other commands.
• Introduce HasRequiredVersion interface and use it when instantiating CommandResponse subclasses that need required version
• Remove all Command copy constructors. Same rationale as the earlier removal of copy methods.
• Switch SelectRowsCommand and NAbRunsCommand to post their parameters as JSON
• Fix NAbReplicate to handle "NaN" values
• Remove CommandException from getHttpRequest() throws list
• Adjust the Demo.java and Test.java tests to match current sample data and Command hierarchy changes

version 4.3.1

Released: 15 January 2023

• Fix regression introduced in 4.3.0: SelectRowsCommand should create a fresh parameter map for every invocation of getParameters()

version 4.3.0

Released: 11 January 2023

• Issue 47030: Switch SelectRowsCommand and NAbRunsCommand to always use POST
• Add support for includeTotalCount, includeMetadata, and ignoreFilter flags to BaseQueryCommand and reconcile duplicate parameter handling code vs. SelectRowsCommand
• Add support for includeTitle and includeViewDataUrl flags to GetQueriesCommand

version 4.2.0

Released: 10 January 2023

• Refactor repository layout, removing unnecessary labkey-client-api folder
• Upgrade to most recent Gradle, Gradle Plugins, and HttpClient versions

version 4.1.0

Released: 15 December 2022

• Migrate internal HTTP handling to use Apache HttpClient 5.2
• Generate and execute path-first URLs
• Add PrimaryStorage a new StorageItemTypes for non-freezer storage

version 4.0.0

Released: 26 October 2022

• Migrate to a new JSON library: JSON-java. The previous library, json-simple is no longer maintained (last released in early 2012) and lacks support for basic features like generics. This is an incompatible API change for developers who write their own Command classes; they will need to update their Command classes if/when they upgrade to v4.0.0. Developers who simply use Command classes should be able to upgrade without changes.
• API changes:
  • Remove copy method from Commands. It was inconsistently implemented and served little purpose.
  • Remove CommandResponse.getSourceCommand. Functionality would vary wildly because of inconsistent Command.copy implementations.
  • Make the properties stashed by ResponseObject immutable.
• Issue 46321: Remove lib directory from fatJar in favor of pulling dependencies via the published pom files when needed
• Remove artifactory plugin since we use the maven publish command now

version 3.1.0

Released: 20 September 2022

• Add support for creating Freezer Manager freezer hierarchies via StorageController APIs (earliest compatible LabKey Server version: 22.10.0)
  • CreateCommand, UpdateCommand, DeleteCommand
• Restore proactive authentication behavior. A change in v3.0.0 caused some invocations of @NoPermissionsRequired actions (e.g., GetContainersCommand) to use guest credentials instead of the configured user credentials. The library now always authenticates using the configured credentials, matching pre-v3.0.0 behavior.

version 3.0.0

Released: 14 September 2022

• Migrate internal HTTP handling to use Apache HttpClient 5.1.x
• Migrate from preemptive to challenge-response Basic authentication
• Switch StopImpersonatingCommand to disable redirects (mimicking previous behavior)
• Add Connection.stopImpersonating() and deprecate stopImpersonate()
• Remove deprecated methods:
  • ApiVersionException() (use constructor that takes contentType)
  • CommandException() (use constructor that takes contentType)
  • Connection.getBaseUrl() (use Connection.getBaseURI())
  • CredentialsProvider.configureRequest() (use variant that takes a URI)
  • Filter.NON_BLANK (use Filter.NONBLANK)
  • Filter.getCaption() (use Filter.getDisplayValue())
  • Filter.getName() (use Filter.getUrlKey())
  • Filter.isDataValueRequired() (use Filter.isValueRequired())
• Remove SAS macros and wrapper classes
• Add CreateFolderCommand
• Add CreateProjectCommand (earliest compatible LabKey Server version: 22.3.0)
• Update LogoutCommand to use POST

version 2.0.0

Released: 25 July 2022

• Require Java 17 to build and run

version 1.5.2

Released: 14 July 2022

• Add Connection.setUserAgent() and Connection.getUserAgent()
• Set Java library user agent to "LabKey Java API"
• Set SAS library user agent to "LabKey SAS API"

version 1.5.1

Released: 7 July 2022

• Fix NPE when saving assay protocol with transform scripts
• Add derivationDataScope to PropertyDescriptor

version 1.5.0

Released: 20 April 2022

• Update gradle and various dependencies
• Update signature of Connection constructor
• Issue 43380: ImportDataCommand missing options supported by the query-import.api endpoint
• Remove CheckForStudyReloadCommand.

version 1.4.0

Released: 16 June 2021

• Issue 43246: Lineage query NPE while processing an UploadedFile
• Additional lineage options and support additional properties in response
• Update dependency version numbers
• Update to Gradle 7.1

version 1.3.2

Released : 05 November 2020

• Fix selectedMetadataInputFormat serialization
• Add some missing dependency declarations

version 1.3.1

Released : 18 September 2020

• Fix pre-population of session ID and CSRF token in Connection
• Identify target server with a URI instead of a String
• Add support for Log4J 2

version 1.3.0

Released : 16 June 2020

• 7368: Conditional Formats of Fields
• Update FileNotificationCommand to do a POST, as now required
• Add documentation

version 1.2.0

Released: 16 April 2020

• small fixes to LABKEY.Experiment APIs
• Support impersonation via Java client API

version 1.1.0

Released: 19 March 2020

• Support for plate metadata in saveBatch and importRun APIs
• Don't post invalid 'rangeURI' to server
• Update source compatibility to 1.8

version 1.0.0

Released: 06 February 2020

• Migration to SemVer for library versioning. With 1.0.0 we will move away from using the LabKey server version and adopt the standard used in our other API libraries. Version 1.0.0 will succeed the previous published version of : 19.1.0.
• Support for truncating tables, there is a new TruncateTableCommand to expose this functionality.
• CRUD operations for Domains.
• Improved support for Assay data import. LoadAssayBatchCommand and SaveAssayRunCommand have been added to allow support for ad-hoc properties.
• New ListDomainsCommand.
• New SaveAssayRunsCommand.
• Update PropertyDescriptor to expose missing value toggling.