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RELEASE_NOTES.md

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Change log

in develop

...

0.8.5 (2024-03-04)

  • ANTLR4 version bump to 4.13.1

0.8.4 (2022-08-02)

  • For duplicated calls - prepends a process name to make the name unique, avoiding exception "two different processes with the same name"
  • Added support for "metadata" field for input files in CWL under development (pending inclusion in CWL standard).

0.8.3 (2022-05-16)

  • Update dxCommon to 0.11.3

0.8.2 (2022-05-16)

  • Updated cwljava with fixes to secondaryFiles with pattern field when parsing workflow-level parameters and the helper function utils.Uris.shortname to generate enum symbols without namespaces

0.8.1 (2022-04-18)

  • Fixes CWL default requirement classnames NetworkAccess, WorkReuse and ToolTimeLimit so the corresponding hints can be recognized by dxCompiler (instead of being defined as GenericHints which are not interpreted during compilation).

0.8.0 (2022-02-08)

  • Breaking
    • Parser API has changed substantially, with parameters added, removed, and rearranged
    • Parser.parse method is now private - use parseString or parseFile instead
    • Removes all options to modify IDs during parsing
  • Handles workflows packed by cwlpack
  • Adds Process.simpleName method to return simplified process name from ID automatically generated by cwlpack --add-ids
  • Adds Identifiable.copySimplifyIds method to deep-copy objects with simplified IDs
  • Adds CwlEnum.symbolNames function for getting enum symbols without any namespace prefixes
  • Adds coerce option to Evaluator.evaluate to actually perform type coercion, rather than just checking that the result is coercible to the specified type
  • Trims StringValue when coercing to primitive types
  • Fixes Evaluator.finalizeInputValue for compound and optional types
  • Evaluator.finalizeInputValue loads file contents from remote file source if file does not exist locally
  • CwlType.coerceTo now returns both the coerced-to type and value
  • Added CwlType.CwlGenericRecord, which is coercible to either CwlInputRecord or CwlOutputRecord
  • Fixes evaluation of values with multiple possible types

0.7.4 (2021-01-05)

  • Updates code to compile with JDK11
  • Updates build environment to JDK11, Scala 2.13.7, and SBT 1.5.7
  • Fix packaging

0.7.2 (2021-12-09)

  • Update dxCommon version

0.7.1 (2021-11-10)

  • Handles error when listing folder during path value finalization

0.7.0 (2021-09-23)

  • Breaking Change: Sink.linkMerge is now Optional
  • Introduces ParserResult class, which is returned from all Parser.parse* methods
  • For packed workflows, parses out $schemas and $namespaces
  • Updates to latest cwljava, which fixes several parsing errors
  • Fixes CwlType.flatten to correctly handle duplicate types
  • Treats scatter sources as identifiers
  • Automatically renames the main process if its name collides with another process
  • Fixes evalution of compound parameter references

0.6.0 (2021-08-31)

  • Set CommandLineTool.successCodes to Set(0) if not specified
  • Fixes deserialization of optional fields
  • Uses the source file name as the process name when processing a $graph where the top-level element ID is 'main'
  • Fixes evaluation for Directory-type values with listings
  • Fixes parsing of LoadListingEnum values
  • Adds option to Parser.parseFile and Parser.parseString to specify that the CWL file is in "packed" form
  • Updates to latest cwljava, which fixes parsing of anonymous schemas in packed documents
  • Correctly handles identifiers with namespaces from imported documents

v0.5.1 (2021-07-28)

  • Fixes error when trying to finalize a File value without location or path
  • Updates dxCommon to 0.2.15-SNAPSHOT
  • Uses FileSource.listing to determine directory listing during finalization
  • Updates to dxCommon 0.7.0

v0.5.0 (2021-03-28)

  • Breaking change: schema types now have id: Option[Identifier] rather than name: Option[String]
  • Parser can now handle $graph style CWL documents
  • Adds dependency on dxCommon library
  • Improves finalization of file values
  • Fixes coercion of StringValue to CwlEnum
  • other bugfixes

v0.4.1 (2021-03-11)

  • Adds EvaluatorContext.createInputs to create an EvaluatorContext from input values
  • Performs "finalization" of input values (setting of missing attributes on File and Directory values) when using EvaluatorContext.createInputs or EvaluatorContext.createStaticInputs

v0.4.0 (2021-03-04)

  • Parser bugfixes
  • Incorporate cwljava/39, which fixes workflow parsing issues
  • Allow duplicate Requirements/Hints and specify priority rules
  • Breaking change: added new CwlMulti type and removed all uses of Vector[CwlType]

v0.3.4 (2021-02-03)

  • Fix parsing of SchemaDefRequirement with nested type references
  • Fix coercion of null and optional ctypes

v0.3.3 (2021-02-02)

  • Rename all CwlValue.apply(JsValue) functions to deserialize - fixes bug with deserializing string values

v0.3.2 (2021-01-27)

  • Handle CwlAny type in Evaluator
  • Update cwljava, which fixes remaning CommandLineTool parsing errors
  • Convert all tool compliance tests to unit tests

v0.3.1 (2021-01-21)

  • Update cwljava, which fixes most CommandLineTool parsing errors
  • Normalize baseuri so schemadef names and type references match

v0.3.0 (2021-01-20)

  • Implement workflow support
  • Use separate classes for input and output record schemas
  • Use SeqMap for RecordSchema type and Object value

v0.2.9 (2021-01-05)

  • Add optional name parameter to Parser.parse* functions, for tools/workflows that do not specify id
  • Fixed bug with Runtime.create
  • Include class attribute when serializing File and Directory values

v0.2.8 (2020-12-14)

  • Fix hint parsing bugs

v0.2.7 (2020-12-14)

  • Implement coercion of values
  • In Evaluator, have all functions that take a Vector of types return the actual type of the evaluated value
  • Add convenience functions to Evaluator
  • Parse hints

v0.2.6 (2020-12-03)

  • Fix several issues with CwlTypes
  • Add Parser.canParse(String) and Parser.parseString functions
  • Add default values and merge function to ReSourceRequirement

v0.2.5 (2020-11-20)

  • Updated cwljava
    • fixes some issues with requirements parsing
    • fixes some tests cases and breaks others

v0.2.4 (2020-11-19)

  • Fix apply functions for CwlValue primitives - correctly handle Scala values

v0.2.3 (2020-11-16)

  • Fix parsing of process requirements

v0.2.2 (2020-11-12)

  • Add Parser.canParse method

v0.2.1 (2020-11-09)

  • Parse identifiers
  • Use file name as tool identifier if id not specified explicitly

v0.2.0 (2020-11-02)

  • Added documentation
  • Fixed conversion of null-valued expression to string
  • Renamed case class CwlExpr -> ParameterValue

v0.1.0 (2020-11-01)

  • Initial release