ARCtrl.Core 3.3.0

• .NETStandard 2.0

  • ARCtrl.CWL (>= 3.3.0)
  • ARCtrl.FileSystem (>= 3.3.0)
  • FSharp.Core (>= 10.1.302)

Rework of CWL handling and RO-Crate conversion to support CWL 1.2 and 1.3 features #654
Various small fixes, including RO-Crate and XLSX parsing #653
Additions:
Rewrite references in record values when the ids of data entities are normalized
Take CWL defaults into the crate of the ARC as well
Link the files a workflow or run needs in the crate of the ARC as well
Write a run value that names the ARC root as a reference to the crate root
Leave the CWL of workflows and runs empty when reading a crate
Make the type rule of run values public as CWLType.admits
Convert the dates of composed workflows and runs to UTC
Take CWL defaults only into the run crate and for null run values
Keep a run out of its own parts when a run value names its folder
Keep the types of both nodes when a graph merges nodes of one id
List files in lists and records of run values in the root of the crate
Write crate dates in UTC and pin them with one timestamp
Check run values against the types of their inputs again
Use the CWL default of an input without a run value
Write directory values of runs as datasets with their files
Report the JavaScript speed tests as JavaScript and write the Python report in UTF-8
Update Fable to 5.26.0
Add CWL decode and encode to the speed tests
Merge origin/main into cwl_yamlicious_2
Add multiple alternative constructors to DU types. Mirror native js tests to native python
update tests further with correct imports from index and more helpers
Add primary constructor tests for js native
Publish crate roots at the local time when no date is given
Walk steps only in a mapping whose class is workflow
Leave out a directory literal that names the arc root explicitly
Read the run folder itself back as a dot
Check referenced and part paths for duplicates with hash sets
Read every crate id with a uri scheme as a url and not as a file of the arc
Keep URLs in job files and compare run folders by segments
List the files that CWL file and directory literals name
Publish crate roots with a date and their profiles as entities
Write step runs as paths from the crate root
List the files a workflow needs in its crate
Resolve dot segments in job file paths
Restructure the CWL tests as shared tables
Drop packed documents and stop on cyclic runs
Read type names and step outputs without validating them
Update Fable to 5.24
Apply the repeated-key rule to every mapping
Make the step id optional and quote YAML 1.1 lookalikes
improve speed of identifier validation by creating the regex only once (#303)
Reject prohibited YAML features and report error locations
make SetAssay, SetStudy, SetWorkflow and SetRun add the entity if no entity with the identifier exists (#565)
Read directives and numbers in scalar fields like cwltool
Read Schema Salad directives
Decode every string field strictly
Keep run references and job files of an ARC
Report decode errors with path and span
Write port schemas under type and drop the Dirent type
Read packed documents and SchemaDefRequirement types
add full arc ro-crate roundtrip test (#651)
Read the type Any, input formats and stream types
normalize ro-crate file and dataset ids to leading ./ on write and read (#615, #607)
add warning for empty study, assay, run and workflow titles in ro-crate export (#613)
Bugfixes:
fix semver comparison not following the spec and parsing failing for versions without minor or patch (#639)
fix ms, po and ro term accessions being written as ols urls instead of obo purls (#551, #391)
fix empty data file paths being resolved to assay and study folders (#593)
fix external files being added to filesystem when reading ro-crate (#650)
fix assay registrations of studies being lost in ro-crate (#651)
fix workflow datamap not being written to ro-crate (#651)
fix datamap fields not being read from compacted ro-crate (#651)
fix cwl input file paths of runs not being read with normalized ro-crate ids (#615)
fix empty input and output cells resulting in ro-crate entities (#585)
fix ro-crate citations using local identifiers instead of doi or pubmed urls (#627)
update exceljs to 0.5.0 to fix reading tables with totals row formulas (#508)