ARCtrl 2.0.0

• .NETStandard 2.0

  • ARCtrl.Contract (>= 2.0.0)
  • ARCtrl.CWL (>= 2.0.0)
  • ARCtrl.FileSystem (>= 2.0.0)
  • ARCtrl.Json (>= 2.0.0)
  • ARCtrl.Spreadsheet (>= 2.0.0)
  • Fable.SimpleHttp (>= 3.5.0)
  • FSharp.Core (>= 8.0.301)

Additions:
add RO-Crate contexts to docs
Update fsspreadsheet
include fable files
Add ARCtrl.ValidationPackages project: - base type model for ValidationPackages and the config file
Add ARCtrl.Yaml: - Uses YAMLicious - tries to mirror ARCtrl.Json - Encoder/Decoder logic for ValidatioNpackages type model
Add contracts for ValidationPackagesConfig
Update to .NET 8, requested PR changes
add fable files
add the fable files for real. fable be fablin'
Add classes for index files :sparkles: #386
Rename ARCtrl.Path to ARCtrl.ArcPathHelper #398
Add CompositeCell.ToDataCell #404
Unifiy expected functionality of CompositeCell conversion utility #402
Add api to include datamap in assay/study #406
add swate prerelease target
rmv comment
add first json logic for datamap :construction:
Add YAML tests for Validation packages, use custom equality
add a test placeholder -.-
Add contract handling for `validation_packages.yml` to top-level ARC API
wip
Add instance method tests for ARCtrl.ValidationPackages
Add Contract tests for ValidationPackagesConfig
Add topm level api tests for ValidationPackagesConfig
Use literal for yaml keys (also in tests)
Use more Record-like ToString() for ValidationPackages and ValidationpackagesConfig
add addColumnFill member function with tests
Additional tests for AddColumnFill
Reviewed AddColumnFill member function and tests
add ARC.ToROCrateJsonString member #344
added functions for checking assay and study metadata sheet names #414
check identifiers when creating assay and study objects #415
add CompositeHeader.IsUnique #416
add  ArcTable cell accession and manipulation functions
make process conversion more robust against different outputs
base spreadsheet parsers on string columns
change main types of spreadsheet parsing collections from list to array
small adjustments to renaming contract handling
add manage-issues.yml
rework datamap to be represented as a row of records
adjust spreadsheet parsing to datamap datamodel change
update templates json parsing
increase robustness against OntologyAnnotation mutability issues
add new uri parsing rules and core tests
make ArcTable header parsing patterns less strict
add toJsonString extensions members
start implementing @id in isa json writer logic
finish implementing @id in isa json writer logic
add study test file for @id json writer
add idmap test case for study
change encoding order of assay properties for isa json parsing
add useIDReferencing flag to JsonController
small change in ArcTable.ToString function to make it more robust
small speed improvement to ArcTable move column
add column move function to ArcTable
added comparison for ontologyannotation and compositeHeader
added fable helper function for comment header creation
add some more comments to isa processType conversion
add comment column json and spreadsheet parser
add comment column header and process converter
add study rename logic
add rename contract and assay rename logic
make ArcTables construction fail for duplicate table names #332
add some additonal info to pyproject.toml
reinclude inclusion of source files in fable folders
Update scripts
Rename one file and rmv most code from md files for maintainability :fire:
Update GettingStarted.md
Finalize docs :book:
Update EXAMPLE_CreateAssayFile.js
Update js docs : book:
added tests to tab-json conversion and parsing
replace "Raw Data File", "Derived Data File" and "Image File" column headers with "Data" #93
add tests for backwards compatability of data headers
add datamap spreadsheet parsing
add datamap spreadsheet parser tests
add datamap contract handling
add datamap contract handling
add datamap contract handling tests
update Data and CompositeCell json parsing
add json parser and tests for updated data objects
move data file outside of process folder
add pending test for losless data parsing in isa json
update prerelease mechanism
Add ToString overrides for study/investigation
Finalize io controller types for fable :sparkles:
rmv old code :fire:
Rename to toStringObject
add README.md reference to setup.cmd
Simplify OntologyAnnotation hashcode and equality :white_check_mark:
Add setup script for windows :construction_worker:
set test with umlauten pending for python
Add ro-crate write tests :white_check_mark:
add some more schema validation tests
add native python tests :white_check_mark:
Make js native tests pass :heavy_check_mark:
update github CI
rmv leftover folder :fire:
Finish json (for now :construction:)
start reworking tests for js and py
move ARCtrl contract tests to Contract test project
move template json tests to json test project
more work on json :construction:
reduce test spreadsheet metadata matching reduction of parser logic
More work on json tests :construction:
Add custom ToString for OntologyAnnotation :art:
Start working on tests :construction:
distribute template across appropriate projects
Add fable json import type #324 #285
add ARC RO-Crate serialization
finish investigation ro-crate
finish moving template json :sparkles:
Finish compressed json logic :sparkles:
Start moving Arc Json logic :construction:
rework ARCAssay and ArcStudy ISAJson serialization
rework ROCrate process serialization
Start with component logic rework :construction:
finish up ISA-JSON conversion for process types :sparkles:
Finish json table logic :sparkles:
Finish json for shared types :sparkles:
start reworking arctrl.json process serialization
Start workin on new Json API layer :construction:
start reworking ARCtrl.json project
rework ARCtrl.Spreadsheet according to datamodel changes
rework ARCtrl.Core types to improve transpiled javascript
restructure ARCtrl.Core (former ARCtrl.ISA) project
restructure project
move all filesystem information into filesystem project
move UIHelper function into compositecell
add addtionalType to ProcessParameterValue
WIP :construction:
Updated tests for jsonld readers. Investigation test still wip.
adapted json export tests for new ro-crate export (Investigation still open)
new ro-crate export and context files
WIP :construction:
WIP :construction:
Updated tests for jsonld readers. Investigation test still wip.
adapted json export tests for new ro-crate export (Investigation still open)
new ro-crate export and context files
Merge pull request #325 from nfdi4plants/performanceReport
several minor adjustments according to change request
update readme with performance report and python links
move performance report into speedtest project
move performance report build targets and create first reports
first draft of performanceReport target
Merge pull request #323 from nfdi4plants/update_js_docs
Update
Merge pull request #320 from nfdi4plants/python_integration
update documentation and add python docs
Merge pull request #317 from nfdi4plants/python_integration
small change to semver in npm
Deletions:
remove entry when delete contract is created for validation packages config file, add related tests
remove UI helper functions #329
Remove ALL tabs from fsproj files
remove erroneous exe output type from testingutils
Bugfixes:
Fix spreadsheet writer for data with freetext :bug::white_check_mark: #405
fix data column spreadsheet export for mixed columns :bug::white_check_mark:
fix module references :bug:
Added missing datamap to compressed study json :bug:
fix study datamap json key name :bug:
Fixed json key naming issue, added tests :bug::white_check_mark:
fix test transpilation for YAML
Fix path helper usage after rebase
fix multi annotationTable writing and unify API #423
small fix for changes to spreadsheet parsing
fix and test rename leading to update contracts when the renamed entity is registered and remove isalight
fixes and tests for updateContracts when assays or studies are added
Fix missing fable includes #369
fix datamap spreadsheet parsing against tests
fix datamap spreadsheet parser against tests
fix tests againsts iri generation changes
fix tests against @id json writer changes
some fixes against study idmap test case
fix id table json parsing tests
small fix for jsnativetests for comment column addition
Merge pull request #358 from nfdi4plants/fixes
Fix python docs for contract logic :bug: #342
test and fix ro-crate propertyValue parsing
add tests and fix empty cell parsing behaviour
Merge pull request #353 from nfdi4plants/jsonLD-fix
rework and fix Spreadsheet reader according to data node changes
adjust and fix spreadsheet writing for data node changes
small fixes for Fable compatability
fix data json parser test
fix non utf8 json output #334
rmv code circumventing fable python bug :fire:
fix OntologyAnnotation Hashcodes :bug:
Fix json tests :heavy_check_mark:
hotfix js schema validation in tests
Fix all warnings by burning unused fable reflection helpers :fire:
Fix test tasks still using mocha
fix json parsing DateTime issues
several python test fixes
move and fix template hashcode and equality tests
Template fixes against json and core tests
move and fix spreadsheet Template tests
fix component name conversion
fix arctrl.core tests and equality of reworked objects
fix rocrate sample and protocol handling
fix rocrate assay serialization
fix wrong encoder/decoder calls :sparkles:
fix arctrl.core tests
fix multiple issues with ro-crate json encoding :bug:
Added fromJsonldString for all ISA-JSON types. Also fixed some bugs.
fix build chain for linux
fix tests :bug: