RELEASE_NOTES.md

2.2.4+05faa0d (Released 2024-11-19)

• Bugfixes:
  • [#9d2ce07] fix technologyPlatform not handling parentheses

2.2.3+440a84e (Released 2024-11-18)

• Additions:
  • [#4429911] loosen constraint on python requests
  • [#852686c] update poetry.lock file
• Bugfixes:
  • [#12e1a89] fix data cells not being written as such in spreadsheets
  • [#f5cc507] fix template variable names
  • [#d6ca1e7] fix python request dependency

2.2.2+4aaa6cf (Released 2024-11-7)

• Bugfixes:
  • [#5aae159] hotfix parsing of old json-ld samples and sources

2.2.1+6f816b8 (Released 2024-11-6)

• Bugfixes:
  • [#17d6e64] fix additionalProperties being lost in RO-Crate write read

2.2.0+fd5eccc (Released 2024-10-24)

• Additions:
  • [#b8640a7] small changes to build-chain according to PR review
  • [#9e43e81] Merge pull request #446 from nfdi4plants/ro-crate-json
  • [#e6becb8] Enable Sequence based metadata data creation for arc assays
  • [#3c383de] Enable the creation of study metadata based on sequences
  • [#12e5d75] Add excel get and create template meta data from sequence of strings
  • [#38b9ce8] Adapt styling
  • [#5e0e10e] Add from and to seq for arc investigation
  • [#8050b1b] Update build-test.yml
  • [#d4687f3] Added unit tests for investigation
  • [#8301e02] restore package.json of ARCtrl
  • [#f525619] restore pagages.lock.json of ARCtrl
  • [#536b988] Apply review changes
  • [#79f4fde] Adapt parameter styling
  • [#36f78d4] small undo of styling change
  • [#0f9028c] Merge pull request #451 from nfdi4plants/Feature_Enable_Sequence_Based_Metadata_Creation
  • [#25c8d3c] include ARCtrl Common props in package for downstream fable transpilation
  • [#97a3d46] move jsonIO dependencies from shared props file directly into project files
  • [#850e889] created "All" Tests project which bundles all other tests
  • [#d5d5201] #433: Add api functions for mandatory dynamic props on some classes
  • [#00c1ca7] add requested changes, add at least some tests
  • [#d35c76a] start working in potential typed ro-crate-json parser
  • [#9f9b9c7] finish up first version of ROCrateObject serialization
  • [#d9fbb33] add ROCrateObject decoder tests
  • [#100fc34] Enable check for metadata sheetname and is meta data sheet
  • [#fc2f7d9] rename ROCrateObject to LDObject
  • [#a0eeeed] Implented review changes
  • [#081ca04] Add cwl model
  • [#ef04da1] Add cwl decode functions
  • [#8cfb04c] Add testing project
  • [#3da6974] change naming of CWL to CWLProcessingUnits
  • [#1932c44] add test strings
  • [#6ae8e47] Add cwl test
  • [#a9e64d3] rewrite tests to be more clear
  • [#a59d834] reorganize tests
  • [#3c5e2f8] dix dockerFile requirement
  • [#3c6c0a3] start separating processunits for better modularity / edge case handling
  • [#13d8a9c] reorder and specify wf specific types
  • [#c7a0082] change in-/outputs to dynamicObj for more flexibility
  • [#9930238] add workflow steps
  • [#0d049b1] add workflow description type
  • [#ccefbff] add steps decoding
  • [#3db45c6] add WorkflowSteps tests
  • [#95dab47] support direct type mappings for inputs and outputs
  • [#0fd5be9] add overflow decoder
  • [#7007a0b] add cmd tool metadata and tests
  • [#3fca0c1] update fsproj
  • [#4ff39f9] Update YAMLicious to version 0.0.2
  • [#ff5af9c] rename Type to Type_ for fable
  • [#379efb4] add failcase to requirements
  • [#44112a8] add wf requirements to decoder
  • [#8b6963e] trim strings for python
  • [#7728ebb] update yamlicious version
  • [#1222f01] add workflow decoding
  • [#83cad3e] add cwl to all test list
  • [#f452622] rename types and tests
  • [#e6d9902] add attachmembers attribute
  • [#070ca96] switch to resizearray and add some comments
  • [#090a214] add optional field to inputs
  • [#de6ef63] change version and class to optional on tool and wf descriptions
  • [#fedc6d4] reorganize modules
  • [#77d1054] make OntologyAnnotation work with localID as TAN
  • [#c3ed011] add template copy tests
  • [#d9e4ae4] small cleanup of CompositeHeader
  • [#68fc64e] add data cell update tests for ArcTable Copy function
  • [#1edfd80] add test against correctly writing valueless ArcTable
  • [#3b0fa76] treat empty strings in OntologyAnnotation as None
  • [#f4cad69] set RO-Crate empty unit test to pending
• Deletions:
  • [#12eb2b9] remove leftover catching of erros in dotnet packaging
  • [#b038cfc] Add '@context' support: - instance methods and static methods for set/tryGet/remove - tests for all classes
  • [#f53e73f] remove try with for dirent initial workdir
  • [#10e40ba] separate processing units and remove module
  • [#b783782] remove type CLWClass :(
  • [#844ca8b] remove underlying modules
• Bugfixes:
  • [#b2b6e8b] Merge pull request #452 from nfdi4plants/nugetFix
  • [#55d360f] fix rebase conflicts, update to DynObj v4.0.3, remove Directory.Build.props
  • [#96231bc] add ROCrateObject writer tests and fix accordingly
  • [#cc77790] hotfix ROCrateObject json writer writing internal keys as fields in json
  • [#63f8cdc] fix references in decode
  • [#cd3cdee] fix cwl type naming
  • [#9c36d2d] fix test fsproj
  • [#bbc5a42] fix optional fields
  • [#86913f6] fix EnvVarRequirement
  • [#27c8037] fix SchemaDefRequirement
  • [#f4a662d] fix SoftwareRequirements
  • [#e44e736] fix workdirReq and resourceReq
  • [#01a3c04] fix direct map decode
  • [#17fabe8] fix for new dynamic obj version
  • [#548b2b7] add metadata and dynobj testing (fix test runs)
  • [#cb87cba] Implement review fix
  • [#b335ddc] test and fix ArcTable copy member deep copying ontology annotations
  • [#b71fb4b] minimal hotfix for writing bodyless tables

2.1.0+99b2659 (Released 2024-10-2)

• Additions:
  • [#28cfd13] add rocrate project
  • [#f71faea] rocrate datamodel wip based on inheritance and single interface
  • [#ef15f35] implement first POC of ISA ROCrate profile
  • [#168ead8] add test project
  • [#2cea57c] update solution
  • [#ccd1805] Unify Inheritance to LDObject
  • [#95cab6f] wip ro-crate tests
  • [#9ef48d7] only use primary constructor
  • [#9deffb7] Add basic tests for I/S/A LDObjects
  • [#4b4a2fc] temp workaround in tests for CSBiology/DynamicObj#25
  • [#f67e78b] Use unblocking version of DynamicObj, introduce runTestProject target
  • [#4e91e9d] finish basic property tests for isa profile types
  • [#8b4368a] Merge pull request #426 from nfdi4plants/ro-crate-data-model
  • [#fdc4773] add tryGetColumnByHeaderBy member and static + tests
  • [#1a5c4d6] Update ArcTable.Tests.fs
  • [#29d1bb2] update to thoth.json.core 0.4.0 and use temporary FsSpreadsheet implementations for js and py
  • [#2e47979] start working on ro-crate-json parsing
  • [#f6afa53] first buildable version after fable restructure
  • [#755879d] move duplicate project references into props files
  • [#93030e9] Make use of Fable.Package.SDK
  • [#99b2659] rename json IO implementations folder to reduce ambiguity in py and javascript packages
• Deletions:
  • [#c71b8a3] correct interface implementation on LDObject, remove interface implementation from Dataset
  • [#c429686] remove javascript and pyton packages from main solution
  • [#3586dee] remove restorelockedmode flag
• Bugfixes:
  • [#9d526b8] add LabProcess tests, fix schematype of LDObject base constructor
  • [#192812d] fix error messages of ROCrate testing utils
  • [#43d65db] various test fixes for Fable logic transition
  • [#8552f9e] fix fable ready packaging and/by update package tags

2.0.1+5e6cc32 (Released 2024-8-29)

• Bugfixes:
  • [#bfaaaf6] fix single dot in paths being interpreted as folder

2.0.0+6c267dd (Released 2024-8-27)

• Additions:
  • [#c250f52] add RO-Crate contexts to docs
  • [#55ad878] Update fsspreadsheet
  • [#263db68] include fable files
  • [#c59b883] Add ARCtrl.ValidationPackages project: - base type model for ValidationPackages and the config file
  • [#cc879fd] Add ARCtrl.Yaml: - Uses YAMLicious - tries to mirror ARCtrl.Json - Encoder/Decoder logic for ValidatioNpackages type model
  • [#c5a9e7c] Add contracts for ValidationPackagesConfig
  • [#532d310] Update to .NET 8, requested PR changes
  • [#137d885] add fable files
  • [#87ed783] add the fable files for real. fable be fablin'
  • [#8b55020] Add classes for index files ✨ #386
  • [#27d259a] Rename ARCtrl.Path to ARCtrl.ArcPathHelper #398
  • [#3e427f1] Add CompositeCell.ToDataCell #404
  • [#bf79874] Unifiy expected functionality of CompositeCell conversion utility #402
  • [#8432507] Add api to include datamap in assay/study #406
  • [#b00b17e] add swate prerelease target
  • [#486d6a7] rmv comment
  • [#d036c31] add first json logic for datamap 🚧
  • [#22b48f5] Add YAML tests for Validation packages, use custom equality
  • [#b510ab2] add a test placeholder -.-
  • [#9c70c5d] Add contract handling for validation_packages.yml to top-level ARC API
  • [#263db27] wip
  • [#6273594] Add instance method tests for ARCtrl.ValidationPackages
  • [#4101dcb] Add Contract tests for ValidationPackagesConfig
  • [#995e2f8] Add topm level api tests for ValidationPackagesConfig
  • [#8de0653] Use literal for yaml keys (also in tests)
  • [#d64f841] Use more Record-like ToString() for ValidationPackages and ValidationpackagesConfig
  • [#88c9b9d] add addColumnFill member function with tests
  • [#e68ca44] Additional tests for AddColumnFill
  • [#df0bda9] Reviewed AddColumnFill member function and tests
  • [#94fba28] add ARC.ToROCrateJsonString member #344
  • [#064b3e0] added functions for checking assay and study metadata sheet names #414
  • [#c5a929d] check identifiers when creating assay and study objects #415
  • [#d40fea9] add CompositeHeader.IsUnique #416
  • [#de4246f] add ArcTable cell accession and manipulation functions
  • [#485d778] make process conversion more robust against different outputs
  • [#0b85fcd] base spreadsheet parsers on string columns
  • [#142b6a2] change main types of spreadsheet parsing collections from list to array
  • [#61eec9f] small adjustments to renaming contract handling
  • [#56f3a7a] add manage-issues.yml
  • [#ee1091f] rework datamap to be represented as a row of records
  • [#2261883] adjust spreadsheet parsing to datamap datamodel change
  • [#aa28494] update templates json parsing
  • [#4358b6a] increase robustness against OntologyAnnotation mutability issues
  • [#44c4ded] add new uri parsing rules and core tests
  • [#758a083] make ArcTable header parsing patterns less strict
  • [#ab38980] add toJsonString extensions members
  • [#108f6f4] start implementing @id in isa json writer logic
  • [#70f9047] finish implementing @id in isa json writer logic
  • [#8bd5d21] add study test file for @id json writer
  • [#85a8e1b] add idmap test case for study
  • [#8c93928] change encoding order of assay properties for isa json parsing
  • [#e138dcc] add useIDReferencing flag to JsonController
  • [#8c192dd] small change in ArcTable.ToString function to make it more robust
  • [#4173454] small speed improvement to ArcTable move column
  • [#fceee84] add column move function to ArcTable
  • [#3620782] added comparison for ontologyannotation and compositeHeader
  • [#0ce1c7c] added fable helper function for comment header creation
  • [#a5f299b] add some more comments to isa processType conversion
  • [#8ef35c2] add comment column json and spreadsheet parser
  • [#ead29a5] add comment column header and process converter
  • [#0b73da2] add study rename logic
  • [#57f3a2e] add rename contract and assay rename logic
  • [#f565309] make ArcTables construction fail for duplicate table names #332
  • [#d986c1a] add some additonal info to pyproject.toml
  • [#99d94a5] reinclude inclusion of source files in fable folders
  • [#d37a71e] Update scripts
  • [#e9c0a2e] Rename one file and rmv most code from md files for maintainability 🔥
  • [#4a2666f] Update GettingStarted.md
  • [#0fab876] Finalize docs 📖
  • [#5194df1] Update EXAMPLE_CreateAssayFile.js
  • [#56ebceb] Update js docs : book:
  • [#a9b4fa1] added tests to tab-json conversion and parsing
  • [#3916bc4] replace "Raw Data File", "Derived Data File" and "Image File" column headers with "Data" #93
  • [#32e1885] add tests for backwards compatability of data headers
  • [#a55279a] add datamap spreadsheet parsing
  • [#239457a] add datamap spreadsheet parser tests
  • [#b54b5a5] add datamap contract handling
  • [#db9fbf8] add datamap contract handling
  • [#890dfd6] add datamap contract handling tests
  • [#08fcb3b] update Data and CompositeCell json parsing
  • [#8c67c36] add json parser and tests for updated data objects
  • [#e5e666e] move data file outside of process folder
  • [#ecd9a17] add pending test for losless data parsing in isa json
  • [#66beafa] update prerelease mechanism
  • [#98c5228] Add ToString overrides for study/investigation
  • [#6b52004] Finalize io controller types for fable ✨
  • [#0ff28ab] rmv old code 🔥
  • [#754cac7] Rename to toStringObject
  • [#98efaa0] add README.md reference to setup.cmd
  • [#d893131] Simplify OntologyAnnotation hashcode and equality ✅
  • [#7d6c107] Add setup script for windows 👷
  • [#232dae3] set test with umlauten pending for python
  • [#c15a2e5] Add ro-crate write tests ✅
  • [#7340910] add some more schema validation tests
  • [#fc8f63e] add native python tests ✅
  • [#e3512c7] Make js native tests pass ✔️
  • [#8d50567] update github CI
  • [#18012b3] rmv leftover folder 🔥
  • [#89f976c] Finish json (for now 🚧)
  • [#5803eb7] start reworking tests for js and py
  • [#766d46a] move ARCtrl contract tests to Contract test project
  • [#3f35262] move template json tests to json test project
  • [#4fc4a07] more work on json 🚧
  • [#cb5da3a] reduce test spreadsheet metadata matching reduction of parser logic
  • [#c885111] More work on json tests 🚧
  • [#adac51c] Add custom ToString for OntologyAnnotation 🎨
  • [#c193629] Start working on tests 🚧
  • [#5f6c65b] distribute template across appropriate projects
  • [#8af7487] Add fable json import type #324 #285
  • [#e3437b2] add ARC RO-Crate serialization
  • [#4cd6d63] finish investigation ro-crate
  • [#39fe3cf] finish moving template json ✨
  • [#c25748a] Finish compressed json logic ✨
  • [#04b097b] Start moving Arc Json logic 🚧
  • [#e710c5a] rework ARCAssay and ArcStudy ISAJson serialization
  • [#437bca3] rework ROCrate process serialization
  • [#19b849a] Start with component logic rework 🚧
  • [#f24259e] finish up ISA-JSON conversion for process types ✨
  • [#a51bfcc] Finish json table logic ✨
  • [#6b670d9] Finish json for shared types ✨
  • [#a29a7f9] start reworking arctrl.json process serialization
  • [#5150773] Start workin on new Json API layer 🚧
  • [#f65d414] start reworking ARCtrl.json project
  • [#b568074] rework ARCtrl.Spreadsheet according to datamodel changes
  • [#2cb9db8] rework ARCtrl.Core types to improve transpiled javascript
  • [#b282dc3] restructure ARCtrl.Core (former ARCtrl.ISA) project
  • [#90520bd] restructure project
  • [#ceefce8] move all filesystem information into filesystem project
  • [#4b2b78f] move UIHelper function into compositecell
  • [#dd69b1f] add addtionalType to ProcessParameterValue
  • [#3bf2a83] WIP 🚧
  • [#f7beae7] Updated tests for jsonld readers. Investigation test still wip.
  • [#d8c4d0a] adapted json export tests for new ro-crate export (Investigation still open)
  • [#d1cbba9] new ro-crate export and context files
  • [#280d3b8] WIP 🚧
  • [#9983642] WIP 🚧
  • [#e7b0015] Updated tests for jsonld readers. Investigation test still wip.
  • [#1cc83f8] adapted json export tests for new ro-crate export (Investigation still open)
  • [#9b0d7b7] new ro-crate export and context files
  • [#0fb24ee] Merge pull request #325 from nfdi4plants/performanceReport
  • [#faaba01] several minor adjustments according to change request
  • [#9c32a3d] update readme with performance report and python links
  • [#9e79685] move performance report into speedtest project
  • [#27aac66] move performance report build targets and create first reports
  • [#41fef58] first draft of performanceReport target
  • [#d64e708] Merge pull request #323 from nfdi4plants/update_js_docs
  • [#1cd68ea] Update
  • [#60d575e] Merge pull request #320 from nfdi4plants/python_integration
  • [#0aefdb2] update documentation and add python docs
  • [#abd3d89] Merge pull request #317 from nfdi4plants/python_integration
  • [#b6e2eca] small change to semver in npm
• Deletions:
  • [#cd1620c] remove entry when delete contract is created for validation packages config file, add related tests
  • [#e50083c] remove UI helper functions #329
  • [#1ce8001] Remove ALL tabs from fsproj files
  • [#f055617] remove erroneous exe output type from testingutils
• Bugfixes:
  • [#ad6f37f] Fix spreadsheet writer for data with freetext 🐛✅ #405
  • [#e358522] fix data column spreadsheet export for mixed columns 🐛✅
  • [#f60e663] fix module references 🐛
  • [#36ab086] Added missing datamap to compressed study json 🐛
  • [#5cfffe9] fix study datamap json key name 🐛
  • [#dc3822f] Fixed json key naming issue, added tests 🐛✅
  • [#a88344a] fix test transpilation for YAML
  • [#ba8d69e] Fix path helper usage after rebase
  • [#d1b9f9b] fix multi annotationTable writing and unify API #423
  • [#621f769] small fix for changes to spreadsheet parsing
  • [#19b6a4c] fix and test rename leading to update contracts when the renamed entity is registered and remove isalight
  • [#4ae6bd0] fixes and tests for updateContracts when assays or studies are added
  • [#4136027] Fix missing fable includes #369
  • [#ff4bad8] fix datamap spreadsheet parsing against tests
  • [#0ead1eb] fix datamap spreadsheet parser against tests
  • [#65274ec] fix tests againsts iri generation changes
  • [#2abd33f] fix tests against @id json writer changes
  • [#f8ae105] some fixes against study idmap test case
  • [#b367d01] fix id table json parsing tests
  • [#3f164c3] small fix for jsnativetests for comment column addition
  • [#6ef030d] Merge pull request #358 from nfdi4plants/fixes
  • [#e2cb695] Fix python docs for contract logic 🐛 #342
  • [#d2d7c53] test and fix ro-crate propertyValue parsing
  • [#8c82636] add tests and fix empty cell parsing behaviour
  • [#30a9bf4] Merge pull request #353 from nfdi4plants/jsonLD-fix
  • [#eebaf4d] rework and fix Spreadsheet reader according to data node changes
  • [#b856188] adjust and fix spreadsheet writing for data node changes
  • [#bc7d952] small fixes for Fable compatability
  • [#4b53ff2] fix data json parser test
  • [#e444944] fix non utf8 json output #334
  • [#025734d] rmv code circumventing fable python bug 🔥
  • [#9f570b3] fix OntologyAnnotation Hashcodes 🐛
  • [#b84919f] Fix json tests ✔️
  • [#d68348e] hotfix js schema validation in tests
  • [#2a999e8] Fix all warnings by burning unused fable reflection helpers 🔥
  • [#562ce65] Fix test tasks still using mocha
  • [#b15a377] fix json parsing DateTime issues
  • [#d5eae8d] several python test fixes
  • [#451ef11] move and fix template hashcode and equality tests
  • [#9da88fe] Template fixes against json and core tests
  • [#97c433e] move and fix spreadsheet Template tests
  • [#fbaa958] fix component name conversion
  • [#6c9123e] fix arctrl.core tests and equality of reworked objects
  • [#da18342] fix rocrate sample and protocol handling
  • [#4b5af05] fix rocrate assay serialization
  • [#cd69fc3] fix wrong encoder/decoder calls ✨
  • [#e053cd9] fix arctrl.core tests
  • [#996ae0e] fix multiple issues with ro-crate json encoding 🐛
  • [#5b0adba] Added fromJsonldString for all ISA-JSON types. Also fixed some bugs.
  • [#2c74476] fix build chain for linux
  • [#295af00] fix tests 🐛

1.2.0+19d850e (Released 2024-3-8)

• Additions:
  • Added Python compatability
  • [#19d850e] several small cleanups according to PR #317 comments
  • [#8becc67] update build project for releasing python package
  • [#df663cb] include python setup in CI
  • [#66b83a2] several small changes to test stack
  • [#3dfaad7] adjustments to web and validation to allowe for python transpilation
  • [#688c628] work on json io support in python
  • [#93b6d94] replace mocha and expecto with pyxpecto
  • [#aa30389] move json schema validation to json tests
  • [#f0bb78d] switch towards using .venv for running transpiled python
  • [#2d35cfb] update Fable and pyxpecto
  • [#32a4128] add hashcode tests
  • [#cc8c116] increase json write test timeout
  • [#3d00621] small adjustments in isa.json
  • [#10c5538] cleanup merge of json-ld and thoth.json
  • [#58b3d5a] merge json-ld changes into thoth.json update changes and refactor
  • [#87ab15d] increase json parsing test timeout
  • [#90c60b9] rework json encoding
  • [#c482c86] finish thoth conversion
  • [#d0a99a3] start reworking json towards net Thoth.Json
  • [#4f77082] Merge pull request #271 from nfdi4plants/jsonld
  • [#3f84e17] increase speed of ARC to Json Type conversion
  • [#5ceb732] bump to 1.1.0
• Bugfixes:
  • [#890048e] set ci fail-fast to false and fix py encoding in windows
  • [#3e403cd] small fix to CI
  • [#b0186f4] small fix to CI
  • [#89aa3c2] fixed python tests to work on all platforms
  • [#4262833] hotfix js webrequest
  • [#f75ce4d] small python tests hotfix
  • [#9385d06] small fixes in python and setup instructions
  • [#b5eaaed] hotfix fable python hashing of person
  • [#556e2bf] fix http requests in python
  • [#c534acf] fix and test comment regex handling for python
  • [#2540056] small fix for compressed json io stringtable conversion fable-compiler/Fable#3771
  • [#92c72ee] array fixes in python compilation
  • [#b55d360] fix and finish up thoth migration

1.1.0+6309e03 (Released 2024-2-15)

• Additions:
  • [#544ffdc] add some additional information to failing spreadsheet parsers #306
  • [#ee67104] create first version of compressed arctable json exporter
  • [#8b36c55] implement stringtable in arctable json compression
  • [#bb98bf4] add compressed study and assay json encoders
  • [#6c5aa85] add tests for compressed json
  • [#689f60c] add more efficient compressed column encoding
  • [#a9fbdf6] add rangeEncoding to compressed json
  • [#8635d76] Improve speed of GetHashCode
  • [#ed0e78e] add GetUpdateContracts functionality
  • [#73ed27e] small clarification on getUpdateContracts
  • [#787368e] reinclude fable reference in isa.json.fsproj
• Deletions:
  • [#f87b4b6] removed unused self reference in assay and study constructors
• Bugfixes:
  • [#c619cd9] small fix to compressed arcTable json
  • [#9d3392d] add update contract tests and fix against them

1.0.7+14c14a9 (Released 2024-1-30)

• Additions:
  • [#14c14a9] update FsSpreadsheet reference
  • [#1d8d7b7] small changes to fillmissing and performance tests
  • [#68c65d0] improve design of speed tests
  • [#d592cf3] small speed increase of setCell
  • [#38fe3a9] rework fillMissing
  • [#ddb8238] improve speed of ArcTable.AddRows
• Bugfixes:
  • [#2caadb7] small fix to addRows

1.0.6+c6d86b1 (Released 2024-1-26)

• Additions:
  • [#c6d86b1] small performance improvement for reading ARCs
  • [#3f8c788] add case for speedtest project
  • [#a90a1f1] improve and test speed of investigation file writer
  • [#123f209] Merge pull request #299 from nfdi4plants/small_cleanup
  • [#70d3c85] Merge pull request #297 from nfdi4plants/table_join_296
  • [#13428ca] Revert unintended change in default!
  • [#66b15f6] Update to v1.0.5
• Deletions:
  • [#d121e5c] remove playground and move speedtest folders

1.0.5+b21e3bc (Released 2024-1-17)

• Additions:
  • [#b21e3bc] Extend ArcTable.Join ✨✅
  • [#a112468] Update readme badge
  • [#a0144e1] Merge pull request #295 from nfdi4plants/Freymaurer-patch-1
  • [#9e5c1f6] Update README.md
  • [#6e0755b] update and release version 1.0.4
• Bugfixes:
  • [#8dd99e8] Merge pull request #294 from nfdi4plants/fix_annotationValue_read

1.0.4+167fae8 (Released 2024-1-15)

• Additions:
  • [#167fae8] add json functions for better function names in js ✨

1.0.3+533dab0 (Released 2024-1-15)

• Additions:
  • [#208839a] change annotationValue of Ontology Annotation to string
  • [#533dab0] Add tests for edgecase ✅
• Bugfixes:
  • [#d42faaf] Fix template read issue. annotationvalue not correctly read 🐛

1.0.2+533dab0 (Released 2024-1-15)

• Additions:
  • [#cc7f35f] add speedtest and make some small experimental changes
  • [#e85dba4] make some validation and checks optional for speed improvements
  • [#208839a] change annotationValue of Ontology Annotation to string
  • [#a1921ef] make fillmissingcells optional for addcolumns
  • [#2aca309] Make ArcStudy IO performance test more strict

1.0.1+5576d43 (Released 2023-12-21)

• Additions:
  • [#66ff8f4] improve github ci
• Bugfixes:
  • [#443272b] Fix .fsproj files
  • [#febb0f6] fix npm release target

1.0.0+b42bd6f (Released 2023-12-21)

• Additions:
  • Complete overhaul of the API.
  • Shifted focus from only ISA to include full ARC.
  • Included Fable compilation to Javascript as first citizen design principles.
  • No direct filesystem access but contract based IO, which allows language agnostic IO.

0.7.0+ac83329 (Released 2023-1-26)

• Additions:
  • latest commit #ac83329
  • [#ac83329] impove QNode usability with documentation

0.6.1+7de6163 (Released 2022-12-7)

• Additions:
  • latest commit #7de6163
  • [#477edad] Renamed src/ISADotnet to src/ISADotNet for linux build due to file name case sensitivity.
  • [#325cb91] add json schema validation functions
  • [#94ef9e5] add isFatal check to json schema validation
  • [#d496857] ease constraints of json schema validation
  • [#7db8fae] validate json against json schema from HLWeil fork
  • [#fdf248d] move jsonSchemaValidation in its own Repo
  • [#5f133db] update dotnet version in cli
  • [#8531aac] add unit retrieval functions to API
  • [#372e07f] rename xlsx metadata headers nfdi4plants/ARCCommander#150
• Bugfixes:
  • [#168890f] fix json schema validation use njonschema instead
  • [#9c66fa8] fix json test files to actually adhere to json schema
  • [#d79605c] fix datamodel according to json schema validation
  • [#8f63206] fix study xlsx reader creating empty lists #71
  • [#6d5ee0c] make DAG creation more robust against missing names fix #51

0.6.0+2150bc9 (Released 2022-9-7)

• Additions:
  • latest commit #2150bc9
  • harmonize xlsx IO with Swate 0.6.0 release
  • add OBO ontology IO
  • extend ontological reasoning
  • extend components and protocol types
  • [#118f404] add simple ontological reasoning for protocol type
  • [#bdf85b2] adjust assay xlsx header renumbering
  • [#59cfdaf] small improvements to Ontology Annotation and Component type
  • [#94b6059] drop protocol rowIndex when calculating rowRange
  • [#4c050d1] revert term accession number changes
  • [#f8f94c6] add components to querymodel and assay xlsx writing
  • [#9b85296] add protocol type and protocol ref to assay and study xlsx writing
  • [#9cb34af] add component to querymodel
  • [#1c66f1f] refactor return values of assay and study xlsx file readers
  • [#1a981e9] add component and protocoltype parsers to assay xlsx table reader
  • [#75afe60] add component and protocol type parser functions
  • [#084cee1] add component casting functions
  • [#ba490a3] added inline documentation for querymodel methods
  • [#f2e05eb] improve Querymodel documentation
  • [#6eb5c44] add additional ontology helper functions to querymodel
  • [#11ef6b8] add ontology search functions
  • [#99e3ebb] add isA and xref search on oboOntology
  • [#af680ec] integrate OBO IO and reasoning
  • [#5ff98d8] extend querymodel by basic ontology logic guided querying
• Bugfixes:
  • [#4b99f26] fix ontologyannotation equality for empty objects
  • [#e6966aa] fix json parsing
  • [#d4987fe] fix assay and study file reading tables
  • [#f9bd7f4] fix component json parsing
  • [#86e1b46] fix assay file writing issues #62 #63 #64
  • [#7385792] fix study and assay xlsx write error

0.5.4+262f787 (Released 2022-7-12)

• Additions:
  • latest commit #262f787
  • [#262f787] improve Querymodel by adding Protocol specific functions
  • [#60e189f] add basic ontology reasoning to QueryModel
  • [#1ba8b0c] move Querymodel into own project

0.5.3+dc96afe (Released 2022-6-29)

• Additions:
  • latest commit #dc96afe
  • [#3b4eec6] add metadata sheets to assay and study xlsx writing
  • [#dc96afe] add QInvestigation to querymodel

0.5.2+43177ae (Released 2022-6-24)

• Additions:
  • latest commit #43177ae
  • [#20b36d5] update readme with querymodel examples
  • [#6640826] add assay xlsx file writer
  • [#113767c] finish up assay xlsx file writer

0.5.1+af3dc20 (Released 2022-6-15)

• Additions:
  • latest commit #af3dc20
• Bugfixes:
  • [#af3dc20] fix querymodel node updating

0.5.0+0646fa9 (Released 2022-6-15)

• Additions:
  • latest commit #0646fa9
  • QueryModel
  • Increase verbosity
  • Fixes
  • [#8701a22] add additional methods to QueryModel
  • [#be34819] add study type to query model
  • [#8b7f1c7] improve query model value retrieval
  • [#ba81b27] add Query model capabilities
  • [#a6470f1] add QProcessSequence type for QueryModel
  • [#2a9613d] small improvement to assay xlsx reading error messaging
  • [#97406b5] Add regex unit tests ✅
  • [#0404cbf] Increase flexibility of regex
  • [#d04650f] move ValueIndex file from ISADotNet.XLSX into ISADotNet
  • [#9787518] rework Assay query model
  • [#19cb0f6] adjust assay file header parsing -can now parse brackets inside brackets -now ignores numbers
  • [#06f1078] increase assay file io fail safety
  • [#74b5b0f] increase xlsx IO verbosity
  • [#b3a0a64] include empty study by default when writing investigation file
  • [#314acc0] extend assay query model methods
  • [#372d5d9] start working on assay query model
  • [#e8e0175] add study xlsx file io
  • [#5e27192] switch to FsSpreadsheet for ExcelIO
  • [#8c788d7] add Process IO functions
  • [#269ce79] assay xlsx file reader always assumes data type for data column
  • [#4105894] add Assay Metadatasheet manipulation functions
• Deletions:
  • [#476105e] temporarily remove linux CI to avoid spam #38 this should definitely be looked into again at a later point
• Bugfixes:
  • [#566115d] fix assay metadatasheet not being read correctly
  • [#f343175] dag vizualization now makes edges distinct per source target pair quick fix for #52
  • [#d1c671d] fix outputByCharacterstic getter function fixes #50
  • [#2101589] fix assay reading no processes as Some empty lists fixes #54

0.4.0+2a9311b (Released 2021-10-22)

• Additions:
  • latest commit #2a9311b
  • [#2a9311b] finalize first DAG visualization draft ✨
  • [#e5ad37a] assign characterstics from assay.xlsx files only to inputs #43
  • [#eb985e3] create first DAG creation function
  • [#a9eddd6] add schema type for DAG
  • [#f60edbd] adjust xlsx io to FSharpSpreadsheetML 0.0.7
  • [#2147cb9] prepare assay xlsx file io for FABLE compatability
  • [#78a667c] add helper methods for assay file value ordering
  • [#ea12093] adjust investigation.xlsx file io for FABLE compatabiity
  • [#9c52b6c] make assay.xlsx file reader save value column ordering
  • [#0b8e26e] add helper functions for assayFile Column Ordering
  • [#e1d1f1a] use old formatted printing for compatibility in ISADotNet.XLSX
  • [#ac15be6] use old formatted printing for compatibility
  • [#c80ec0a] Add check to exclude whitespaces from being valid values (Issue #37).
  • [#0847b38] init ISADotNet.Viz
• Bugfixes:
  • [#3fd7fca] several fixes for xlsx io
  • [#edeed88] Update tan issue fix (Issue #35).
  • [#20cff8c] Update worksheet name fix (Issue #34).
  • [#f989114] Fix wrong term accessions (Issue #35).
  • [#4f851d9] Fix worksheet naming bug in CommonAPI (Issue #34).
  • [#f88320f] fix rowMajorAssay to maintain value order

0.3.3+2da8c3a (Released 2021-9-10)

• Additions:
  • latest commit #2da8c3a
• Bugfixes:
  • [#2da8c3a] fix prerelease targets

0.3.2+4233b78 (Released 2021-9-9)

• Additions:
  • latest commit #4233b78
  • [#4233b78] move SwateCustomXml datamodel to ISADotNet
  • [#f7511ad] increase function parameter consistency
  • [#249f1af] add ISA Assay Common API parser
  • [#9890b6a] Unify naming as requested (PR #31).
  • [#a48d571] Add FromStringWithNumber for ProtocolParameter (Issue #24).
  • [#b511949] add isa xlsx stream reader/writer functions
  • [#91e9ea5] Add GetName, GetNameWithNumber for xxValue DataModel (Issue #24).
  • [#035ed55] Add FromString, FromStringWithNumber for OntologyAnnotation, Factor, MaterialAttribute (Issue #24)
  • [#6f883e6] Add GetValue logic for FactorValue, MaterialAttributeValue, ProcessParameterValue (Issue #24)
  • [#01db12b] add json readers/writers

0.3.0+993781f (Released 2021-9-6)

• Additions:
  • latest commit #993781f
  • [#993781f] small adjustment to assay.xlsx reader
  • [#81a8130] reduce protocol splitting complexity of assay.xlsx reader
  • [#700bf6d] update tests to match assay.xlsx reader changes
  • [#d65a86b] adjust assay.xlsx header parsers to new swate format

0.2.6+0fa5cb5 (Released 2021-8-25)

• Additions:
  • latest commit #0fa5cb5
  • [#a5b970f] add pretty printer example script
• Bugfixes:
  • [#17200f7] fix missing commas in json deserializer
  • [#24f9872] Fix Person.removeByFullName error

0.2.5+02f30a0 (Released 2021-3-26)

• Additions:
  • latest commit #02f30a0
  • [#6c23554] add compact pretty printers
  • [#ac52305] add data column reader to assay reader
  • [#c4f6df3] add cyjs assay visualisation script
  • [#327d9eb] add assay file data column parser
  • [#f783a15] bump to 0.2.4
• Bugfixes:
  • [#02f30a0] fix process compact printer

0.2.4+1c7ed14 (Released 2021-3-24)

• Additions:
  • latest commit #1c7ed14
  • [#0c9b3e9] bump to 0.2.3
• Bugfixes:
  • [#1c7ed14] fix: remove printf from assay file reader

0.2.3+3536cd3 (Released 2021-3-23)

• Additions:
  • latest commit #3536cd3
• Bugfixes:
  • [#3536cd3] fix assay file reader sample updating

0.2.2+83de052 (Released 2021-3-22)

• Additions:
  • latest commit #83de052
  • [#c44316c] add process sequence convencience functions
  • [#f62e7be] make assay file parser take column header number
  • [#e2c267f] add functions for accessing numbered parameters
• Bugfixes:
  • [#83de052] fix process filterByProtocolName

0.2.1+ae00b13 (Released 2021-3-22)

• Additions:
  • latest commit #ae00b13
  • ISAXlsx Assay File Reader Tests
  • [#93e32c4] bump to 0.2.0
  • [#e6d53bf] rename assay file node getter functions
  • [#9b4884c] small adjustemt to assay file sample column handling
  • [#261e28a] add assay file io tests
  • [#1cc8a95] add assay file io tests
  • [#cd74341] add assay sample getter functions
  • Assay Parameters accession functions
  • [#ddab453] add additional assay parameter convenience functions
  • [#622b834] add assay factors and characteristics convenience functions
  • [#ae00b13] add parameter value parsing functions
• Bugfixes:
  • ISAXlsx Assay File Reader Fixes
  • [#2886bb5] fix assay file reader crashing when no custom xml is present closes #18
  • [#bc848e7] fix assay file io sample merging

0.2.0+1c7c8c6 (Released 2021-3-7)

• Additions:
  • latest commit #1c7c8c6
  • Add ISAXlsx Assay File Reader
  • [#9398ccb] add assay file io tests
  • [#9a86d09] add swate customXml parsing
  • [#7c9340b] comment Assay File IO functions and modules
  • [#2a62081] add sample alignment to assay file reader
  • [#1ba9aa9] add protocol splitting to assay file reader
  • [#50c2411] tidy up ISADotNet.XLSX library structure
  • [#dc98abe] add UpdateByExistingAppendLists option to record type updater
  • [#6cedda2] add assay file reader
  • [#0e1b990] add assayFile MetaDataReader and tests
  • [#e33517b] add assayfile process parsing functions
  • [#8de1b95] add additional assay file column parsers
  • [#803f642] add assay file parameter reading
• Bugfixes:
  • [#3af8dcd] fix assay file parameter values being parsed incorrectly
  • [#d1e7aef] fix AssayFileReader switching table headers

0.1.1+93e1117 (Released 2021-2-17)

• Additions:
  • latest commit #93e1117
  • [#93e1117] add assayFile init function
  • [#4c3e434] make investigation file prefixes optional
  • [#235b714] Create README.md

0.1.0+5f34043 (Released 2021-2-8)

• Additions:
  • latest commit #5f34043
  • [#9b00412] Modernize library structure
  • [#7f126ed] Modernize library structure
  • [#400211a] Apply requested changes
  • [#a05b17e] Update global.json to "latestMajor"
  • [#23a6d87] Add --noapidocs flag to docs tasks
  • [#ad13b35] Merge pull request #9 from Freymaurer/developer
  • [#79b9bc2] Merge pull request #13 from Freymaurer/developer
  • [#5f34043] Merge pull request #14 from Freymaurer/developer
• Bugfixes:
  • [#fa4d1c5] fix remove functions fixes #8

0.0.4+2f78a5fa (Released 2023-8-3)

• Additions:
  • latest commit #2f78a5fa
  • • Add append optional list functionality when updating record types
  • • Add tests
  • • Soften version constraint of FSharp.Core package dependancy

0.0.2 (Released 2023-8-3)

* Increased the minimum version of the System.Json.Text dependancy
* Minor additions to the API functions

0.0.1 (Released 2023-8-3)

* Moved Project from nfdi4Plants/ArcCommander
* Full ISA Datamodel
* Reworked API
* ISA XLSX Investigation file parser
* Added ISA Json IO