3.1.0+a36ace7f (Released 2026-6-22)
Additions:
[#c9df71d5 ] add forceOverwrite flag to write contract handling
[#c38d4365 ] add start_as_task to python imports
[#2dc34a94 ] Add tryGetTable + tests
[#fadb506d ] add .swp files to gitignore
Deletions:
[#28bd9b9a ] remove text file overwriting in ARC.GetWriteContracts()
Bugfixes:
[#722239c8 ] fix contract io tests writing into same test file
[#49692b8d ] last fixes to GetWriteContracts fixes
[#9ed0594d ] fix empty datamap returning HashCode 0
[#56c51317 ] fixed changes
3.0.5+48b19118 (Released 2026-4-20)
Additions:
Bugfixes:
[#8966d3c2 ] hotfix CompositeCell Hash clashes in Javascript through linear probing
3.0.4+eb91229b (Released 2026-3-30)
Additions:
[#bb749d61 ] add dockerRun options and ID
[#80729c7a ] add tests for complex wf and dockerRun/ID
[#cf3460c2 ] update yamlicious and de/encoders to match new scalar behavior
[#401303f5 ] add support for union-valued CWL array items
Bugfixes:
3.0.3+681187d0 (Released 2026-3-3) 3.0.2+b00b50cf (Released 2026-3-2)
Additions:
[#4ab85c26 ] add function to create full LDGraph from ARC
[#28a96a1d ] update YAMLicious version
Bugfixes:
[#2c1e1de7 ] fix sdDatePublished key name #582
3.0.1+a6b1138f (Released 2026-2-27) 3.0.0+3de66bcb (Released 2026-2-19)
Additions:
[#c2d0f529 ] add intent field to all processing units
[#3c4bd8c5 ] add deeply nested step dependency tests
[#dea546f5 ] add empty input edge case tests
[#27d623dc ] include operations in related files
[#09f7bec7 ] add handling of step reuse
[#e8e9e974 ] add pending tests for minor missing spec cases
[#43ee136b ] add pending tests for reuse of the same unit in steps across wfs
[#9d166c02 ] compare example generated graphs to expected graphs
[#7fd7ab10 ] update graph readme
[#0d650158 ] add comments
[#6a181b3e ] move yamlobjects to utils
[#4f30855c ] create mkstep helper
[#55c1c698 ] replace alternate constructor with static member
[#3768e21f ] add create functions for graph types
[#92bf4274 ] move requirement defaults
[#c2ea2f3b ] rename and reformat testlist
[#6bca58c5 ] add workflowgraph to py and js solution
[#6d6510fa ] add edge-case coverage for cwl requirements
[#3b5ac1a0 ] harden cwl requirement edge-case handling
[#f0189b71 ] add/update tests for req/hint extensions
[#6404ea26 ] extend cwl requirement and hint models
[#23cf7c46 ] add comments to graph functions
[#9ab37570 ] move extension to main type
[#644659d3 ] update cwl tests for payload requirements
[#9a981e17 ] add directive and payload requirement tests
[#dc0d1e36 ] encode canonical requirement directive forms
[#e454e00a ] decode schemasalad directives in requirements
[#7968774b ] add schemasalad requirement models
[#fca5d589 ] add secondary path/missing branch tests
[#44dac4a8 ] add mutation and initialworkdir tests
[#e98235b6 ] add helpers to update processingunits/wfsteps
[#835a1209 ] enable more options for initialworkdir
[#74232cf3 ] add set to inputs/outputs
[#3914b3be ] add fable packaging tags
[#0479ac89 ] update path handling for linux
[#ed65dddb ] extend workflowgraph tests
[#515fcb1d ] tighten graph rendering
[#be8bd3b6 ] restore node shapes
[#0f89c1fc ] normalize pu labels
[#db89c010 ] reconnect workflow links
[#7a272cf9 ] group io in mermaid
[#d65bd658 ] simplify mermaid rendering
[#08926004 ] refine workflowgraph core
[#09204928 ] document workflowgraph outputs
[#ee3734d8 ] add workflowgraph tests
[#0eff24b1 ] wire workflowgraph in arctrl
[#23ffa64a ] add workflowgraph core
[#6f9a2a96 ] document expressiontool mapping
[#ea8567aa ] add expressiontool decode encode tests
[#c33df386 ] wire expressiontool in workflow conversion
[#8a410554 ] add expressiontool processing unit support
[#d0dc323f ] add more tests for implemented functions and roundtrips
[#54eeff18 ] add tests for new fields and decode/encode logic
[#5a58d4f2 ] simplify run resolver
[#c95ff9fc ] encode/decode added fields, unify hint/requirement order
[#ece2aa99 ] add wfsteps outside for safer type implementation
[#08d877e1 ] add missing fields
[#08fbadf2 ] add CWLRunResolver to py and js projects
[#9993bc0f ] add tests for full run parsing and update wf parsing tests
[#819f6e0d ] add wf/run tests for data model
[#8bde74ec ] move real wf test files and add contract samples
[#7fe00866 ] move step resolver to separate file to us it uniformly, add relative path handling
[#07deade2 ] test parsing of workflowsteps from files during conversion
[#3aeb9b90 ] update wf tests for wfsteps
[#cbad414f ] add recursive workflow step parsing to conversion
[#20a71add ] sanitize yaml, decode/encode for updated wfsteps
[#fd9f115c ] complete workflowsteps fields and types
[#dbb170cf ] add filebased test workflow
[#65691231 ] Add support for CWL requirements mapping and JSON syntax
[#28c7a2c0 ] add new empty array option after yamlicious changes
[#d9d1180d ] apply helper functions in all relevant tests
[#bb511441 ] further improve error handling
[#8b0b9f52 ] explain workaround and enum order
[#c07fcadc ] add helper functions for cwl test type creation
[#a6c3fde5 ] change to string interpolation
[#92811b18 ] add tests for edge cases
[#9c5de864 ] move typechecks to encode
[#14c614b4 ] improve error handling
[#77e7a7d5 ] encode function for yaml flowstyle, which yamlicious can now read
[#47cd6a79 ] decompose to yaml flowstyle, which yamlicious can now read
[#7b4266bc ] update yamlicious
[#8145af40 ] add cwl to json encode/decode roundtrip tests
[#70065e24 ] add missing custom equality
[#fd6a12ee ] include yamlControler in .fsproj
[#0ac443e5 ] add cwl type ro-crate conversion tests
[#59be9947 ] simplify array handling and add json converter for complex types
[#2ff2d825 ] add cwl types to json and py
[#c90a701b ] add yamlcontroler
Deletions:
[#84b040dc ] remove unused matchcase
[#f4c37415 ] remove unused options from step creat function
[#e7d9eb76 ] remove legacy dockerreq decode and apply create function everywhere
[#fac25294 ] merge and then remove workflowstepops
[#f093535a ] remove private
[#ed415edc ] remove namespace from test
[#948ee96c ] Delete tests/TestingUtils/TestObjects.IO/SimpleARCWithCWL/.gitignore
[#e5ee5ab5 ] remove duplicate normalizePath
Bugfixes:
[#466aa14d ] fix spec cases and add abstract cwl (operation)
[#349378a4 ] try fix path error for linux
[#01e45dd0 ] fix naming consitency and redundant function duplication
[#c2835779 ] refresh cwl requirement test fixtures
[#4a777659 ] fix path for wf resolver handling
[#96f47ee1 ] fix cwl file location
[#3774becb ] update cwl fixture paths
[#ccdd4915 ] add simplearcwithcwl fixture
[#2ca57bde ] move cwl sample fixtures
[#1a58f0eb ] add expressiontool test fixtures
[#25864586 ] fix match guards and req/hint ordering in steps
[#e04f2da8 ] fix error handling
[#27cf55cc ] fix record schema reading
[#2bd868a2 ] fix handling of simple types within complex types
[#445dd29a ] fix transpilation issues
3.0.0-beta.16+3d215088 (Released 2026-1-15)
Additions:
[#841914d0 ] add custom equaltiy to cwltype and mutually recursive types
[#eca0b6f2 ] add missing properties to main wf of run, expand tests
[#12e8d516 ] change naming and use static members for property names
[#d7fa4d7d ] write creators and dateCreated to WorkflowProtocol as well
[#c0b8da3a ] add checks for mandatory parent profile fields
[#b9e89003 ] optionally allow skipping broken runs and worklows for RO-Crate conversion
[#e0315b0c ] set dataplant as workflow publisher during conversion
[#5a74153b ] change name to take from titel to match mapping file
[#b47526de ] take name and description from run/wf, make license mandatory
[#23a815fa ] add automatic workflow and run profile export
[#4d4ad978 ] add files and workflow to hasParts during run conversion
[#7ad8b0e4 ] add workflow to hasParts of workflow in conversion
[#cd97732e ] add mainEntity during conversion to rocrate run
[#45d2ba15 ] Unify CWL type system with mutual recursion and Union support
[#b78841c1 ] allow empty outputs, cleanup
[#ec97b23d ] Add support for records
[#34bc061e ] add list decoding/encoding for source in inputStep
[#b2cafe13 ] add decoders to processing units
[#df648f1b ] bump yamlicious version for multiline doc handling
[#9db593ec ] update logo
[#5d6abf2a ] Rename tests DataMap to Datamap in Tests
Deletions:
[#d4fbac35 ] remove print
[#4f6ca3dc ] add main entityCheck and fallback for executingLabProtocol during run decomposition
[#b0365fea ] Delete duplicate tests/TestingUtils/Descriptions.fs
Bugfixes:
[#d028b933 ] fix description exected newlines
[#5d1f000f ] add fixes for cwl doc and label reading
3.0.0-beta.15+b5d48ed9 (Released 2025-12-4)
Additions:
[#5d6abf2a ] Rename tests DataMap to Datamap in Tests
Bugfixes:
[#8fb1cbac ] test and fix bug where nullValues could not be parsed from JSON-LD
[#92ccbd20 ] fix arc run conversion failing for matching table and cwl input names
[#ae82d6d5 ] fix naming of DataMap to Datamap
[#f3677f5b ] test and fix LDNode parsing of bool properties
3.0.0-beta.14+b22a48f6 (Released 2025-12-3) * Rename DataMap to Datamap!
Additions:
[#5b41cc0b ] bump to 3.0.0-beta.13
[#10a9e512 ] make columnIndex point to newly created term #507
[#20e5041b ] add Datamap and DataContext to index.ts and init .py
[#61ad36f8 ] change propertyNames of Datamap from uppercase to lowercase
[#b22a48f6 ] Rename DataMap references to Datamap
Bugfixes:
[#ae82d6d5 ] fix naming of DataMap to Datamap
[#f3677f5b ] test and fix LDNode parsing of bool properties
3.0.0-beta.13+46b2f157 (Released 2025-11-25) * Implement ARC WR RO-Crate profile
Additions:
[#1ead1b1b ] add ARC wr ro crate model (WIP)
[#745b237d ] add formal parameter
[#da3919f1 ] add computational workflow
[#73ca8dc4 ] add software source code profile
[#1a3a9346 ] add createaction
[#e3deae4b ] add workflowprotocol
[#2834a60b ] add ARCWorkflow to Dataset
[#9b872b48 ] add arcrun
[#68fe82a8 ] add workflowinvocation
[#f996717d ] implement first approach to conversion of Workflow object
[#a8614a50 ] rename CWL Description to ProcessingUnit and add parsers
[#2ef72329 ] add CWLProcessingUnit as property to ArcRun and ArcWorkflow
[#2fd83c0c ] include cwl files in ARC Scaffold parsing
[#a9e08c73 ] add workflow and run cwl parsing tests
[#3da2226c ] add CWLParameterReference type
[#b26929d5 ] add YAML parameter file parsing
[#3ab9f11e ] add direct parameterfile decode function
[#57336cd3 ] add cwl yml input parameters to run object and arc parsing
[#c99f8110 ] first version of parsing to arc-wr-ro-crate
[#6292ada2 ] add basic WR to RO-Crate conversion tests
[#0c76db22 ] update rocrate workflow and run compose functions to include fs information
[#4c202c6a ] various changes to ROCrate conversion of CWLInputs
[#6b33fc55 ] improve cwl ro-crate conversion to include parameter types
[#f9e657ec ] add some cwl test objects and ro-crate conversion tests
[#cb330cac ] finish up first batch of cwl ro-crate parser tests
[#f5645713 ] add some basic ro-crate to scaffold workflow converter functions
[#8e891c0f ] finish first implementation to workflow ro-crate reader
[#d675282c ] add ArcWorkflow ROCrate Conversion tests
[#57ac6cef ] finish up first version of workflow and run ro-crate conversion and roundabout tests
[#76b10538 ] some restructuring of the ro-crate types and conversion functions
[#eac84fed ] add setup instructions and script for unix
[#e2ad4b91 ] add default programmingLanguages for RO-Crate export
[#db5f90e3 ] make ldcontext resolove http and https as interchangeable
[#4834ec27 ] update index.ts and rocrate.py
Deletions:
[#14cda2bd ] remove some unnecessary fields from ROCrate Workflow
Bugfixes:
[#3ecb5288 ] fix tests for dotnet sequences
[#21d2e174 ] some fixes and adjustments to JSON-LD base types
[#c028132a ] fix and add formalparameter ro-crate conversion tests
[#f704bd13 ] add first cwlROCrate roundabout tests and according fixes
[#a15d8c76 ] additional fixes towards Workflow Invocation conversion
[#63325d45 ] fix workflowinvcation writing test failing
[#6d0b67ec ] small fix to createAction URL and WorkflowInput additionalType
[#14afa248 ] fix FormalParameter lacking additional type property when being written
[#2791d96e ] fix ld context term resolving for compacted https insensitity
[#a5409491 ] update ro-crate context from1.2-DRAFT to 1.2 and fix bioschemas property urls
[#cc788b37 ] fix test failing for updated ro-crate context
3.0.0-beta.12+cf08594b (Released 2025-11-5)
Additions:
Bugfixes:
[#aedf8cba ] Fix space in error message for invalid identifier
3.0.0-beta.11+adde9c7b (Released 2025-10-31)
Additions:
Bugfixes:
[#29544557 ] fix read license always containing default path
3.0.0-beta.10+fe1c178d (Released 2025-10-30)
Additions:
[#33dc55e8 ] make autofill of sparse columns default behaviour in ArcTable column getters
3.0.0-beta.9+3aef1ad3 (Released 2025-10-28)
Deletions:
[#0671bbb9 ] remove cwl references from top level ARC object
Bugfixes:
[#342953d2 ] add tests and fixes for run and workflow rename and remove functionality
3.0.0-beta.8+1e8ec499 (Released 2025-10-28)
Bugfixes:
[#1e8ec499 ] Apply several hotfixes around workflow and run 🐛
3.0.0-beta.7+e314b7b2 (Released 2025-10-27) 3.0.0-beta.6+0b552d70 (Released 2025-10-27)
Additions:
[#6b4e11ce ] bump to 3.0.0-beta.5
[#38ffdcd8 ] Add license logic to ARC class + tests ✨
[#d9d1dcf2 ] license object in ROCrate is CreativeWork and Scaffold parser checks more different potential License paths
[#2b59ea8b ] add license rename contract function
Deletions:
[#0b552d70 ] remove treeshake from typescript bundling to include more functions in package
Bugfixes:
[#c1dda5a9 ] fix ro-crate license parser
[#0abcddb0 ] add additional license parsing tests and according fixes
3.0.0-beta.5+f74b2d99 (Released 2025-10-23)
Additions:
[#70cdacff ] bump to 3.0.0-beta.4
[#e8a74ffa ] Implement run and workflow json methods
[#168dec1b ] various small changes to run and workflow json parsing according to PR review #558
3.0.0-beta.4+79c230b2 (Released 2025-10-22)
Additions:
[#7fcf7d3a ] bump to 3.0.0-beta.3
[#c68f3ec8 ] Add .zenodo.json for metadata and contributors
[#d9124d2a ] Update contributors with project member types
[#4dccaaa1 ] various small changes to citability
[#ca57190d ] Add Mühlhaus, Timo to contributors in .zenodo.json
[#c861dbdf ] make OntologyAnnotation equality TSR case insensitive
[#4fe6c226 ] add issue id to ldgraph parser test name
[#3f77dd54 ] update FsSpreadsheet dependency to 7.0.0
[#a6adeb92 ] Add ToJsonString and FromJsonString to datamap
[#869d6e09 ] Add unit tests
[#51d26af9 ] stop vite minifying ts source code for packaging
[#5b84a774 ] improve access to non-manually exported typescript functions
3.0.0-beta.3+2f33c59 (Released 2025-7-29)
Additions:
[#e683d69 ] add --fail-on-focused-tests to dotnet pyxpecto tests
[#70ab794 ] streamline build logic ✨
[#43757e6 ] add test files
[#52ba8df ] implement and test composeFile considering FileSystem
[#c7ca1bb ] add tryGetPath function to FileSystemTree
[#f648699 ] establish async dynamic import logic ✅
Bugfixes:
[#386560b ] test and fix rocrate containing enough information to reconstruct annotated files and folder in FileSystemTree
3.0.0-beta.2+e74c9f8 (Released 2025-7-25)
Additions:
[#2290d57 ] add ldgraph and ldnode to JsonController
[#7d14d88 ] minimal implementation of reading filepaths from RO-Crate
[#eccb4f8 ] fix ro_crate writig duplicating data file paths #513
3.0.0-beta.1+a98b25f (Released 2025-7-22)
Additions:
[#4a51552 ] add tests to reproduce isa and rocrate json import error #512
[#8d97118 ] expose default .gitattributes contract equal to .gitignore #534
[#589322a ] continue reworking ArcTable according to change requests in #537
[#995e668 ] continue reworking ArcTable according to change requests in #537
[#70ccc25 ] small performance improvement to ArcTable.GetColumn
[#0a69048 ] extend and run performance tests
[#02efde4 ] adjust ArcTable json parsing according to changes in ArcTable structure
[#8bdd981 ] update ArcTable compressed json parsing
[#8f127ba ] add and run performance tests
[#7be7abf ] update default ArcTable json parsing
[#86e2a22 ] heavily improve performance of ArcTable addRow and addColumn
[#5213ffd ] improve performance of Annotation Table Read
[#0713287 ] change OntologyAnnotation TanInfo computation time
[#913ee6e ] implement fillmissingcells
[#3711615 ] adjust tests according to ArcTable rework
[#10671d5 ] finish up first version of ArcTable rework in source code
[#df14ca0 ] start reworking ArcTable references
[#233344d ] finish up first version of reworked ArcTable
[#179bcdb ] finish up first version of ArcTableValues type
[#d3f27b1 ] continue reworking arcTable by adding ArcTableValues type
[#0651f02 ] Start working on ArcTable redesign ✨
[#ceb6c2b ] Add (more) tests for ArcInvestigation functionality
[#e87294f ] Add in-memory spreadsheet file for tests
[#b847725 ] Update fromRows function for ArcInvestigation module
[#e0e5f6e ] improve performance import to include preparation and repeated testing
[#81d65c5 ] force python dict usage in compressed json writing
[#1a73116 ] improve LDContext Dictionary access speed
[#311603c ] change ro-crate labprocess id generation to include study or assay name
[#4d1bb7a ] add test against distinct ro-crate process ids for same table names
Deletions:
[#5fcfda1 ] add preliminary removeRowRange function
Bugfixes:
[#9a9c015 ] various small fixes and comments according to PR #539 review
[#8de07fe ] fix processes with underscore names being incorrectly parsed back to Scaffold tables #512
[#61ea221 ] datamap comment headers now contain "Comment" prefix #515
[#f1d5e16 ] fix scaffold reader assigning assay datamap to study
[#3e30224 ] small fixes to ArcTable according to PR comments
[#4ff9bc4 ] small fix to ArcTable
[#585017d ] small fixes to ArcTable functions
[#0895fd1 ] remove erase from ColumnRefValues to fix js and py
[#be5876b ] fix final tests against dotnet for table rework
[#a8f5c5e ] fix some ArcTable tests
[#be45cbc ] fix arctable cell addition and retrieval according to tests
[#214160c ] some fixes to ArcTable according to tests
[#a3eec49 ] small fixes against tests for ArcTable rework
[#fd94ddb ] some fixes on ArcTable against tests
3.0.0-alpha.4+16a8bb6 (Released 2025-5-28) * Python performance improvements
* Fix duplicate Process IDs for Tables with same name
Additions:
[#e0e5f6e ] improve performance import to include preparation and repeated testing
[#81d65c5 ] force python dict usage in compressed json writing
[#1a73116 ] improve LDContext Dictionary access speed
[#311603c ] change ro-crate labprocess id generation to include study or assay name
[#4d1bb7a ] add test against distinct ro-crate process ids for same table names
Bugfixes:
[#7696eeb ] fix duplicate Process IDs for Tables with same name
[#1321320 ] small name fix of test
3.0.0-alpha.3+ae0e326 (Released 2025-5-19) * Switch from poetry to uv for python project management
* make native tests actually use core transpilations
* improve imports in python and js
Additions:
[#1ecbc2e ] make jsnative tests use core transpilation
[#e6a61c1 ] make pynative tests use core transpilation
[#8d3c511 ] switch from poetry to uv for python project management
[#44d0a76 ] improve python package accessibility
[#593866c ] add rocrate module to typescript package
Bugfixes:
[#753528d ] small fix to include dev dependencies in python setup
3.0.0-alpha.2+4273dfa (Released 2025-5-15) * Fix critical typescript error
Bugfixes:
[#4273dfa ] fix typescript type declarations not being exported
3.0.0-alpha.1+a081b85 (Released 2025-5-15) * Add Run and Workflow isa xlsx files
* Add fields to Assay
* Add fields to Datamap
* Flattened ArcInvestigation into ARC class
Additions:
[#d33f5a0 ] cleanup version control and release tag generation
[#0de2c57 ] bump node version in ci to 18
[#af9edf5 ] cleanup npm dependencies
[#a295671 ] finish up release pipeline rework
[#9637108 ] continue reworking package build tasks
[#7828ea6 ] adjust python transpilation and build chain to ts changes
[#04cc5cb ] switch from vite packaging to tsc
[#9dad19a ] Update DesignPrinciples.md
[#2074e77 ] small tweaks to ts packaging
[#963dc90 ] continue working on build targets for ts release
[#76893ef ] refactor js fs bindings and finish up vitest implementation
[#61781cb ] start working on typescript support
[#a64d7c0 ] add workflow and run contract handling tests
[#83ec141 ] add workflow and run contract handling
[#9f11b5f ] add run spreadsheet parser and tests
[#36e0407 ] update and test ArcInvestigation Run and Workflow handling
[#fdb299b ] add ArcRun Type
[#618c33f ] implement and test ArcWorkflow Spreadsheet parsing
[#8560e8b ] start working on workflow spreadsheet parsing
[#839c70b ] add identifier, title and description to assay according to specification changes
[#3d424b8 ] add ArcWorkflow type
[#6211557 ] update methods and tests according to ARC ISA flattening
[#f72aecf ] start flattening ARC class
[#1d81138 ] include label in datamap spreadsheet parsing
[#bb772de ] bump to 2.5.1
Deletions:
[#8f49f11 ] remove py index file generation
Bugfixes:
[#a36aa3f ] try fix esbuild in ci
[#a2622a2 ] fix jsnativetests copying correct index file
[#521ad99 ] fixes and cleanup to ts packaging
[#b3685f9 ] update to vitest and fix jsnative tests
[#811545f ] add tests for arcworkflow and arcrun and according fixes
[#4b9d5e6 ] small fix to assay/study rename/remove failing in python
2.5.1+9f76bf1 (Released 2025-3-27) 2.5.0+b9de3c1 (Released 2025-3-26) * RO-Crate rework (https://github.com/nfdi4plants/ARCtrl/pull/496)
Additions:
[#b9de3c1 ] Merge pull request #502 from nfdi4plants/datamap_rocrate
[#38e512b ] make file paths from datamap absolute in RO-Crate
[#d6f802d ] start working on Datamap RO-Crate parser
[#b3d1537 ] Merge pull request #496 from nfdi4plants/ld-object-context
[#0d82e3c ] added doi and pubmed helper functions to LDPropertyValue and LDScholarlyArticle converters
[#4beb8cd ] bump to 2.4.0
Bugfixes:
[#589a332 ] add fixed propertyID to RO-Crate Fragment Descriptor
[#19774ab ] small fixes and adjustments for ro-crate export
[#7c35f44 ] update ro-crate testfile with datamap and small fix
[#20459ed ] add ro_crate conversion tests and fixes
[#60f0ad2 ] add tests and fixes for datamap RO-Crate conversion
[#f997440 ] reinclude isaprofile types and prefix static class names with LD
2.4.0+4a309c7 (Released 2025-3-7)
Additions:
[#d2e1f99 ] add ArcTable related helper functions
[#c1a34d6 ] Update documentation link in README.md
[#921594e ] make xlsx controller use async calls in javascript
[#8e78499 ] add some missing XlsxHelper functions
[#5ce39f9 ] RO-Crate export: added default publication date
[#5d498cb ] RO-Crate context: changed headline to name
[#b047349 ] Added dataFiles to Study RO-Crate export
[#7cfcece ] add logo references to ReadMe
[#5369bad ] small changes to logos - make hand lighter - higher quality
[#d95455d ] added ARCtrl logos
Bugfixes:
[#e4f9b91 ] fix datamap reader failing for empty datamap files
[#651fd8e ] fix filesystem access related tests failing in linux CI
[#134caf8 ] RO-Crate export: fixed default publication date
[#d353a43 ] RO-Crate export: fixed paths/ids for directories
[#4813991 ] RO-Crate context: fixed conformsTo mapping
2.3.1+56da453 (Released 2024-12-5)
Additions:
[#51eb019 ] rename top-level ARC IO functions
2.3.0+13842ba (Released 2024-12-4) * Cross-language file access functionality is here!
Additions:
[#94714ba ] add level synchronous IO functions for dotnet and python
[#5c1f99e ] finish up basic cross language IO and tests
[#8c6d20d ] finish up python io
[#ac29af6 ] finish up first version python arc io
[#a6438eb ] start working on python arc IO
[#2b754f5 ] finish up first working version of javascript arc io
[#c20e8c1 ] add preliminary promise catch mechanic for js io tests
[#a5c195b ] some cleanup for js fs IO
[#cca43e8 ] add first wip version of js file system access
[#a4a991a ] switch all file system access to async/promise functionality
Deletions:
[#3934047 ] remove second namespace definition in xlsx controller file
Bugfixes:
[#ce001af ] fix test file path handling for js in linux
[#4dd085a ] fix js io helpers aganst basic tests
[#2478640 ] fix js base level IO tests
[#02384d8 ] fix tests for dotnet again
[#1929830 ] further fixes for js file io
[#7bc9e5a ] add exceljs requirement and fix fileysystem helper file name
[#e72c01e ] some more fixes for js file io
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:
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:
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) 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) 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) 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:
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:
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
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