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Complete project structure rework #330

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merged 64 commits into from
Apr 3, 2024
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9b0d7b7
new ro-crate export and context files
floWetzels Mar 11, 2024
1cc83f8
adapted json export tests for new ro-crate export (Investigation stil…
floWetzels Mar 11, 2024
5b0adba
Added fromJsonldString for all ISA-JSON types. Also fixed some bugs.
floWetzels Mar 13, 2024
e7b0015
Updated tests for jsonld readers. Investigation test still wip.
floWetzels Mar 13, 2024
9983642
WIP :construction:
Freymaurer Mar 17, 2024
280d3b8
WIP :construction:
Freymaurer Mar 18, 2024
d1cbba9
new ro-crate export and context files
floWetzels Mar 11, 2024
d8c4d0a
adapted json export tests for new ro-crate export (Investigation stil…
floWetzels Mar 11, 2024
f7beae7
Updated tests for jsonld readers. Investigation test still wip.
floWetzels Mar 13, 2024
3bf2a83
WIP :construction:
Freymaurer Mar 17, 2024
996ae0e
fix multiple issues with ro-crate json encoding :bug:
Freymaurer Mar 19, 2024
dd69b1f
add addtionalType to ProcessParameterValue
Freymaurer Mar 19, 2024
4b2b78f
move UIHelper function into compositecell
HLWeil Mar 20, 2024
ceefce8
move all filesystem information into filesystem project
HLWeil Mar 20, 2024
90520bd
restructure project
HLWeil Mar 20, 2024
b282dc3
restructure ARCtrl.Core (former ARCtrl.ISA) project
HLWeil Mar 20, 2024
2cb9db8
rework ARCtrl.Core types to improve transpiled javascript
HLWeil Mar 21, 2024
b568074
rework ARCtrl.Spreadsheet according to datamodel changes
HLWeil Mar 21, 2024
f65d414
start reworking ARCtrl.json project
HLWeil Mar 21, 2024
5150773
Start workin on new Json API layer :construction:
Freymaurer Mar 21, 2024
e053cd9
fix arctrl.core tests
HLWeil Mar 21, 2024
a29a7f9
start reworking arctrl.json process serialization
HLWeil Mar 21, 2024
6b670d9
Finish json for shared types :sparkles:
Freymaurer Mar 21, 2024
a51bfcc
Finish json table logic :sparkles:
Freymaurer Mar 21, 2024
f24259e
finish up ISA-JSON conversion for process types :sparkles:
Freymaurer Mar 22, 2024
cd69fc3
fix wrong encoder/decoder calls :sparkles:
Freymaurer Mar 22, 2024
19b849a
Start with component logic rework :construction:
Freymaurer Mar 22, 2024
437bca3
rework ROCrate process serialization
HLWeil Mar 22, 2024
e710c5a
rework ARCAssay and ArcStudy ISAJson serialization
HLWeil Mar 22, 2024
04b097b
Start moving Arc Json logic :construction:
Freymaurer Mar 22, 2024
c25748a
Finish compressed json logic :sparkles:
Freymaurer Mar 25, 2024
39fe3cf
finish moving template json :sparkles:
Freymaurer Mar 25, 2024
4b5af05
fix rocrate assay serialization
HLWeil Mar 25, 2024
da18342
fix rocrate sample and protocol handling
HLWeil Mar 25, 2024
4cd6d63
finish investigation ro-crate
HLWeil Mar 25, 2024
e3437b2
add ARC RO-Crate serialization
HLWeil Mar 25, 2024
8af7487
Add fable json import type #324 #285
Freymaurer Mar 25, 2024
5f6c65b
distribute template across appropriate projects
HLWeil Mar 26, 2024
c193629
Start working on tests :construction:
Freymaurer Mar 26, 2024
6c9123e
fix arctrl.core tests and equality of reworked objects
HLWeil Mar 26, 2024
fbaa958
fix component name conversion
HLWeil Mar 26, 2024
adac51c
Add custom ToString for OntologyAnnotation :art:
Freymaurer Mar 27, 2024
c885111
More work on json tests :construction:
Freymaurer Mar 27, 2024
cb5da3a
reduce test spreadsheet metadata matching reduction of parser logic
HLWeil Mar 27, 2024
4fc4a07
more work on json :construction:
Freymaurer Mar 27, 2024
3f35262
move template json tests to json test project
HLWeil Mar 27, 2024
766d46a
move ARCtrl contract tests to Contract test project
HLWeil Mar 27, 2024
97c433e
move and fix spreadsheet Template tests
HLWeil Mar 27, 2024
9da88fe
Template fixes against json and core tests
HLWeil Mar 27, 2024
5803eb7
start reworking tests for js and py
HLWeil Mar 28, 2024
451ef11
move and fix template hashcode and equality tests
HLWeil Mar 28, 2024
89f976c
Finish json (for now :construction:)
Freymaurer Mar 28, 2024
d5eae8d
several python test fixes
HLWeil Mar 28, 2024
18012b3
rmv leftover folder :fire:
Freymaurer Mar 28, 2024
8d50567
update github CI
Freymaurer Mar 28, 2024
e3512c7
Make js native tests pass :heavy_check_mark:
Freymaurer Mar 28, 2024
b15a377
fix json parsing DateTime issues
HLWeil Mar 29, 2024
562ce65
Fix test tasks still using mocha
Freymaurer Apr 2, 2024
2a999e8
Fix all warnings by burning unused fable reflection helpers :fire:
Freymaurer Apr 2, 2024
fc8f63e
add native python tests :white_check_mark:
Freymaurer Apr 2, 2024
7340910
add some more schema validation tests
HLWeil Apr 2, 2024
d68348e
hotfix js schema validation in tests
HLWeil Apr 2, 2024
c15a2e5
Add ro-crate write tests :white_check_mark:
Freymaurer Apr 3, 2024
232dae3
set test with umlauten pending for python
Freymaurer Apr 3, 2024
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3 changes: 0 additions & 3 deletions .github/workflows/build-test.yml
Original file line number Diff line number Diff line change
Expand Up @@ -35,9 +35,6 @@ jobs:
- name: install node modules
working-directory: ./
run: npm install --ignore-scripts
- name: install node modules ISA
working-directory: ./src/ISA
run: npm install

# SETUP PYTHON
- name: Setup Python
Expand Down
1 change: 1 addition & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -363,3 +363,4 @@ tmp/
/tests/**/py
/tests/UI/cypress/screenshots/Tests/Dictionary.cy.js
/tests/ISA/ISA.Tests/py
/ro-crate-test.json
114 changes: 55 additions & 59 deletions ARCtrl.sln
Original file line number Diff line number Diff line change
Expand Up @@ -25,28 +25,8 @@ Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "src", "src", "{6DA2330B-D40
EndProject
Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "Build", "build\Build.fsproj", "{5EAFB0CD-1168-4FCA-AA61-E96AD6C85819}"
EndProject
Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "ISA", "ISA", "{C61B3F43-2255-4585-9110-F8AB74F02654}"
ProjectSection(SolutionItems) = preProject
src\ISA\package.json = src\ISA\package.json
src\ISA\README.md = src\ISA\README.md
EndProjectSection
EndProject
Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.ISA", "src\ISA\ISA\ARCtrl.ISA.fsproj", "{67CF6725-6AC0-47FB-A725-6DC2192713B5}"
EndProject
Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.ISA.Json", "src\ISA\ISA.Json\ARCtrl.ISA.Json.fsproj", "{2CA397B2-0220-49A3-AD79-2F9F53633EC1}"
EndProject
Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "tests", "tests", "{64B34A6E-318D-4E6E-9262-CE52C9B85A38}"
EndProject
Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "ISA", "ISA", "{D1BBD7AE-35C8-498F-BABA-C93FFAE68037}"
EndProject
Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ISA.Tests", "tests\ISA\ISA.Tests\ISA.Tests.fsproj", "{36EAC61E-4318-47AD-ABC8-87BC2A8C9908}"
EndProject
Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ISA.Json.Tests", "tests\ISA\ISA.Json.Tests\ISA.Json.Tests.fsproj", "{04789F17-3DC2-4A09-848D-376E5D269740}"
EndProject
Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.ISA.Spreadsheet", "src\ISA\ISA.Spreadsheet\ARCtrl.ISA.Spreadsheet.fsproj", "{07C7942E-FC34-4C27-82C1-6B2972654BA7}"
EndProject
Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ISA.Spreadsheet.Tests", "tests\ISA\ISA.Spreadsheet.Tests\ISA.Spreadsheet.Tests.fsproj", "{656E8DAF-EFCF-472E-91D0-987D09B74523}"
EndProject
Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "JavaScript", "JavaScript", "{913222CA-261F-49CB-A823-CC7C335F964A}"
ProjectSection(SolutionItems) = preProject
tests\JavaScript\ARCtrl.Index.js = tests\JavaScript\ARCtrl.Index.js
Expand All @@ -63,12 +43,29 @@ Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.Tests", "tests\ARCtr
EndProject
Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.Contract", "src\Contract\ARCtrl.Contract.fsproj", "{1945EE8A-F105-43A9-91C9-8C4422B9873E}"
EndProject
Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "FileSystem.Tests", "tests\FileSystem\FileSystem.Tests.fsproj", "{D9FE196B-AC21-4C3E-B9AE-DDDEC2158BC3}"
EndProject
Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "TestingUtils", "tests\TestingUtils\TestingUtils.fsproj", "{AA011593-6603-4E16-A7B0-0ED3862511DE}"
EndProject
Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "Speedtest", "tests\Speedtest\Speedtest.fsproj", "{6EFC7E7D-840E-4506-ADBC-37130A21D1C0}"
EndProject
Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.Json", "src\Json\ARCtrl.Json.fsproj", "{6DCF93BA-A918-42A0-BAD7-A11B72ADFFE6}"
EndProject
Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.Spreadsheet", "src\Spreadsheet\ARCtrl.Spreadsheet.fsproj", "{74EF1B45-C7B7-4281-BDDB-7A653F9F935E}"
EndProject
Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.Core", "src\Core\ARCtrl.Core.fsproj", "{FDA13C07-2E22-49D5-A317-7A68DC359894}"
EndProject
Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.Core.Tests", "tests\Core\ARCtrl.Core.Tests.fsproj", "{EDC4FB2B-40CF-4AFD-90C7-CF88C2745789}"
EndProject
Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.Json.Tests", "tests\Json\ARCtrl.Json.Tests.fsproj", "{9E1FF103-B5BD-44B6-B839-0E1FED2C49EC}"
EndProject
Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.Spreadsheet.Tests", "tests\Spreadsheet\ARCtrl.Spreadsheet.Tests.fsproj", "{03F4E6D0-CFE7-44A6-994B-778B3DF6532C}"
EndProject
Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.FileSystem.Tests", "tests\FileSystem\ARCtrl.FileSystem.Tests.fsproj", "{704935A5-68F2-4070-8A55-AFF8F66ACAD6}"
EndProject
Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Python", "Python", "{501F6D1E-6300-4CA4-8E61-3523BCF4D533}"
ProjectSection(SolutionItems) = preProject
tests\Python\test_index.py = tests\Python\test_index.py
EndProjectSection
EndProject
Global
GlobalSection(SolutionConfigurationPlatforms) = preSolution
Debug|Any CPU = Debug|Any CPU
Expand All @@ -87,30 +84,6 @@ Global
{5EAFB0CD-1168-4FCA-AA61-E96AD6C85819}.Debug|Any CPU.Build.0 = Debug|Any CPU
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Expand All @@ -123,10 +96,6 @@ Global
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Expand All @@ -135,28 +104,55 @@ Global
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{801247D5-7EE5-49C8-AB26-F822A415BA49} = {64B34A6E-318D-4E6E-9262-CE52C9B85A38}
{1945EE8A-F105-43A9-91C9-8C4422B9873E} = {6DA2330B-D407-4FB1-AF05-B0184034EC44}
{D9FE196B-AC21-4C3E-B9AE-DDDEC2158BC3} = {64B34A6E-318D-4E6E-9262-CE52C9B85A38}
{AA011593-6603-4E16-A7B0-0ED3862511DE} = {64B34A6E-318D-4E6E-9262-CE52C9B85A38}
{6EFC7E7D-840E-4506-ADBC-37130A21D1C0} = {64B34A6E-318D-4E6E-9262-CE52C9B85A38}
{6DCF93BA-A918-42A0-BAD7-A11B72ADFFE6} = {6DA2330B-D407-4FB1-AF05-B0184034EC44}
{74EF1B45-C7B7-4281-BDDB-7A653F9F935E} = {6DA2330B-D407-4FB1-AF05-B0184034EC44}
{FDA13C07-2E22-49D5-A317-7A68DC359894} = {6DA2330B-D407-4FB1-AF05-B0184034EC44}
{EDC4FB2B-40CF-4AFD-90C7-CF88C2745789} = {64B34A6E-318D-4E6E-9262-CE52C9B85A38}
{9E1FF103-B5BD-44B6-B839-0E1FED2C49EC} = {64B34A6E-318D-4E6E-9262-CE52C9B85A38}
{03F4E6D0-CFE7-44A6-994B-778B3DF6532C} = {64B34A6E-318D-4E6E-9262-CE52C9B85A38}
{704935A5-68F2-4070-8A55-AFF8F66ACAD6} = {64B34A6E-318D-4E6E-9262-CE52C9B85A38}
{501F6D1E-6300-4CA4-8E61-3523BCF4D533} = {64B34A6E-318D-4E6E-9262-CE52C9B85A38}
EndGlobalSection
GlobalSection(ExtensibilityGlobals) = postSolution
SolutionGuid = {1E354DE6-99BA-421E-9EF8-E808B855A85F}
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3 changes: 2 additions & 1 deletion build/GenerateIndexJs.fs
Original file line number Diff line number Diff line change
Expand Up @@ -94,7 +94,8 @@ let ARCtrl_generate(rootPath: string) =
"Template"
"Templates"
"Organisation"
"JsWeb"
"WebController"
"ARC"
"JsonController"
|]
generateIndexfile(rootPath, "index.js", whiteList)
29 changes: 14 additions & 15 deletions build/GenerateIndexPy.fs
Original file line number Diff line number Diff line change
Expand Up @@ -25,21 +25,20 @@ let classes =
"__future__", "annotations"
"collections.abc", "Callable"
"typing", "Any"
".ISA.ISA.JsonTypes.comment", "Comment"
".ISA.ISA.JsonTypes.ontology_annotation","OntologyAnnotation";
".ISA.ISA.JsonTypes.person", "Person";
".ISA.ISA.JsonTypes.publication", "Publication";
".ISA.ISA.ArcTypes.composite_header", "IOType"
".ISA.ISA.ArcTypes.composite_header", "CompositeHeader";
".ISA.ISA.ArcTypes.composite_cell", "CompositeCell"
".ISA.ISA.ArcTypes.composite_column", "CompositeColumn"
".ISA.ISA.ArcTypes.arc_table", "ArcTable"
".ISA.ISA.ArcTypes.arc_types", "ArcAssay";
".ISA.ISA.ArcTypes.arc_types", "ArcStudy";
".ISA.ISA.ArcTypes.arc_types", "ArcInvestigation";
".Templates.template", "Template"
".Templates.templates", "Templates"
".Templates.template", "Organisation"
".Core.comment", "Comment"
".Core.ontology_annotation","OntologyAnnotation";
".Core.person", "Person";
".Core.publication", "Publication";
".Core.Table.composite_header", "IOType"
".Core.Table.composite_header", "CompositeHeader";
".Core.Table.composite_cell", "CompositeCell"
".Core.Table.composite_column", "CompositeColumn"
".Core.Table.arc_table", "ArcTable"
".Core.arc_types", "ArcAssay";
".Core.arc_types", "ArcStudy";
".Core.arc_types", "ArcInvestigation";
".Core.template", "Template"
".json", "JsonController"
".arc","ARC"
|]

Expand Down
12 changes: 9 additions & 3 deletions build/ProjectInfo.fs
Original file line number Diff line number Diff line change
Expand Up @@ -7,9 +7,9 @@ let project = "ARCtrl"
/// Dotnet and JS test paths
let testProjects =
[
"tests/ISA/ISA.Tests"
"tests/ISA/ISA.Json.Tests"
"tests/ISA/ISA.Spreadsheet.Tests"
"tests/Core"
"tests/Json"
"tests/Spreadsheet"
"tests/FileSystem"
"tests/ARCtrl"
]
Expand All @@ -20,6 +20,12 @@ let jsTestProjects =
"tests/JavaScript"
]

/// Native JS test paths
let pyTestProjects =
[
"tests/Python"
]

let solutionFile = $"{project}.sln"

let configuration = "Release"
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22 changes: 10 additions & 12 deletions build/TestTasks.fs
Original file line number Diff line number Diff line change
Expand Up @@ -33,19 +33,17 @@ module RunTests =
run dotnet $"fable {path} -o {path}/js" ""
// run mocha in target path to execute tests
// "--timeout 20000" is used, because json schema validation takes a bit of time.
run npx $"mocha {path}/js --timeout 20000" ""
run node $"{path}/js/Main.js" ""
}

/// <summary>
/// Until we reach full Py compatibility we use these paths to check only compatible projects
/// </summary>
let testProjectsPy =
[
//"tests/ISA/ISA.Tests"
//"tests/ISA/ISA.Json.Tests"
//"tests/ISA/ISA.Spreadsheet.Tests"
"tests/ARCtrl"
]
let runTestsPyNative = BuildTask.create "runTestsPyNative" [clean; build] {
Trace.traceImportant "Start native Python tests"
for path in ProjectInfo.pyTestProjects do
// transpile library for native access
run dotnet $"fable src/ARCtrl -o {path}/ARCtrl --lang python" ""
GenerateIndexPy.ARCtrl_generate($"{path}/ARCtrl")
run python $"-m pytest {path}" ""
}

let runTestsPy = BuildTask.create "runTestsPy" [clean; build] {
for path in ProjectInfo.testProjects do
Expand All @@ -61,6 +59,6 @@ module RunTests =
|> Seq.iter dotnetRun
}

let runTests = BuildTask.create "RunTests" [clean; build; RunTests.runTestsJs; RunTests.runTestsJsNative; RunTests.runTestsPy; RunTests.runTestsDotnet] {
let runTests = BuildTask.create "RunTests" [clean; build; RunTests.runTestsJs; RunTests.runTestsJsNative; RunTests.runTestsPy; RunTests.runTestsPyNative; RunTests.runTestsDotnet] {
()
}
6 changes: 6 additions & 0 deletions docs/scripts_js/Contracts.js
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,12 @@ import {Xlsx} from "fsspreadsheet";
import fs from "fs";
import path from "path";

export function normalizePathSeparators (str) {
const normalizedPath = path.normalize(str)
return normalizedPath.replace(/\\/g, '/');
}


// Write

export function normalizePathSeparators (str) {
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1 change: 0 additions & 1 deletion package-lock.json

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

13 changes: 6 additions & 7 deletions package.json
Original file line number Diff line number Diff line change
Expand Up @@ -6,12 +6,12 @@
"bundlejs": "dotnet fable ./src/ARCtrl -o ./dist/js",
"prebundlets": "mkdirp .\\dist/ts && dotnet fable clean -o ./dist/ts --yes --extension .ts",
"bundlets": "dotnet fable ./src/ARCtrl -o ./dist/ts --lang ts",
"pretestJson": "dotnet fable tests/ISA/ISA.Json.Tests -o tests/ISA/ISA.Json.Tests/js",
"testJson": "mocha tests/ISA/ISA.Json.Tests/js --timeout 20000",
"pretestXlsx": "dotnet fable tests/ISA/ISA.Spreadsheet.Tests -o tests/ISA/ISA.Spreadsheet.Tests/js",
"testXlsx": "mocha tests/ISA/ISA.Spreadsheet.Tests/js --timeout 20000",
"pretestIsa": "dotnet fable tests/ISA/ISA.Tests -o tests/ISA/ISA.Tests/js",
"testIsa": "mocha tests/ISA/ISA.Tests/js",
"pretestJson": "dotnet fable tests/Json -o tests/Json/js",
"testJson": "mocha tests/Json/js --timeout 20000",
"pretestXlsx": "dotnet fable tests/Spreadsheet -o tests/Spreadsheet/js",
"testXlsx": "mocha tests/Spreadsheet/js --timeout 20000",
"pretestIsa": "dotnet fable tests/Core -o tests/Core/js",
"testIsa": "mocha tests/Core/js",
"pretestFiles": "dotnet fable tests/FileSystem -o tests/FileSystem/js",
"testFiles": "mocha tests/FileSystem/js",
"pretestArctrl": "dotnet fable tests/ARCtrl -o tests/ARCtrl/js",
Expand All @@ -22,7 +22,6 @@
"pretestui": "dotnet fable src/ARCtrl -o tests/UI/ARCtrl ",
"testui": "cd tests/UI & npx cypress run --component ",
"testpy": "",
"postinstall": "cd src/ISA && npm install",
"devui": "cd tests/UI & npx vite"
},
"author": "Heinrich Lukas Weil <[email protected]> (https://github.com/HLWeil)",
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