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Merge pull request #480 from nfdi4plants/arcIO_async
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Rename top-level ARC IO functions
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@HLWeil
HLWeil authored Dec 5, 2024
2 parents 5e85024 + 51eb019 commit 56da453
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Showing 2 changed files with 100 additions and 57 deletions.
127 changes: 85 additions & 42 deletions src/ARCtrl/ARC.fs
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Original file line number Diff line number Diff line change
Expand Up @@ -89,15 +89,15 @@ type ARC(?isa : ArcInvestigation, ?cwl : unit, ?fs : FileSystem.FileSystem) =
with get() = _fs
and set(fs) = _fs <- fs

member this.WriteAsync(arcPath) =
member this.TryWriteAsync(arcPath) =
this.GetWriteContracts()
|> fullFillContractBatchAsync arcPath

member this.UpdateAsync(arcPath) =
member this.TryUpdateAsync(arcPath) =
this.GetUpdateContracts()
|> fullFillContractBatchAsync arcPath

static member loadAsync (arcPath : string) =
static member tryLoadAsync (arcPath : string) =
crossAsync {

let! paths = FileSystemHelper.getAllFilePathsAsync arcPath
Expand Down Expand Up @@ -138,7 +138,7 @@ type ARC(?isa : ArcInvestigation, ?cwl : unit, ?fs : FileSystem.FileSystem) =
s.ToUpdateContract()
|]

member this.RemoveAssayAsync(arcPath : string, assayIdentifier: string) =
member this.TryRemoveAssayAsync(arcPath : string, assayIdentifier: string) =
this.GetAssayRemoveContracts(assayIdentifier)
|> fullFillContractBatchAsync arcPath

Expand All @@ -160,7 +160,7 @@ type ARC(?isa : ArcInvestigation, ?cwl : unit, ?fs : FileSystem.FileSystem) =
yield! this.GetUpdateContracts()
|]

member this.RenameAssayAsync(arcPath : string, oldAssayIdentifier: string, newAssayIdentifier: string) =
member this.TryRenameAssayAsync(arcPath : string, oldAssayIdentifier: string, newAssayIdentifier: string) =
this.GetAssayRenameContracts(oldAssayIdentifier,newAssayIdentifier)
|> fullFillContractBatchAsync arcPath

Expand All @@ -179,7 +179,7 @@ type ARC(?isa : ArcInvestigation, ?cwl : unit, ?fs : FileSystem.FileSystem) =
isa.ToUpdateContract()
|]

member this.RemoveStudyAsync(arcPath : string, studyIdentifier: string) =
member this.TryRemoveStudyAsync(arcPath : string, studyIdentifier: string) =
this.GetStudyRemoveContracts(studyIdentifier)
|> fullFillContractBatchAsync arcPath

Expand All @@ -201,60 +201,103 @@ type ARC(?isa : ArcInvestigation, ?cwl : unit, ?fs : FileSystem.FileSystem) =
yield! this.GetUpdateContracts()
|]

member this.RenameStudyAsync(arcPath : string, oldStudyIdentifier: string, newStudyIdentifier: string) =
member this.TryRenameStudyAsync(arcPath : string, oldStudyIdentifier: string, newStudyIdentifier: string) =
this.GetStudyRenameContracts(oldStudyIdentifier,newStudyIdentifier)
|> fullFillContractBatchAsync arcPath


member this.WriteAsync(arcPath) =
crossAsync {
let! result = this.TryWriteAsync(arcPath)
match result with
| Ok _ -> ()
| Error errors ->
let appended = errors |> Array.map (fun e -> e.ToString()) |> String.concat "\n"
failwithf "Could not write ARC, failed with the following errors %s" appended
}

member this.UpdateAsync(arcPath) =
crossAsync {
let! result = this.TryUpdateAsync(arcPath)
match result with
| Ok _ -> ()
| Error errors ->
let appended = errors |> Array.map (fun e -> e.ToString()) |> String.concat "\n"
failwithf "Could not update ARC, failed with the following errors %s" appended
}

member this.RemoveAssayAsync(arcPath, assayIdentifier) =
crossAsync {
let! result = this.TryRemoveAssayAsync(arcPath, assayIdentifier)
match result with
| Ok _ -> ()
| Error errors ->
let appended = errors |> Array.map (fun e -> e.ToString()) |> String.concat "\n"
failwithf "Could not remove assay, failed with the following errors %s" appended
}

member this.RenameAssayAsync(arcPath, oldAssayIdentifier, newAssayIdentifier) =
crossAsync {
let! result = this.TryRenameAssayAsync(arcPath, oldAssayIdentifier, newAssayIdentifier)
match result with
| Ok _ -> ()
| Error errors ->
let appended = errors |> Array.map (fun e -> e.ToString()) |> String.concat "\n"
failwithf "Could not rename assay, failed with the following errors %s" appended
}

member this.RemoveStudyAsync(arcPath, studyIdentifier) =
crossAsync {
let! result = this.TryRemoveStudyAsync(arcPath, studyIdentifier)
match result with
| Ok _ -> ()
| Error errors ->
let appended = errors |> Array.map (fun e -> e.ToString()) |> String.concat "\n"
failwithf "Could not remove study, failed with the following errors %s" appended
}

member this.RenameStudyAsync(arcPath, oldStudyIdentifier, newStudyIdentifier) =
crossAsync {
let! result = this.TryRenameStudyAsync(arcPath, oldStudyIdentifier, newStudyIdentifier)
match result with
| Ok _ -> ()
| Error errors ->
let appended = errors |> Array.map (fun e -> e.ToString()) |> String.concat "\n"
failwithf "Could not rename study, failed with the following errors %s" appended
}

static member loadAsync (arcPath) =
crossAsync {
let! result = ARC.tryLoadAsync arcPath
match result with
| Ok arc -> return arc
| Error errors ->
let appended = errors |> Array.map (fun e -> e.ToString()) |> String.concat "\n"
failwithf "Could not load ARC, failed with the following errors %s" appended
return (ARC())
}

#if FABLE_COMPILER_PYTHON || !FABLE_COMPILER
member this.Write(arcPath) =
match Async.RunSynchronously (this.WriteAsync(arcPath)) with
| Ok _ -> ()
| Error errors ->
let appended = errors |> Array.map (fun e -> e.ToString()) |> String.concat "\n"
failwithf "Could not write ARC, failed with the following errors %s" appended
Async.RunSynchronously (this.WriteAsync(arcPath))

member this.Update(arcPath) =
match Async.RunSynchronously (this.UpdateAsync(arcPath)) with
| Ok _ -> ()
| Error errors ->
let appended = errors |> Array.map (fun e -> e.ToString()) |> String.concat "\n"
failwithf "Could not update ARC, failed with the following errors %s" appended
Async.RunSynchronously (this.UpdateAsync(arcPath))

member this.RemoveAssay(arcPath, assayIdentifier) =
match Async.RunSynchronously (this.RemoveAssayAsync(arcPath, assayIdentifier)) with
| Ok _ -> ()
| Error errors ->
let appended = errors |> Array.map (fun e -> e.ToString()) |> String.concat "\n"
failwithf "Could not remove assay, failed with the following errors %s" appended
Async.RunSynchronously (this.RemoveAssayAsync(arcPath, assayIdentifier))

member this.RenameAssay(arcPath, oldAssayIdentifier, newAssayIdentifier) =
match Async.RunSynchronously (this.RenameAssayAsync(arcPath, oldAssayIdentifier, newAssayIdentifier)) with
| Ok _ -> ()
| Error errors ->
let appended = errors |> Array.map (fun e -> e.ToString()) |> String.concat "\n"
failwithf "Could not rename assay, failed with the following errors %s" appended
Async.RunSynchronously (this.RenameAssayAsync(arcPath, oldAssayIdentifier, newAssayIdentifier))

member this.RemoveStudy(arcPath, studyIdentifier) =
match Async.RunSynchronously (this.RemoveStudyAsync(arcPath, studyIdentifier)) with
| Ok _ -> ()
| Error errors ->
let appended = errors |> Array.map (fun e -> e.ToString()) |> String.concat "\n"
failwithf "Could not remove study, failed with the following errors %s" appended
Async.RunSynchronously (this.RemoveStudyAsync(arcPath, studyIdentifier))

member this.RenameStudy(arcPath, oldStudyIdentifier, newStudyIdentifier) =
match Async.RunSynchronously (this.RenameStudyAsync(arcPath, oldStudyIdentifier, newStudyIdentifier)) with
| Ok _ -> ()
| Error errors ->
let appended = errors |> Array.map (fun e -> e.ToString()) |> String.concat "\n"
failwithf "Could not rename study, failed with the following errors %s" appended
Async.RunSynchronously (this.RenameStudyAsync(arcPath, oldStudyIdentifier, newStudyIdentifier))

static member load (arcPath) =
match Async.RunSynchronously (ARC.loadAsync arcPath) with
| Ok arc -> arc
| Error errors ->
let appended = errors |> Array.map (fun e -> e.ToString()) |> String.concat "\n"
failwithf "Could not load ARC, failed with the following errors %s" appended
Async.RunSynchronously (ARC.loadAsync arcPath)
#endif


Expand Down
30 changes: 15 additions & 15 deletions tests/ARCtrl/ARCtrl.Tests.fs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -949,7 +949,7 @@ let tests_load =
testList "Load" [
testCaseCrossAsync "simpleARC" (crossAsync {
let p = TestObjects.IO.testSimpleARC
let! result = ARC.loadAsync(p)
let! result = ARC.tryLoadAsync(p)
let result = Expect.wantOk result "ARC should load successfully"

Expect.isSome result.ISA "Should contain an ISA part"
Expand Down Expand Up @@ -979,7 +979,7 @@ let tests_write =
let p = ArcPathHelper.combine TestObjects.IO.testResultsFolder "ARC_Write_Empty"
let a = ARC()

let! result = a.WriteAsync(p)
let! result = a.TryWriteAsync(p)

Expect.wantOk result "ARC should write successfully" |> ignore

Expand Down Expand Up @@ -1014,7 +1014,7 @@ let tests_write =
arc.ISA <- Some i
arc.UpdateFileSystem()

let! result = arc.WriteAsync(p)
let! result = arc.TryWriteAsync(p)
Expect.wantOk result "ARC should write successfully" |> ignore

let expectedPaths =
Expand Down Expand Up @@ -1046,7 +1046,7 @@ let tests_write =
testCaseCrossAsync "LoadSimpleARCAndAddAssay" (crossAsync {
let p = ArcPathHelper.combine TestObjects.IO.testResultsFolder "ARC_Write_SimpleARCWithAssay"

let! readResult = ARC.loadAsync(TestObjects.IO.testSimpleARC)
let! readResult = ARC.tryLoadAsync(TestObjects.IO.testSimpleARC)
let arc = Expect.wantOk readResult "ARC should load correctly"

let i = arc.ISA.Value
Expand All @@ -1060,7 +1060,7 @@ let tests_write =

arc.UpdateFileSystem()

let! writeResult = arc.WriteAsync(p)
let! writeResult = arc.TryWriteAsync(p)

Expect.wantOk writeResult "ARC should write successfully" |> ignore

Expand Down Expand Up @@ -1131,7 +1131,7 @@ let tests_Update =
arc.ISA <- Some i
arc.UpdateFileSystem()

let! writeResult = arc.WriteAsync(p)
let! writeResult = arc.TryWriteAsync(p)

Expect.wantOk writeResult "ARC should write successfully" |> ignore

Expand All @@ -1141,7 +1141,7 @@ let tests_Update =
arc.ISA <- Some i
arc.UpdateFileSystem()

let! updateResult = arc.UpdateAsync(p)
let! updateResult = arc.TryUpdateAsync(p)

Expect.wantOk updateResult "ARC should update successfully" |> ignore

Expand Down Expand Up @@ -1194,14 +1194,14 @@ let tests_renameAssay =
arc.ISA <- Some i
arc.UpdateFileSystem()

let! updateResult = arc.WriteAsync(p)
let! updateResult = arc.TryWriteAsync(p)

Expect.wantOk updateResult "ARC should write successfully" |> ignore

// rename assay
let newAssayName = "MyNewAssay"

let! renameResult = arc.RenameAssayAsync(p,assayName, newAssayName)
let! renameResult = arc.TryRenameAssayAsync(p,assayName, newAssayName)
Expect.wantOk renameResult "Assay should be renamed successfully" |> ignore

let expectedPaths =
Expand Down Expand Up @@ -1247,14 +1247,14 @@ let tests_RenameStudy =
arc.ISA <- Some i
arc.UpdateFileSystem()

let! writeResult = arc.WriteAsync(p)
let! writeResult = arc.TryWriteAsync(p)

Expect.wantOk writeResult "ARC should write successfully" |> ignore

// rename study
let newStudyName = "MyNewStudy"

let! renameResult = arc.RenameStudyAsync(p,studyName, newStudyName)
let! renameResult = arc.TryRenameStudyAsync(p,studyName, newStudyName)
Expect.wantOk renameResult "Study should be renamed successfully" |> ignore

let expectedPaths =
Expand Down Expand Up @@ -1301,13 +1301,13 @@ let tests_RemoveAssay =
arc.ISA <- Some i
arc.UpdateFileSystem()

let! writeResult = arc.WriteAsync(p)
let! writeResult = arc.TryWriteAsync(p)

Expect.wantOk writeResult "ARC should write successfully" |> ignore

// remove assay

let! removeResult = arc.RemoveAssayAsync(p,assayName)
let! removeResult = arc.TryRemoveAssayAsync(p,assayName)
Expect.wantOk removeResult "Assay should be removed successfully" |> ignore

let expectedPaths =
Expand Down Expand Up @@ -1349,13 +1349,13 @@ let tests_RemoveStudy =
arc.ISA <- Some i
arc.UpdateFileSystem()

let! writeResult = arc.WriteAsync(p)
let! writeResult = arc.TryWriteAsync(p)

Expect.wantOk writeResult "ARC should write successfully" |> ignore

// remove study

let! removeResult = arc.RemoveStudyAsync(p,studyName)
let! removeResult = arc.TryRemoveStudyAsync(p,studyName)
Expect.wantOk removeResult "Study should be removed successfully" |> ignore

let expectedPaths =
Expand Down

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