Various read write fixes #257
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HLWeil
commented
Nov 19, 2023
HLWeil
commented
- Reading ISA from Contracts will now not return Assay and Study objects, when they are only registered in the investigation file, but have no corresponding folder/file in the filesystem.
- added a ARC.setFileSystem method, [BUG] Deleting assay from ARC will produce faulty write contracts #250
- investigation spreadsheet writer previously failed when it contained a study that was only registered, but no corresponding study object
- reworked test objects for full arc read-in
Freymaurer
reviewed
Nov 20, 2023
| @@ -194,7 +194,8 @@ module ArcInvestigation = | |||
| yield SparseRow.fromValues [contactsLabel] | |||
| yield! Contacts.toRows (Some contactsLabelPrefix) (List.ofArray investigation.Contacts) | |||
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| for study in investigation.RegisteredStudies do | |||
| for studyIdentifier in investigation.RegisteredStudyIdentifiers do | |||
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What exactly is happening here? Can you add a few comments?
| @@ -19,7 +19,7 @@ let [<Literal>] ValidStudyFileNamePattern = @"^(studies(\/|\\))?(?<identifier>" | |||
| let checkValidCharacters (identifier: string) = | |||
| let regex = new Regex(ValidIdentifierPattern) | |||
| let isValid = regex.IsMatch(identifier) | |||
| if not isValid then failwith "New identifier contains forbidden characters! Allowed characters are: letters, digits, underscore (_), dash (-) and whitespace ( )." | |||
| if not isValid then failwith $"New identifier \"{identifier}\"contains forbidden characters! Allowed characters are: letters, digits, underscore (_), dash (-) and whitespace ( )." | |||
HLWeil
commented
Nov 20, 2023
| @@ -71,6 +71,25 @@ type ARC(?isa : ISA.ArcInvestigation, ?cwl : CWL.CWL, ?fs : FileSystem.FileSyste | |||
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| member this.FileSystem | |||
| with get() = _fs | |||
| and set(fs) = _fs <- fs | |||
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| member this.RemoveAssay(assayIdentifier: string) = | |||
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These functions should contain update contracts for all registering objects (study,investigation)
Additional helpers:
- ContractCreator Type extensions for ArcInvestigation, ArcStudy and ArcAssay in Contract namespace
Freymaurer
approved these changes
Nov 20, 2023
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