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nfdi4plants / ARCCommander

Tool to manage your ARCs
MIT License
11 stars 9 forks source link

[BUG] Adding assay performer fails and argument -s is irritating #214

Closed andreaschrader closed 10 months ago

andreaschrader commented 11 months ago

Describe the bug

When registering an assay performer, the argument -a is not recognized. 

arc a person register -s MY_STUDY -a MY_ASSAY -l LASTNAME -f FIRSTNAME

and

arc a person register-a MY_ASSAY -l LASTNAME -f FIRSTNAME

do not work:

ERROR: ERROR: unrecognized argument: '-a'.

When reading the help, it says --assayidentifier or -s. This is irritating. However I executed this as well.

arc a person register -s MY_ASSAY -l LASTNAME -f FIRSTNAME

Start processing command with the arguments: Address:Field "" Affiliation:Field "" AssayIdentifier:Field "MY_ASSAY" Email:Field "" Fax:Field "" FirstName:Field "FIRSTNAME" LastName:Field "LASTNAME" MidInitials:Field "" ORCID:Field "" Phone:Field "" Roles:Field "" RolesTermAccessionNumber:Field "" RolesTermSourceREF:Field ""

Start Person Register Done processing command. ERROR: System.Exception: Metadata sheetname Investigation could not be found System.Exception: Metadata sheetname Investigation could not be found at Microsoft.FSharp.Core.PrintfModule.PrintFormatToStringThenFail@1448.Invoke(String message) at ArcCommander.APIs.AssayAPI.Contacts.register(ArcConfiguration arcConfiguration, FSharpMap2 personArgs) at ArcCommander.Program.handleAssayContactsSubCommands@128-2.Invoke(ArcConfiguration arcConfiguration, FSharpMap2 personArgs) at ArcCommander.Program.processCommand[a,T](ArcConfiguration arcConfiguration, FSharpFunc2 commandF, ParseResults1 r) at ArcCommander.Program.handleAssayContactsSubCommands(ArcConfiguration arcConfiguration, AssayPersonCommand contactsVerb) at ArcCommander.Program.handleAssaySubCommands(ArcConfiguration arcConfiguration, AssayCommand assayVerb) at ArcCommander.Program.handleCommand(ArcConfiguration arcConfiguration, ArcCommand command) at ArcCommander.Program.main(String[] argv)

Moreover, the assay performer fields in the isa.assay.xlsx file remain empty and nothing is added to the isa.investigation.xlsx file.

Expected behavior arc a person register -a MY_ASSAY -l LASTNAME -f FIRSTNAME

with --assayidentifier or -a to pass the assay identifier

and with the information being added to the isa.assay.xlsx file as well as to the isa.investigation.xlsx file.

OS and framework information (please complete the following information):

HLWeil commented 11 months ago

Ah okay I see, the short-hand flag is of course flat out wrong and needs to be updated.

We're currently working on integrating the new back-end https://github.com/nfdi4plants/ARCtrl into the ArcCommander (It is also the back-end for the ARCitect). This should also fix many of the issues the ArcCommander has, as the ARCtrl is already well tested. Just as a heads-up.