ArcInvestigation level assays #184
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Freymaurer
commented
Sep 8, 2023
Freymaurer
commented
- Add parent option for ArcAssay and ArcStudy
- Move full ArcAssays out of ArcStudy to ArcInvestigation
HLWeil
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CI bugged?
Everything works for me locally. I even tried cloning the repo again (which also worked). |
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Also: The
https://github.com/nfdi4plants/ARCtrl/blob/developer_TopLevelAssays/src/ARCtrl/ARCtrl.fs |
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Any ideas? @Freymaurer @kMutagene |
src/ISA/ISA/ArcTypes/ArcTable.fs
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| @@ -32,6 +32,14 @@ type ArcTable = | |||
| Values = System.Collections.Generic.Dictionary<int*int,CompositeCell>() | |||
| } | |||
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| static member initWithHeaders(name,headers : ResizeArray<CompositeHeader>) = | |||
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createFromHeaders
src/ISA/ISA/ArcTypes/ArcTable.fs
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| @@ -156,7 +164,7 @@ type ArcTable = | |||
| column.Cells |> Array.iteri (fun rowIndex v -> Unchecked.setCellAt(columnIndex,rowIndex,v) this.Values) | |||
| Unchecked.fillMissingCells this.Headers this.Values | |||
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| static member updatetColumn (columnIndex:int, header: CompositeHeader, ?cells: CompositeCell []) = | |||
| static member updatedColumn (columnIndex:int, header: CompositeHeader, ?cells: CompositeCell []) = | |||
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Please update to make difference to setColumn clear
src/ISA/ISA/ArcTypes/ArcTable.fs
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| |> fun (headers, rows) -> ArcTable.create(name,headers,rows) | ||
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| /// This method is meant to update an ArcTable stored as a protocol in a study or investigation file with the information from an ArcTable actually stored as an annotation table | ||
| member this.UpdateReferenceByAnnotationTable(table:ArcTable) = |
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Maybe move to a less discoverable location
| for c in table.Columns do | ||
| this.AddColumn(c.Header, cells = c.Cells,forceReplace = true) | ||
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| static member SplitByColumnValues(columnIndex) = |
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SplitByColumnValuesAt; and comment, that this divided table rows
| ArcTable.createFromRows(table.Name,headers,rows) | ||
| ) | ||
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| static member SplitByColumnValuesByHeader(header : CompositeHeader) = |
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SplitByColumnValues, and add comment that this divides table by rows
| @@ -275,6 +278,16 @@ module Unchecked = | |||
| for missingColumn,missingRow in missingKeys do | |||
| setCellAt (missingColumn,missingRow,empty) values | |||
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| /// Increases the table size to the given new row count and fills the new rows with the last value of the column | |||
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Maybe combine with fillMissingCells and add a flag to use empty or last value
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Now that I think about it, it doesn't really match. ExtendRows does not fill up empty cells in a previously sparse table, but extends the table to a new given rowCount.
| |> ArcTables | ||
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| static member updateReferenceTablesBySheets (referenceTables : ArcTables,sheetTables : ArcTables,?keepUnusedRefTables : bool) : ArcTables = | ||
| let keepUnusedRefTables = Option.defaultValue false keepUnusedRefTables |
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Can we move this somewhere less visible?
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Will first make a static member out of it. We need a place for more complex operations that do not necessarily belong to a downstream repository.
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Whoops, this comment belongs to your comment above. Still my point remains.
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Maybe a module similiar to module ARCtrl.ISA.IdentifierSetters at the end of the arctypes folder with extensions?
src/ISA/ISA/Update.fs
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| @@ -1,5 +1,17 @@ | |||
| namespace ARCtrl.ISA.Aux | |||
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| module List = | |||
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make this internal? So we never flood namespaces.
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