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ArcInvestigation level assays #184
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Freymaurer
commented
Sep 8, 2023
- Add parent option for ArcAssay and ArcStudy
- Move full ArcAssays out of ArcStudy to ArcInvestigation
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Also: The https://github.com/nfdi4plants/ARCtrl/blob/developer_TopLevelAssays/src/ARCtrl/ARCtrl.fs |
Any ideas? @Freymaurer @kMutagene |
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Please update naming and visibility issues ❤️
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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👍 lgtm