Merge pull request #581 from nfdi4plants/Debug_Excel_FixFindAllChildT…

…erms

implement working updated version of findAllChildTerms

src/Client/OfficeInterop/OfficeInterop.fs

@@ -9,7 +9,7 @@ open GlobalBindings
 
 open Shared
 open Database
-open DTO
+open DTOs.TermQuery
 
 open OfficeInterop
 open OfficeInterop.ExcelUtil
@@ -1635,7 +1635,7 @@ let validateSelectedAndNeighbouringBuildingBlocks () =
 /// <param name="names"></param>
 let searchTermInDatabase name =
     promise {
-        let term = TermQuery.create(name, searchMode=Database.FullTextSearch.Exact)
+        let term = TermQueryDto.create(name, searchMode=Database.FullTextSearch.Exact)
         let! results = Async.StartAsPromise(Api.ontology.searchTerm term)
         let result = Array.tryHead results
         return result
@@ -1650,7 +1650,7 @@ let searchTermsInDatabase names =
         let terms =
             names
             |> List.map (fun name ->
-                TermQuery.create(name, searchMode=Database.FullTextSearch.Exact)
+                TermQueryDto.create(name, searchMode=Database.FullTextSearch.Exact)
             )
             |> Array.ofSeq
         let! result = Async.StartAsPromise(Api.ontology.searchTerms terms)

src/Client/SharedComponents/TermSearchInput.fs

@@ -6,7 +6,8 @@ open Browser.Types
 open ARCtrl
 open Shared
 open Shared.Database
-open DTO
+open Shared.DTOs.TermQuery
+open Shared.DTOs.ParentTermQuery
 open Fable.Core.JsInterop
 
 module TermSearchAux =
@@ -30,22 +31,23 @@ module TermSearchAux =
 
     let searchByName(query: string, setResults: Term [] -> unit) =
         async {
-            let query = TermQuery.create(query, 10)
+            let query = TermQueryDto.create(query, 10)
             let! terms = Api.ontology.searchTerm query
             setResults terms
         }
 
     let searchByParent(query: string, parentTAN: string, setResults: Term [] -> unit) =
         async {
-            let query = TermQuery.create(query, 50, parentTAN)
+            let query = TermQueryDto.create(query, 50, parentTAN)
             let! terms = Api.ontology.searchTerm query
             setResults terms
         }
 
-    let searchAllByParent(parentTAN: string, setResults: Term [] -> unit) =
+    let findAllChildTerms(parentTAN: string, setResults: Term [] -> unit) =
         async {
-            let! terms = Api.api.getAllTermsByParentTerm <| Shared.SwateObsolete.TermMinimal.create "" parentTAN
-            setResults terms
+            let query = ParentTermQueryDto.create(parentTAN, 50)
+            let! terms = Api.ontology.findAllChildTerms query
+            setResults terms.results
         }
 
     let allByParentSearch (
@@ -61,7 +63,7 @@ module TermSearchAux =
                 async {
                     ClickOutsideHandler.AddListener(SelectAreaID, fun e -> stopSearch())
                 }
-                searchAllByParent(parent.TermAccessionShort, fun terms -> setSearchTreeState {Results = terms; SearchIs = SearchIs.Done})
+                findAllChildTerms(parent.TermAccessionShort, fun terms -> setSearchTreeState {Results = terms; SearchIs = SearchIs.Done})
             ]
             |> Async.Parallel
             |> Async.Ignore

src/Server/Api/IOntologyAPI.fs

@@ -3,7 +3,8 @@ module API.IOntologyAPI
 open Shared
 open Database
 
-open DTO
+open DTOs.TermQuery
+open DTOs.ParentTermQuery
 open Fable.Remoting.Server
 open Fable.Remoting.Giraffe
 open ARCtrl
@@ -26,7 +27,7 @@ module Helper =
     module V3 =
         open ARCtrl.Helper.Regex.ActivePatterns
 
-        let searchSingleTerm credentials (content: TermQuery) =
+        let searchSingleTerm credentials (content: TermQueryDto) =
             async {
                 let dbSearchRes =
                     match content.query.Trim() with
@@ -46,12 +47,20 @@ module Helper =
                 return dbSearchRes
             }
 
+        let searchChildTerms credentials (content: ParentTermQueryDto) =
+            async {
+                let dbSearchRes = 
+                    Term.Term(credentials).findAllChildTerms(content.parentTermId, ?limit=content.limit) |> Array.ofSeq
+
+                return dbSearchRes
+            }
+
 open Helper
 
 [<RequireQualifiedAccess>]
 module V3 =
 
-    let ontologyApi (credentials : Helper.Neo4JCredentials) : IOntologyAPIv3 =
+    let ontologyApi (credentials: Helper.Neo4JCredentials) : IOntologyAPIv3 =
         {
             //Development
             getTestNumber = 
@@ -68,7 +77,7 @@ module V3 =
                             Helper.V3.searchSingleTerm credentials query
                     ]
                     let! results = asyncQueries |> Async.Parallel
-                    let zipped = Array.map2 (fun a b -> TermQueryResults.create(a,b)) queries results
+                    let zipped = Array.map2 (fun a b -> TermQueryDtoResults.create(a,b)) queries results
                     return zipped
                 }
             getTermById = fun id  ->
@@ -80,6 +89,12 @@ module V3 =
                         | 0 -> None
                         | _ -> failwith $"Found multiple terms with the same accession: {id}" // must be multiples as negative cannot exist for length
                 }
+            findAllChildTerms  = fun content ->
+                async {
+                    let! results = Helper.V3.searchChildTerms credentials content
+                    let zipped = ParentTermQueryDtoResults.create(content, results)
+                    return zipped
+                }
         }
 
     let createIOntologyApi credentials =
@@ -97,7 +112,7 @@ open Shared.SwateObsolete.Regex
 module V1 =
 
     /// <summary>Deprecated</summary>
-    let ontologyApi (credentials : Helper.Neo4JCredentials) : IOntologyAPIv1 =
+    let ontologyApi (credentials: Helper.Neo4JCredentials) : IOntologyAPIv1 =
         /// We use sorensen dice to avoid scoring mutliple occassions of the same word (Issue https://github.com/nfdi4plants/Swate/issues/247)
         let sorensenDiceSortTerms (searchStr:string) (terms: Term []) =
             terms |> SorensenDice.sortBySimilarity searchStr (fun term -> term.Name)
@@ -193,7 +208,7 @@ module V1 =
                     return filteredResult
                 }
 
-            getUnitTermSuggestions = fun (max:int,typedSoFar:string) ->
+            getUnitTermSuggestions = fun (max:int, typedSoFar:string) ->
                 async {
                     let dbSearchRes =
                         match typedSoFar with
@@ -207,7 +222,7 @@ module V1 =
                     return res
                 }
 
-            getTermsByNames = fun (queryArr) ->
+            getTermsByNames = fun queryArr ->
                 async {
                     // check if search string is empty. This case should delete TAN- and TSR- values in table
                     let filteredQueries = queryArr |> Array.filter (fun x -> x.Term.Name <> "" || x.Term.TermAccession <> "")
@@ -224,7 +239,7 @@ module V1 =
                                 Term.TermQuery.getByName(searchTerm.Term.Name, searchType=FullTextSearch.Exact)
                         )
                     let result =
-                        Helper.Neo4j.runQueries(queries,credentials)
+                        Helper.Neo4j.runQueries(queries, credentials)
                         |> Array.map2 (fun termSearchable dbResults ->
                             // replicate if..elif..else conditions from 'queries'
                             if termSearchable.Term.TermAccession <> "" then

src/Server/Database/Term.fs

@@ -1,7 +1,6 @@
 module Database.Term
 
 open Neo4j.Driver
-open Shared.DTO
 open Shared.Database
 open Shared.SwateObsolete
 open Helper
@@ -103,7 +102,7 @@ type Term(?credentials:Neo4JCredentials, ?session:IAsyncSession) =
         let limit = defaultArg limit 5
         let searchNameQuery = Queries.NameQueryFullText ("node", limit=true)
         let searchTreeQuery =
-          """MATCH (node:Term)
+            """MATCH (node:Term)
     WHERE node.accession IN $AccessionList
     MATCH (endNode:Term {accession: $Parent})
     MATCH (node)
@@ -185,6 +184,47 @@ type Term(?credentials:Neo4JCredentials, ?session:IAsyncSession) =
             printfn "%s" exn.Message
             [||]
 
+    /// <summary>
+    /// Find all child terms of a given parent
+    /// </summary>
+    /// <param name="parentId"></param>
+    /// <param name="limit"></param>
+    member this.findAllChildTerms(parentId: string, ?limit: int) =
+        let limit = defaultArg limit 5
+
+        let query =
+            """MATCH (child)-[:is_a*]->(:Term {accession: $Parent})
+            RETURN child.accession, child.name, child.definition, child.is_obsolete
+            LIMIT $Limit"""
+
+        let config = Action<TransactionConfigBuilder>(fun (config : TransactionConfigBuilder) -> config.WithTimeout(TimeSpan.FromSeconds(0.5)) |> ignore)
+        use session = if session.IsSome then session.Value else Neo4j.establishConnection(credentials.Value)
+        let main = 
+            task {
+                let! tree_query = 
+                    let parameters = System.Collections.Generic.Dictionary<string,obj>([
+                        KeyValuePair("Parent", box parentId);
+                        KeyValuePair("Limit", box limit)
+                    ])
+                    session.RunAsync(query, parameters, config)
+
+                let! tree_records = tree_query.ToListAsync()
+                let tree_results =
+                    [|
+                        for record in tree_records do
+                            yield Term.asTerm("child") record
+                    |]
+            return tree_results
+            }
+        try
+            main.Result
+        with
+            | exn -> 
+            printfn "%s" exn.Message
+            [||]
+
+        //Neo4j.runQuery(query, param, (Term.asTerm("child")), ?session=session, ?credentials=credentials)
+
     /// This function will allow for raw apache lucene input. It is possible to search either term name or description or both.
     /// The function will error if both term name and term description are None.
     member this.getByAdvancedTermSearch(advancedSearchOptions:Shared.AdvancedSearchTypes.AdvancedSearchOptions) =

src/Server/Database/TreeSearch.fs

@@ -3,7 +3,7 @@ module Database.TreeSearch
 open System
 open Neo4j.Driver
 
-open Shared.DTO
+open Shared.DTOs
 open Shared.Database
 open Shared.Database.TreeTypes
 

src/Shared/DTOs/ParentTermQueryDto.fs

@@ -0,0 +1,21 @@
+module Shared.DTOs.ParentTermQuery
+
+open Shared
+
+type ParentTermQueryDto = {
+    parentTermId: string
+    limit: int option
+} with
+    static member create(parentTermId, ?limit) = {
+        parentTermId = parentTermId
+        limit = limit
+    }
+
+type ParentTermQueryDtoResults = {
+    query: ParentTermQueryDto
+    results: Database.Term []
+} with
+    static member create(query, results) = {
+        query = query
+        results = results
+    }

src/Shared/DTO.fs → src/Shared/DTOs/TermQueryDto.fs

@@ -1,10 +1,8 @@
-module Shared.DTO
+module Shared.DTOs.TermQuery
 
-open ARCtrl
+open Shared
 
-open Database
-
-type TermQuery = {
+type TermQueryDto = {
     query: string
     limit: int option
     parentTermId: string option
@@ -19,12 +17,11 @@ type TermQuery = {
         searchMode = searchMode
     }
 
-type TermQueryResults = {
-    query: TermQuery
-    results: Term []
+type TermQueryDtoResults = {
+    query: TermQueryDto
+    results: Database.Term []
 } with
     static member create(query, results) = {
         query = query
         results = results
-    }
-
+    }

src/Shared/Shared.fs

@@ -3,7 +3,8 @@ namespace Shared
 open System
 open Shared
 open Database
-open DTO
+open DTOs.TermQuery
+open DTOs.ParentTermQuery
 
 [<AutoOpen>]
 module Regex =
@@ -46,10 +47,12 @@ module SorensenDice =
 
 type IOntologyAPIv3 = {
     // Development
-    getTestNumber : unit -> Async<int>
-    searchTerm: TermQuery -> Async<Term []>
-    searchTerms: TermQuery[] -> Async<TermQueryResults[]>
-    getTermById: string -> Async<Term option>
+    getTestNumber           : unit                  -> Async<int>
+    searchTerm              : TermQueryDto          -> Async<Term []>
+    searchTerms             : TermQueryDto[]        -> Async<TermQueryDtoResults[]>
+    getTermById             : string                -> Async<Term option>
+    findAllChildTerms       : ParentTermQueryDto    -> Async<ParentTermQueryDtoResults>
+
 }
 
 /// Development api

src/Shared/Shared.fsproj

@@ -5,10 +5,11 @@
   </PropertyGroup>
   <ItemGroup>
     <Compile Include="Database.fs" />
+    <Compile Include="DTOs\ParentTermQueryDto.fs" />
+    <Compile Include="DTOs\TermQueryDto.fs" />
     <Compile Include="Extensions.fs" />
     <Compile Include="StaticTermCollection.fs" />
     <Compile Include="URLs.fs" />
-    <Compile Include="DTO.fs" />
     <Compile Include="ARCtrl.Helper.fs" />
     <Compile Include="AdvancedSearchTypes.fs" />
     <Compile Include="Shared.fs" />