Add Spawn API endpoints.

.assets/assets/manifest.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8" standalone="yes"?>
 <OfficeApp xmlns="http://schemas.microsoft.com/office/appforoffice/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.microsoft.com/office/officeappbasictypes/1.0" xmlns:ov="http://schemas.microsoft.com/office/taskpaneappversionoverrides" xsi:type="TaskPaneApp">
   <Id>5d6f5462-3401-48ec-9406-d12882e9ad83</Id>
-  <Version>0.4.5</Version>
+  <Version>0.4.6</Version>
   <ProviderName>Computational Systems Biology</ProviderName>
   <DefaultLocale>en-US</DefaultLocale>
   <DisplayName DefaultValue="Swate"/>

RELEASE_NOTES.md

@@ -1,3 +1,8 @@
+### 0.4.6+9cad63e (Released 2021-3-12)
+* Additions:
+    * latest commit #9cad63e
+    * [[#9cad63e](https://github.com/nfdi4plants/Swate/commit/9cad63e1cd456b377fe42ce1d5488412eacf19db)] Merge pull request #141 from nfdi4plants/kevinf-patch-0.4.5
+
 ### 0.4.5+b360273 (Released 2021-3-12)
 * Additions:
     * latest commit #b360273

manifest.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8" standalone="yes"?>
 <OfficeApp xmlns="http://schemas.microsoft.com/office/appforoffice/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.microsoft.com/office/officeappbasictypes/1.0" xmlns:ov="http://schemas.microsoft.com/office/taskpaneappversionoverrides" xsi:type="TaskPaneApp">
   <Id>5d6f5462-3401-48ec-9406-d12882e9ad83</Id>
-  <Version>0.4.5</Version>
+  <Version>0.4.6</Version>
   <ProviderName>Computational Systems Biology</ProviderName>
   <DefaultLocale>en-US</DefaultLocale>
   <DisplayName DefaultValue="Swate"/>

src/Client/Messages.fs

@@ -278,11 +278,11 @@ type Model = {
 
 and Msg =
     | Bounce                of (System.TimeSpan*string*Msg)
+    | DebouncerSelfMsg      of Debouncer.SelfMessage<Msg>
     | Api                   of ApiMsg
     | Dev                   of DevMsg
     | TermSearch            of TermSearchMsg
     | AdvancedSearch        of AdvancedSearchMsg
-    | DebouncerSelfMsg      of Debouncer.SelfMessage<Msg>
     | ExcelInterop          of ExcelInteropMsg
     | StyleChange           of StyleChangeMsg
     | PersistentStorage     of PersistentStorageMsg

src/Client/Model.fs

@@ -73,13 +73,18 @@ type AdvancedTermSearchOptions = {
         }
 
 type TermSearchState = {
+
     TermSearchText          : string
+
     SelectedTerm            : DbDomain.Term option
     TermSuggestions         : DbDomain.Term []
+
     ParentOntology          : OntologyInfo option
     SearchByParentOntology  : bool
+
     HasSuggestionsLoading   : bool
     ShowSuggestions         : bool
+
 } with
     static member init () = {
         TermSearchText              = ""

src/Server/Docs/DocsAnnotationAPIvs1.fs

@@ -108,21 +108,68 @@ let annotatorApiDocsv1 =
 
         ////////
         annotatorDocsv1.route <@ fun api -> api.getTermSuggestionsByParentTerm @>
-        |> annotatorDocsv1.alias "Get Terms By Parent Ontology (<code>getTermSuggestionsByParentTerm</code>)"
+        |> annotatorDocsv1.alias "Get Terms By Parent Ontology Term (<code>getTermSuggestionsByParentTerm</code>)"
         |> annotatorDocsv1.description (
             createDocumentationDescription
                 "This is a <code>getTermSuggestions</code> variant, used to reduce the number of possible hits searching only data that is in a \"is_a\" relation to the parent ontology (written at the top of the column)."
                 "If a column with a parent ontology is selected, the app will add this to the 'TermSearch' field in a static button. This can be toggled but a small slider below. If this alternative term search is active then <code>getTermSuggestionsByParentTerm</code> is executed."
                 (Some [|
                     Parameter.create "n" ParamInteger "This parameter sets the number of returned results."
                     Parameter.create "queryString" ParamString "This parameter is used to search the Term.Name column for hits."
-                    Parameter.create "parentOntology" ParamString "This parameter is used to search <b>only</b> is_a relationships by the parentOntology (Term.Name)."
+                    Parameter.create "parentOntology" DocsFunctions.PredefinedParams.OntologyInfoType "This parameter is used to search <b>only</b> is_a relationships by the parentOntology (Term.Name, Term.Accession)."
                 |])
                 "This function returns an array of matching Database.Term entries in the form of <code>DbDomain.Term []</code>."
                 (Parameter.create "Term []" (PredefinedParams.TermType |> ParamArray) "Array of database Term entries.")
         )
         |> annotatorDocsv1.example <@ fun api -> api.getTermSuggestionsByParentTerm (5,"micrOTOF-Q",PredefinedParams.Examples.ontologyInfoExmp) @>
 
+        ////////
+        annotatorDocsv1.route <@ fun api -> api.getAllTermsByParentTerm @>
+        |> annotatorDocsv1.alias "Get All Terms By Parent Ontology Term (<code>getAllTermsByParentTerm</code>)"
+        |> annotatorDocsv1.description (
+            createDocumentationDescription
+                "This is a <code>getTermSuggestions</code> variant, used to reduce the number of possible hits searching only data that is in a \"is_a\" relation to the parent ontology (written at the top of the column)."
+                "If a column with a parent ontology is selected, the app will add this to the 'TermSearch' field in a static button. This can be toggled but a small slider below. If this alternative term search is active then <code>getAllTermsByParentTerm</code> and the input field is still empty, a double click will trigger this search."
+                (Some [|
+                    Parameter.create "parentOntology" DocsFunctions.PredefinedParams.OntologyInfoType "This parameter is used to search <b>only</b> is_a relationships by the parentOntology (Term.Name, Term.Accession)."
+                |])
+                "This function returns an array of matching Database.Term entries in the form of <code>DbDomain.Term []</code>."
+                (Parameter.create "Term []" (PredefinedParams.TermType |> ParamArray) "Array of database Term entries.")
+        )
+        |> annotatorDocsv1.example <@ fun api -> api.getAllTermsByParentTerm PredefinedParams.Examples.ontologyInfoExmp @>
+
+        ////////
+        annotatorDocsv1.route <@ fun api -> api.getTermSuggestionsByChildTerm @>
+        |> annotatorDocsv1.alias "Get Terms By Child Ontology Term (<code>getTermSuggestionsByChildTerm</code>)"
+        |> annotatorDocsv1.description (
+            createDocumentationDescription
+                "This function does something similiar to <code>getTermSuggestionsByParentTerm</code>. But instead of searching children in a is_a directed search, it searches all parents in a is_a directed search."
+                "It is used purely as API endpoint for Spawn, but might be implemented for Swate in the future."
+                (Some [|
+                    Parameter.create "n" ParamInteger "This parameter sets the number of returned results."
+                    Parameter.create "queryString" ParamString "This parameter is used to search the Term.Name column for hits."
+                    Parameter.create "parentOntology" DocsFunctions.PredefinedParams.OntologyInfoType "This parameter is used to search <b>only</b> is_a relationships by the parentOntology (Term.Name, Term.Accession)."
+                |])
+                "This function returns an array of matching Database.Term entries in the form of <code>DbDomain.Term []</code>."
+                (Parameter.create "Term []" (PredefinedParams.TermType |> ParamArray) "Array of database Term entries.")
+        )
+        |> annotatorDocsv1.example <@ fun api -> api.getTermSuggestionsByChildTerm (5,"inst",PredefinedParams.Examples.ontologyInfoExmp2) @>
+
+        ////////
+        annotatorDocsv1.route <@ fun api -> api.getAllTermsByChildTerm @>
+        |> annotatorDocsv1.alias "Get All Terms By Child Ontology Term (<code>getAllTermsByChildTerm</code>)"
+        |> annotatorDocsv1.description (
+            createDocumentationDescription
+                "This is a <code>getTermSuggestions</code> variant, used to reduce the number of possible hits searching only data that is in a \"is_a\" relation to the child ontology term."
+                "It is used purely as API endpoint for Spawn, but might be implemented for Swate in the future."
+                (Some [|
+                    Parameter.create "parentOntology" DocsFunctions.PredefinedParams.OntologyInfoType "This parameter is used to search <b>only</b> is_a relationships by the parentOntology (Term.Name, Term.Accession)."
+                |])
+                "This function returns an array of matching Database.Term entries in the form of <code>DbDomain.Term []</code>."
+                (Parameter.create "Term []" (PredefinedParams.TermType |> ParamArray) "Array of database Term entries.")
+        )
+        |> annotatorDocsv1.example <@ fun api -> api.getAllTermsByParentTerm (PredefinedParams.Examples.ontologyInfoExmp2) @>
+
         ////////
         annotatorDocsv1.route <@ fun api -> api.getTermsForAdvancedSearch @>
         |> annotatorDocsv1.alias "Get Terms Advanced Search (<code>getTermsForAdvancedSearch</code>)"

src/Server/Docs/DocsFunctions.fs

@@ -129,6 +129,7 @@ module PredefinedParams =
     module Examples =
 
         let ontologyInfoExmp:OntologyInfo = OntologyInfo.create "Instrument Model" "MS:1000031"
+        let ontologyInfoExmp2:OntologyInfo = OntologyInfo.create "Q TRAP" "MS:1000187"
 
         let unitOntologyExmp:DbDomain.Ontology = {
             ID = 1L

src/Server/OntologyDB.fs

@@ -160,6 +160,36 @@ let getTermSuggestionsByParentTerm cString (query:string, parentTerm:string) =
                     (reader.GetBoolean(6))
     |]
 
+let getTermSuggestionsByChildTerm cString (query:string, childTerm:string) =
+
+    use connection = establishConnection cString
+    connection.Open()
+    use getTermSuggestionsCmd = new MySqlCommand("getTermSuggestionsByChildTerm",connection)
+    getTermSuggestionsCmd.CommandType <- CommandType.StoredProcedure
+
+    let queryParam              = getTermSuggestionsCmd.Parameters.Add("query",MySqlDbType.VarChar)
+    let childOntologyParam     = getTermSuggestionsCmd.Parameters.Add("childOntology",MySqlDbType.VarChar)
+
+    queryParam              .Value <- query
+    childOntologyParam      .Value <- childTerm
+
+    use reader = getTermSuggestionsCmd.ExecuteReader()
+    [|
+        while reader.Read() do
+            yield
+                DbDomain.createTerm
+                    (reader.GetInt64(0))
+                    (reader.GetString(1))
+                    (reader.GetInt64(2))
+                    (reader.GetString(3))
+                    (reader.GetString(4))
+                    (if (reader.IsDBNull(5)) then
+                        None
+                    else
+                        Some (reader.GetString(5)))
+                    (reader.GetBoolean(6))
+    |]
+
 let getTermByParentTermOntologyInfo cString (query:string, parentTerm:OntologyInfo) =
 
     let hasAccession = parentTerm.TermAccession <> ""
@@ -240,6 +270,45 @@ let getAllTermsByParentTermOntologyInfo cString (parentTerm:OntologyInfo) =
                     (reader.GetBoolean(6))
     |]
 
+let getAllTermsByChildTermOntologyInfo cString (childTerm:OntologyInfo) =
+
+    let hasAccession = childTerm.TermAccession <> ""
+
+    use connection = establishConnection cString
+    connection.Open()
+    use cmd =
+        if hasAccession then
+            new MySqlCommand("getAllTermsByChildTermAndAccession",connection)
+        else
+            new MySqlCommand("getAllTermsByChildTerm",connection)
+
+    cmd.CommandType <- CommandType.StoredProcedure
+
+    let parentOntologyParam     = cmd.Parameters.Add("childOntology",MySqlDbType.VarChar)
+
+    parentOntologyParam     .Value <- childTerm.Name
+
+    if hasAccession then
+        let accessionParam = cmd.Parameters.Add("childTermAccession", MySqlDbType.VarChar)
+        accessionParam      .Value <- childTerm.TermAccession
+
+    use reader = cmd.ExecuteReader()
+    [|
+        while reader.Read() do
+            yield
+                DbDomain.createTerm
+                    (reader.GetInt64(0))
+                    (reader.GetString(1))
+                    (reader.GetInt64(2))
+                    (reader.GetString(3))
+                    (reader.GetString(4))
+                    (if (reader.IsDBNull(5)) then
+                        None
+                    else
+                        Some (reader.GetString(5)))
+                    (reader.GetBoolean(6))
+    |]
+
 let getTermSuggestionsByParentTermAndAccession cString (query:string, parentTerm:string, parentTermAccession:string) =
 
     use connection = establishConnection cString
@@ -272,6 +341,38 @@ let getTermSuggestionsByParentTermAndAccession cString (query:string, parentTerm
                     (reader.GetBoolean(6))
     |]
 
+let getTermSuggestionsByChildTermAndAccession cString (query:string, childTerm:string, childTermAccession:string) =
+
+    use connection = establishConnection cString
+    connection.Open()
+    use getTermSuggestionsCmd = new MySqlCommand("getTermSuggestionsByChildTermAndAccession",connection)
+    getTermSuggestionsCmd.CommandType <- CommandType.StoredProcedure
+
+    let queryParam                  = getTermSuggestionsCmd.Parameters.Add("query",MySqlDbType.VarChar)
+    let childOntologyParam         = getTermSuggestionsCmd.Parameters.Add("childOntology",MySqlDbType.VarChar)
+    let childTermAccessionParam    = getTermSuggestionsCmd.Parameters.Add("childTermAccession",MySqlDbType.VarChar)
+
+    queryParam              .Value <- query
+    childOntologyParam     .Value <- childTerm
+    childTermAccessionParam.Value <- childTermAccession
+
+    use reader = getTermSuggestionsCmd.ExecuteReader()
+    [|
+        while reader.Read() do
+            yield
+                DbDomain.createTerm
+                    (reader.GetInt64(0))
+                    (reader.GetString(1))
+                    (reader.GetInt64(2))
+                    (reader.GetString(3))
+                    (reader.GetString(4))
+                    (if (reader.IsDBNull(5)) then
+                        None
+                    else
+                        Some (reader.GetString(5)))
+                    (reader.GetBoolean(6))
+    |]
+
 let getUnitTermSuggestions cString (query:string) =
 
     use connection = establishConnection cString

src/Server/Server.fs

@@ -109,9 +109,42 @@ let annotatorApi cString = {
     getAllTermsByParentTerm = fun (parentTerm:OntologyInfo) ->
         async {
             let searchRes =
-                OntologyDB.getAllTermsByParentTermOntologyInfo
+                OntologyDB.getAllTermsByParentTermOntologyInfo cString parentTerm
 
-            return searchRes cString parentTerm
+            return searchRes  
+        }
+
+    getTermSuggestionsByChildTerm = fun (max:int,typedSoFar:string,childTerm:OntologyInfo) ->
+        async {
+
+            let searchRes =
+                match typedSoFar with
+                | HelperFunctions.Regex HelperFunctions.isAccessionPattern foundAccession ->
+                    OntologyDB.getTermByAccession cString foundAccession
+                | _ ->
+                    let like =
+                        if childTerm.TermAccession = ""
+                        then
+                            OntologyDB.getTermSuggestionsByChildTerm cString (typedSoFar,childTerm.Name)
+                        else
+                            OntologyDB.getTermSuggestionsByChildTermAndAccession cString (typedSoFar,childTerm.Name,childTerm.TermAccession)
+                    let searchSet = typedSoFar |> Suggestion.createBigrams
+                    like
+                    |> Array.sortByDescending (fun sugg ->
+                            Suggestion.sorensenDice (Suggestion.createBigrams sugg.Name) searchSet
+                    )
+
+                    |> fun x -> x |> Array.take (if x.Length > max then max else x.Length)
+
+            return searchRes
+        }
+
+    getAllTermsByChildTerm = fun (childTerm:OntologyInfo) ->
+        async {
+            let searchRes =
+                OntologyDB.getAllTermsByChildTermOntologyInfo cString childTerm
+
+            return searchRes  
         }
 
     getTermsForAdvancedSearch = fun (ontOpt,searchName,mustContainName,searchDefinition,mustContainDefinition,keepObsolete) ->

src/Server/Version.fs

@@ -3,11 +3,11 @@ namespace System
 open System.Reflection
 
 [<assembly: AssemblyTitleAttribute("SWATE")>]
-[<assembly: AssemblyVersionAttribute("0.4.5")>]
+[<assembly: AssemblyVersionAttribute("0.4.6")>]
 [<assembly: AssemblyMetadataAttribute("ReleaseDate","12/03/2021")>]
 do ()
 
 module internal AssemblyVersionInformation =
     let [<Literal>] AssemblyTitle = "SWATE"
-    let [<Literal>] AssemblyVersion = "0.4.5"
+    let [<Literal>] AssemblyVersion = "0.4.6"
     let [<Literal>] AssemblyMetadata_ReleaseDate = "12/03/2021"

src/Shared/Shared.fs

@@ -227,6 +227,10 @@ type IAnnotatorAPIv1 = {
     getTermSuggestionsByParentTerm      : (int*string*OntologyInfo)                                     -> Async<DbDomain.Term []>
     ///
     getAllTermsByParentTerm             : OntologyInfo                                                  -> Async<DbDomain.Term []>
+    /// (nOfReturnedResults*queryString*parentOntology). If parentOntology = "" then isNull -> Error.
+    getTermSuggestionsByChildTerm       : (int*string*OntologyInfo)                                     -> Async<DbDomain.Term []>
+    ///
+    getAllTermsByChildTerm              : OntologyInfo                                                  -> Async<DbDomain.Term []>
     /// (ontOpt,searchName,mustContainName,searchDefinition,mustContainDefinition,keepObsolete)
     getTermsForAdvancedSearch           : (DbDomain.Ontology option*string*string*string*string*bool)   -> Async<DbDomain.Term []>