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add blanks for everything
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@Koeng101
Koeng101 committed Dec 26, 2023
1 parent c51aff9 commit 4b4d293
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Showing 4 changed files with 3,359 additions and 819 deletions.
243 changes: 164 additions & 79 deletions api/api/api.go
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Original file line number Diff line number Diff line change
Expand Up @@ -96,7 +96,7 @@ func InitializeApp() App {
app.Router.HandleFunc("/", indexHandler)
app.Router.Handle("/static/", http.StripPrefix("/static/", http.FileServer(http.FS(subFS))))
app.Router.HandleFunc("/scalar/", scalarHandler(jsonSwagger))
app.Router.HandleFunc("/api.json", func(w http.ResponseWriter, r *http.Request) { _, _ = w.Write(jsonSwagger) })
app.Router.HandleFunc("/spec.json", func(w http.ResponseWriter, r *http.Request) { _, _ = w.Write(jsonSwagger) })

// Lua handlers.
app.Router.HandleFunc("/api/execute_lua", appImpl.PostExecuteLua)
Expand All @@ -115,7 +115,7 @@ func InitializeApp() App {
app.Router.HandleFunc("/api/pcr/simple_pcr", appImpl.PostPcrSimplePcr)

// Synthesis handlers.
app.Router.HandleFunc("/api/synthesis/fragment", appImpl.PostSynthesisFragment)
app.Router.HandleFunc("/api/synthesis/fragment", appImpl.PostCloningFragment)

return app
}
Expand Down Expand Up @@ -165,9 +165,9 @@ func (app *App) ExecuteLua(data string, attachments []gen.Attachment) (string, s
L.SetGlobal("translate", L.NewFunction(app.LuaCdsTranslate))

// Add simulate functions
L.SetGlobal("fragment", L.NewFunction(app.LuaSimulateFragment))
L.SetGlobal("complex_pcr", L.NewFunction(app.LuaSimulateComplexPcr))
L.SetGlobal("pcr", L.NewFunction(app.LuaSimulatePcr))
L.SetGlobal("fragment", L.NewFunction(app.LuaCloningFragment))
L.SetGlobal("complex_pcr", L.NewFunction(app.LuaPcrComplexPcr))
L.SetGlobal("pcr", L.NewFunction(app.LuaPcrSimplePcr))

// Execute the Lua script
if err := L.DoString(data); err != nil {
Expand Down Expand Up @@ -267,6 +267,7 @@ func (app *App) LuaIoFastaParse(L *lua.LState) int {
func (app *App) PostIoFastaWrite(ctx context.Context, request gen.PostIoFastaWriteRequestObject) (gen.PostIoFastaWriteResponseObject, error) {
return nil, nil
}
func (app *App) LuaIoFastaWrite(L *lua.LState) int { return 0 }

func (app *App) PostIoGenbankParse(ctx context.Context, request gen.PostIoGenbankParseRequestObject) (gen.PostIoGenbankParseResponseObject, error) {
genbankString := *request.Body
Expand Down Expand Up @@ -298,14 +299,47 @@ func (app *App) LuaIoGenbankParse(L *lua.LState) int {
func (app *App) PostIoGenbankWrite(ctx context.Context, request gen.PostIoGenbankWriteRequestObject) (gen.PostIoGenbankWriteResponseObject, error) {
return nil, nil
}
func (app *App) LuaIoGenbankWrite(L *lua.LState) int { return 0 }

func (app *App) PostIoFastqParse(ctx context.Context, request gen.PostIoFastqParseRequestObject) (gen.PostIoFastqParseResponseObject, error) {
return nil, nil
}
func (app *App) LuaIoFastqParse(L *lua.LState) int { return 0 }

func (app *App) PostIoFastqWrite(ctx context.Context, request gen.PostIoFastqWriteRequestObject) (gen.PostIoFastqWriteResponseObject, error) {
return nil, nil
}
func (app *App) LuaIoFastqWrite(L *lua.LState) int { return 0 }

func (app *App) PostIoSlow5Parse(ctx context.Context, request gen.PostIoSlow5ParseRequestObject) (gen.PostIoSlow5ParseResponseObject, error) {
return nil, nil
}
func (app *App) LuaIoSlow5Parse(L *lua.LState) int { return 0 }

func (app *App) PostIoSlow5Write(ctx context.Context, request gen.PostIoSlow5WriteRequestObject) (gen.PostIoSlow5WriteResponseObject, error) {
return nil, nil
}
func (app *App) LuaIoSlow5Write(L *lua.LState) int { return 0 }

func (app *App) PostIoSlow5SvbCompress(ctx context.Context, request gen.PostIoSlow5SvbCompressRequestObject) (gen.PostIoSlow5SvbCompressResponseObject, error) {
return nil, nil
}
func (app *App) LuaIoSlow5SvbCompress(L *lua.LState) int { return 0 }

func (app *App) PostIoSlow5SvbDecompress(ctx context.Context, request gen.PostIoSlow5SvbDecompressRequestObject) (gen.PostIoSlow5SvbDecompressResponseObject, error) {
return nil, nil
}
func (app *App) LuaIoSlow5SvbDecompress(L *lua.LState) int { return 0 }

func (app *App) PostIoPileupParse(ctx context.Context, request gen.PostIoPileupParseRequestObject) (gen.PostIoPileupParseResponseObject, error) {
return nil, nil
}
func (app *App) LuaIoPileupParse(L *lua.LState) int { return 0 }

func (app *App) PostIoPileupWrite(ctx context.Context, request gen.PostIoPileupWriteRequestObject) (gen.PostIoPileupWriteResponseObject, error) {
return nil, nil
}
func (app *App) LuaIoPileupWrite(L *lua.LState) int { return 0 }

/*
*****************************************************************************
Expand Down Expand Up @@ -457,8 +491,8 @@ func (app *App) PostPcrComplexPcr(ctx context.Context, request gen.PostPcrComple
return gen.PostPcrComplexPcr200JSONResponse(amplicons), nil
}

// LuaSimulateComplexPcr implements complex pcr in lua.
func (app *App) LuaSimulateComplexPcr(L *lua.LState) int {
// LuaPcrComplexPcr implements complex pcr in lua.
func (app *App) LuaPcrComplexPcr(L *lua.LState) int {
templates, err := luaStringArrayToGoSlice(L, 1)
if err != nil {
L.RaiseError(err.Error())
Expand Down Expand Up @@ -494,8 +528,8 @@ func (app *App) PostPcrSimplePcr(ctx context.Context, request gen.PostPcrSimpleP
return gen.PostPcrSimplePcr200JSONResponse(amplicons[0]), nil
}

// LuaSimulatePcr implements pcr in lua
func (app *App) LuaSimulatePcr(L *lua.LState) int {
// LuaPcrSimplePcr implements pcr in lua
func (app *App) LuaPcrSimplePcr(L *lua.LState) int {
template := L.ToString(1)
forwardPrimer := L.ToString(2)
reversePrimer := L.ToString(3)
Expand All @@ -514,18 +548,27 @@ func (app *App) LuaSimulatePcr(L *lua.LState) int {
func (app *App) PostPcrPrimersDebruijnBarcodes(ctx context.Context, request gen.PostPcrPrimersDebruijnBarcodesRequestObject) (gen.PostPcrPrimersDebruijnBarcodesResponseObject, error) {
return nil, nil
}
func (app *App) LuaPcrPrimersDebruijnBarcodes(L *lua.LState) int { return 0 }

func (app *App) PostPcrPrimersMarmurDoty(ctx context.Context, request gen.PostPcrPrimersMarmurDotyRequestObject) (gen.PostPcrPrimersMarmurDotyResponseObject, error) {
return nil, nil
}
func (app *App) LuaPcrPrimersMarmurDoty(L *lua.LState) int { return 0 }

func (app *App) PostPcrPrimersSantaLucia(ctx context.Context, request gen.PostPcrPrimersSantaLuciaRequestObject) (gen.PostPcrPrimersSantaLuciaResponseObject, error) {
return nil, nil
}
func (app *App) LuaPcrPrimersSantaLucia(L *lua.LState) int { return 0 }

func (app *App) PostPcrPrimersMeltingTemperature(ctx context.Context, request gen.PostPcrPrimersMeltingTemperatureRequestObject) (gen.PostPcrPrimersMeltingTemperatureResponseObject, error) {
return nil, nil
}
func (app *App) LuaPcrPrimersMeltingTemperature(L *lua.LState) int { return 0 }

func (app *App) PostPcrPrimersDesignPrimers(ctx context.Context, request gen.PostPcrPrimersDesignPrimersRequestObject) (gen.PostPcrPrimersDesignPrimersResponseObject, error) {
return nil, nil
}
func (app *App) LuaPcrPrimersDesignPrimers(L *lua.LState) int { return 0 }

/*
*****************************************************************************
Expand All @@ -538,27 +581,30 @@ func (app *App) PostPcrPrimersMeltingTemperature(ctx context.Context, request ge
func (app *App) PostCloningGoldengate(ctx context.Context, request gen.PostCloningGoldengateRequestObject) (gen.PostCloningGoldengateResponseObject, error) {
return nil, nil
}
func (app *App) LuaCloningGoldengate(L *lua.LState) int { return 0 }
func (app *App) PostCloningLigate(ctx context.Context, request gen.PostCloningLigateRequestObject) (gen.PostCloningLigateResponseObject, error) {
return nil, nil
}
func (app *App) LuaCloningLigate(L *lua.LState) int { return 0 }
func (app *App) PostCloningRestrictionDigest(ctx context.Context, request gen.PostCloningRestrictionDigestRequestObject) (gen.PostCloningRestrictionDigestResponseObject, error) {
return nil, nil
}
func (app *App) PostSynthesisFragment(ctx context.Context, request gen.PostSynthesisFragmentRequestObject) (gen.PostSynthesisFragmentResponseObject, error) {
func (app *App) LuaCloningRestrictionDigest(L *lua.LState) int { return 0 }
func (app *App) PostCloningFragment(ctx context.Context, request gen.PostCloningFragmentRequestObject) (gen.PostCloningFragmentResponseObject, error) {
var excludeOverhangs []string
overhangs := *request.Body.ExcludeOverhangs
if overhangs != nil {
excludeOverhangs = overhangs
}
fragments, efficiency, err := fragment.Fragment(request.Body.Sequence, request.Body.MinFragmentSize, request.Body.MaxFragmentSize, excludeOverhangs)
if err != nil {
return gen.PostSynthesisFragment500TextResponse(fmt.Sprintf("Got internal server error: %s", err)), nil
return gen.PostCloningFragment500TextResponse(fmt.Sprintf("Got internal server error: %s", err)), nil
}
return gen.PostSynthesisFragment200JSONResponse{Fragments: fragments, Efficiency: float32(efficiency)}, nil
return gen.PostCloningFragment200JSONResponse{Fragments: fragments, Efficiency: float32(efficiency)}, nil
}

// LuaSimulateFragment implements fragment in lua.
func (app *App) LuaSimulateFragment(L *lua.LState) int {
// LuaCloningFragment implements fragment in lua.
func (app *App) LuaCloningFragment(L *lua.LState) int {
sequence := L.ToString(1)
minFragmentSize := L.ToInt(2)
maxFragmentSize := L.ToInt(3)
Expand Down Expand Up @@ -591,17 +637,20 @@ func (app *App) LuaSimulateFragment(L *lua.LState) int {
*****************************************************************************
*/

//func (app *App) x(ctx context.Context, request gen.RequestObject) (gen.ResponseObject, error) {
// return nil, nil
//}
//
//func (app *App) x(ctx context.Context, request gen.RequestObject) (gen.ResponseObject, error) {
// return nil, nil
//}
//
//func (app *App) x(ctx context.Context, request gen.RequestObject) (gen.ResponseObject, error) {
// return nil, nil
//}
func (app *App) PostFoldingZuker(ctx context.Context, request gen.PostFoldingZukerRequestObject) (gen.PostFoldingZukerResponseObject, error) {
return nil, nil
}
func (app *App) LuaFoldingZuker(L *lua.LState) int { return 0 }

func (app *App) PostFoldingLinearfoldContraFoldV2(ctx context.Context, request gen.PostFoldingLinearfoldContraFoldV2RequestObject) (gen.PostFoldingLinearfoldContraFoldV2ResponseObject, error) {
return nil, nil
}
func (app *App) LuaFoldingLinearfoldContraFoldV2(L *lua.LState) int { return 0 }

func (app *App) PostFoldingLinearfoldViennaRnaFold(ctx context.Context, request gen.PostFoldingLinearfoldViennaRnaFoldRequestObject) (gen.PostFoldingLinearfoldViennaRnaFoldResponseObject, error) {
return nil, nil
}
func (app *App) LuaFoldingLinearfoldViennaRnaFold(L *lua.LState) int { return 0 }

/*
*****************************************************************************
Expand All @@ -611,12 +660,15 @@ func (app *App) LuaSimulateFragment(L *lua.LState) int {
*****************************************************************************
*/

//func (app *App) x(ctx context.Context, request gen.RequestObject) (gen.ResponseObject, error) {
// return nil, nil
//}
//func (app *App) x(ctx context.Context, request gen.RequestObject) (gen.ResponseObject, error) {
// return nil, nil
//}
func (app *App) PostSeqhash(ctx context.Context, request gen.PostSeqhashRequestObject) (gen.PostSeqhashResponseObject, error) {
return nil, nil
}
func (app *App) LuaSeqhash(L *lua.LState) int { return 0 }

func (app *App) PostSeqhashFragment(ctx context.Context, request gen.PostSeqhashFragmentRequestObject) (gen.PostSeqhashFragmentResponseObject, error) {
return nil, nil
}
func (app *App) LuaSeqhashFragment(L *lua.LState) int { return 0 }

/*
*****************************************************************************
Expand All @@ -626,24 +678,35 @@ func (app *App) LuaSimulateFragment(L *lua.LState) int {
*****************************************************************************
*/

//func (app *App) x(ctx context.Context, request gen.RequestObject) (gen.ResponseObject, error) {
// return nil, nil
//}
//func (app *App) x(ctx context.Context, request gen.RequestObject) (gen.ResponseObject, error) {
// return nil, nil
//}
//func (app *App) x(ctx context.Context, request gen.RequestObject) (gen.ResponseObject, error) {
// return nil, nil
//}
//func (app *App) x(ctx context.Context, request gen.RequestObject) (gen.ResponseObject, error) {
// return nil, nil
//}
//func (app *App) x(ctx context.Context, request gen.RequestObject) (gen.ResponseObject, error) {
// return nil, nil
//}
//func (app *App) x(ctx context.Context, request gen.RequestObject) (gen.ResponseObject, error) {
// return nil, nil
//}
func (app *App) PostCodonTablesFromGenbank(ctx context.Context, request gen.PostCodonTablesFromGenbankRequestObject) (gen.PostCodonTablesFromGenbankResponseObject, error) {
return nil, nil
}
func (app *App) LuaCodonTablesFromGenbank(L *lua.LState) int { return 0 }

func (app *App) PostCodonTablesNew(ctx context.Context, request gen.PostCodonTablesNewRequestObject) (gen.PostCodonTablesNewResponseObject, error) {
return nil, nil
}
func (app *App) LuaCodonTablesNew(L *lua.LState) int { return 0 }

func (app *App) PostCodonTablesCompromiseTables(ctx context.Context, request gen.PostCodonTablesCompromiseTablesRequestObject) (gen.PostCodonTablesCompromiseTablesResponseObject, error) {
return nil, nil
}
func (app *App) LuaCodonTablesCompromiseTables(L *lua.LState) int { return 0 }

func (app *App) PostCodonTablesAddTables(ctx context.Context, request gen.PostCodonTablesAddTablesRequestObject) (gen.PostCodonTablesAddTablesResponseObject, error) {
return nil, nil
}
func (app *App) LuaCodonTablesAddTables(L *lua.LState) int { return 0 }

func (app *App) GetCodonTablesDefaultOrganisms(ctx context.Context, request gen.GetCodonTablesDefaultOrganismsRequestObject) (gen.GetCodonTablesDefaultOrganismsResponseObject, error) {
return nil, nil
}
func (app *App) LuaCodonTablesDefaultOrganisms(L *lua.LState) int { return 0 }

func (app *App) PostCodonTablesGetOrganismTable(ctx context.Context, request gen.PostCodonTablesGetOrganismTableRequestObject) (gen.PostCodonTablesGetOrganismTableResponseObject, error) {
return nil, nil
}
func (app *App) LuaCodonTablesGetOrganismTable(L *lua.LState) int { return 0 }

/*
*****************************************************************************
Expand All @@ -653,18 +716,25 @@ func (app *App) LuaSimulateFragment(L *lua.LState) int {
*****************************************************************************
*/

//func (app *App) x(ctx context.Context, request gen.RequestObject) (gen.ResponseObject, error) {
// return nil, nil
//}
//func (app *App) x(ctx context.Context, request gen.RequestObject) (gen.ResponseObject, error) {
// return nil, nil
//}
//func (app *App) x(ctx context.Context, request gen.RequestObject) (gen.ResponseObject, error) {
// return nil, nil
//}
//func (app *App) x(ctx context.Context, request gen.RequestObject) (gen.ResponseObject, error) {
// return nil, nil
//}
func (app *App) PostAlignNeedlemanWunsch(ctx context.Context, request gen.PostAlignNeedlemanWunschRequestObject) (gen.PostAlignNeedlemanWunschResponseObject, error) {
return nil, nil
}
func (app *App) LuaAlignNeedlemanWunsch(L *lua.LState) int { return 0 }

func (app *App) PostAlignSmithWaterman(ctx context.Context, request gen.PostAlignSmithWatermanRequestObject) (gen.PostAlignSmithWatermanResponseObject, error) {
return nil, nil
}
func (app *App) LuaAlignSmithWaterman(L *lua.LState) int { return 0 }

func (app *App) PostAlignMash(ctx context.Context, request gen.PostAlignMashRequestObject) (gen.PostAlignMashResponseObject, error) {
return nil, nil
}
func (app *App) LuaPostAlignMash(L *lua.LState) int { return 0 }

func (app *App) PostAlignMashMany(ctx context.Context, request gen.PostAlignMashManyRequestObject) (gen.PostAlignMashManyResponseObject, error) {
return nil, nil
}
func (app *App) LuaAlignMashMany(L *lua.LState) int { return 0 }

/*
*****************************************************************************
Expand All @@ -674,15 +744,15 @@ func (app *App) LuaSimulateFragment(L *lua.LState) int {
*****************************************************************************
*/

//func (app *App) x(ctx context.Context, request gen.RequestObject) (gen.ResponseObject, error) {
// return nil, nil
//}
//func (app *App) x(ctx context.Context, request gen.RequestObject) (gen.ResponseObject, error) {
// return nil, nil
//}
//func (app *App) x(ctx context.Context, request gen.RequestObject) (gen.ResponseObject, error) {
// return nil, nil
//}
func (app *App) PostUtilsReverseComplement(ctx context.Context, request gen.PostUtilsReverseComplementRequestObject) (gen.PostUtilsReverseComplementResponseObject, error) {
return nil, nil
}
func (app *App) Lua(L *lua.LState) int { return 0 }

func (app *App) PostUtilsIsPalindromic(ctx context.Context, request gen.PostUtilsIsPalindromicRequestObject) (gen.PostUtilsIsPalindromicResponseObject, error) {
return nil, nil
}
func (app *App) LuaUtilsIsPalindromic(L *lua.LState) int { return 0 }

/*
*****************************************************************************
Expand All @@ -692,15 +762,30 @@ func (app *App) LuaSimulateFragment(L *lua.LState) int {
*****************************************************************************
*/

func (app *App) PostRandomRandomDna(ctx context.Context, request gen.PostRandomRandomDnaRequestObject) (gen.PostRandomRandomDnaResponseObject, error) {
return nil, nil
}
func (app *App) LuaRandomRandomDna(L *lua.LState) int { return 0 }

func (app *App) PostRandomRandomRna(ctx context.Context, request gen.PostRandomRandomRnaRequestObject) (gen.PostRandomRandomRnaResponseObject, error) {
return nil, nil
}
func (app *App) LuaRandomRandomRna(L *lua.LState) int { return 0 }

func (app *App) PostRandomRandomProtein(ctx context.Context, request gen.PostRandomRandomProteinRequestObject) (gen.PostRandomRandomProteinResponseObject, error) {
return nil, nil
}
func (app *App) LuaRandomRandomProtein(L *lua.LState) int { return 0 }

/*
*****************************************************************************
# Template for functions
*****************************************************************************
*/
//func (app *App) Lua(L *lua.LState) int { return 0 }
//func (app *App) x(ctx context.Context, request gen.RequestObject) (gen.ResponseObject, error) {
// return nil, nil
//}
//
//func (app *App) x(ctx context.Context, request gen.RequestObject) (gen.ResponseObject, error) {
// return nil, nil
//}
//
//func (app *App) x(ctx context.Context, request gen.RequestObject) (gen.ResponseObject, error) {
// return nil, nil
//}
//
//func (app *App) Lua(L *lua.LState) int { return 0 }
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