@nfdi4plants/arctrl 1.0.7 → 1.2.0

package/ISA/ISA.Json/Protocol.js

@@ -1,19 +1,25 @@
-import { value as value_19 } from "../../fable_modules/fable-library.4.5.0/Option.js";
+import { value as value_13 } from "../../fable_modules/fable-library-js.4.13.0/Option.js";
 import { URIModule_toString } from "../ISA/JsonTypes/URI.js";
-import { toString, nil, object as object_18 } from "../../fable_modules/Thoth.Json.10.1.0/Encode.fs.js";
-import { choose } from "../../fable_modules/fable-library.4.5.0/List.js";
-import { uncurry2, equals } from "../../fable_modules/fable-library.4.5.0/Util.js";
-import { empty, singleton, append, delay, toList } from "../../fable_modules/fable-library.4.5.0/Seq.js";
-import { ConverterOptions__set_IncludeType_Z1FBCCD16, ConverterOptions__set_SetID_Z1FBCCD16, ConverterOptions_$ctor, ConverterOptions__get_IncludeType, ConverterOptions__get_SetID } from "./ConverterOptions.js";
-import { tryInclude } from "./GEncode.js";
+import { ofArray, choose } from "../../fable_modules/fable-library-js.4.13.0/List.js";
+import { equals } from "../../fable_modules/fable-library-js.4.13.0/Util.js";
+import { Json } from "../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+import { empty, singleton, append, delay, toList } from "../../fable_modules/fable-library-js.4.13.0/Seq.js";
+import { ConverterOptions__set_IncludeContext_Z1FBCCD16, ConverterOptions__set_IncludeType_Z1FBCCD16, ConverterOptions__set_SetID_Z1FBCCD16, ConverterOptions_$ctor, ConverterOptions__get_IncludeContext, ConverterOptions__get_IncludeType, ConverterOptions__get_SetID } from "./ConverterOptions.js";
+import { tryIncludeList, tryInclude } from "./GEncode.js";
+import { list as list_1 } from "../../fable_modules/Thoth.Json.Core.0.2.1/Encode.fs.js";
 import { OntologyAnnotation_decoder, OntologyAnnotation_encoder } from "./Ontology.js";
-import { list as list_1, string, object as object_19 } from "../../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
-import { fromJsonString, uri } from "./Decode.js";
+import { context_jsonvalue } from "./context/rocrate/isa_protocol_parameter_context.js";
+import { list as list_2, string, object } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
+import { uri } from "./Decode.js";
 import { ProtocolParameter } from "../ISA/JsonTypes/ProtocolParameter.js";
-import { replace } from "../../fable_modules/fable-library.4.5.0/String.js";
-import { Result_Map } from "../../fable_modules/fable-library.4.5.0/Choice.js";
+import { fromString } from "../../fable_modules/Thoth.Json.JavaScript.0.1.0/Decode.fs.js";
+import { replace, printf, toText } from "../../fable_modules/fable-library-js.4.13.0/String.js";
+import { toString } from "../../fable_modules/Thoth.Json.JavaScript.0.1.0/Encode.fs.js";
+import { context_jsonvalue as context_jsonvalue_1 } from "./context/rocrate/isa_component_context.js";
+import { Result_Map } from "../../fable_modules/fable-library-js.4.13.0/Result.js";
 import { Component, Component_decomposeName_Z721C83C5 } from "../ISA/JsonTypes/Component.js";
-import { decoder as decoder_3, encoder } from "./Comment.js";
+import { decoder as decoder_1, encoder } from "./Comment.js";
+import { context_jsonvalue as context_jsonvalue_2 } from "./context/rocrate/isa_protocol_context.js";
 import { Protocol } from "../ISA/JsonTypes/Protocol.js";
 
 export function ProtocolParameter_genID(pp) {
@@ -35,7 +41,7 @@ export function ProtocolParameter_genID(pp) {
         }
         switch (matchResult) {
             case 0:
-                return "#Param_" + value_19(n_1.ID);
+                return "#Param_" + value_13(n_1.ID);
             default:
                 return "#EmptyProtocolParameter";
         }
@@ -46,36 +52,32 @@ export function ProtocolParameter_genID(pp) {
 }
 
 export function ProtocolParameter_encoder(options, oa) {
-    return object_18(choose((tupledArg) => {
+    return new Json(5, [choose((tupledArg) => {
         const v = tupledArg[1];
-        if (equals(v, nil)) {
+        if (equals(v, new Json(3, []))) {
             return void 0;
         }
         else {
             return [tupledArg[0], v];
         }
-    }, toList(delay(() => {
-        let value, s;
-        return append(ConverterOptions__get_SetID(options) ? singleton(["@id", (value = ProtocolParameter_genID(oa), (typeof value === "string") ? ((s = value, s)) : nil)]) : singleton(tryInclude("@id", (value_2) => {
-            let s_1;
-            const value_3 = value_2;
-            return (typeof value_3 === "string") ? ((s_1 = value_3, s_1)) : nil;
-        }, oa["ID"])), delay(() => {
-            let value_5, s_2;
-            return append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", (value_5 = "ProtocolParameter", (typeof value_5 === "string") ? ((s_2 = value_5, s_2)) : nil)]) : empty(), delay(() => singleton(tryInclude("parameterName", (oa_1) => OntologyAnnotation_encoder(options, oa_1), oa["ParameterName"]))));
-        }));
-    }))));
+    }, toList(delay(() => append(ConverterOptions__get_SetID(options) ? singleton(["@id", new Json(0, [ProtocolParameter_genID(oa)])]) : singleton(tryInclude("@id", (value_1) => (new Json(0, [value_1])), oa.ID)), delay(() => append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", list_1(ofArray([new Json(0, ["ProtocolParameter"]), new Json(0, ["ArcProtocolParameter"])]))]) : empty(), delay(() => append(singleton(tryInclude("parameterName", (oa_1) => OntologyAnnotation_encoder(options, oa_1), oa.ParameterName)), delay(() => (ConverterOptions__get_IncludeContext(options) ? singleton(["@context", context_jsonvalue]) : empty()))))))))))]);
 }
 
 export function ProtocolParameter_decoder(options) {
-    return (path) => ((v) => object_19((get$) => {
+    return object((get$) => {
         let objectArg, arg_3, objectArg_1;
-        return new ProtocolParameter((objectArg = get$.Optional, objectArg.Field("@id", uri)), (arg_3 = OntologyAnnotation_decoder(options), (objectArg_1 = get$.Optional, objectArg_1.Field("parameterName", uncurry2(arg_3)))));
-    }, path, v));
+        return new ProtocolParameter((objectArg = get$.Optional, objectArg.Field("@id", uri)), (arg_3 = OntologyAnnotation_decoder(options), (objectArg_1 = get$.Optional, objectArg_1.Field("parameterName", arg_3))));
+    });
 }
 
 export function ProtocolParameter_fromJsonString(s) {
-    return fromJsonString(uncurry2(ProtocolParameter_decoder(ConverterOptions_$ctor())), s);
+    const matchValue = fromString(ProtocolParameter_decoder(ConverterOptions_$ctor()), s);
+    if (matchValue.tag === 1) {
+        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
+    }
+    else {
+        return matchValue.fields[0];
+    }
 }
 
 export function ProtocolParameter_toString(p) {
@@ -85,11 +87,16 @@ export function ProtocolParameter_toString(p) {
 /**
  * exports in json-ld format
  */
-export function ProtocolParameter_toStringLD(p) {
+export function ProtocolParameter_toJsonldString(p) {
     let returnVal;
     return toString(2, ProtocolParameter_encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), p));
 }
 
+export function ProtocolParameter_toJsonldStringWithContext(a) {
+    let returnVal;
+    return toString(2, ProtocolParameter_encoder((returnVal = ConverterOptions_$ctor(), (((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), ConverterOptions__set_IncludeContext_Z1FBCCD16(returnVal, true)), returnVal)), a));
+}
+
 export function Component_genID(c) {
     const matchValue = c.ComponentName;
     if (matchValue == null) {
@@ -101,48 +108,47 @@ export function Component_genID(c) {
 }
 
 export function Component_encoder(options, oa) {
-    return object_18(choose((tupledArg) => {
+    return new Json(5, [choose((tupledArg) => {
         const v = tupledArg[1];
-        if (equals(v, nil)) {
+        if (equals(v, new Json(3, []))) {
             return void 0;
         }
         else {
             return [tupledArg[0], v];
         }
-    }, toList(delay(() => {
-        let value, s;
-        return append(ConverterOptions__get_SetID(options) ? singleton(["@id", (value = Component_genID(oa), (typeof value === "string") ? ((s = value, s)) : nil)]) : empty(), delay(() => {
-            let value_2, s_1;
-            return append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", (value_2 = "Component", (typeof value_2 === "string") ? ((s_1 = value_2, s_1)) : nil)]) : empty(), delay(() => append(singleton(tryInclude("componentName", (value_4) => {
-                let s_2;
-                const value_5 = value_4;
-                return (typeof value_5 === "string") ? ((s_2 = value_5, s_2)) : nil;
-            }, oa["ComponentName"])), delay(() => singleton(tryInclude("componentType", (oa_1) => OntologyAnnotation_encoder(options, oa_1), oa["ComponentType"]))))));
-        }));
-    }))));
-}
-
-export function Component_decoder(options, s, json) {
-    return Result_Map((c) => {
-        let patternInput;
-        const matchValue = c.ComponentName;
-        if (matchValue == null) {
-            patternInput = [void 0, void 0];
-        }
-        else {
-            const tupledArg = Component_decomposeName_Z721C83C5(matchValue);
-            patternInput = [tupledArg[0], tupledArg[1]];
-        }
-        return new Component(c.ComponentName, patternInput[0], patternInput[1], c.ComponentType);
-    }, object_19((get$) => {
-        let objectArg, arg_3, objectArg_1;
-        return new Component((objectArg = get$.Optional, objectArg.Field("componentName", uri)), void 0, void 0, (arg_3 = OntologyAnnotation_decoder(options), (objectArg_1 = get$.Optional, objectArg_1.Field("componentType", uncurry2(arg_3)))));
-    }, s, json));
+    }, toList(delay(() => append(ConverterOptions__get_SetID(options) ? singleton(["@id", new Json(0, [Component_genID(oa)])]) : empty(), delay(() => append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", list_1(ofArray([new Json(0, ["Component"]), new Json(0, ["ArcComponent"])]))]) : empty(), delay(() => append(singleton(tryInclude("componentName", (value_3) => (new Json(0, [value_3])), oa.ComponentName)), delay(() => append(singleton(tryInclude("componentType", (oa_1) => OntologyAnnotation_encoder(options, oa_1), oa.ComponentType)), delay(() => (ConverterOptions__get_IncludeContext(options) ? singleton(["@context", context_jsonvalue_1]) : empty()))))))))))))]);
+}
+
+export function Component_decoder(options) {
+    return {
+        Decode(s, json) {
+            return Result_Map((c) => {
+                let patternInput;
+                const matchValue = c.ComponentName;
+                if (matchValue == null) {
+                    patternInput = [void 0, void 0];
+                }
+                else {
+                    const tupledArg = Component_decomposeName_Z721C83C5(matchValue);
+                    patternInput = [tupledArg[0], tupledArg[1]];
+                }
+                return new Component(c.ComponentName, patternInput[0], patternInput[1], c.ComponentType);
+            }, object((get$) => {
+                let objectArg, arg_3, objectArg_1;
+                return new Component((objectArg = get$.Optional, objectArg.Field("componentName", uri)), void 0, void 0, (arg_3 = OntologyAnnotation_decoder(options), (objectArg_1 = get$.Optional, objectArg_1.Field("componentType", arg_3))));
+            }).Decode(s, json));
+        },
+    };
 }
 
 export function Component_fromJsonString(s) {
-    let options;
-    return fromJsonString(uncurry2((options = ConverterOptions_$ctor(), (s_1) => ((json) => Component_decoder(options, s_1, json)))), s);
+    const matchValue = fromString(Component_decoder(ConverterOptions_$ctor()), s);
+    if (matchValue.tag === 1) {
+        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
+    }
+    else {
+        return matchValue.fields[0];
+    }
 }
 
 export function Component_toJsonString(p) {
@@ -152,19 +158,67 @@ export function Component_toJsonString(p) {
 /**
  * exports in json-ld format
  */
-export function Component_toStringLD(p) {
+export function Component_toJsonldString(p) {
     let returnVal;
     return toString(2, Component_encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), p));
 }
 
-export function Protocol_genID(p) {
+export function Component_toJsonldStringWithContext(a) {
+    let returnVal;
+    return toString(2, Component_encoder((returnVal = ConverterOptions_$ctor(), (((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), ConverterOptions__set_IncludeContext_Z1FBCCD16(returnVal, true)), returnVal)), a));
+}
+
+export function Protocol_genID(studyName, assayName, processName, p) {
     const matchValue = p.ID;
     if (matchValue == null) {
         const matchValue_1 = p.Uri;
         if (matchValue_1 == null) {
             const matchValue_2 = p.Name;
             if (matchValue_2 == null) {
-                return "#EmptyProtocol";
+                let matchResult, an, pn, sn, pn_1, sn_1, pn_2;
+                if (studyName == null) {
+                    if (assayName == null) {
+                        if (processName != null) {
+                            matchResult = 2;
+                            pn_2 = processName;
+                        }
+                        else {
+                            matchResult = 3;
+                        }
+                    }
+                    else {
+                        matchResult = 3;
+                    }
+                }
+                else if (assayName == null) {
+                    if (processName != null) {
+                        matchResult = 1;
+                        pn_1 = processName;
+                        sn_1 = studyName;
+                    }
+                    else {
+                        matchResult = 3;
+                    }
+                }
+                else if (processName != null) {
+                    matchResult = 0;
+                    an = assayName;
+                    pn = processName;
+                    sn = studyName;
+                }
+                else {
+                    matchResult = 3;
+                }
+                switch (matchResult) {
+                    case 0:
+                        return (((("#Protocol_" + replace(sn, " ", "_")) + "_") + replace(an, " ", "_")) + "_") + replace(pn, " ", "_");
+                    case 1:
+                        return (("#Protocol_" + replace(sn_1, " ", "_")) + "_") + replace(pn_1, " ", "_");
+                    case 2:
+                        return "#Protocol_" + replace(pn_2, " ", "_");
+                    default:
+                        return "#EmptyProtocol";
+                }
             }
             else {
                 return "#Protocol_" + replace(matchValue_2, " ", "_");
@@ -179,64 +233,49 @@ export function Protocol_genID(p) {
     }
 }
 
-export function Protocol_encoder(options, oa) {
-    return object_18(choose((tupledArg) => {
+export function Protocol_encoder(options, studyName, assayName, processName, oa) {
+    return new Json(5, [choose((tupledArg) => {
         const v = tupledArg[1];
-        if (equals(v, nil)) {
+        if (equals(v, new Json(3, []))) {
             return void 0;
         }
         else {
             return [tupledArg[0], v];
         }
-    }, toList(delay(() => {
-        let value, s;
-        return append(ConverterOptions__get_SetID(options) ? singleton(["@id", (value = Protocol_genID(oa), (typeof value === "string") ? ((s = value, s)) : nil)]) : singleton(tryInclude("@id", (value_2) => {
-            let s_1;
-            const value_3 = value_2;
-            return (typeof value_3 === "string") ? ((s_1 = value_3, s_1)) : nil;
-        }, oa["ID"])), delay(() => {
-            let value_5, s_2;
-            return append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", (value_5 = "Protocol", (typeof value_5 === "string") ? ((s_2 = value_5, s_2)) : nil)]) : empty(), delay(() => append(singleton(tryInclude("name", (value_7) => {
-                let s_3;
-                const value_8 = value_7;
-                return (typeof value_8 === "string") ? ((s_3 = value_8, s_3)) : nil;
-            }, oa["Name"])), delay(() => append(singleton(tryInclude("protocolType", (oa_1) => OntologyAnnotation_encoder(options, oa_1), oa["ProtocolType"])), delay(() => append(singleton(tryInclude("description", (value_10) => {
-                let s_4;
-                const value_11 = value_10;
-                return (typeof value_11 === "string") ? ((s_4 = value_11, s_4)) : nil;
-            }, oa["Description"])), delay(() => append(singleton(tryInclude("uri", (value_13) => {
-                let s_5;
-                const value_14 = value_13;
-                return (typeof value_14 === "string") ? ((s_5 = value_14, s_5)) : nil;
-            }, oa["Uri"])), delay(() => append(singleton(tryInclude("version", (value_16) => {
-                let s_6;
-                const value_17 = value_16;
-                return (typeof value_17 === "string") ? ((s_6 = value_17, s_6)) : nil;
-            }, oa["Version"])), delay(() => append(singleton(tryInclude("parameters", (oa_2) => ProtocolParameter_encoder(options, oa_2), oa["Parameters"])), delay(() => append(singleton(tryInclude("components", (oa_3) => Component_encoder(options, oa_3), oa["Components"])), delay(() => singleton(tryInclude("comments", (comment) => encoder(options, comment), oa["Comments"]))))))))))))))))));
-        }));
-    }))));
+    }, toList(delay(() => append(ConverterOptions__get_SetID(options) ? singleton(["@id", new Json(0, [Protocol_genID(studyName, assayName, processName, oa)])]) : singleton(tryInclude("@id", (value_1) => (new Json(0, [value_1])), oa.ID)), delay(() => append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", list_1(ofArray([new Json(0, ["Protocol"]), new Json(0, ["ArcProtocol"])]))]) : empty(), delay(() => append(singleton(tryInclude("name", (value_5) => (new Json(0, [value_5])), oa.Name)), delay(() => append(singleton(tryInclude("protocolType", (oa_1) => OntologyAnnotation_encoder(options, oa_1), oa.ProtocolType)), delay(() => append(singleton(tryInclude("description", (value_7) => (new Json(0, [value_7])), oa.Description)), delay(() => append(singleton(tryInclude("uri", (value_9) => (new Json(0, [value_9])), oa.Uri)), delay(() => append(singleton(tryInclude("version", (value_11) => (new Json(0, [value_11])), oa.Version)), delay(() => append(singleton(tryIncludeList("parameters", (oa_2) => ProtocolParameter_encoder(options, oa_2), oa.Parameters)), delay(() => append(singleton(tryIncludeList("components", (oa_3) => Component_encoder(options, oa_3), oa.Components)), delay(() => append(singleton(tryIncludeList("comments", (comment) => encoder(options, comment), oa.Comments)), delay(() => (ConverterOptions__get_IncludeContext(options) ? singleton(["@context", context_jsonvalue_2]) : empty()))))))))))))))))))))))))]);
 }
 
 export function Protocol_decoder(options) {
-    return (path_6) => ((v) => object_19((get$) => {
-        let objectArg, objectArg_1, arg_5, objectArg_2, objectArg_3, objectArg_4, objectArg_5, arg_13, decoder, objectArg_6, objectArg_7, arg_17, decoder_2, objectArg_8;
-        return new Protocol((objectArg = get$.Optional, objectArg.Field("@id", uri)), (objectArg_1 = get$.Optional, objectArg_1.Field("name", string)), (arg_5 = OntologyAnnotation_decoder(options), (objectArg_2 = get$.Optional, objectArg_2.Field("protocolType", uncurry2(arg_5)))), (objectArg_3 = get$.Optional, objectArg_3.Field("description", string)), (objectArg_4 = get$.Optional, objectArg_4.Field("uri", uri)), (objectArg_5 = get$.Optional, objectArg_5.Field("version", string)), (arg_13 = ((decoder = ProtocolParameter_decoder(options), (path_3) => ((value_3) => list_1(uncurry2(decoder), path_3, value_3)))), (objectArg_6 = get$.Optional, objectArg_6.Field("parameters", uncurry2(arg_13)))), (objectArg_7 = get$.Optional, objectArg_7.Field("components", (path_4, value_4) => list_1((s_2, json_2) => Component_decoder(options, s_2, json_2), path_4, value_4))), (arg_17 = ((decoder_2 = decoder_3(options), (path_5) => ((value_5) => list_1(uncurry2(decoder_2), path_5, value_5)))), (objectArg_8 = get$.Optional, objectArg_8.Field("comments", uncurry2(arg_17)))));
-    }, path_6, v));
+    return object((get$) => {
+        let objectArg, objectArg_1, arg_5, objectArg_2, objectArg_3, objectArg_4, objectArg_5, arg_13, objectArg_6, arg_15, objectArg_7, arg_17, objectArg_8;
+        return new Protocol((objectArg = get$.Optional, objectArg.Field("@id", uri)), (objectArg_1 = get$.Optional, objectArg_1.Field("name", string)), (arg_5 = OntologyAnnotation_decoder(options), (objectArg_2 = get$.Optional, objectArg_2.Field("protocolType", arg_5))), (objectArg_3 = get$.Optional, objectArg_3.Field("description", string)), (objectArg_4 = get$.Optional, objectArg_4.Field("uri", uri)), (objectArg_5 = get$.Optional, objectArg_5.Field("version", string)), (arg_13 = list_2(ProtocolParameter_decoder(options)), (objectArg_6 = get$.Optional, objectArg_6.Field("parameters", arg_13))), (arg_15 = list_2(Component_decoder(options)), (objectArg_7 = get$.Optional, objectArg_7.Field("components", arg_15))), (arg_17 = list_2(decoder_1(options)), (objectArg_8 = get$.Optional, objectArg_8.Field("comments", arg_17))));
+    });
 }
 
 export function Protocol_fromJsonString(s) {
-    return fromJsonString(uncurry2(Protocol_decoder(ConverterOptions_$ctor())), s);
+    const matchValue = fromString(Protocol_decoder(ConverterOptions_$ctor()), s);
+    if (matchValue.tag === 1) {
+        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
+    }
+    else {
+        return matchValue.fields[0];
+    }
 }
 
 export function Protocol_toJsonString(p) {
-    return toString(2, Protocol_encoder(ConverterOptions_$ctor(), p));
+    return toString(2, Protocol_encoder(ConverterOptions_$ctor(), void 0, void 0, void 0, p));
 }
 
 /**
  * exports in json-ld format
  */
-export function Protocol_toStringLD(p) {
+export function Protocol_toJsonldString(p) {
+    let returnVal;
+    return toString(2, Protocol_encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), void 0, void 0, void 0, p));
+}
+
+export function Protocol_toJsonldStringWithContext(a) {
     let returnVal;
-    return toString(2, Protocol_encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), p));
+    return toString(2, Protocol_encoder((returnVal = ConverterOptions_$ctor(), (((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), ConverterOptions__set_IncludeContext_Z1FBCCD16(returnVal, true)), returnVal)), void 0, void 0, void 0, a));
 }
 

package/ISA/ISA.Json/Publication.js

@@ -1,15 +1,18 @@
-import { replace } from "../../fable_modules/fable-library.4.5.0/String.js";
-import { toString, nil, object as object_12 } from "../../fable_modules/Thoth.Json.10.1.0/Encode.fs.js";
-import { choose } from "../../fable_modules/fable-library.4.5.0/List.js";
-import { uncurry2, equals } from "../../fable_modules/fable-library.4.5.0/Util.js";
-import { empty, singleton, append, delay, toList } from "../../fable_modules/fable-library.4.5.0/Seq.js";
-import { ConverterOptions__set_IncludeType_Z1FBCCD16, ConverterOptions__set_SetID_Z1FBCCD16, ConverterOptions_$ctor, ConverterOptions__get_IncludeType, ConverterOptions__get_SetID } from "./ConverterOptions.js";
-import { tryInclude } from "./GEncode.js";
+import { printf, toText, replace } from "../../fable_modules/fable-library-js.4.13.0/String.js";
+import { ofArray, choose } from "../../fable_modules/fable-library-js.4.13.0/List.js";
+import { equals } from "../../fable_modules/fable-library-js.4.13.0/Util.js";
+import { Json } from "../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+import { empty, singleton, append, delay, toList } from "../../fable_modules/fable-library-js.4.13.0/Seq.js";
+import { ConverterOptions__set_IncludeContext_Z1FBCCD16, ConverterOptions__set_IncludeType_Z1FBCCD16, ConverterOptions__set_SetID_Z1FBCCD16, ConverterOptions_$ctor, ConverterOptions__get_IncludeContext, ConverterOptions__get_IncludeType, ConverterOptions__get_SetID } from "./ConverterOptions.js";
+import { tryIncludeArray, tryInclude } from "./GEncode.js";
 import { OntologyAnnotation_decoder, OntologyAnnotation_encoder } from "./Ontology.js";
 import { decoder as decoder_2, encoder as encoder_1 } from "./Comment.js";
-import { array, string, object as object_13 } from "../../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
-import { fromJsonString as fromJsonString_1, uri } from "./Decode.js";
+import { context_jsonvalue } from "./context/rocrate/isa_publication_context.js";
+import { uri, object } from "./Decode.js";
+import { array, string } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
 import { Publication } from "../ISA/JsonTypes/Publication.js";
+import { fromString } from "../../fable_modules/Thoth.Json.JavaScript.0.1.0/Decode.fs.js";
+import { toString } from "../../fable_modules/Thoth.Json.JavaScript.0.1.0/Encode.fs.js";
 
 export function genID(p) {
     const matchValue = p.DOI;
@@ -34,48 +37,34 @@ export function genID(p) {
 }
 
 export function encoder(options, oa) {
-    return object_12(choose((tupledArg) => {
+    return new Json(5, [choose((tupledArg) => {
         const v = tupledArg[1];
-        if (equals(v, nil)) {
+        if (equals(v, new Json(3, []))) {
             return void 0;
         }
         else {
             return [tupledArg[0], v];
         }
-    }, toList(delay(() => {
-        let value, s;
-        return append(ConverterOptions__get_SetID(options) ? singleton(["@id", (value = genID(oa), (typeof value === "string") ? ((s = value, s)) : nil)]) : empty(), delay(() => {
-            let value_2, s_1;
-            return append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", (value_2 = "Publication", (typeof value_2 === "string") ? ((s_1 = value_2, s_1)) : nil)]) : empty(), delay(() => append(singleton(tryInclude("pubMedID", (value_4) => {
-                let s_2;
-                const value_5 = value_4;
-                return (typeof value_5 === "string") ? ((s_2 = value_5, s_2)) : nil;
-            }, oa["PubMedID"])), delay(() => append(singleton(tryInclude("doi", (value_7) => {
-                let s_3;
-                const value_8 = value_7;
-                return (typeof value_8 === "string") ? ((s_3 = value_8, s_3)) : nil;
-            }, oa["DOI"])), delay(() => append(singleton(tryInclude("authorList", (value_10) => {
-                let s_4;
-                const value_11 = value_10;
-                return (typeof value_11 === "string") ? ((s_4 = value_11, s_4)) : nil;
-            }, oa["Authors"])), delay(() => append(singleton(tryInclude("title", (value_13) => {
-                let s_5;
-                const value_14 = value_13;
-                return (typeof value_14 === "string") ? ((s_5 = value_14, s_5)) : nil;
-            }, oa["Title"])), delay(() => append(singleton(tryInclude("status", (oa_1) => OntologyAnnotation_encoder(options, oa_1), oa["Status"])), delay(() => singleton(tryInclude("comments", (comment) => encoder_1(options, comment), oa["Comments"]))))))))))))));
-        }));
-    }))));
+    }, toList(delay(() => append(ConverterOptions__get_SetID(options) ? singleton(["@id", new Json(0, [genID(oa)])]) : empty(), delay(() => append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", new Json(0, ["Publication"])]) : empty(), delay(() => append(singleton(tryInclude("pubMedID", (value_2) => (new Json(0, [value_2])), oa.PubMedID)), delay(() => append(singleton(tryInclude("doi", (value_4) => (new Json(0, [value_4])), oa.DOI)), delay(() => append(singleton(tryInclude("authorList", (value_6) => (new Json(0, [value_6])), oa.Authors)), delay(() => append(singleton(tryInclude("title", (value_8) => (new Json(0, [value_8])), oa.Title)), delay(() => append(singleton(tryInclude("status", (oa_1) => OntologyAnnotation_encoder(options, oa_1), oa.Status)), delay(() => append(singleton(tryIncludeArray("comments", (comment) => encoder_1(options, comment), oa.Comments)), delay(() => (ConverterOptions__get_IncludeContext(options) ? singleton(["@context", context_jsonvalue]) : empty()))))))))))))))))))))]);
 }
 
+export const allowedFields = ofArray(["@id", "pubMedID", "doi", "authorList", "title", "status", "comments", "@type", "@context"]);
+
 export function decoder(options) {
-    return (path_4) => ((v) => object_13((get$) => {
-        let objectArg, objectArg_1, objectArg_2, objectArg_3, arg_9, objectArg_4, arg_11, decoder_1, objectArg_5;
-        return new Publication((objectArg = get$.Optional, objectArg.Field("pubMedID", uri)), (objectArg_1 = get$.Optional, objectArg_1.Field("doi", string)), (objectArg_2 = get$.Optional, objectArg_2.Field("authorList", string)), (objectArg_3 = get$.Optional, objectArg_3.Field("title", string)), (arg_9 = OntologyAnnotation_decoder(options), (objectArg_4 = get$.Optional, objectArg_4.Field("status", uncurry2(arg_9)))), (arg_11 = ((decoder_1 = decoder_2(options), (path_3) => ((value_3) => array(uncurry2(decoder_1), path_3, value_3)))), (objectArg_5 = get$.Optional, objectArg_5.Field("comments", uncurry2(arg_11)))));
-    }, path_4, v));
+    return object(allowedFields, (get$) => {
+        let objectArg, objectArg_1, objectArg_2, objectArg_3, arg_9, objectArg_4, arg_11, objectArg_5;
+        return new Publication((objectArg = get$.Optional, objectArg.Field("pubMedID", uri)), (objectArg_1 = get$.Optional, objectArg_1.Field("doi", string)), (objectArg_2 = get$.Optional, objectArg_2.Field("authorList", string)), (objectArg_3 = get$.Optional, objectArg_3.Field("title", string)), (arg_9 = OntologyAnnotation_decoder(options), (objectArg_4 = get$.Optional, objectArg_4.Field("status", arg_9))), (arg_11 = array(decoder_2(options)), (objectArg_5 = get$.Optional, objectArg_5.Field("comments", arg_11))));
+    });
 }
 
 export function fromJsonString(s) {
-    return fromJsonString_1(uncurry2(decoder(ConverterOptions_$ctor())), s);
+    const matchValue = fromString(decoder(ConverterOptions_$ctor()), s);
+    if (matchValue.tag === 1) {
+        throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
+    }
+    else {
+        return matchValue.fields[0];
+    }
 }
 
 export function toJsonString(p) {
@@ -85,8 +74,13 @@ export function toJsonString(p) {
 /**
  * exports in json-ld format
  */
-export function toStringLD(p) {
+export function toJsonldString(p) {
     let returnVal;
     return toString(2, encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), p));
 }
 
+export function toJsonldStringWithContext(a) {
+    let returnVal;
+    return toString(2, encoder((returnVal = ConverterOptions_$ctor(), (((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), ConverterOptions__set_IncludeContext_Z1FBCCD16(returnVal, true)), returnVal)), a));
+}
+

package/ISA/ISA.Json/StringTable.js

@@ -0,0 +1,44 @@
+import { item, map, setItem, fill } from "../../fable_modules/fable-library-js.4.13.0/Array.js";
+import { iterate } from "../../fable_modules/fable-library-js.4.13.0/Seq.js";
+import { Json } from "../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+import { int, string, array as array_1 } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
+import { Dict_tryFind } from "../ISA/Helper.js";
+import { addToDict } from "../../fable_modules/fable-library-js.4.13.0/MapUtil.js";
+import { FSharpResult$2 } from "../../fable_modules/fable-library-js.4.13.0/Result.js";
+
+export function StringTable_arrayFromMap(otm) {
+    const a = fill(new Array(otm.size), 0, otm.size, "");
+    iterate((kv) => {
+        setItem(a, kv[1], kv[0]);
+    }, otm);
+    return a;
+}
+
+export function StringTable_encoder(ot) {
+    return new Json(6, [map((value) => (new Json(0, [value])), ot)]);
+}
+
+export const StringTable_decoder = array_1(string);
+
+export function StringTable_encodeString(otm, s) {
+    const matchValue = Dict_tryFind(s, otm);
+    if (matchValue == null) {
+        const i_1 = otm.size | 0;
+        addToDict(otm, s, i_1);
+        return new Json(7, [i_1 >>> 0]);
+    }
+    else {
+        const i = matchValue | 0;
+        return new Json(7, [i >>> 0]);
+    }
+}
+
+export function StringTable_decodeString(ot) {
+    return {
+        Decode(s, json) {
+            const matchValue = int.Decode(s, json);
+            return (matchValue.tag === 1) ? (new FSharpResult$2(1, [matchValue.fields[0]])) : (new FSharpResult$2(0, [item(matchValue.fields[0], ot)]));
+        },
+    };
+}
+