@nfdi4plants/arctrl 2.5.1 → 3.0.0-alpha.1

package/dist/ts/cjs/ts/Json/Person.js

@@ -0,0 +1,338 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.ISAJson_decoder = exports.ISAJson_allowedFields = exports.ROCrate_decodeAuthorListString = exports.ROCrate_decoder = exports.ROCrate_Affiliation_decoder = exports.decoder = void 0;
+exports.encoder = encoder;
+exports.ROCrate_genID = ROCrate_genID;
+exports.ROCrate_Affiliation_encoder = ROCrate_Affiliation_encoder;
+exports.ROCrate_encoder = ROCrate_encoder;
+exports.ROCrate_encodeAuthorListString = ROCrate_encodeAuthorListString;
+exports.ISAJson_encoder = ISAJson_encoder;
+const List_js_1 = require("@fable-org/fable-library-js/List.js");
+const Option_js_1 = require("@fable-org/fable-library-js/Option.js");
+const Encode_js_1 = require("./Encode.js");
+const OntologyAnnotation_js_1 = require("./OntologyAnnotation.js");
+const Comment_js_1 = require("./Comment.js");
+const Seq_js_1 = require("@fable-org/fable-library-js/Seq.js");
+const Person_js_1 = require("../Core/Person.js");
+const Decode_fs_js_1 = require("../fable_modules/Thoth.Json.Core.0.4.0/Decode.fs.js");
+const String_js_1 = require("@fable-org/fable-library-js/String.js");
+const isa_organization_context_js_1 = require("./context/rocrate/isa_organization_context.js");
+const isa_person_context_js_1 = require("./context/rocrate/isa_person_context.js");
+const Array_js_1 = require("@fable-org/fable-library-js/Array.js");
+const Conversion_js_1 = require("../Core/Conversion.js");
+const IDTable_js_1 = require("./IDTable.js");
+const Decode_js_1 = require("./Decode.js");
+function encoder(person) {
+    const values_1 = (0, List_js_1.choose)((tupledArg) => (0, Option_js_1.map)((v_1) => [tupledArg[0], v_1], tupledArg[1]), (0, List_js_1.ofArray)([(0, Encode_js_1.tryInclude)("firstName", (value) => ({
+            Encode(helpers) {
+                return helpers.encodeString(value);
+            },
+        }), person.FirstName), (0, Encode_js_1.tryInclude)("lastName", (value_2) => ({
+            Encode(helpers_1) {
+                return helpers_1.encodeString(value_2);
+            },
+        }), person.LastName), (0, Encode_js_1.tryInclude)("midInitials", (value_4) => ({
+            Encode(helpers_2) {
+                return helpers_2.encodeString(value_4);
+            },
+        }), person.MidInitials), (0, Encode_js_1.tryInclude)("orcid", (value_6) => ({
+            Encode(helpers_3) {
+                return helpers_3.encodeString(value_6);
+            },
+        }), person.ORCID), (0, Encode_js_1.tryInclude)("email", (value_8) => ({
+            Encode(helpers_4) {
+                return helpers_4.encodeString(value_8);
+            },
+        }), person.EMail), (0, Encode_js_1.tryInclude)("phone", (value_10) => ({
+            Encode(helpers_5) {
+                return helpers_5.encodeString(value_10);
+            },
+        }), person.Phone), (0, Encode_js_1.tryInclude)("fax", (value_12) => ({
+            Encode(helpers_6) {
+                return helpers_6.encodeString(value_12);
+            },
+        }), person.Fax), (0, Encode_js_1.tryInclude)("address", (value_14) => ({
+            Encode(helpers_7) {
+                return helpers_7.encodeString(value_14);
+            },
+        }), person.Address), (0, Encode_js_1.tryInclude)("affiliation", (value_16) => ({
+            Encode(helpers_8) {
+                return helpers_8.encodeString(value_16);
+            },
+        }), person.Affiliation), (0, Encode_js_1.tryIncludeSeq)("roles", OntologyAnnotation_js_1.OntologyAnnotation_encoder, person.Roles), (0, Encode_js_1.tryIncludeSeq)("comments", Comment_js_1.encoder, person.Comments)]));
+    return {
+        Encode(helpers_9) {
+            const arg = (0, Seq_js_1.map)((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_9)], values_1);
+            return helpers_9.encodeObject(arg);
+        },
+    };
+}
+exports.decoder = (0, Decode_fs_js_1.object)((get$) => {
+    let objectArg, objectArg_1, objectArg_2, objectArg_3, objectArg_4, objectArg_5, objectArg_6, objectArg_7, objectArg_8, arg_19, objectArg_9, arg_21, objectArg_10;
+    return new Person_js_1.Person((0, Option_js_1.unwrap)((objectArg = get$.Optional, objectArg.Field("orcid", Decode_fs_js_1.string))), (0, Option_js_1.unwrap)((objectArg_1 = get$.Optional, objectArg_1.Field("lastName", Decode_fs_js_1.string))), (0, Option_js_1.unwrap)((objectArg_2 = get$.Optional, objectArg_2.Field("firstName", Decode_fs_js_1.string))), (0, Option_js_1.unwrap)((objectArg_3 = get$.Optional, objectArg_3.Field("midInitials", Decode_fs_js_1.string))), (0, Option_js_1.unwrap)((objectArg_4 = get$.Optional, objectArg_4.Field("email", Decode_fs_js_1.string))), (0, Option_js_1.unwrap)((objectArg_5 = get$.Optional, objectArg_5.Field("phone", Decode_fs_js_1.string))), (0, Option_js_1.unwrap)((objectArg_6 = get$.Optional, objectArg_6.Field("fax", Decode_fs_js_1.string))), (0, Option_js_1.unwrap)((objectArg_7 = get$.Optional, objectArg_7.Field("address", Decode_fs_js_1.string))), (0, Option_js_1.unwrap)((objectArg_8 = get$.Optional, objectArg_8.Field("affiliation", Decode_fs_js_1.string))), (0, Option_js_1.unwrap)((arg_19 = (0, Decode_fs_js_1.resizeArray)(OntologyAnnotation_js_1.OntologyAnnotation_decoder), (objectArg_9 = get$.Optional, objectArg_9.Field("roles", arg_19)))), (0, Option_js_1.unwrap)((arg_21 = (0, Decode_fs_js_1.resizeArray)(Comment_js_1.decoder), (objectArg_10 = get$.Optional, objectArg_10.Field("comments", arg_21)))));
+});
+function ROCrate_genID(p) {
+    const orcid = (0, Seq_js_1.tryPick)((c) => {
+        const matchValue = c.Name;
+        const matchValue_1 = c.Value;
+        let matchResult, n, v;
+        if (matchValue != null) {
+            if (matchValue_1 != null) {
+                matchResult = 0;
+                n = (0, Option_js_1.value)(matchValue);
+                v = (0, Option_js_1.value)(matchValue_1);
+            }
+            else {
+                matchResult = 1;
+            }
+        }
+        else {
+            matchResult = 1;
+        }
+        switch (matchResult) {
+            case 0:
+                if (((n === "orcid") ? true : (n === "Orcid")) ? true : (n === "ORCID")) {
+                    return v;
+                }
+                else {
+                    return undefined;
+                }
+            default:
+                return undefined;
+        }
+    }, p.Comments);
+    if (orcid == null) {
+        const matchValue_3 = p.EMail;
+        if (matchValue_3 == null) {
+            const matchValue_4 = p.FirstName;
+            const matchValue_5 = p.MidInitials;
+            const matchValue_6 = p.LastName;
+            let matchResult_1, fn, ln, mn, fn_1, ln_1, ln_2, fn_2;
+            if (matchValue_4 == null) {
+                if (matchValue_5 == null) {
+                    if (matchValue_6 != null) {
+                        matchResult_1 = 2;
+                        ln_2 = (0, Option_js_1.value)(matchValue_6);
+                    }
+                    else {
+                        matchResult_1 = 4;
+                    }
+                }
+                else {
+                    matchResult_1 = 4;
+                }
+            }
+            else if (matchValue_5 == null) {
+                if (matchValue_6 == null) {
+                    matchResult_1 = 3;
+                    fn_2 = (0, Option_js_1.value)(matchValue_4);
+                }
+                else {
+                    matchResult_1 = 1;
+                    fn_1 = (0, Option_js_1.value)(matchValue_4);
+                    ln_1 = (0, Option_js_1.value)(matchValue_6);
+                }
+            }
+            else if (matchValue_6 != null) {
+                matchResult_1 = 0;
+                fn = (0, Option_js_1.value)(matchValue_4);
+                ln = (0, Option_js_1.value)(matchValue_6);
+                mn = (0, Option_js_1.value)(matchValue_5);
+            }
+            else {
+                matchResult_1 = 4;
+            }
+            switch (matchResult_1) {
+                case 0:
+                    return (((("#" + (0, String_js_1.replace)(fn, " ", "_")) + "_") + (0, String_js_1.replace)(mn, " ", "_")) + "_") + (0, String_js_1.replace)(ln, " ", "_");
+                case 1:
+                    return (("#" + (0, String_js_1.replace)(fn_1, " ", "_")) + "_") + (0, String_js_1.replace)(ln_1, " ", "_");
+                case 2:
+                    return "#" + (0, String_js_1.replace)(ln_2, " ", "_");
+                case 3:
+                    return "#" + (0, String_js_1.replace)(fn_2, " ", "_");
+                default:
+                    return "#EmptyPerson";
+            }
+        }
+        else {
+            return (0, Option_js_1.value)(matchValue_3);
+        }
+    }
+    else {
+        return (0, Option_js_1.value)(orcid);
+    }
+}
+function ROCrate_Affiliation_encoder(affiliation) {
+    let value_1;
+    const idStr = `#Organization_${affiliation}`;
+    const values_1 = [["@type", {
+                Encode(helpers) {
+                    return helpers.encodeString("Organization");
+                },
+            }], ["@id", (value_1 = (0, String_js_1.replace)(idStr, " ", "_"), {
+                Encode(helpers_1) {
+                    return helpers_1.encodeString(value_1);
+                },
+            })], ["name", {
+                Encode(helpers_2) {
+                    return helpers_2.encodeString(affiliation);
+                },
+            }], ["@context", isa_organization_context_js_1.context_jsonvalue]];
+    return {
+        Encode(helpers_3) {
+            const arg = (0, Seq_js_1.map)((tupledArg) => [tupledArg[0], tupledArg[1].Encode(helpers_3)], values_1);
+            return helpers_3.encodeObject(arg);
+        },
+    };
+}
+exports.ROCrate_Affiliation_decoder = (0, Decode_fs_js_1.object)((get$) => {
+    const objectArg = get$.Required;
+    return objectArg.Field("name", Decode_fs_js_1.string);
+});
+function ROCrate_encoder(oa) {
+    let value;
+    const values_1 = (0, List_js_1.choose)((tupledArg) => (0, Option_js_1.map)((v_1) => [tupledArg[0], v_1], tupledArg[1]), (0, List_js_1.ofArray)([["@id", (value = ROCrate_genID(oa), {
+                Encode(helpers) {
+                    return helpers.encodeString(value);
+                },
+            })], ["@type", {
+                Encode(helpers_1) {
+                    return helpers_1.encodeString("Person");
+                },
+            }], (0, Encode_js_1.tryInclude)("orcid", (value_2) => ({
+            Encode(helpers_2) {
+                return helpers_2.encodeString(value_2);
+            },
+        }), oa.ORCID), (0, Encode_js_1.tryInclude)("firstName", (value_4) => ({
+            Encode(helpers_3) {
+                return helpers_3.encodeString(value_4);
+            },
+        }), oa.FirstName), (0, Encode_js_1.tryInclude)("lastName", (value_6) => ({
+            Encode(helpers_4) {
+                return helpers_4.encodeString(value_6);
+            },
+        }), oa.LastName), (0, Encode_js_1.tryInclude)("midInitials", (value_8) => ({
+            Encode(helpers_5) {
+                return helpers_5.encodeString(value_8);
+            },
+        }), oa.MidInitials), (0, Encode_js_1.tryInclude)("email", (value_10) => ({
+            Encode(helpers_6) {
+                return helpers_6.encodeString(value_10);
+            },
+        }), oa.EMail), (0, Encode_js_1.tryInclude)("phone", (value_12) => ({
+            Encode(helpers_7) {
+                return helpers_7.encodeString(value_12);
+            },
+        }), oa.Phone), (0, Encode_js_1.tryInclude)("fax", (value_14) => ({
+            Encode(helpers_8) {
+                return helpers_8.encodeString(value_14);
+            },
+        }), oa.Fax), (0, Encode_js_1.tryInclude)("address", (value_16) => ({
+            Encode(helpers_9) {
+                return helpers_9.encodeString(value_16);
+            },
+        }), oa.Address), (0, Encode_js_1.tryInclude)("affiliation", ROCrate_Affiliation_encoder, oa.Affiliation), (0, Encode_js_1.tryIncludeSeq)("roles", OntologyAnnotation_js_1.OntologyAnnotation_ROCrate_encoderDefinedTerm, oa.Roles), (0, Encode_js_1.tryIncludeSeq)("comments", Comment_js_1.ROCrate_encoderDisambiguatingDescription, oa.Comments), ["@context", isa_person_context_js_1.context_jsonvalue]]));
+    return {
+        Encode(helpers_10) {
+            const arg = (0, Seq_js_1.map)((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_10)], values_1);
+            return helpers_10.encodeObject(arg);
+        },
+    };
+}
+exports.ROCrate_decoder = (0, Decode_fs_js_1.object)((get$) => {
+    let objectArg, objectArg_1, objectArg_2, objectArg_3, objectArg_4, objectArg_5, objectArg_6, objectArg_7, objectArg_8, arg_19, objectArg_9, arg_21, objectArg_10;
+    return new Person_js_1.Person((0, Option_js_1.unwrap)((objectArg = get$.Optional, objectArg.Field("orcid", Decode_fs_js_1.string))), (0, Option_js_1.unwrap)((objectArg_1 = get$.Optional, objectArg_1.Field("lastName", Decode_fs_js_1.string))), (0, Option_js_1.unwrap)((objectArg_2 = get$.Optional, objectArg_2.Field("firstName", Decode_fs_js_1.string))), (0, Option_js_1.unwrap)((objectArg_3 = get$.Optional, objectArg_3.Field("midInitials", Decode_fs_js_1.string))), (0, Option_js_1.unwrap)((objectArg_4 = get$.Optional, objectArg_4.Field("email", Decode_fs_js_1.string))), (0, Option_js_1.unwrap)((objectArg_5 = get$.Optional, objectArg_5.Field("phone", Decode_fs_js_1.string))), (0, Option_js_1.unwrap)((objectArg_6 = get$.Optional, objectArg_6.Field("fax", Decode_fs_js_1.string))), (0, Option_js_1.unwrap)((objectArg_7 = get$.Optional, objectArg_7.Field("address", Decode_fs_js_1.string))), (0, Option_js_1.unwrap)((objectArg_8 = get$.Optional, objectArg_8.Field("affiliation", exports.ROCrate_Affiliation_decoder))), (0, Option_js_1.unwrap)((arg_19 = (0, Decode_fs_js_1.resizeArray)(OntologyAnnotation_js_1.OntologyAnnotation_ROCrate_decoderDefinedTerm), (objectArg_9 = get$.Optional, objectArg_9.Field("roles", arg_19)))), (0, Option_js_1.unwrap)((arg_21 = (0, Decode_fs_js_1.resizeArray)(Comment_js_1.ROCrate_decoderDisambiguatingDescription), (objectArg_10 = get$.Optional, objectArg_10.Field("comments", arg_21)))));
+});
+/**
+ * This is only used for ro-crate creation. In ISA publication authors are only a string. ro-crate requires person object.
+ * Therefore, we try to split the string by common separators and create a minimal person object for ro-crate.
+ */
+function ROCrate_encodeAuthorListString(authorList) {
+    const values_2 = (0, Array_js_1.map)((name) => {
+        const values_1 = (0, List_js_1.choose)((tupledArg) => (0, Option_js_1.map)((v_1) => [tupledArg[0], v_1], tupledArg[1]), (0, List_js_1.ofArray)([["@type", {
+                    Encode(helpers) {
+                        return helpers.encodeString("Person");
+                    },
+                }], (0, Encode_js_1.tryInclude)("name", (value_1) => ({
+                Encode(helpers_1) {
+                    return helpers_1.encodeString(value_1);
+                },
+            }), name), ["@context", isa_person_context_js_1.contextMinimal_jsonValue]]));
+        return {
+            Encode(helpers_2) {
+                const arg = (0, Seq_js_1.map)((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_2)], values_1);
+                return helpers_2.encodeObject(arg);
+            },
+        };
+    }, (0, Array_js_1.map)((s) => s.trim(), (0, String_js_1.split)(authorList, [(authorList.indexOf("\t") >= 0) ? "\t" : ((authorList.indexOf(";") >= 0) ? ";" : ",")], undefined, 0)));
+    return {
+        Encode(helpers_3) {
+            const arg_1 = (0, Array_js_1.map)((v_3) => v_3.Encode(helpers_3), values_2);
+            return helpers_3.encodeArray(arg_1);
+        },
+    };
+}
+exports.ROCrate_decodeAuthorListString = (0, Decode_fs_js_1.map)((v) => (0, String_js_1.join)(", ", v), (0, Decode_fs_js_1.array)((0, Decode_fs_js_1.object)((get$) => {
+    let objectArg;
+    return (0, Option_js_1.defaultArg)((objectArg = get$.Optional, objectArg.Field("name", Decode_fs_js_1.string)), "");
+})));
+exports.ISAJson_allowedFields = (0, List_js_1.ofArray)(["@id", "firstName", "lastName", "midInitials", "email", "phone", "fax", "address", "affiliation", "roles", "comments", "@type", "@context"]);
+function ISAJson_encoder(idMap, person) {
+    const f = (person_1) => {
+        const person_2 = (0, Conversion_js_1.Person_setCommentFromORCID)(person_1);
+        const values_1 = (0, List_js_1.choose)((tupledArg) => (0, Option_js_1.map)((v_1) => [tupledArg[0], v_1], tupledArg[1]), (0, List_js_1.ofArray)([(0, Encode_js_1.tryInclude)("@id", (value) => ({
+                Encode(helpers) {
+                    return helpers.encodeString(value);
+                },
+            }), ROCrate_genID(person_2)), (0, Encode_js_1.tryInclude)("firstName", (value_2) => ({
+                Encode(helpers_1) {
+                    return helpers_1.encodeString(value_2);
+                },
+            }), person_2.FirstName), (0, Encode_js_1.tryInclude)("lastName", (value_4) => ({
+                Encode(helpers_2) {
+                    return helpers_2.encodeString(value_4);
+                },
+            }), person_2.LastName), (0, Encode_js_1.tryInclude)("midInitials", (value_6) => ({
+                Encode(helpers_3) {
+                    return helpers_3.encodeString(value_6);
+                },
+            }), person_2.MidInitials), (0, Encode_js_1.tryInclude)("email", (value_8) => ({
+                Encode(helpers_4) {
+                    return helpers_4.encodeString(value_8);
+                },
+            }), person_2.EMail), (0, Encode_js_1.tryInclude)("phone", (value_10) => ({
+                Encode(helpers_5) {
+                    return helpers_5.encodeString(value_10);
+                },
+            }), person_2.Phone), (0, Encode_js_1.tryInclude)("fax", (value_12) => ({
+                Encode(helpers_6) {
+                    return helpers_6.encodeString(value_12);
+                },
+            }), person_2.Fax), (0, Encode_js_1.tryInclude)("address", (value_14) => ({
+                Encode(helpers_7) {
+                    return helpers_7.encodeString(value_14);
+                },
+            }), person_2.Address), (0, Encode_js_1.tryInclude)("affiliation", (value_16) => ({
+                Encode(helpers_8) {
+                    return helpers_8.encodeString(value_16);
+                },
+            }), person_2.Affiliation), (0, Encode_js_1.tryIncludeSeq)("roles", OntologyAnnotation_js_1.OntologyAnnotation_encoder, person_2.Roles), (0, Encode_js_1.tryIncludeSeq)("comments", Comment_js_1.encoder, person_2.Comments)]));
+        return {
+            Encode(helpers_9) {
+                const arg = (0, Seq_js_1.map)((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_9)], values_1);
+                return helpers_9.encodeObject(arg);
+            },
+        };
+    };
+    if (idMap != null) {
+        return (0, IDTable_js_1.encode)(ROCrate_genID, f, person, (0, Option_js_1.value)(idMap));
+    }
+    else {
+        return f(person);
+    }
+}
+exports.ISAJson_decoder = (0, Decode_js_1.Decode_objectNoAdditionalProperties)(exports.ISAJson_allowedFields, (get$) => {
+    let objectArg, objectArg_1, objectArg_2, objectArg_3, objectArg_4, objectArg_5, objectArg_6, objectArg_7, arg_17, objectArg_8, arg_19, objectArg_9;
+    return (0, Conversion_js_1.Person_setOrcidFromComments)(new Person_js_1.Person(undefined, (0, Option_js_1.unwrap)((objectArg = get$.Optional, objectArg.Field("lastName", Decode_fs_js_1.string))), (0, Option_js_1.unwrap)((objectArg_1 = get$.Optional, objectArg_1.Field("firstName", Decode_fs_js_1.string))), (0, Option_js_1.unwrap)((objectArg_2 = get$.Optional, objectArg_2.Field("midInitials", Decode_fs_js_1.string))), (0, Option_js_1.unwrap)((objectArg_3 = get$.Optional, objectArg_3.Field("email", Decode_fs_js_1.string))), (0, Option_js_1.unwrap)((objectArg_4 = get$.Optional, objectArg_4.Field("phone", Decode_fs_js_1.string))), (0, Option_js_1.unwrap)((objectArg_5 = get$.Optional, objectArg_5.Field("fax", Decode_fs_js_1.string))), (0, Option_js_1.unwrap)((objectArg_6 = get$.Optional, objectArg_6.Field("address", Decode_fs_js_1.string))), (0, Option_js_1.unwrap)((objectArg_7 = get$.Optional, objectArg_7.Field("affiliation", Decode_fs_js_1.string))), (0, Option_js_1.unwrap)((arg_17 = (0, Decode_fs_js_1.resizeArray)(OntologyAnnotation_js_1.OntologyAnnotation_decoder), (objectArg_8 = get$.Optional, objectArg_8.Field("roles", arg_17)))), (0, Option_js_1.unwrap)((arg_19 = (0, Decode_fs_js_1.resizeArray)(Comment_js_1.decoder), (objectArg_9 = get$.Optional, objectArg_9.Field("comments", arg_19))))));
+});

package/dist/ts/cjs/ts/Json/Process/AssayMaterials.js

@@ -0,0 +1,21 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.encoder = encoder;
+const ProcessSequence_js_1 = require("../../Core/Process/ProcessSequence.js");
+const List_js_1 = require("@fable-org/fable-library-js/List.js");
+const Option_js_1 = require("@fable-org/fable-library-js/Option.js");
+const Encode_js_1 = require("../Encode.js");
+const Sample_js_1 = require("./Sample.js");
+const Material_js_1 = require("./Material.js");
+const Seq_js_1 = require("@fable-org/fable-library-js/Seq.js");
+function encoder(idMap, ps) {
+    const samples = (0, ProcessSequence_js_1.getSamples)(ps);
+    const materials = (0, ProcessSequence_js_1.getMaterials)(ps);
+    const values_1 = (0, List_js_1.choose)((tupledArg) => (0, Option_js_1.map)((v_1) => [tupledArg[0], v_1], tupledArg[1]), (0, List_js_1.ofArray)([(0, Encode_js_1.tryIncludeList)("samples", (oa) => (0, Sample_js_1.ISAJson_encoder)(idMap, oa), samples), (0, Encode_js_1.tryIncludeList)("otherMaterials", (c) => (0, Material_js_1.ISAJson_encoder)(idMap, c), materials)]));
+    return {
+        Encode(helpers) {
+            const arg = (0, Seq_js_1.map)((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers)], values_1);
+            return helpers.encodeObject(arg);
+        },
+    };
+}

package/dist/ts/cjs/ts/Json/Process/Component.js

@@ -0,0 +1,47 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.ISAJson_decoder = exports.ROCrate_decoder = exports.ROCrate_encoder = void 0;
+exports.ISAJson_genID = ISAJson_genID;
+exports.ISAJson_encoder = ISAJson_encoder;
+const PropertyValue_js_1 = require("../PropertyValue.js");
+const Component_js_1 = require("../../Core/Process/Component.js");
+const Option_js_1 = require("@fable-org/fable-library-js/Option.js");
+const List_js_1 = require("@fable-org/fable-library-js/List.js");
+const Encode_js_1 = require("../Encode.js");
+const OntologyAnnotation_js_1 = require("../OntologyAnnotation.js");
+const Seq_js_1 = require("@fable-org/fable-library-js/Seq.js");
+const Decode_fs_js_1 = require("../../fable_modules/Thoth.Json.Core.0.4.0/Decode.fs.js");
+const Decode_js_1 = require("../Decode.js");
+exports.ROCrate_encoder = PropertyValue_js_1.encoder;
+exports.ROCrate_decoder = (0, PropertyValue_js_1.decoder)(Component_js_1.Component_createAsPV);
+function ISAJson_genID(c) {
+    return (0, PropertyValue_js_1.genID)(c);
+}
+function ISAJson_encoder(idMap, c) {
+    const values_1 = (0, List_js_1.choose)((tupledArg) => (0, Option_js_1.map)((v_1) => [tupledArg[0], v_1], tupledArg[1]), (0, List_js_1.ofArray)([(0, Encode_js_1.tryInclude)("componentName", (value) => ({
+            Encode(helpers) {
+                return helpers.encodeString(value);
+            },
+        }), (0, Component_js_1.Component__get_ComponentName)(c)), (0, Encode_js_1.tryInclude)("componentType", (oa) => (0, OntologyAnnotation_js_1.OntologyAnnotation_ISAJson_encoder)(idMap, oa), c.ComponentType)]));
+    return {
+        Encode(helpers_1) {
+            const arg = (0, Seq_js_1.map)((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_1)], values_1);
+            return helpers_1.encodeObject(arg);
+        },
+    };
+}
+exports.ISAJson_decoder = (0, Decode_fs_js_1.object)((get$) => {
+    let objectArg_1;
+    let name;
+    const objectArg = get$.Optional;
+    name = objectArg.Field("componentName", Decode_js_1.Decode_uri);
+    let patternInput_1;
+    if (name == null) {
+        patternInput_1 = [undefined, undefined];
+    }
+    else {
+        const patternInput = (0, Component_js_1.Component_decomposeName_Z721C83C5)((0, Option_js_1.value)(name));
+        patternInput_1 = [patternInput[0], patternInput[1]];
+    }
+    return new Component_js_1.Component(patternInput_1[0], patternInput_1[1], (objectArg_1 = get$.Optional, objectArg_1.Field("componentType", OntologyAnnotation_js_1.OntologyAnnotation_ISAJson_decoder)));
+});

package/dist/ts/cjs/ts/Json/Process/Factor.js

@@ -0,0 +1,58 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.decoder = void 0;
+exports.genID = genID;
+exports.encoder = encoder;
+const Option_js_1 = require("@fable-org/fable-library-js/Option.js");
+const OntologyAnnotation_js_1 = require("../OntologyAnnotation.js");
+const Factor_js_1 = require("../../Core/Process/Factor.js");
+const List_js_1 = require("@fable-org/fable-library-js/List.js");
+const Encode_js_1 = require("../Encode.js");
+const Comment_js_1 = require("../Comment.js");
+const Seq_js_1 = require("@fable-org/fable-library-js/Seq.js");
+const IDTable_js_1 = require("../IDTable.js");
+const Decode_fs_js_1 = require("../../fable_modules/Thoth.Json.Core.0.4.0/Decode.fs.js");
+function genID(f) {
+    const matchValue = f.Name;
+    if (matchValue == null) {
+        const matchValue_1 = f.FactorType;
+        if (matchValue_1 == null) {
+            return "#EmptyFactor";
+        }
+        else {
+            return `#Factor/${(0, OntologyAnnotation_js_1.OntologyAnnotation_ROCrate_genID)((0, Option_js_1.value)(matchValue_1))}`;
+        }
+    }
+    else {
+        return `#Factor/${(0, Option_js_1.value)(matchValue)}`;
+    }
+}
+function encoder(idMap, value) {
+    const f_1 = (value_1) => {
+        const values_1 = (0, List_js_1.choose)((tupledArg) => (0, Option_js_1.map)((v_1) => [tupledArg[0], v_1], tupledArg[1]), (0, List_js_1.ofArray)([(0, Encode_js_1.tryInclude)("@id", (value_2) => ({
+                Encode(helpers) {
+                    return helpers.encodeString(value_2);
+                },
+            }), genID(value_1)), (0, Encode_js_1.tryInclude)("factorName", (value_4) => ({
+                Encode(helpers_1) {
+                    return helpers_1.encodeString(value_4);
+                },
+            }), value_1.Name), (0, Encode_js_1.tryInclude)("factorType", (oa) => (0, OntologyAnnotation_js_1.OntologyAnnotation_ISAJson_encoder)(idMap, oa), value_1.FactorType), (0, Encode_js_1.tryIncludeSeq)("comments", (comment) => (0, Comment_js_1.ISAJson_encoder)(idMap, comment), (0, Option_js_1.defaultArg)(value_1.Comments, []))]));
+        return {
+            Encode(helpers_2) {
+                const arg = (0, Seq_js_1.map)((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_2)], values_1);
+                return helpers_2.encodeObject(arg);
+            },
+        };
+    };
+    if (idMap != null) {
+        return (0, IDTable_js_1.encode)(genID, f_1, value, (0, Option_js_1.value)(idMap));
+    }
+    else {
+        return f_1(value);
+    }
+}
+exports.decoder = (0, Decode_fs_js_1.object)((get$) => {
+    let objectArg, objectArg_1, arg_5, objectArg_2;
+    return new Factor_js_1.Factor((objectArg = get$.Optional, objectArg.Field("factorName", Decode_fs_js_1.string)), (objectArg_1 = get$.Optional, objectArg_1.Field("factorType", OntologyAnnotation_js_1.OntologyAnnotation_ISAJson_decoder)), (arg_5 = (0, Decode_fs_js_1.resizeArray)(Comment_js_1.ISAJson_decoder), (objectArg_2 = get$.Optional, objectArg_2.Field("comments", arg_5))));
+});

package/dist/ts/cjs/ts/Json/Process/FactorValue.js

@@ -0,0 +1,47 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.ISAJson_decoder = exports.ROCrate_decoder = exports.ROCrate_encoder = void 0;
+exports.ISAJson_genID = ISAJson_genID;
+exports.ISAJson_encoder = ISAJson_encoder;
+const PropertyValue_js_1 = require("../PropertyValue.js");
+const FactorValue_js_1 = require("../../Core/Process/FactorValue.js");
+const Option_js_1 = require("@fable-org/fable-library-js/Option.js");
+const List_js_1 = require("@fable-org/fable-library-js/List.js");
+const Encode_js_1 = require("../Encode.js");
+const Factor_js_1 = require("./Factor.js");
+const Value_js_1 = require("./Value.js");
+const OntologyAnnotation_js_1 = require("../OntologyAnnotation.js");
+const Seq_js_1 = require("@fable-org/fable-library-js/Seq.js");
+const IDTable_js_1 = require("../IDTable.js");
+const Decode_fs_js_1 = require("../../fable_modules/Thoth.Json.Core.0.4.0/Decode.fs.js");
+const Decode_js_1 = require("../Decode.js");
+exports.ROCrate_encoder = PropertyValue_js_1.encoder;
+exports.ROCrate_decoder = (0, PropertyValue_js_1.decoder)(FactorValue_js_1.FactorValue_createAsPV);
+function ISAJson_genID(fv) {
+    return (0, PropertyValue_js_1.genID)(fv);
+}
+function ISAJson_encoder(idMap, fv) {
+    const f = (fv_1) => {
+        const values_1 = (0, List_js_1.choose)((tupledArg) => (0, Option_js_1.map)((v_1) => [tupledArg[0], v_1], tupledArg[1]), (0, List_js_1.ofArray)([(0, Encode_js_1.tryInclude)("@id", (value) => ({
+                Encode(helpers) {
+                    return helpers.encodeString(value);
+                },
+            }), ISAJson_genID(fv_1)), (0, Encode_js_1.tryInclude)("category", (value_2) => (0, Factor_js_1.encoder)(idMap, value_2), fv_1.Category), (0, Encode_js_1.tryInclude)("value", (value_3) => (0, Value_js_1.encoder)(idMap, value_3), fv_1.Value), (0, Encode_js_1.tryInclude)("unit", (oa) => (0, OntologyAnnotation_js_1.OntologyAnnotation_ISAJson_encoder)(idMap, oa), fv_1.Unit)]));
+        return {
+            Encode(helpers_1) {
+                const arg = (0, Seq_js_1.map)((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_1)], values_1);
+                return helpers_1.encodeObject(arg);
+            },
+        };
+    };
+    if (idMap != null) {
+        return (0, IDTable_js_1.encode)(ISAJson_genID, f, fv, (0, Option_js_1.value)(idMap));
+    }
+    else {
+        return f(fv);
+    }
+}
+exports.ISAJson_decoder = (0, Decode_fs_js_1.object)((get$) => {
+    let objectArg, objectArg_1, objectArg_2, objectArg_3;
+    return new FactorValue_js_1.FactorValue((objectArg = get$.Optional, objectArg.Field("@id", Decode_js_1.Decode_uri)), (objectArg_1 = get$.Optional, objectArg_1.Field("category", Factor_js_1.decoder)), (objectArg_2 = get$.Optional, objectArg_2.Field("value", Value_js_1.decoder)), (objectArg_3 = get$.Optional, objectArg_3.Field("unit", OntologyAnnotation_js_1.OntologyAnnotation_ISAJson_decoder)));
+});

package/dist/ts/cjs/ts/Json/Process/Material.js

@@ -0,0 +1,120 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.ISAJson_decoder = exports.ISAJson_allowedFields = exports.ROCrate_decoder = void 0;
+exports.ROCrate_genID = ROCrate_genID;
+exports.ROCrate_encoder = ROCrate_encoder;
+exports.ISAJson_encoder = ISAJson_encoder;
+const Option_js_1 = require("@fable-org/fable-library-js/Option.js");
+const String_js_1 = require("@fable-org/fable-library-js/String.js");
+const Material_js_1 = require("../../Core/Process/Material.js");
+const List_js_1 = require("@fable-org/fable-library-js/List.js");
+const Encode_fs_js_1 = require("../../fable_modules/Thoth.Json.Core.0.4.0/Encode.fs.js");
+const Encode_js_1 = require("../Encode.js");
+const MaterialType_js_1 = require("./MaterialType.js");
+const MaterialAttributeValue_js_1 = require("./MaterialAttributeValue.js");
+const isa_material_context_js_1 = require("../context/rocrate/isa_material_context.js");
+const Seq_js_1 = require("@fable-org/fable-library-js/Seq.js");
+const Decode_fs_js_1 = require("../../fable_modules/Thoth.Json.Core.0.4.0/Decode.fs.js");
+const Decode_js_1 = require("../Decode.js");
+const IDTable_js_1 = require("../IDTable.js");
+function ROCrate_genID(m) {
+    const matchValue = m.ID;
+    if (matchValue == null) {
+        const matchValue_1 = m.Name;
+        if (matchValue_1 == null) {
+            return "#EmptyMaterial";
+        }
+        else {
+            return "#Material_" + (0, String_js_1.replace)((0, Option_js_1.value)(matchValue_1), " ", "_");
+        }
+    }
+    else {
+        return (0, Option_js_1.value)(matchValue);
+    }
+}
+function ROCrate_encoder(oa) {
+    let value;
+    const values_1 = (0, List_js_1.choose)((tupledArg) => (0, Option_js_1.map)((v_1) => [tupledArg[0], v_1], tupledArg[1]), (0, List_js_1.ofArray)([["@id", (value = ROCrate_genID(oa), {
+                Encode(helpers) {
+                    return helpers.encodeString(value);
+                },
+            })], ["@type", (0, Encode_fs_js_1.list)((0, List_js_1.singleton)({
+                Encode(helpers_1) {
+                    return helpers_1.encodeString("Material");
+                },
+            }))], ["additionalType", {
+                Encode(helpers_2) {
+                    return helpers_2.encodeString("Material");
+                },
+            }], (0, Encode_js_1.tryInclude)("name", (value_3) => ({
+            Encode(helpers_3) {
+                return helpers_3.encodeString(value_3);
+            },
+        }), oa.Name), (0, Encode_js_1.tryInclude)("type", MaterialType_js_1.ROCrate_encoder, oa.MaterialType), (0, Encode_js_1.tryIncludeListOpt)("characteristics", MaterialAttributeValue_js_1.ROCrate_encoder, oa.Characteristics), (0, Encode_js_1.tryIncludeListOpt)("derivesFrom", ROCrate_encoder, oa.DerivesFrom), ["@context", isa_material_context_js_1.context_jsonvalue]]));
+    return {
+        Encode(helpers_4) {
+            const arg = (0, Seq_js_1.map)((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_4)], values_1);
+            return helpers_4.encodeObject(arg);
+        },
+    };
+}
+exports.ROCrate_decoder = (() => {
+    const decode = () => (0, Decode_fs_js_1.object)((get$) => {
+        let objectArg_2, objectArg_3, objectArg_4, arg_11, objectArg_5, arg_13, objectArg_6;
+        let matchValue;
+        const objectArg = get$.Optional;
+        matchValue = objectArg.Field("additionalType", Decode_js_1.Decode_uri);
+        let matchResult;
+        if (matchValue == null) {
+            matchResult = 0;
+        }
+        else if ((0, Option_js_1.value)(matchValue) === "Material") {
+            matchResult = 0;
+        }
+        else {
+            matchResult = 1;
+        }
+        switch (matchResult) {
+            case 1: {
+                const objectArg_1 = get$.Required;
+                objectArg_1.Field("FailBecauseNotSample", Decode_fs_js_1.unit);
+                break;
+            }
+        }
+        return new Material_js_1.Material((objectArg_2 = get$.Optional, objectArg_2.Field("@id", Decode_js_1.Decode_uri)), (objectArg_3 = get$.Optional, objectArg_3.Field("name", Decode_fs_js_1.string)), (objectArg_4 = get$.Optional, objectArg_4.Field("type", MaterialType_js_1.ROCrate_decoder)), (arg_11 = (0, Decode_fs_js_1.list)(MaterialAttributeValue_js_1.ROCrate_decoder), (objectArg_5 = get$.Optional, objectArg_5.Field("characteristics", arg_11))), (arg_13 = (0, Decode_fs_js_1.list)(decode()), (objectArg_6 = get$.Optional, objectArg_6.Field("derivesFrom", arg_13))));
+    });
+    return decode();
+})();
+function ISAJson_encoder(idMap, c) {
+    const f = (oa) => {
+        const values_1 = (0, List_js_1.choose)((tupledArg) => (0, Option_js_1.map)((v_1) => [tupledArg[0], v_1], tupledArg[1]), (0, List_js_1.ofArray)([(0, Encode_js_1.tryInclude)("@id", (value) => ({
+                Encode(helpers) {
+                    return helpers.encodeString(value);
+                },
+            }), ROCrate_genID(oa)), (0, Encode_js_1.tryInclude)("name", (value_2) => ({
+                Encode(helpers_1) {
+                    return helpers_1.encodeString(value_2);
+                },
+            }), oa.Name), (0, Encode_js_1.tryInclude)("type", MaterialType_js_1.ISAJson_encoder, oa.MaterialType), (0, Encode_js_1.tryIncludeListOpt)("characteristics", (oa_1) => (0, MaterialAttributeValue_js_1.ISAJson_encoder)(idMap, oa_1), oa.Characteristics), (0, Encode_js_1.tryIncludeListOpt)("derivesFrom", (c_1) => ISAJson_encoder(idMap, c_1), oa.DerivesFrom)]));
+        return {
+            Encode(helpers_2) {
+                const arg = (0, Seq_js_1.map)((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_2)], values_1);
+                return helpers_2.encodeObject(arg);
+            },
+        };
+    };
+    if (idMap != null) {
+        return (0, IDTable_js_1.encode)(ROCrate_genID, f, c, (0, Option_js_1.value)(idMap));
+    }
+    else {
+        return f(c);
+    }
+}
+exports.ISAJson_allowedFields = (0, List_js_1.ofArray)(["@id", "@type", "name", "type", "characteristics", "derivesFrom", "@context"]);
+exports.ISAJson_decoder = (() => {
+    const decode = () => (0, Decode_js_1.Decode_objectNoAdditionalProperties)(exports.ISAJson_allowedFields, (get$) => {
+        let objectArg, objectArg_1, objectArg_2, arg_7, objectArg_3, arg_9, objectArg_4;
+        return new Material_js_1.Material((objectArg = get$.Optional, objectArg.Field("@id", Decode_js_1.Decode_uri)), (objectArg_1 = get$.Optional, objectArg_1.Field("name", Decode_fs_js_1.string)), (objectArg_2 = get$.Optional, objectArg_2.Field("type", MaterialType_js_1.ISAJson_decoder)), (arg_7 = (0, Decode_fs_js_1.list)(MaterialAttributeValue_js_1.ISAJson_decoder), (objectArg_3 = get$.Optional, objectArg_3.Field("characteristics", arg_7))), (arg_9 = (0, Decode_fs_js_1.list)(decode()), (objectArg_4 = get$.Optional, objectArg_4.Field("derivesFrom", arg_9))));
+    });
+    return decode();
+})();