Merge pull request #18 from bcgsc/feature/hard-code-reverse-names

Feature/hard code reverse names

src/class.ts

@@ -53,20 +53,6 @@ const createClassDefinition = (opt: ClassDefinitionInput): ClassDefinition => {
         isEdge = true;
     }
 
-    let reverseName;
-
-    if (opt.isEdge) {
-        if (name.endsWith('Of')) {
-            reverseName = `Has${name.slice(0, name.length - 2)}`;
-        } else if (name.endsWith('By')) {
-            reverseName = `${name.slice(0, name.length - 3)}s`;
-        } else if (name === 'Infers') {
-            reverseName = 'InferredBy';
-        } else {
-            reverseName = `${name.slice(0, name.length - 1)}dBy`;
-        }
-    }
-
     let defaultRoutes: Expose;
 
     if (opt.isAbstract || opt.embedded) {
@@ -91,8 +77,6 @@ const createClassDefinition = (opt: ClassDefinitionInput): ClassDefinition => {
         embedded: Boolean(opt.embedded),
         indices: opt.indices || [],
         permissions: { ...defaultPermissions(routes), ...(opt.permissions || {}) },
-        reverseName,
-
     };
 };
 

src/definitions/edges.ts

@@ -22,20 +22,23 @@ const edgeModels: PartialSchemaDefn = {
         indices: [activeUUID('E'), defineSimpleIndex({ model: 'E', property: 'createdAt' })],
     },
     AliasOf: {
+        reverseName: 'HasAlias',
         description: 'The source record is an equivalent representation of the target record, both of which are from the same source',
     },
-    Cites: { description: 'Generally refers to relationships between publications. For example, some article cites another' },
-    CrossReferenceOf: { description: 'The source record is an equivalent representation of the target record from a different source' },
-    DeprecatedBy: { description: 'The target record is a newer version of the source record' },
-    ElementOf: { description: 'The source record is part of (or contained within) the target record' },
-    GeneralizationOf: { description: 'The source record is a less specific (or more general) instance of the target record' },
+    Cites: { reverseName: 'CitedBy', description: 'Generally refers to relationships between publications. For example, some article cites another' },
+    CrossReferenceOf: { reverseName: 'HasCrossReference', description: 'The source record is an equivalent representation of the target record from a different source' },
+    DeprecatedBy: { reverseName: 'Deprecates', description: 'The target record is a newer version of the source record' },
+    ElementOf: { reverseName: 'HasElement', description: 'The source record is part of (or contained within) the target record' },
+    GeneralizationOf: { reverseName: 'HasGeneralization', description: 'The source record is a less specific (or more general) instance of the target record' },
     Infers: {
         description: 'Given the source record, the target record is also expected. For example given some genomic variant we infer the protein change equivalent',
         sourceModel: 'Variant',
         targetModel: 'Variant',
+        reverseName: 'InferredBy',
     },
-    SubClassOf: { description: 'The source record is a subset of the target record' },
+    SubClassOf: { reverseName: 'HasSubclass', description: 'The source record is a subset of the target record' },
     TargetOf: {
+        reverseName: 'HasTarget',
         description: 'The source record is a target of the target record. For example some gene is the target of a particular drug',
         properties: [
             { ...BASE_PROPERTIES.in },
@@ -59,20 +62,8 @@ for (const name of [
     'TargetOf',
 ]) {
     const sourceProp = { name: 'source', type: 'link' as const, linkedClass: 'Source' };
-    let reverseName;
-
-    if (name.endsWith('Of')) {
-        reverseName = `Has${name.slice(0, name.length - 2)}`;
-    } else if (name.endsWith('By')) {
-        reverseName = `${name.slice(0, name.length - 3)}s`;
-    } else if (name === 'Infers') {
-        reverseName = 'InferredBy';
-    } else {
-        reverseName = `${name.slice(0, name.length - 1)}dBy`;
-    }
     edgeModels[name] = {
         isEdge: true,
-        reverseName,
         inherits: ['E'],
         sourceModel: 'Ontology',
         targetModel: 'Ontology',

src/definitions/index.ts

@@ -129,7 +129,7 @@ const BASE_SCHEMA: PartialSchemaDefn = {
                 mandatory: true,
                 nullable: false,
                 description: 'The timestamp at which this terms of use was put into action',
-                default: timeStampNow,
+                generateDefault: timeStampNow,
                 generated: true,
                 examples: [1547245339649],
             }, {
@@ -155,7 +155,7 @@ const initializeSchema = (
     for (const name of Object.keys(inputSchema)) {
         if (name !== 'Permissions' && !inputSchema[name].embedded) {
             permissionsProperties.push({
-                min: PERMISSIONS.NONE, max: PERMISSIONS.ALL, type: 'integer', nullable: false, readOnly: false, name,
+                minimum: PERMISSIONS.NONE, maximum: PERMISSIONS.ALL, type: 'integer', nullable: false, readOnly: false, name,
             });
         }
     }

src/definitions/ontology.ts

@@ -70,7 +70,7 @@ const models: PartialSchemaDefn = {
             {
                 name: 'name',
                 nullable: false,
-                default: (record) => record.sourceId,
+                generateDefault: (record) => record?.sourceId,
                 description: 'Name of the term',
                 nonEmpty: true,
                 generationDependencies: true,
@@ -107,7 +107,7 @@ const models: PartialSchemaDefn = {
             { name: 'url', type: 'string' },
             {
                 ...BASE_PROPERTIES.displayName,
-                default: util.displayOntology,
+                generateDefault: util.displayOntology,
             },
         ],
         isAbstract: true,
@@ -246,7 +246,7 @@ const models: PartialSchemaDefn = {
             },
             {
                 ...BASE_PROPERTIES.displayName,
-                default: util.displayFeature,
+                generateDefault: util.displayFeature,
             },
         ],
     },

src/definitions/position.ts

@@ -19,7 +19,7 @@ const models: PartialSchemaDefn = {
         embedded: true,
         properties: [
             {
-                name: 'pos', type: 'integer', min: 1, mandatory: true, examples: [12], nullable: true, description: 'The Amino Acid number',
+                name: 'pos', type: 'integer', minimum: 1, mandatory: true, examples: [12], nullable: true, description: 'The Amino Acid number',
             },
             {
                 name: 'refAA', type: 'string', cast: util.uppercase, examples: ['G'], pattern: '^[A-Z*?]$', description: 'The reference Amino Acid (single letter notation)',
@@ -35,10 +35,10 @@ const models: PartialSchemaDefn = {
                 name: 'arm', mandatory: true, nullable: false, choices: ['p', 'q'],
             },
             {
-                name: 'majorBand', type: 'integer', min: 1, examples: ['11'],
+                name: 'majorBand', type: 'integer', minimum: 1, examples: ['11'],
             },
             {
-                name: 'minorBand', type: 'integer', min: 1, examples: ['1'],
+                name: 'minorBand', type: 'integer', minimum: 1, examples: ['1'],
             },
         ],
     },
@@ -47,23 +47,23 @@ const models: PartialSchemaDefn = {
         inherits: ['Position'],
         embedded: true,
         properties: [{
-            name: 'pos', type: 'integer', min: 1, mandatory: true, nullable: true, description: 'The genomic/nucleotide number',
+            name: 'pos', type: 'integer', minimum: 1, mandatory: true, nullable: true, description: 'The genomic/nucleotide number',
         }],
     },
     ExonicPosition: {
         routes: EXPOSE_NONE,
         inherits: ['Position'],
         embedded: true,
         properties: [{
-            name: 'pos', type: 'integer', min: 1, mandatory: true, nullable: true, description: 'The exon number',
+            name: 'pos', type: 'integer', minimum: 1, mandatory: true, nullable: true, description: 'The exon number',
         }],
     },
     IntronicPosition: {
         routes: EXPOSE_NONE,
         inherits: ['Position'],
         embedded: true,
         properties: [{
-            name: 'pos', type: 'integer', min: 1, mandatory: true, nullable: true,
+            name: 'pos', type: 'integer', minimum: 1, mandatory: true, nullable: true,
         }],
     },
     CdsPosition: {
@@ -85,7 +85,7 @@ const models: PartialSchemaDefn = {
         embedded: true,
         properties: [
             {
-                name: 'pos', type: 'integer', min: 1, mandatory: true, examples: [55], nullable: true,
+                name: 'pos', type: 'integer', minimum: 1, mandatory: true, examples: [55], nullable: true,
             },
             {
                 name: 'offset', type: 'integer', examples: [-11], description: 'distance from the nearest exon boundary (pos)',
@@ -100,7 +100,7 @@ const models: PartialSchemaDefn = {
         embedded: true,
         properties: [
             {
-                name: 'pos', type: 'integer', min: 1, mandatory: true, examples: [55], nullable: true,
+                name: 'pos', type: 'integer', minimum: 1, mandatory: true, examples: [55], nullable: true,
             },
             {
                 name: 'offset', type: 'integer', examples: [-11], description: 'distance from the nearest cds exon boundary',

src/definitions/statement.ts

@@ -89,13 +89,15 @@ const models: PartialSchemaDefn = {
                 name: 'displayNameTemplate',
                 description: 'The template used in building the display name',
                 type: 'string',
-                default: (record) => {
+                generateDefault: (record) => {
                     try {
-                        return chooseDefaultTemplate(record);
-                    } catch (err) {
-                        return DEFAULT_TEMPLATE;
-                    }
+                        if (record) {
+                            return chooseDefaultTemplate(record);
+                        }
+                    } catch (err) { }
+                    return DEFAULT_TEMPLATE;
                 },
+                generationDependencies: true,
                 cast: util.castString, // skip default lowercasing
             },
         ],

src/definitions/util.ts

@@ -86,7 +86,7 @@ const BASE_PROPERTIES: { [P in BasePropertyName]: PropertyDefinitionInput } = {
         readOnly: true,
         description: 'Internal identifier for tracking record history',
         cast: util.castUUID,
-        default: uuidV4 as () => string,
+        generateDefault: uuidV4 as () => string,
         generated: true,
         examples: ['4198e211-e761-4771-b6f8-dadbcc44e9b9'],
     },
@@ -96,7 +96,7 @@ const BASE_PROPERTIES: { [P in BasePropertyName]: PropertyDefinitionInput } = {
         mandatory: true,
         nullable: false,
         description: 'The timestamp at which the record was created',
-        default: util.timeStampNow,
+        generateDefault: util.timeStampNow,
         generated: true,
         examples: [1547245339649],
     },
@@ -106,7 +106,7 @@ const BASE_PROPERTIES: { [P in BasePropertyName]: PropertyDefinitionInput } = {
         mandatory: true,
         nullable: false,
         description: 'The timestamp at which the record was last updated',
-        default: util.timeStampNow,
+        generateDefault: util.timeStampNow,
         generated: true,
         examples: [1547245339649],
     },
@@ -180,7 +180,7 @@ const BASE_PROPERTIES: { [P in BasePropertyName]: PropertyDefinitionInput } = {
         name: 'displayName',
         type: 'string',
         description: 'Optional string used for display in the web application. Can be overwritten w/o tracking',
-        default: (rec) => rec.name || null,
+        generateDefault: (rec) => rec?.name || null,
         generationDependencies: true,
         cast: util.castString,
     },

src/definitions/variant.ts

@@ -75,7 +75,7 @@ const models: PartialSchemaDefn = {
                 type: 'string',
                 generationDependencies: true,
                 generated: true,
-                default: (record) => generateBreakRepr(record.break1Start, record.break1End),
+                generateDefault: (record) => generateBreakRepr(record.break1Start, record.break1End),
                 cast: castBreakRepr,
             },
             {
@@ -92,7 +92,7 @@ const models: PartialSchemaDefn = {
                 type: 'string',
                 generationDependencies: true,
                 generated: true,
-                default: (record) => generateBreakRepr(record.break2Start, record.break2End),
+                generateDefault: (record) => generateBreakRepr(record.break2Start, record.break2End),
                 cast: castBreakRepr,
             },
             {

src/property.ts

@@ -58,15 +58,15 @@ export const validateProperty = (prop: PropertyDefinition, inputValue: unknown):
             });
         }
         if (castValue !== null) {
-            if (prop.min !== undefined && prop.min !== null && castValue < prop.min) {
+            if (prop.minimum !== undefined && prop.minimum !== null && castValue < prop.minimum) {
                 throw new ValidationError({
-                    message: `Violated the minimum value constraint of ${prop.name} (${castValue} < ${prop.min})`,
+                    message: `Violated the minimum value constraint of ${prop.name} (${castValue} < ${prop.minimum})`,
                     field: prop.name,
                 });
             }
-            if (prop.max !== undefined && prop.max !== null && castValue > prop.max) {
+            if (prop.maximum !== undefined && prop.maximum !== null && castValue > prop.maximum) {
                 throw new ValidationError({
-                    message: `Violated the maximum value constraint of ${prop.name} (${castValue} > ${prop.max})`,
+                    message: `Violated the maximum value constraint of ${prop.name} (${castValue} > ${prop.maximum})`,
                     field: prop.name,
                 });
             }
@@ -116,10 +116,9 @@ export const validateProperty = (prop: PropertyDefinition, inputValue: unknown):
 export const createPropertyDefinition = (opt: PropertyDefinitionInput): PropertyDefinition => {
     const {
         type: inputType,
-        default: inputDefault,
         ...rest
     } = opt;
-    const defaultType = ((opt.min !== undefined || opt.max !== undefined) && !opt.type)
+    const defaultType = ((opt.minimum !== undefined || opt.maximum !== undefined) && !opt.type)
         ? 'integer'
         : 'string';
     const type: DbType = inputType || defaultType;
@@ -148,17 +147,6 @@ export const createPropertyDefinition = (opt: PropertyDefinitionInput): Property
         }
     }
 
-    let generateDefault,
-        defaultValue: undefined | unknown;
-
-    if (opt.default !== undefined) {
-        if (opt.default instanceof Function) {
-            generateDefault = opt.default;
-        } else {
-            defaultValue = opt.default;
-        }
-    }
-
     const castFunction = opt.cast || defaultCast;
     let choices: undefined | unknown[];
 
@@ -170,8 +158,6 @@ export const createPropertyDefinition = (opt: PropertyDefinitionInput): Property
         ...rest,
         type,
         cast: castFunction,
-        default: defaultValue,
-        generateDefault,
         description: opt.description || '',
         generated: Boolean(opt.generated),
         generationDependencies: Boolean(opt.generationDependencies),

src/schema.ts

@@ -1,5 +1,5 @@
 import {
-    PropertyDefinition, ClassDefinition, GraphRecord, ClassMapping,
+    PropertyDefinition, ClassDefinition, GraphRecord, ClassMapping, StatementRecord,
 } from './types';
 import { ValidationError } from './error';
 import { validateProperty } from './property';
@@ -84,12 +84,12 @@ class SchemaDefinition {
     * Returns preview of given record based on its '@class' value
     * @param {Object} obj - Record to be parsed.
     */
-    getPreview(obj: GraphRecord): string {
+    getPreview(obj: Partial<GraphRecord>): string {
         if (obj && typeof obj === 'object') {
             if (obj['@class'] === 'Statement') {
                 const { content } = sentenceTemplates.generateStatementSentence(
                     this.getPreview.bind(this),
-                    obj,
+                    obj as StatementRecord,
                 );
                 return content;
             }
@@ -101,7 +101,7 @@ class SchemaDefinition {
                 return obj.name;
             }
             if (obj['@rid']) {
-                return obj['@rid'];
+                return `${obj['@rid']}`;
             }
             if (Array.isArray(obj)) { // embedded link set
                 return `${obj.length}`;
@@ -342,14 +342,14 @@ class SchemaDefinition {
      */
     formatRecord(
         modelName: unknown,
-        record: GraphRecord,
+        record: Record<string, unknown>,
         opt: {
             dropExtra?: boolean;
             addDefaults?: boolean;
             ignoreExtra?: boolean;
             ignoreMissing?: boolean;
         } = {},
-    ): GraphRecord {
+    ): Partial<GraphRecord> {
         const model = this.get(modelName);
         // add default options
         const {
@@ -421,7 +421,7 @@ class SchemaDefinition {
         for (let [attr, value] of Object.entries(formattedRecord)) {
             let { linkedClass, type, iterable } = properties[attr];
 
-            if (type.startsWith('embedded') && linkedClass !== undefined && value) {
+            if (type.startsWith('embedded') && linkedClass !== undefined && value && typeof value === 'object') {
                 if (value['@class'] && value['@class'] !== linkedClass) {
                     // record has a class type that doesn't match the expected linkedClass, is it a subclass of it?
                     if (this.ancestors(value['@class']).includes(linkedClass)) {
@@ -431,11 +431,11 @@ class SchemaDefinition {
                     }
                 }
                 if (type === 'embedded' && typeof value === 'object') {
-                    value = this.formatRecord(linkedClass, value);
-                } else if (iterable) {
+                    value = this.formatRecord(linkedClass, value as Record<string, unknown>);
+                } else if (iterable && Array.isArray(value)) {
                     value = Array.from(
                         value,
-                        (v) => this.formatRecord(linkedClass, v as GraphRecord),
+                        (v) => this.formatRecord(linkedClass, v),
                     );
                 }
             }