myst-frontmatter - npm Package Compare versions

Comparing version 1.1.1 to 1.1.2

dist/frontmatter/types.d.ts

 import type { CreditRole } from 'credit-roles';
 import type { Licenses } from '../licenses/types.js';
+export interface Affiliation {
+    id?: string;
+    name?: string;
+    institution?: string;
+    department?: string;
+    address?: string;
+    city?: string;
+    state?: string;
+    postal_code?: string;
+    country?: string;
+    collaboration?: boolean;
+    isni?: string;
+    ringgold?: number;
+    ror?: string;
+    url?: string;
+    email?: string;
+    phone?: string;
+    fax?: string;
+}
 export type AuthorRoles = CreditRole | string;
 export interface Author {
+    id?: string;
     name?: string;
@@ -9,10 +29,23 @@ userId?: string;
     corresponding?: boolean;
+    equal_contributor?: boolean;
+    deceased?: boolean;
     email?: string;
     roles?: AuthorRoles[];
     affiliations?: string[];
-    collaborations?: string[];
     twitter?: string;
     github?: string;
-    website?: string;
+    url?: string;
+    note?: string;
+    phone?: string;
+    fax?: string;
 }
+/**
+ * Object to hold items referenced in multiple parts of frontmatter
+ *
+ * These will be normalized to the top level and replaced with ids elsewhere
+ */
+export type ReferenceStash = {
+    affiliations?: Affiliation[];
+    authors?: Author[];
+};
 export type Biblio = {
@@ -115,2 +148,3 @@ volume?: string | number;
     authors?: Author[];
+    affiliations?: Affiliation[];
     venue?: Venue;
@@ -117,0 +151,0 @@ github?: string;

dist/frontmatter/validators.d.ts

 import type { ValidationOptions } from 'simple-validators';
-import type { Author, Biblio, Export, Jupytext, KernelSpec, Numbering, PageFrontmatter, ProjectFrontmatter, SiteFrontmatter, Venue, Thebe, BinderHubOptions, JupyterServerOptions, JupyterLocalOptions } from './types.js';
+import type { Author, Biblio, Export, Jupytext, KernelSpec, Numbering, PageFrontmatter, ProjectFrontmatter, SiteFrontmatter, Venue, Thebe, BinderHubOptions, JupyterServerOptions, JupyterLocalOptions, ReferenceStash, Affiliation } from './types.js';
 export declare const SITE_FRONTMATTER_KEYS: string[];
@@ -9,2 +9,20 @@ export declare const PROJECT_FRONTMATTER_KEYS: string[];
 /**
+ * Update stash of authors/affiliations based on input value
+ *
+ * Input may be:
+ *   - string name
+ *   - string id
+ *   - object without id
+ *   - object with id
+ *
+ * This function will normalize all of the above to an id and if a corresponding
+ * object does not yet exist in the stash, it will be added. The id is returned.
+ *
+ * This function will warn if two objects are explicitly defined with the same id.
+ */
+export declare function validateAndStashObject<T extends {
+    id?: string;
+    name?: string;
+}>(input: any, stash: ReferenceStash, kind: keyof ReferenceStash, validateFn: (v: any, o: ValidationOptions) => T | undefined, opts: ValidationOptions): string | undefined;
+/**
  * Validate Venue object against the schema
@@ -16,5 +34,12 @@ *
 /**
+ * Validate Affiliation object against the schema
+ */
+export declare function validateAffiliation(input: any, opts: ValidationOptions): Affiliation | {
+    id: string;
+    name: string;
+} | undefined;
+/**
  * Validate Author object against the schema
  */
-export declare function validateAuthor(input: any, opts: ValidationOptions): Author | undefined;
+export declare function validateAuthor(input: any, stash: ReferenceStash, opts: ValidationOptions): Author | undefined;
 /**
@@ -70,3 +95,3 @@ * Validate Biblio object
  */
-export declare function fillPageFrontmatter(pageFrontmatter: PageFrontmatter, projectFrontmatter: ProjectFrontmatter): PageFrontmatter;
+export declare function fillPageFrontmatter(pageFrontmatter: PageFrontmatter, projectFrontmatter: ProjectFrontmatter, opts: ValidationOptions): PageFrontmatter;
 /**
@@ -73,0 +98,0 @@ * Unnest `kernelspec` from `jupyter.kernelspec`

dist/frontmatter/validators.js

 import { doi } from 'doi-utils';
 import { credit } from 'credit-roles';
 import { orcid } from 'orcid';
-import { defined, incrementOptions, fillMissingKeys, filterKeys, validateBoolean, validateDate, validateEmail, validateEnum, validateKeys, validateList, validateObject, validateObjectKeys, validateString, validateUrl, validationError, validationWarning, } from 'simple-validators';
+import { defined, incrementOptions, fillMissingKeys, filterKeys, validateBoolean, validateDate, validateEmail, validateEnum, validateKeys, validateList, validateObject, validateObjectKeys, validateString, validateUrl, validationError, validationWarning, validateNumber, } from 'simple-validators';
 import { validateLicenses } from '../licenses/validators.js';
 import { BinderProviders, ExportFormats } from './types.js';
+import { createHash } from 'node:crypto';
 export const SITE_FRONTMATTER_KEYS = [
@@ -20,2 +21,3 @@ 'title',
     'keywords',
+    'affiliations',
 ];
@@ -60,3 +62,23 @@ export const PROJECT_FRONTMATTER_KEYS = [
 ];
+const AFFILIATION_KEYS = [
+    'id',
+    'address',
+    'city',
+    'state',
+    'postal_code',
+    'country',
+    'name',
+    'institution',
+    'department',
+    'collaboration',
+    'isni',
+    'ringgold',
+    'ror',
+    'url',
+    'email',
+    'phone',
+    'fax',
+];
 const AUTHOR_KEYS = [
+    'id',
     'userId',
@@ -66,2 +88,4 @@ 'name',
     'corresponding',
+    'equal_contributor',
+    'deceased',
     'email',
@@ -73,3 +97,6 @@ 'roles',
     'github',
-    'website',
+    'url',
+    'note',
+    'phone',
+    'fax',
 ];
@@ -79,3 +106,10 @@ const AUTHOR_ALIASES = {
     affiliation: 'affiliations',
+    website: 'url',
 };
+const AFFILIATION_ALIASES = {
+    ref: 'id',
+    region: 'state',
+    province: 'state',
+    website: 'url',
+};
 const BIBLIO_KEYS = ['volume', 'issue', 'first_page', 'last_page'];
@@ -145,3 +179,68 @@ const THEBE_KEYS = [
 }
+function stashPlaceholder(value) {
+    return { id: value, name: value };
+}
 /**
+ * Return true if object:
+ *   - has 2 keys and only 2 keys: id and name
+ *   - the values for id and name are the same
+ */
+function isStashPlaceholder(object) {
+    return Object.keys(object).length === 2 && object.name && object.id && object.name === object.id;
+}
+function normalizedString(value) {
+    return JSON.stringify(Object.entries(value).sort());
+}
+/**
+ * Update stash of authors/affiliations based on input value
+ *
+ * Input may be:
+ *   - string name
+ *   - string id
+ *   - object without id
+ *   - object with id
+ *
+ * This function will normalize all of the above to an id and if a corresponding
+ * object does not yet exist in the stash, it will be added. The id is returned.
+ *
+ * This function will warn if two objects are explicitly defined with the same id.
+ */
+export function validateAndStashObject(input, stash, kind, validateFn, opts) {
+    var _a;
+    const lookup = {};
+    (_a = stash[kind]) === null || _a === void 0 ? void 0 : _a.forEach((item) => {
+        if (item.id)
+            lookup[item.id] = item;
+    });
+    if (typeof input === 'string' && Object.keys(lookup).includes(input)) {
+        // Handle case where input is id and object already exists
+        return input;
+    }
+    const value = validateFn(input, opts);
+    if (!value)
+        return;
+    // Only warn on duplicate if the new object is not a placeholder
+    let warnOnDuplicate = !isStashPlaceholder(value);
+    if (!value.id) {
+        // If object is defined without an id, generate a unique id
+        value.id = createHash('md5').update(normalizedString(value)).digest('hex');
+        // Do not warn on duplicates for hash ids; any duplicates here are identical
+        warnOnDuplicate = false;
+    }
+    if (!Object.keys(lookup).includes(value.id)) {
+        // Handle case of new id - add stash value
+        lookup[value.id] = value;
+    }
+    else if (isStashPlaceholder(lookup[value.id])) {
+        // Handle case of existing placeholder { id: value, name: value } - replace stash value
+        lookup[value.id] = value;
+    }
+    else if (warnOnDuplicate) {
+        // Warn on duplicate id - lose new object
+        validationWarning(`duplicate id for ${kind} found in frontmatter: ${value.id}`, opts);
+    }
+    stash[kind] = Object.values(lookup);
+    return value.id;
+}
+/**
  * Validate Venue object against the schema
@@ -174,7 +273,84 @@ *
 /**
+ * Validate Affiliation object against the schema
+ */
+export function validateAffiliation(input, opts) {
+    if (typeof input === 'string') {
+        input = stashPlaceholder(input);
+    }
+    const value = validateObjectKeys(input, { optional: AFFILIATION_KEYS, alias: AFFILIATION_ALIASES }, opts);
+    if (value === undefined)
+        return undefined;
+    const output = {};
+    if (defined(value.id)) {
+        output.id = validateString(value.id, incrementOptions('id', opts));
+    }
+    if (defined(value.name)) {
+        output.name = validateString(value.name, incrementOptions('name', opts));
+    }
+    if (defined(value.institution)) {
+        output.institution = validateString(value.institution, incrementOptions('institution', opts));
+    }
+    if (defined(value.department)) {
+        output.department = validateString(value.department, incrementOptions('department', opts));
+    }
+    if (defined(value.address)) {
+        output.address = validateString(value.address, incrementOptions('address', opts));
+    }
+    if (defined(value.city)) {
+        output.city = validateString(value.city, incrementOptions('city', opts));
+    }
+    if (defined(value.state)) {
+        output.state = validateString(value.state, incrementOptions('state', opts));
+    }
+    if (defined(value.postal_code)) {
+        output.postal_code = validateString(value.postal_code, incrementOptions('postal_code', opts));
+    }
+    if (defined(value.country)) {
+        output.country = validateString(value.country, incrementOptions('country', opts));
+    }
+    // Both ISNI and ROR validation should occur similar to orcid (maybe in that same lib?)
+    if (defined(value.isni)) {
+        output.isni = validateString(value.isni, incrementOptions('isni', opts));
+    }
+    if (defined(value.ror)) {
+        output.ror = validateString(value.ror, incrementOptions('ror', opts));
+    }
+    if (defined(value.ringgold)) {
+        output.ringgold = validateNumber(value.ringgold, {
+            min: 1000,
+            max: 999999,
+            ...incrementOptions('ringgold', opts),
+        });
+    }
+    if (defined(value.collaboration)) {
+        output.collaboration = validateBoolean(value.collaboration, incrementOptions('collaboration', opts));
+    }
+    if (defined(value.email)) {
+        output.email = validateEmail(value.email, incrementOptions('email', opts));
+    }
+    if (defined(value.url)) {
+        output.url = validateUrl(value.url, incrementOptions('url', opts));
+    }
+    if (defined(value.phone)) {
+        output.phone = validateString(value.phone, incrementOptions('phone', opts));
+    }
+    if (defined(value.fax)) {
+        output.fax = validateString(value.fax, incrementOptions('fax', opts));
+    }
+    // If affiliation only has an id, give it a matching name; this is equivalent to the case
+    // where a simple string is provided as an affiliation.
+    if (Object.keys(output).length === 1 && output.id) {
+        return stashPlaceholder(output.id);
+    }
+    else if (!output.name && !output.institution) {
+        validationWarning('affiliation should include name or institution', opts);
+    }
+    return output;
+}
+/**
  * Validate Author object against the schema
  */
-export function validateAuthor(input, opts) {
+export function validateAuthor(input, stash, opts) {
     if (typeof input === 'string') {
-        input = { name: input };
+        input = { id: input, name: input };
     }
@@ -185,2 +361,5 @@ const value = validateObjectKeys(input, { optional: AUTHOR_KEYS, alias: AUTHOR_ALIASES }, opts);
     const output = {};
+    if (defined(value.id)) {
+        output.id = validateString(value.id, incrementOptions('id', opts));
+    }
     if (defined(value.userId)) {
@@ -193,2 +372,5 @@ // TODO: Better userId validation - length? regex?
     }
+    else {
+        validationWarning('author should include name', opts);
+    }
     if (defined(value.orcid)) {
@@ -212,2 +394,8 @@ const orcidOpts = incrementOptions('orcid', opts);
     }
+    if (defined(value.equal_contributor)) {
+        output.equal_contributor = validateBoolean(value.equal_contributor, incrementOptions('equal_contributor', opts));
+    }
+    if (defined(value.deceased)) {
+        output.deceased = validateBoolean(value.deceased, incrementOptions('deceased', opts));
+    }
     if (defined(value.email)) {
@@ -234,2 +422,5 @@ output.email = validateEmail(value.email, incrementOptions('email', opts));
     }
+    if (defined(value.collaborations)) {
+        validationError('collaborations must be defined in frontmatter as affiliations with "collaboration: true"', incrementOptions('collaborations', opts));
+    }
     if (defined(value.affiliations)) {
@@ -239,20 +430,8 @@ const affiliationsOpts = incrementOptions('affiliations', opts);
         if (typeof affiliations === 'string') {
-            affiliations = affiliations.split(';');
+            affiliations = affiliations.split(';').map((aff) => aff.trim());
         }
         output.affiliations = validateList(affiliations, affiliationsOpts, (aff) => {
-            var _a;
-            return (_a = validateString(aff, affiliationsOpts)) === null || _a === void 0 ? void 0 : _a.trim();
+            return validateAndStashObject(aff, stash, 'affiliations', validateAffiliation, affiliationsOpts);
         });
     }
-    if (defined(value.collaborations)) {
-        const collaborationsOpts = incrementOptions('collaborations', opts);
-        let collaborations = value.collaborations;
-        if (typeof collaborations === 'string') {
-            collaborations = collaborations.split(';');
-        }
-        output.collaborations = validateList(collaborations, collaborationsOpts, (col) => {
-            var _a;
-            return (_a = validateString(col, collaborationsOpts)) === null || _a === void 0 ? void 0 : _a.trim();
-        });
-    }
     if (defined(value.twitter)) {
@@ -264,5 +443,14 @@ output.twitter = validateString(value.twitter, incrementOptions('twitter', opts));
     }
-    if (defined(value.website)) {
-        output.website = validateUrl(value.website, incrementOptions('website', opts));
+    if (defined(value.url)) {
+        output.url = validateUrl(value.url, incrementOptions('url', opts));
     }
+    if (defined(value.phone)) {
+        output.phone = validateString(value.phone, incrementOptions('phone', opts));
+    }
+    if (defined(value.fax)) {
+        output.fax = validateString(value.fax, incrementOptions('fax', opts));
+    }
+    if (defined(value.note)) {
+        output.note = validateString(value.note, incrementOptions('note', opts));
+    }
     return output;
@@ -623,2 +811,13 @@ }
     }
+    const stash = {};
+    if (defined(value.affiliations)) {
+        const affiliationsOpts = incrementOptions('affiliations', opts);
+        let affiliations = value.affiliations;
+        if (typeof affiliations === 'string') {
+            affiliations = affiliations.split(';').map((aff) => aff.trim());
+        }
+        validateList(affiliations, affiliationsOpts, (aff) => {
+            return validateAndStashObject(aff, stash, 'affiliations', validateAffiliation, affiliationsOpts);
+        });
+    }
     if (defined(value.authors)) {
@@ -631,3 +830,3 @@ let authors = value.authors;
         output.authors = validateList(authors, incrementOptions('authors', opts), (author, index) => {
-            return validateAuthor(author, incrementOptions(`authors.${index}`, opts));
+            return validateAuthor(author, stash, incrementOptions(`authors.${index}`, opts));
         });
@@ -656,2 +855,5 @@ // Ensure there is a corresponding author if an email is provided
     }
+    if (stash.affiliations) {
+        output.affiliations = stash.affiliations;
+    }
     return output;
@@ -838,3 +1040,3 @@ }
  */
-export function fillPageFrontmatter(pageFrontmatter, projectFrontmatter) {
+export function fillPageFrontmatter(pageFrontmatter, projectFrontmatter, opts) {
     var _a, _b, _c, _d;
@@ -859,2 +1061,37 @@ const frontmatter = fillMissingKeys(pageFrontmatter, projectFrontmatter, USE_PROJECT_FALLBACK);
     }
+    // Replace affiliation placeholders with extra affiliations available on the project/page
+    let affiliations;
+    let extraAffiliations;
+    // Currently, affiliations are connected only to authors, so we look at
+    // which frontmatter (project or page) has authors defined, and use the
+    // affiliations from there. However, we still use the other affiliations
+    // to fill out any placeholders where affiliations have id only.
+    if (projectFrontmatter.authors && !pageFrontmatter.authors) {
+        affiliations = projectFrontmatter.affiliations;
+        extraAffiliations = pageFrontmatter.affiliations;
+    }
+    else {
+        affiliations = pageFrontmatter.affiliations;
+        extraAffiliations = projectFrontmatter.affiliations;
+    }
+    if (affiliations) {
+        const projectAffLookup = {};
+        extraAffiliations === null || extraAffiliations === void 0 ? void 0 : extraAffiliations.forEach((aff) => {
+            if (aff.id && !isStashPlaceholder(aff)) {
+                projectAffLookup[aff.id] = aff;
+            }
+        });
+        frontmatter.affiliations = affiliations.map((aff) => {
+            if (!aff.id || !projectAffLookup[aff.id]) {
+                return aff;
+            }
+            else if (isStashPlaceholder(aff)) {
+                return projectAffLookup[aff.id];
+            }
+            else if (normalizedString(aff) !== normalizedString(projectAffLookup[aff.id])) {
+                validationWarning(`Duplicate affiliation id within project: ${aff.id}`, incrementOptions('affiliations', opts));
+            }
+            return aff;
+        });
+    }
     return frontmatter;
@@ -861,0 +1098,0 @@ }

package.json

 {
   "name": "myst-frontmatter",
-  "version": "1.1.1",
+  "version": "1.1.2",
   "sideEffects": false,
@@ -35,3 +35,3 @@ "license": "MIT",
   "dependencies": {
-    "credit-roles": "^2.0.0",
+    "credit-roles": "^2.1.0",
     "doi-utils": "^2.0.0",
@@ -38,0 +38,0 @@ "orcid": "^1.0.0",

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Found 1 instance in 1 package

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A new npm collaborator published a version of the package for the first time. New collaborators are usually benign additions to a project, but do indicate a change to the security surface area of a package.

Found 1 instance in 1 package

Fixed alerts

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Improved metrics

Total package byte prevSize

115531

increased by11.44%

Lines of code

3456

increased by9.37%

Worsened metrics

Number of medium supply chain risk alerts

1

increased byInfinity%

Dependency changes

• Updatedcredit-roles@^2.1.0