Merge pull request #13 from elifesciences/pub-year-volume

Pub year volume

examples/generated/04.reviewed_preprintv1.json

@@ -297,7 +297,15 @@
           "item": {
             "type": "preprint",
             "doi": "10.7554/eLife.80494.1",
-            "versionIdentifier": "1"
+            "versionIdentifier": "1",
+            "publicationYear": 2022,
+            "embodimentOf": {
+              "type": "manuscript",
+              "doi": "10.7554/eLife.80494",
+              "identifier": "80494",
+              "volumeIdentifier": "11",
+              "electronicArticleIdentifier": "RP80494"
+            }
           },
           "status": "manuscript-published",
           "happened": "2022-10-20T00:00:00.000Z"
@@ -329,4 +337,4 @@
       "previous-step": "_:b2"
     }
   }
-}
+}

src/docmap-generator.ts

@@ -25,21 +25,23 @@ import {
   Url,
   VersionOfRecord,
   WebPage,
+  Work,
 } from './docmap';
 
 type Steps = {
   'first-step': string,
   steps: Map<string, Step>
 };
 
-export const generatePreprint = (doi: DOI, published?: Date, url?: Url, version?: string, content?: Manifestation[], license?: string): Preprint => ({
+export const generatePreprint = (doi: DOI, published?: Date, url?: Url, version?: string, content?: Manifestation[], license?: string, work?: Work): Preprint => ({
   type: ExpressionType.Preprint,
   doi,
   url,
   published,
   versionIdentifier: version,
   content,
   license,
+  embodimentOf: work,
 });
 
 export const generateRevisedPreprint = (doi: DOI, published?: Date, url?: Url, version?: string, content?: Manifestation[]): RevisedPreprint => ({
@@ -112,6 +114,14 @@ export const generateWebContent = (url: Url): WebPage => ({
   url,
 });
 
+export const generateWork = (doi?: DOI, identifier?: string, volumeIdentifier?: string, electronicArticleIdentifier?: string): Work => ({
+  type: 'manuscript',
+  doi,
+  identifier,
+  volumeIdentifier,
+  electronicArticleIdentifier,
+});
+
 export const generatePersonParticipant = (name: string, role: string): Participant => ({
   actor: {
     name,

src/docmap-parser.test.ts

@@ -385,4 +385,23 @@ describe('docmap-parser', () => {
     expect(parsedData.versions[0].preprint.license).toStrictEqual('http://creativecommons.org/licenses/by/4.0/');
     expect(parsedData.versions[0].license).toStrictEqual('http://creativecommons.org/licenses/by/4.0/');
   });
+
+  it('extracts embodimentOf, if present', () => {
+    const parsedData = parseDocMap(fixtures.preprintWithWorkAsOutput());
+
+    expect(parsedData.manuscript).toStrictEqual({
+      doi: '10.1101/123456',
+      volume: '1',
+      eLocationId: 'RP123456',
+    });
+  });
+
+  it('extracts partial embodimentOf, if present', () => {
+    const parsedData = parseDocMap(fixtures.preprintWithPartialWorkAsOutput());
+
+    expect(parsedData.manuscript).toStrictEqual({
+      doi: '10.1101/123456',
+      eLocationId: 'RP123456',
+    });
+  });
 });

src/docmap-parser.ts

@@ -80,11 +80,30 @@ export type VersionedReviewedPreprint = ReviewedPreprint & {
   versionIdentifier: string,
 };
 
+export type Manuscript = {
+  doi?: string,
+  volume?: string,
+  eLocationId?: string,
+};
+
 export type ManuscriptData = {
   id: string,
+  manuscript?: Manuscript,
   versions: VersionedReviewedPreprint[],
 };
 
+const getManuscriptFromExpression = (expression: Expression): Manuscript | false => {
+  if (!expression.embodimentOf) {
+    return false;
+  }
+
+  return {
+    doi: expression.embodimentOf.doi,
+    volume: expression.embodimentOf.volumeIdentifier,
+    eLocationId: expression.embodimentOf.electronicArticleIdentifier,
+  };
+};
+
 const getPreprintFromExpression = (expression: Expression): Preprint => {
   if (!expression.doi) {
     throw Error('Cannot identify Expression by DOI');
@@ -171,13 +190,27 @@ const addPreprintDescribedBy = (expression: Expression, preprintCollection: Arra
   return newPreprint;
 };
 
-const findAndUpdateOrAddPreprintDescribedBy = (expression: Expression, preprintCollection: Array<ReviewedPreprint>): ReviewedPreprint => {
+const findAndUpdateOrAddPreprintDescribedBy = (expression: Expression, preprintCollection: Array<ReviewedPreprint>, manuscript: Manuscript): ReviewedPreprint => {
+  const foundManuscriptData = getManuscriptFromExpression(expression);
+  const existingManuscript = manuscript;
+  if (foundManuscriptData) {
+    if (foundManuscriptData.doi) {
+      existingManuscript.doi = foundManuscriptData.doi;
+    }
+    if (foundManuscriptData.eLocationId) {
+      existingManuscript.eLocationId = foundManuscriptData.eLocationId;
+    }
+    if (foundManuscriptData.volume) {
+      existingManuscript.volume = foundManuscriptData.volume;
+    }
+  }
   const foundPreprint = findPreprintDescribedBy(expression, preprintCollection);
   if (!foundPreprint) {
     return addPreprintDescribedBy(expression, preprintCollection);
   }
   // Update fields, default to any data already there.
   updateReviewedPreprintFrom(foundPreprint, expression);
+
   return foundPreprint;
 };
 
@@ -314,36 +347,36 @@ const getAuthorResponse = (step: Step): { preprint: Item, authorResponse: Item }
   return (authorResponseOutputs.length === 1 && items.preprintInputs.length === 1) ? { preprint: items.preprintInputs[0], authorResponse: authorResponseOutputs[0] } : false;
 };
 
-const parseStep = (step: Step, preprints: Array<ReviewedPreprint>): Array<ReviewedPreprint> => {
+const parseStep = (step: Step, preprints: Array<ReviewedPreprint>, manuscript: Manuscript): Array<ReviewedPreprint> => {
   const preprintPublishedAssertion = step.assertions.find((assertion) => assertion.status === AssertionStatus.Published);
   if (preprintPublishedAssertion) {
     // Update type and sent for review date
-    const preprint = findAndUpdateOrAddPreprintDescribedBy(preprintPublishedAssertion.item, preprints);
+    const preprint = findAndUpdateOrAddPreprintDescribedBy(preprintPublishedAssertion.item, preprints, manuscript);
     preprint.publishedDate = preprintPublishedAssertion.happened ?? preprint.publishedDate;
   }
 
   const inferredPublished = getPublishedPreprint(step);
   if (inferredPublished) {
-    findAndUpdateOrAddPreprintDescribedBy(inferredPublished, preprints);
+    findAndUpdateOrAddPreprintDescribedBy(inferredPublished, preprints, manuscript);
   }
 
   const preprintUnderReviewAssertion = step.assertions.find((assertion) => assertion.status === AssertionStatus.UnderReview);
   if (preprintUnderReviewAssertion) {
     // Update type and sent for review date
-    const preprint = findAndUpdateOrAddPreprintDescribedBy(preprintUnderReviewAssertion.item, preprints);
+    const preprint = findAndUpdateOrAddPreprintDescribedBy(preprintUnderReviewAssertion.item, preprints, manuscript);
     preprint.sentForReviewDate = preprintUnderReviewAssertion.happened;
   }
 
   const inferredRepublished = getRepublishedPreprint(step);
   if (inferredRepublished) {
     // preprint input, preprint output, but no evaluations = superceed input preprint with output Reviewed Preprint
-    const preprint = findAndUpdateOrAddPreprintDescribedBy(inferredRepublished.originalExpression, preprints);
+    const preprint = findAndUpdateOrAddPreprintDescribedBy(inferredRepublished.originalExpression, preprints, manuscript);
     republishPreprintAs(inferredRepublished.republishedExpression, preprint);
   }
 
   const inferredPeerReviewed = getPeerReviewedPreprint(step);
   if (inferredPeerReviewed) {
-    const preprint = findAndUpdateOrAddPreprintDescribedBy(inferredPeerReviewed.peerReviewedPreprint, preprints);
+    const preprint = findAndUpdateOrAddPreprintDescribedBy(inferredPeerReviewed.peerReviewedPreprint, preprints, manuscript);
     setPeerReviewFrom(step.actions, preprint);
     preprint.reviewedDate = preprint.peerReview?.evaluationSummary?.date;
 
@@ -355,13 +388,13 @@ const parseStep = (step: Step, preprints: Array<ReviewedPreprint>): Array<Review
 
   const newVersionPreprint = getNewVersionPreprint(step);
   if (newVersionPreprint) {
-    findAndUpdateOrAddPreprintDescribedBy(newVersionPreprint.newVersionExpression, preprints);
+    findAndUpdateOrAddPreprintDescribedBy(newVersionPreprint.newVersionExpression, preprints, manuscript);
   }
 
   // sometimes author response is a separate step, find those and add the author response
   const authorResponse = getAuthorResponse(step);
   if (authorResponse) {
-    const preprint = findAndUpdateOrAddPreprintDescribedBy(authorResponse.preprint, preprints);
+    const preprint = findAndUpdateOrAddPreprintDescribedBy(authorResponse.preprint, preprints, manuscript);
     setPeerReviewFrom(step.actions, preprint);
     preprint.authorResponseDate = authorResponse.authorResponse.published;
   }
@@ -430,8 +463,9 @@ export const parsePreprintDocMap = (docMap: DocMap | string): ManuscriptData =>
   const stepsIterator = getSteps(docMapStruct);
   let currentStep = stepsIterator.next().value;
   let preprints: Array<ReviewedPreprint> = [];
+  const manuscript: Manuscript = {};
   while (currentStep) {
-    preprints = parseStep(currentStep, preprints);
+    preprints = parseStep(currentStep, preprints, manuscript);
     currentStep = stepsIterator.next().value;
   }
 
@@ -442,6 +476,7 @@ export const parsePreprintDocMap = (docMap: DocMap | string): ManuscriptData =>
   const { id, versions } = finaliseVersions(preprints);
   return {
     id,
+    manuscript,
     versions,
   };
 };

src/docmap.ts

@@ -38,6 +38,7 @@ export type Expression = {
   doi?: DOI,
   content?: Manifestation[],
   license?: string,
+  embodimentOf?: Work,
 };
 
 export type Manifestation = {
@@ -115,6 +116,14 @@ export type Assertion = {
   happened?: Date,
 };
 
+export type Work = {
+  type: 'manuscript',
+  doi?: DOI,
+  identifier?: string,
+  volumeIdentifier?: string,
+  electronicArticleIdentifier?: string,
+};
+
 export type Step = {
   assertions: Assertion[],
   inputs: Input[],

src/test-fixtures/docmapGenerators.ts

@@ -15,6 +15,7 @@ import {
   generateStep,
   generateUnderReviewAssertion,
   generateWebContent,
+  generateWork,
 } from '../docmap-generator';
 
 const publisher = {
@@ -46,6 +47,20 @@ export const fixtures = {
     return generateDocMap('test', publisher, firstStep);
   },
 
+  preprintWithWorkAsOutput: (): DocMap => {
+    const work = generateWork('10.1101/123456', '123456', '1', 'RP123456');
+    const preprint = generatePreprint('preprint/article1', new Date('2022-03-01'), undefined, undefined, undefined, undefined, work);
+    const firstStep = generateStep([], [generateAction([], [preprint])], []);
+    return generateDocMap('test', publisher, firstStep);
+  },
+
+  preprintWithPartialWorkAsOutput: (): DocMap => {
+    const work = generateWork('10.1101/123456', '123456', undefined, 'RP123456');
+    const preprint = generatePreprint('preprint/article1', new Date('2022-03-01'), undefined, undefined, undefined, undefined, work);
+    const firstStep = generateStep([], [generateAction([], [preprint])], []);
+    return generateDocMap('test', publisher, firstStep);
+  },
+
   simplePreprintWithUrlAsOutput: (): DocMap => {
     const preprint = generatePreprint('preprint/article1', new Date('2022-03-01'), 'https://somewhere.org/preprint/article1');
     const firstStep = generateStep([], [generateAction([], [preprint])], []);