Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Added support for corrected assertions in docmap #92

Merged
merged 11 commits into from
Jun 20, 2024
Merged
Show file tree
Hide file tree
Changes from 2 commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 6 additions & 0 deletions src/generators/docmap-generators.ts
Original file line number Diff line number Diff line change
Expand Up @@ -209,6 +209,12 @@ export const generatePeerReviewedAssertion = (item: Item, date?: Date): Assertio
happened: date,
});

export const generateCorrectedAssertion = (item: Item, date?: Date): Assertion => ({
item,
status: AssertionStatus.Corrected,
happened: date,
});

export const generateEnhancedAssertion = (item: Item, date?: Date): Assertion => ({
item,
status: AssertionStatus.Enhanced,
Expand Down
22 changes: 22 additions & 0 deletions src/parser/docmap-parser.test.ts
Original file line number Diff line number Diff line change
Expand Up @@ -445,6 +445,28 @@ describe('docmap-parser', () => {
});
});

it('can parse a docmap with an inference of version of record corrected from input/outputs', () => {
const parsedData = parseDocMap(fixtures.inferredVersionOfRecordCorrected());

expect(parsedData.versions.length).toStrictEqual(1);
expect(parsedData.versions[0]).toMatchObject<VersionedPreprint>({
doi: 'vor/article1',
id: 'vor/article1',
publishedDate: new Date('2024-05-09'),
url: 'https://version-of-record',
content: [
'https://doi.org/version-of-record',
'https://doi.org/version-of-record-corrected',
'https://doi.org/version-of-record-corrected-again',
],
versionIdentifier: '1',
correctedDate: [
new Date('2024-06-09'),
new Date('2024-06-10'),
],
});
});

it('inference of reviewed preprint from input/outputs', () => {
const parsedData = parseDocMap(fixtures.inferredReviewedPreprint());

Expand Down
14 changes: 14 additions & 0 deletions src/parser/docmap-parser.ts
Original file line number Diff line number Diff line change
Expand Up @@ -67,6 +67,7 @@ type Preprint = {
url?: string,
content?: string[],
license?: string,
correctedDate?: Date[],
};

type ReviewedPreprint = {
Expand All @@ -80,6 +81,7 @@ type ReviewedPreprint = {
reviewedDate?: Date,
authorResponseDate?: Date,
license?: string,
correctedDate?: Date[],
};

type RelatedContentItem = {
Expand Down Expand Up @@ -454,6 +456,18 @@ const parseStep = (step: Step, preprints: Array<ReviewedPreprint>, manuscript: M
preprint.sentForReviewDate = preprintUnderReviewAssertion.happened;
}

const preprintCorrectedAssertion = step.assertions.find((assertion) => assertion.status === AssertionStatus.Corrected);
if (preprintCorrectedAssertion) {
// Update type and sent for review date
const preprint = findAndUpdateOrAddPreprintDescribedBy(preprintCorrectedAssertion.item, preprints, manuscript);
if (preprintCorrectedAssertion.happened) {
if (!Array.isArray(preprint.correctedDate)) {
preprint.correctedDate = [];
}
preprint.correctedDate.push(preprintCorrectedAssertion.happened);
}
}

const inferredRepublished = getRepublishedPreprint(step);
if (inferredRepublished) {
// preprint input, preprint output, but no evaluations = supersede input preprint with output Reviewed Preprint
Expand Down
54 changes: 53 additions & 1 deletion src/test-fixtures/docmap-parser.ts
Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,9 @@ import {
generateUnderReviewAssertion,
generateWebContent,
generateManuscript,
generateInsight, generateVersionOfRecord,
generateInsight,
generateVersionOfRecord,
generateCorrectedAssertion,
} from '../generators/docmap-generators';

const publisher = {
Expand Down Expand Up @@ -548,6 +550,56 @@ export const fixtures = {
return generateDocMap('test', publisher, firstStep);
},

inferredVersionOfRecordCorrected: (): DocMap => {
nlisgo marked this conversation as resolved.
Show resolved Hide resolved
const versionOfRecordOutput = generateVersionOfRecord(new Date('2024-05-09'), [generateWebContent('https://doi.org/version-of-record')], 'vor/article1', 'https://version-of-record');
const versionOfRecord = {
type: versionOfRecordOutput.type,
doi: versionOfRecordOutput.doi,
versionIdentifier: versionOfRecordOutput.versionIdentifier,
};
const firstStep = generateStep([], [generateAction([], [versionOfRecordOutput])], []);
const nextStep = addNextStep(firstStep, generateStep(
[{
...versionOfRecord,
identifier: versionOfRecordOutput.identifier,
}],
[
generateAction([], [
{
...versionOfRecord,
content: [
generateWebContent('https://doi.org/version-of-record-corrected')
],
},
]),
],
[
generateCorrectedAssertion(versionOfRecord, new Date('2024-06-09')),
],
));
addNextStep(nextStep, generateStep(
[{
...versionOfRecord,
identifier: versionOfRecordOutput.identifier,
}],
[
generateAction([], [
{
...versionOfRecord,
content: [
generateWebContent('https://doi.org/version-of-record-corrected-again')
],
},
]),
],
[
generateCorrectedAssertion(versionOfRecord, new Date('2024-06-10')),
],
));

return generateDocMap('test', publisher, firstStep);
},

preprintWithPublishedDateAndNoAssertedPublishDate: (): DocMap => {
const preprint = generatePreprint('preprint/article1');
const preprintWithDate = generatePreprint('preprint/article1', new Date('2022-03-01'));
Expand Down
1 change: 1 addition & 0 deletions src/types/docmap.ts
Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,7 @@ export enum AssertionStatus {
VersionOfRecord = 'version-of-record',
Revised = 'revised',
Republished = 'republished',
Corrected = 'corrected',
}

export type Assertion = {
Expand Down