Skip to content

Commit

Permalink
refactor: ♻️ updates to zenodo workflow (#84)
Browse files Browse the repository at this point in the history 
* refactor: ♻️ update on the zenodo ui

* fix: 🐛 patch existing Zenodo dep template being applied in wrong cases

* fix: 🐛 no contributor roles patch

* fix: update for codemeta license field

* fix: update for codemeta contributor roles

* fix: 🐛 preserve db license id and content when github api returns no assertion

* fix: update for codemeta license field

* fix: update zenodo success message

* fix: 🐛 delete zenodo deposition upon uninstallation, throw new errors on zenodo workflow

* fix: update for citation license field

* refactor: ♻️ update db when pull request is created by codefair

* fix: 🐛 contributor key wrong for valid codemeta

* fix: 🐛 validations on code meta UI, wip patching error message on zenodo publication UI

* fix: 🐛 remove info alert box for metadata info

* fix: 🐛 preserve contributor and author roles when codemeta.json file exists

* refactor: ♻️ consider the both valid keys for schema contributor

* fix: 🐛 preserve related links and funding organization

* fix: 🐛 patch zenodo authors having extra creators

* 🐛 fix: update modal content based on explicit response

* refactor: ♻️ null values rather than undefined for fallback value

* refactor: ♻️ update on accessing contributor role details

* fix: 🐛 empty modal on zenodo release

* fix: 🐛 verify state of pull request if PR url exists in db

* fix: 🐛 update metadata details in db after updating for Zenodo

* refactor: ♻️ don't update updated_at value in db

---------

Co-authored-by: Sanjay Soundarajan <sanjay.16@live.com>
  • Loading branch information
@slugb0t @megasanjay
slugb0t and megasanjay authored Oct 16, 2024
1 parent 77dd9c1 commit 26b688c
Show file tree
Hide file tree
Showing 11 changed files with 513 additions and 263 deletions.
113 changes: 72 additions & 41 deletions bot/archival/index.js
View file
Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ export async function applyArchivalTemplate(
const releaseBadgeButton = `[![Create Release](https://img.shields.io/badge/Create_Release-00bcd4.svg)](${badgeURL})`
const newReleaseText = `To make your software FAIR, it is necessary to archive it in an archival repository like Zenodo every time you make a release. When you are ready to make your next release, click the "Create release" button below to easily create a FAIR release where your metadata files are updated (including with a DOI) before creating a GitHub release and archiving it.\n\n`

if (!existingZenodoDep) {
if (!existingZenodoDep && !existingZenodoDep?.last_published_zenodo_doi) {
// Entry does not exist in db, create a new one
// await zenDepositionCollection.create({
// data: {
Expand All @@ -58,7 +58,7 @@ export async function applyArchivalTemplate(
}
});

// Fetch the DOI content
// Fetch the DOI content
const lastVersion = existingZenodoDep.github_tag_name;
const zenodoId = existingZenodoDep.zenodo_id;
const zenodoDoi = existingZenodoDep.last_published_zenodo_doi;
Expand Down Expand Up @@ -97,18 +97,18 @@ export async function createNewZenodoDeposition(zenodoToken) {
*/
export async function fetchExistingZenodoDeposition(zenodoToken, depositionId) {
const zenodoDeposition = await fetch(
`${ZENODO_API_ENDPOINT}/deposit/depositions/${depositionId}?access_token=${zenodoToken}`,
`${ZENODO_API_ENDPOINT}/deposit/depositions/${depositionId}`,
{
method: "GET",
headers: {
"Content-Type": "application/json",
"Authorization": `Bearer ${zenodoToken}`,
},
},
);

if (!zenodoDeposition.ok) {
consola.error("Error fetching the Zenodo deposition:", zenodoDeposition);
throw new Error(`Failed to fetch the Zenodo deposition. Status: ${zenodoDeposition.statusText}`);
const errorText = await zenodoDeposition.text();
throw new Error(`Failed to fetch the Zenodo deposition. Status: ${zenodoDeposition.status}: ${zenodoDeposition.statusText}. Error: ${errorText}`);
}

const zenodoDepositionInfo = await zenodoDeposition.json();
Expand All @@ -126,17 +126,15 @@ export async function createNewVersionOfDeposition(zenodoToken, depositionId) {
`${ZENODO_API_ENDPOINT}/deposit/depositions/${depositionId}/actions/newversion`,
{
method: "POST",
headers: {
"Content-Type": "application/json",
headers: {
Authorization: `Bearer ${zenodoToken}`, // Use Authorization header instead of query parameter
},
},
);

// Delete all the files in the deposition draft
if (!zenodoRecord.ok) {
consola.error("Error creating new version of Zenodo deposition:", zenodoRecord);
throw new Error(`Failed to create new version of Zenodo deposition. Status: ${zenodoRecord.statusText}`);
const errorText = await zenodoRecord.text();
throw new Error(`Failed to create a new version of Zenodo deposition. Status: ${zenodoRecord.status}: ${zenodoRecord.statusText}. Error: ${errorText}`, { cause: errorText });
}

const responseText = await zenodoRecord.json();
Expand All @@ -158,14 +156,15 @@ export async function getZenodoDepositionInfo(
const newZenodoDeposition = await createNewZenodoDeposition(zenodoToken);
return newZenodoDeposition;
} catch (error) {
throw new Error ("Error creating new Zenodo deposition:", error);
throw new Error (`Error creating new Zenodo deposition: ${error}`, { cause: error });
}
} else {
try {
// Fetch existing Zenodo deposition
const zenodoDepositionInfo = await fetchExistingZenodoDeposition(zenodoToken, depositionId);

// Check if the deposition is published
// Check if the deposition is a draft or contains a draft

if (zenodoDepositionInfo.submitted === false){
// Delete the files in the draft
for (const file of zenodoDepositionInfo.files) {
Expand All @@ -175,8 +174,34 @@ export async function getZenodoDepositionInfo(
return zenodoDepositionInfo;
}

// TODO: Check if the deposition is a draft or contains a draft
// consola.info("DONT LOST IT")
// consola.info(zenodoDepositionInfo.links)
// consola.info(zenodoDepositionInfo.links.latest_draft)
// if (zenodoDepositionInfo.links && zenodoDepositionInfo.links.latest_draft) {
// // Fetch the draft, delete the files and then return deposition info
// const draftZenodoRecord = await fetch(zenodoDepositionInfo.links.latest_draft, {
// method: "GET",
// headers: {
// "Content-Type": "application/json",
// Authorization: `Bearer ${zenodoToken}`,
// },
// });

// if (!draftZenodoRecord.ok) {
// consola.error("Error fetching the latest draft of Zenodo deposition:", draftZenodoRecord);
// const errorText = await draftZenodoRecord.text();
// throw new Error(`Failed to fetch the latest draft of Zenodo deposition. Status: ${draftZenodoRecord.status}: ${draftZenodoRecord.statusText}. Error: ${errorText}`, { cause: errorText });
// }

// const draftZenodoVersion = await draftZenodoRecord.json();
// consola.info("HEHEHEHEHE")
// consola.warn(draftZenodoVersion);
// return draftZenodoVersion;
// }

// Create a new version of an existing Zenodo deposition
// consola.info(`Creating a new version of Zenodo deposition ${depositionId}...`);
consola.info(`Creating a new version of Zenodo deposition ${depositionId}...`);
const responseText = await createNewVersionOfDeposition(zenodoToken, depositionId);
const latestDraftLink = responseText.links.latest_draft;

Expand All @@ -191,7 +216,8 @@ export async function getZenodoDepositionInfo(

if (!draftZenodoRecord.ok) {
consola.error("Error fetching the latest draft of Zenodo deposition:", draftZenodoRecord);
throw new Error(`Failed to fetch the latest draft of Zenodo deposition. Status: ${draftZenodoRecord.statusText}`);
const errorText = await draftZenodoRecord.text();
throw new Error(`Failed to fetch the latest draft of Zenodo deposition. Status: ${draftZenodoRecord.status}: ${draftZenodoRecord.statusText}. Error: ${errorText}`, { cause: errorText });
}

const newZenodoVersion = await draftZenodoRecord.json();
Expand All @@ -202,7 +228,7 @@ export async function getZenodoDepositionInfo(
}
}

consola.success("New version of Zenodo deposition created successfully!");
consola.success("New draft version of Zenodo deposition created successfully!");
return newZenodoVersion;
} catch (error) {
consola.error("Error fetching the Zenodo deposition:", error);
Expand All @@ -219,23 +245,31 @@ export async function getZenodoDepositionInfo(
export async function getZenodoMetadata(codemetadata, repository) {
const new_date = new Date().toISOString().split('T')[0];
const codeMetaContent = JSON.parse(codemetadata);
const zenodoCreators = codeMetaContent.author.map((author) => {
const zenodoCreators = codeMetaContent.author
.filter((author) => author?.type !== "Role") // Exclude authors with type "Role"
.map((author) => {
const tempObj = {};
tempObj.name = author.familyName
? `${author.familyName}, ${author.givenName}`

// Format the name as "Family name, Given names"
tempObj.name = author.familyName
? `${author.familyName}, ${author.givenName}`
: author.givenName;

if (author.affiliation) {
tempObj.affiliation = author.affiliation;

// Add affiliation if present
if (author.affiliation && author.affiliation.name) {
tempObj.affiliation = author.affiliation.name;
}


// Add ORCID if present
if (author.orcid) {
tempObj.orcid = author.orcid;
}

return tempObj;
});

console.log(zenodoCreators);

if (!codeMetaContent.license) {
// fetch from the db
consola.warn(`No license found in the codemeta.json file. Fetching from the database...`);
Expand Down Expand Up @@ -389,23 +423,20 @@ export async function uploadReleaseAssetsToZenodo(
* @param {String} fileId - Zenodo file ID
*/
export async function deleteFileFromZenodo(depositionId, zenodoToken, fileId) {
try {
const deleteFile = await fetch(
`${ZENODO_API_ENDPOINT}/deposit/depositions/${depositionId}/files/${fileId}?access_token=${zenodoToken}`,
{
method: "DELETE",
headers: {},
body: JSON.stringify({}),
},
);

if (!deleteFile.ok) {
consola.error(deleteFile);
throw new Error(`Failed to delete file from Zenodo. Status: ${deleteFile.statusText}`);
}
const deleteFile = await fetch(
`${ZENODO_API_ENDPOINT}/deposit/depositions/${depositionId}/files/${fileId}?access_token=${zenodoToken}`,
{
method: "DELETE",
headers: {},
body: JSON.stringify({}),
},
);

consola.success("File successfully deleted from Zenodo!");
} catch (error) {
throw new Error(`Error deleting file from Zenodo: ${error}`);
if (!deleteFile.ok) {
consola.error(deleteFile);
const errorText = await deleteFile.text();
throw new Error(`Failed to delete file from Zenodo. Status: ${deleteFile.status}: ${deleteFile.statusText}. Error: ${errorText}`);
}

consola.success("File successfully deleted from Zenodo!");
}
Loading

0 comments on commit 26b688c

Please sign in to comment.