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Add Zotero.Retractions.getRetractionsFromJSON()

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Addresses #1703
This commit is contained in:
Dan Stillman 2019-06-12 01:05:49 -04:00
parent 5b9b39dfb7
commit b4b19c4811
2 changed files with 188 additions and 15 deletions
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173
chrome/content/zotero/xpcom/retractions.js
View file

@ -106,6 +106,120 @@ Zotero.Retractions = {
return this._retractedItems.has(item.id);
},
getRetractionsFromJSON: Zotero.serial(async function (jsonItems) {
// TODO: Save as retractions-cache with etag and cache and use for other checks
var keyCache = this._keyCache;
if (!keyCache) {
this._keyCache = keyCache = {
[this.TYPE_DOI]: new Map(),
[this.TYPE_PMID]: new Map(),
};
}
var matchingIndexes = new Set();
var valuesToCheck = [];
for (let i = 0; i < jsonItems.length; i++) {
let json = jsonItems[i];
// DOI
let doi;
if (json.DOI) {
doi = json.DOI;
}
else if (json.extra) {
let fields = Zotero.Utilities.Internal.extractExtraFields(json.extra);
let extraField = fields.get('DOI');
if (extraField && extraField.value) {
doi = extraField.value;
}
}
if (doi) {
doi = Zotero.Utilities.cleanDOI(doi);
}
if (doi) {
valuesToCheck.push({
type: this.TYPE_DOI,
value: doi,
index: i
});
}
// PMID
if (json.extra) {
let pmid = this._extractPMID(json.extra);
if (pmid) {
valuesToCheck.push({
type: this.TYPE_PMID,
value: pmid,
index: i
});
}
}
}
// Check all possible values
var keyIndexes = new Map();
var prefixStringsToCheck = [];
for (let { type, value, index } of valuesToCheck) {
// See if we've already cached a result for this key
let key = this._valueToKey(type, value);
let cachedResult = keyCache[type].get(key);
if (cachedResult !== undefined) {
if (cachedResult) {
matchingIndexes.add(index);
}
continue;
}
// Otherwise, check prefix against list
let prefixStr = this._getPrefixString(type, value, this._getCachedPrefixLength(type));
if (this._cachePrefixList.has(prefixStr)) {
prefixStringsToCheck.push(prefixStr);
// Map key to array index
let indexes = keyIndexes.get(key);
if (!indexes) {
indexes = new Set();
keyIndexes.set(key, indexes);
}
indexes.add(index);
}
// Set all keys to false in the cache. Any that match will be set to true below.
keyCache[type].set(key, false);
}
if (prefixStringsToCheck.length) {
let possibleMatches = await this._downloadPossibleMatches(prefixStringsToCheck);
for (let row of possibleMatches) {
if (row.doi) {
let indexes = keyIndexes.get(row.doi);
if (indexes !== undefined) {
for (let index of indexes) {
matchingIndexes.add(index);
}
}
keyCache[this.TYPE_DOI].set(row.doi, true);
}
if (row.pmid) {
let indexes = keyIndexes.get(row.pmid);
if (indexes !== undefined) {
for (let index of indexes) {
matchingIndexes.add(index);
}
}
keyCache[this.TYPE_PMID].set(row.pmid, true);
}
}
}
// TODO: Save key cache to disk with current ETag
return [...matchingIndexes];
}),
libraryHasRetractedItems: function (libraryID) {
return !!(this._retractedItemsByLibrary[libraryID]
&& this._retractedItemsByLibrary[libraryID].size);
@ -131,9 +245,9 @@ Zotero.Retractions = {
// Update Retracted Items virtual collection
if (Zotero.Libraries.exists(libraryID)
// Changed
&& (previous != current ||
&& (previous != current
// Explicitly hidden
(current && !Zotero.Utilities.Internal.getVirtualCollectionStateForLibrary(libraryID, 'retracted')))) {
|| (current && !Zotero.Utilities.Internal.getVirtualCollectionStateForLibrary(libraryID, 'retracted')))) {
let promises = [];
for (let zp of Zotero.getZoteroPanes()) {
promises.push(zp.setVirtual(libraryID, 'retracted', current));
@ -291,7 +405,8 @@ Zotero.Retractions = {
this._queuedPrefixStrings.clear();
var addedItems = [];
try {
addedItems = await this._downloadPossibleMatches(prefixStrings);
let possibleMatches = await this._downloadPossibleMatches(prefixStrings);
addedItems = await this._addPossibleMatches(possibleMatches);
}
catch (e) {
// Add back to queue on failure
@ -382,7 +497,8 @@ Zotero.Retractions = {
if (prefixesToSend.size) {
// TODO: Diff list and remove existing retractions that are missing
await this._downloadPossibleMatches([...prefixesToSend]);
let possibleMatches = await this._downloadPossibleMatches([...prefixesToSend]);
await this._addPossibleMatches(possibleMatches);
}
else {
Zotero.debug("No possible retractions");
@ -391,8 +507,10 @@ Zotero.Retractions = {
await this._saveCacheFile(list, etag, doiPrefixLength, pmidPrefixLength);
}),
/**
* @return {Number[]} - Array of added item ids
* @param {String[]} prefixStrings
* @return {Object[]} - Results from API search
*/
_downloadPossibleMatches: async function (prefixStrings) {
var req = await Zotero.HTTP.request(
@ -408,10 +526,17 @@ Zotero.Retractions = {
+ Zotero.Utilities.pluralize(results.length, ['match', 'matches']));
results.push(...this._fixedResults);
return results;
},
/**
* @param {Object[]} - Results from API search
* @return {Number[]} - Array of added item ids
*/
_addPossibleMatches: async function (possibleMatches) {
// Look in the key mappings for local items that match and add them as retractions
var addedItemIDs = new Set();
for (let row of results) {
for (let row of possibleMatches) {
if (row.doi) {
let ids = this._keyItems[this.TYPE_DOI].get(row.doi);
if (ids) {
@ -506,13 +631,31 @@ Zotero.Retractions = {
return value;
},
_getDOIPrefix: function (value, length) {
var hash = this._valueToKey(this.TYPE_DOI, value);
return hash.substr(0, length);
_getPrefixString: function (type, value, length) {
switch (type) {
case this.TYPE_DOI: {
let hash = this._valueToKey(this.TYPE_DOI, value);
return this.TYPE_DOI + hash.substr(0, length);
}
case this.TYPE_PMID: {
return this.TYPE_PMID + value.substr(0, length);
}
}
throw new Error("Unsupported type " + type);
},
_getPMIDPrefix: function (value, length) {
return value.substr(0, length);
_getCachedPrefixLength: function (type) {
switch (type) {
case this.TYPE_DOI: {
return this._cacheDOIPrefixLength;
}
case this.TYPE_PMID: {
return this._cachePMIDPrefixLength;
}
}
throw new Error("Unsupported type " + type);
},
_cacheKeyMappings: async function () {
@ -603,7 +746,7 @@ Zotero.Retractions = {
let doi = this._getItemDOI(item);
if (doi) {
this._addItemKeyMapping(this.TYPE_DOI, doi, item.id);
let prefixStr = this.TYPE_DOI + this._getDOIPrefix(doi, this._cacheDOIPrefixLength);
let prefixStr = this._getPrefixString(this.TYPE_DOI, doi, this._cacheDOIPrefixLength);
if (this._cachePrefixList.has(prefixStr)) {
this._queuedPrefixStrings.add(prefixStr);
}
@ -611,7 +754,7 @@ Zotero.Retractions = {
let pmid = this._getItemPMID(item);
if (pmid) {
this._addItemKeyMapping(this.TYPE_PMID, pmid, item.id);
let prefixStr = this.TYPE_PMID + this._getPMIDPrefix(pmid, this._cachePMIDPrefixLength);
let prefixStr = this._getPrefixString(this.TYPE_PMID, pmid, this._cachePMIDPrefixLength);
if (this._cachePrefixList.has(prefixStr)) {
this._queuedPrefixStrings.add(prefixStr);
}
@ -855,6 +998,6 @@ Zotero.Retractions = {
},
_fixedResults: [
{ date: "1977-04-15", pmid: 993, retractionPMID: 195582, reasons: ["Results Not Reproducible"], urls: []}
{ date: "1977-04-15", pmid: 993, retractionPMID: 195582, reasons: ["Results Not Reproducible"], urls: [] }
]
};

30
test/tests/retractionsTest.js
View file

@ -73,6 +73,36 @@ describe("Retractions", function() {
throw new Error("'collapsed' attribute not found");
}
describe("#getRetractionsFromJSON()", function () {
it("should identify object with retracted DOI", async function () {
var spy = sinon.spy(Zotero.HTTP, 'request');
var json = [
{
},
{
DOI: retractedDOI
},
{
DOI: '10.1234/abcd'
}
];
var indexes = await Zotero.Retractions.getRetractionsFromJSON(json);
assert.sameMembers(indexes, [1]);
assert.equal(spy.callCount, 1);
indexes = await Zotero.Retractions.getRetractionsFromJSON(json);
assert.sameMembers(indexes, [1]);
// Result should've been cached, so we should have it without another API request
assert.equal(spy.callCount, 1);
spy.restore();
});
});
describe("Notification Banner", function () {
it("should show banner when retracted item is added", async function () {
var banner = win.document.getElementById('retracted-items-container');