jenkins-bot has submitted this change and it was merged. (
https://gerrit.wikimedia.org/r/331879 )
Change subject: Added verification to PMCID and PMID parameters in
"addPubMedIndentifiers"
......................................................................
Added verification to PMCID and PMID parameters in "addPubMedIndentifiers"
Bug: T149513
Change-Id: I7695e65efb7019ab4f161d258e50c49f9c792bd8
---
M lib/Exporter.js
M test/features/scraping/index.js
2 files changed, 22 insertions(+), 6 deletions(-)
Approvals:
jenkins-bot: Verified
Mvolz: Looks good to me, approved
diff --git a/lib/Exporter.js b/lib/Exporter.js
index 895e263..942e60e 100644
--- a/lib/Exporter.js
+++ b/lib/Exporter.js
@@ -276,6 +276,8 @@
var citation = cr.response.body[0];
var gotData = false; // Whether or not we retrieved any useful data from
PubMed
+ var rePMCID = new RegExp('\\bPMC\\d{7}\\b');
+ var rePMID = new RegExp('^[1-9]\\d{0,7}\\b');
// Try to get PMCID or PMID from extra field
if ((!citation.PMCID || !citation.PMID) && citation.extra) {
//get pmid from extra fields
@@ -283,8 +285,10 @@
for (var f in extraFields) {
//could add them all, but let's not do this in case of conflicting
fields
var keyValue = extraFields[f].split(': ');
- if (keyValue[0] === 'PMID' || keyValue[0] === 'PMCID') {
- citation[keyValue[0]] = keyValue[1].trim().replace('PMC','');
+ if (keyValue[0] === 'PMID' && keyValue[1].trim().match(rePMID)) {
+ citation['PMID'] = keyValue[1].trim();
+ } else if (keyValue[0] === 'PMCID' &&
keyValue[1].trim().match(rePMCID)) {
+ citation['PMCID'] = keyValue[1].trim();
}
}
}
@@ -295,7 +299,7 @@
}
// Fill in remaining IDs from pubmed api
- return pubMedRequest((citation.DOI || (citation.PMCID ? "PMC" +
citation.PMCID : false) || citation.PMID),
+ return pubMedRequest((citation.DOI || (citation.PMCID ? citation.PMCID :
false) || citation.PMID),
userAgent, defaultLogger).then(function(results){
if (!citation.PMID && results.records[0].pmid){
gotData = true;
@@ -303,7 +307,7 @@
}
if (!citation.PMCID && results.records[0].pmcid) {
gotData = true;
- citation.PMCID = results.records[0].pmcid.replace('PMC','');
+ citation.PMCID = results.records[0].pmcid;
}
if (!citation.DOI && results.records[0].doi) {
gotData = true;
@@ -599,4 +603,4 @@
module.exports.fixURL = fixURL;
module.exports.validateISSN = validateISSN;
-module.exports.validateISBN = validateISBN;
\ No newline at end of file
+module.exports.validateISBN = validateISBN;
diff --git a/test/features/scraping/index.js b/test/features/scraping/index.js
index ddd3ca6..c3b92d7 100644
--- a/test/features/scraping/index.js
+++ b/test/features/scraping/index.js
@@ -97,7 +97,19 @@
assert.deepEqual(res.body[0].publicationTitle, undefined); //TODO:
Investigate why this is undefined
});
});
+ it('PMCID but no PMID', function() {
+
+ it('webpage', function() {
+ return server.query('PMC2096233',
+ 'mediawiki', 'en', 'true').then(function(res) {
+ assert.status(res, 200);
+ console.log(res);
+ assert.deepEqual(!!res.body[0].PMCID, true, 'PMC2096233');
+ assert.deepEqual(res.body[0].PMID, undefined, 'PMID is null');
+ });
+ });
+
+ });
});
-
--
To view, visit https://gerrit.wikimedia.org/r/331879
To unsubscribe, visit https://gerrit.wikimedia.org/r/settings
Gerrit-MessageType: merged
Gerrit-Change-Id: I7695e65efb7019ab4f161d258e50c49f9c792bd8
Gerrit-PatchSet: 10
Gerrit-Project: mediawiki/services/citoid
Gerrit-Branch: master
Gerrit-Owner: Filip <r...@protonmail.com>
Gerrit-Reviewer: Filip <r...@protonmail.com>
Gerrit-Reviewer: Mobrovac <mobro...@wikimedia.org>
Gerrit-Reviewer: Mvolz <mv...@wikimedia.org>
Gerrit-Reviewer: jenkins-bot <>
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