Unicodesnowman has uploaded a new change for review.
https://gerrit.wikimedia.org/r/176887
Change subject: Add requestFromPMID (and aliases for PMCID, Manuscript ID),
which fetches DOI and grabs response of that
......................................................................
Add requestFromPMID (and aliases for PMCID, Manuscript ID), which fetches DOI
and grabs response of that
Change-Id: I1852f9820d9a0e1af0f30003d84846b435095e16
---
M lib/requests.js
1 file changed, 73 insertions(+), 2 deletions(-)
git pull ssh://gerrit.wikimedia.org:29418/mediawiki/services/citoid
refs/changes/87/176887/1
diff --git a/lib/requests.js b/lib/requests.js
index dfde7d2..932330a 100644
--- a/lib/requests.js
+++ b/lib/requests.js
@@ -12,6 +12,7 @@
var scrape = require('./scrape.js').scrape;
var zoteroRequest = require('./zotero.js').zoteroRequest;
var util = require('util');
+var request = require('request');
/**
* runner function to use for a url
@@ -99,6 +100,69 @@
});
};
+/**
+ * parses a PMID, PMCID (must begin with PMC), manuscript ID, finds the DOI,
and runs requestFromDOI
+ * @param {[type]} requestedPMID want metadata from this PMID / PMCID /
manuscript ID
+ * @param {[type]} opts zoteroRequest options object
+ * @param {Function} callback callback (error, statusCode, body)
+ */
+
+var requestFromPMID = function (requestedPMID, opts, callback){
+ var pmidLink =
'http://www.ncbi.nlm.nih.gov/pmc/utils/idconv/v1.0/?tool=citoid&email=citoid@mediawiki&format=json&ids='+requestedPMID;
+ requestJSON(pmidLink, {}, function(error, obj){
+ if(error){
+ callback(error, null, "");
+ }
+ else if(obj.status !== "ok"){
+ log.error("PubMed returned unrecognized status code: "
+ obj.status);
+ callback("PubMed returned unrecognized status", 200,
"");
+ }
+ else {
+ if(obj.records.length > 0){
+ var doi = obj.records[0].doi;
+ console.log("Got DOI " + doi);
+ requestFromDOI(doi, opts, callback);
+ } else {
+ log.error("No records retrieved from PubMed for
" + requestedPMID);
+ callback("No records rerieved from PubMed",
200, "");
+ }
+ }
+
+ });
+};
+
+/**
+ * fetch and parse a JSON endpoint, returns the JS object.
+ * @param {[type]} url JSON endpoint to fetch and parse
+ * @param {[type]} opts request options object
+ * @param {Function} callback callback (error, object)
+ */
+
+var requestJSON = function (url, opts, callback){
+ opts.url = url;
+ request(opts, function(error, response, body){
+ log.info("JSON query made for: " + url);
+ if ( error ) {
+ log.error(error);
+ return callback(true, "");
+ }
+ else if ( response.statusCode !== 200 ) {
+ log.error("JSON query returned HTTP status code " +
response.statusCode);
+ return callback(true, "");
+ }
+ else {
+ try {
+ var jsonObj = JSON.parse(body);
+ return callback(false, jsonObj);
+ } catch ( error ) {
+ log.error("Error when parsing JSON response: " + error);
+ return callback(true, "");
+ }
+ }
+ });
+};
+
+
/*Test methods in main */
if (require.main === module) {
var opts = {
@@ -110,9 +174,16 @@
requestFromURL("http://example.com";, opts, function (error, statusCode,
body){
console.log(body);
});
+
+ requestFromPMID("23193287", opts, function(error, statusCode, body){
+ console.log(body);
+ });
}
module.exports = {
requestFromURL: requestFromURL,
- requestFromDOI: requestFromDOI
-};
\ No newline at end of file
+ requestFromDOI: requestFromDOI,
+ requestFromPMID: requestFromPMID,
+ requestFromPMCID: requestFromPMID, // alias
+ requestFromManuscript: requestFromPMID // alias
+};
--
To view, visit https://gerrit.wikimedia.org/r/176887
To unsubscribe, visit https://gerrit.wikimedia.org/r/settings
Gerrit-MessageType: newchange
Gerrit-Change-Id: I1852f9820d9a0e1af0f30003d84846b435095e16
Gerrit-PatchSet: 1
Gerrit-Project: mediawiki/services/citoid
Gerrit-Branch: master
Gerrit-Owner: Unicodesnowman <[email protected]>
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