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PMC: allow saving from PDF pages
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see https://forums.zotero.org/discussion/comment/268749#Comment_268749
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@adam3smith
adam3smith committed Jan 26, 2017
1 parent d0976b0 commit 7dba7c6
Showing 1 changed file with 121 additions and 34 deletions.
155 changes: 121 additions & 34 deletions PubMed Central.js
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
"inRepository": true,
"translatorType": 4,
"browserSupport": "gcsibv",
"lastUpdated": "2017-01-10 22:34:30"
"lastUpdated": "2017-01-26 04:49:54"
}

function detectWeb(doc, url) {
Expand All @@ -29,7 +29,7 @@ function doWeb(doc, url) {
if (!ids) {
return true;
}
var pmcids = new Array();
var pmcids = [];
for (var i in ids) {
pmcids.push(i);
}
Expand All @@ -40,6 +40,10 @@ function doWeb(doc, url) {
var pdf = getPDF(doc,'//td[@class="format-menu"]//a[contains(@href,".pdf")]'
+ '|//div[@class="format-menu"]//a[contains(@href,".pdf")]'
+ '|//aside[@id="jr-alt-p"]/div/a[contains(@href,".pdf")]');
//if we're looking at a pdf, just use the current url
if (!pdf && url.search(/\/pdf\/.+.pdf/)!=-1) {
pdf = url;
}
var pdfCollection = {};

if(pdf) pdfCollection[pmcid] = pdf;
Expand Down Expand Up @@ -95,7 +99,6 @@ function lookupPMCIDs(ids, doc, pdfLink) {

text = text.replace(/<xref[^<\/]*<\/xref>/g, ""); //Strip xref cross reference from e.g. title
//Z.debug(text)

var parser = new DOMParser();
var doc = parser.parseFromString(text, "text/xml");

Expand Down Expand Up @@ -129,7 +132,7 @@ function lookupPMCIDs(ids, doc, pdfLink) {
newItem.abstractNote = abstract;
} else {
var abstractSections = ZU.xpath(article, 'abstract/sec');
var abstract = [];
abstract = [];
for (var j in abstractSections) {
abstract.push(ZU.xpathText(abstractSections[j], 'title') + "\n" + ZU.xpathText(abstractSections[j], 'p'));
}
Expand Down Expand Up @@ -220,39 +223,46 @@ function lookupPMCIDs(ids, doc, pdfLink) {
var testCases = [
{
"type": "web",
"url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2377243/?tool=pmcentrez",
"url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2377243/?tool=pmcentrez",
"items": [
{
"itemType": "journalArticle",
"title": "Effects of long-term low-dose oxygen supplementation on the epithelial function, collagen metabolism and interstitial fibrogenesis in the guinea pig lung",
"creators": [
{
"lastName": "Aoki",
"firstName": "Takuya"
"firstName": "Takuya",
"creatorType": "author"
},
{
"lastName": "Yamasawa",
"firstName": "Fumihiro"
"firstName": "Fumihiro",
"creatorType": "author"
},
{
"lastName": "Kawashiro",
"firstName": "Takeo"
"firstName": "Takeo",
"creatorType": "author"
},
{
"lastName": "Shibata",
"firstName": "Tetsuichi"
"firstName": "Tetsuichi",
"creatorType": "author"
},
{
"lastName": "Ishizaka",
"firstName": "Akitoshi"
"firstName": "Akitoshi",
"creatorType": "author"
},
{
"lastName": "Urano",
"firstName": "Tetsuya"
"firstName": "Tetsuya",
"creatorType": "author"
},
{
"lastName": "Okada",
"firstName": "Yasumasa"
"firstName": "Yasumasa",
"creatorType": "author"
}
],
"date": "2008",
Expand Down Expand Up @@ -286,57 +296,66 @@ var testCases = [
},
{
"type": "web",
"url": "http://www.ncbi.nlm.nih.gov/pmc/?term=anger",
"url": "https://www.ncbi.nlm.nih.gov/pmc/?term=anger",
"items": "multiple"
},
{
"type": "web",
"url": "http://www.ncbi.nlm.nih.gov/pmc/issues/184700/",
"url": "https://www.ncbi.nlm.nih.gov/pmc/issues/184700/",
"items": "multiple"
},
{
"type": "web",
"url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3139813/?report=classic",
"url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3139813/?report=classic",
"items": [
{
"itemType": "journalArticle",
"title": "Evaluation Metrics for Biostatistical and Epidemiological Collaborations",
"creators": [
{
"lastName": "Rubio",
"firstName": "Doris McGartland"
"firstName": "Doris McGartland",
"creatorType": "author"
},
{
"lastName": "del Junco",
"firstName": "Deborah J."
"firstName": "Deborah J.",
"creatorType": "author"
},
{
"lastName": "Bhore",
"firstName": "Rafia"
"firstName": "Rafia",
"creatorType": "author"
},
{
"lastName": "Lindsell",
"firstName": "Christopher J."
"firstName": "Christopher J.",
"creatorType": "author"
},
{
"lastName": "Oster",
"firstName": "Robert A."
"firstName": "Robert A.",
"creatorType": "author"
},
{
"lastName": "Wittkowski",
"firstName": "Knut M."
"firstName": "Knut M.",
"creatorType": "author"
},
{
"lastName": "Welty",
"firstName": "Leah J."
"firstName": "Leah J.",
"creatorType": "author"
},
{
"lastName": "Li",
"firstName": "Yi-Ju"
"firstName": "Yi-Ju",
"creatorType": "author"
},
{
"lastName": "DeMets",
"firstName": "Dave"
"firstName": "Dave",
"creatorType": "author"
}
],
"date": "2011-10-15",
Expand Down Expand Up @@ -370,36 +389,41 @@ var testCases = [
},
{
"type": "web",
"url": "http://www.ncbi.nlm.nih.gov/pmc/?term=test",
"url": "https://www.ncbi.nlm.nih.gov/pmc/?term=test",
"items": "multiple"
},
{
"type": "web",
"url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2801612/?report=reader",
"url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2801612/?report=reader",
"items": [
{
"itemType": "journalArticle",
"title": "Cdk4 Regulates Recruitment of Quiescent ?-Cells and Ductal Epithelial Progenitors to Reconstitute ?-Cell Mass",
"title": "Cdk4 Regulates Recruitment of Quiescent β-Cells and Ductal Epithelial Progenitors to Reconstitute β-Cell Mass",
"creators": [
{
"lastName": "Lee",
"firstName": "Ji-Hyeon"
"firstName": "Ji-Hyeon",
"creatorType": "author"
},
{
"lastName": "Jo",
"firstName": "Junghyo"
"firstName": "Junghyo",
"creatorType": "author"
},
{
"lastName": "Hardikar",
"firstName": "Anandwardhan A."
"firstName": "Anandwardhan A.",
"creatorType": "author"
},
{
"lastName": "Periwal",
"firstName": "Vipul"
"firstName": "Vipul",
"creatorType": "author"
},
{
"lastName": "Rane",
"firstName": "Sushil G."
"firstName": "Sushil G.",
"creatorType": "author"
}
],
"date": "2010-1-13",
Expand All @@ -411,7 +435,6 @@ var testCases = [
"journalAbbreviation": "PLoS One",
"libraryCatalog": "PubMed Central",
"publicationTitle": "PLoS ONE",
"shortTitle": "Cdk4 Regulates Recruitment of Quiescent ?",
"url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2801612/",
"volume": "5",
"attachments": [
Expand All @@ -430,6 +453,70 @@ var testCases = [
"seeAlso": []
}
]
},
{
"type": "web",
"url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4368415/pdf/imr0264-0088.pdf",
"items": [
{
"itemType": "journalArticle",
"title": "The human immune response to tuberculosis and its treatment: a view from the blood",
"creators": [
{
"lastName": "Cliff",
"firstName": "Jacqueline M",
"creatorType": "author"
},
{
"lastName": "Kaufmann",
"firstName": "Stefan H E",
"creatorType": "author"
},
{
"lastName": "McShane",
"firstName": "Helen",
"creatorType": "author"
},
{
"lastName": "van Helden",
"firstName": "Paul",
"creatorType": "author"
},
{
"lastName": "O'Garra",
"firstName": "Anne",
"creatorType": "author"
}
],
"date": "2015-3",
"DOI": "10.1111/imr.12269",
"ISSN": "0105-2896",
"abstractNote": "The immune response upon infection with the pathogen Mycobacterium tuberculosis is poorly understood, hampering the discovery of new treatments and the improvements in diagnosis. In the last years, a blood transcriptional signature in tuberculosis has provided knowledge on the immune response occurring during active tuberculosis disease. This signature was absent in the majority of asymptomatic individuals who are latently infected with M. tuberculosis (referred to as latent). Using modular and pathway analyses of the complex data has shown, now in multiple studies, that the signature of active tuberculosis is dominated by overexpression of interferon-inducible genes (consisting of both type I and type II interferon signaling), myeloid genes, and inflammatory genes. There is also downregulation of genes encoding B and T-cell function. The blood signature of tuberculosis correlates with the extent of radiographic disease and is diminished upon effective treatment suggesting the possibility of new improved strategies to support diagnostic assays and methods for drug treatment monitoring. The signature suggested a previously under-appreciated role for type I interferons in development of active tuberculosis disease, and numerous mechanisms have now been uncovered to explain how type I interferon impedes the protective response to M. tuberculosis infection.",
"extra": "PMID: 25703554\nPMCID: PMC4368415",
"issue": "1",
"journalAbbreviation": "Immunol Rev",
"libraryCatalog": "PubMed Central",
"pages": "88-102",
"publicationTitle": "Immunological Reviews",
"shortTitle": "The human immune response to tuberculosis and its treatment",
"url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4368415/",
"volume": "264",
"attachments": [
{
"title": "PubMed Central Link",
"mimeType": "text/html",
"snapshot": false
},
{
"title": "PubMed Central Full Text PDF",
"mimeType": "application/pdf"
}
],
"tags": [],
"notes": [],
"seeAlso": []
}
]
}
]
/** END TEST CASES **/
/** END TEST CASES **/

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