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{ | |
"translatorID": "e16095ae-986c-4117-9cb6-20f3b7a52f64", | |
"label": "Protein Data Bank", | |
"creator": "Philipp Zumstein", | |
"target": "^https?://www\\.(pdb|rcsb)\\.org/pdb/", | |
"minVersion": "3.0", | |
"maxVersion": "", | |
"priority": 100, | |
"inRepository": true, | |
"translatorType": 4, | |
"browserSupport": "gcsibv", | |
"lastUpdated": "2017-06-03 18:51:04" | |
} | |
/* | |
***** BEGIN LICENSE BLOCK ***** | |
Copyright © 2017 Philipp Zumstein | |
This file is part of Zotero. | |
Zotero is free software: you can redistribute it and/or modify | |
it under the terms of the GNU Affero General Public License as published by | |
the Free Software Foundation, either version 3 of the License, or | |
(at your option) any later version. | |
Zotero is distributed in the hope that it will be useful, | |
but WITHOUT ANY WARRANTY; without even the implied warranty of | |
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
GNU Affero General Public License for more details. | |
You should have received a copy of the GNU Affero General Public License | |
along with Zotero. If not, see <http://www.gnu.org/licenses/>. | |
***** END LICENSE BLOCK ***** | |
*/ | |
function detectWeb(doc, url) { | |
if (url.indexOf("results.do") != -1 && getSearchResults(doc, true)) { | |
return "multiple"; | |
} else if (url.indexOf("structureId") != -1) { | |
return "journalArticle"; | |
} | |
} | |
function getSearchResults(doc, checkOnly) { | |
var items = {}; | |
var found = false; | |
var rows = ZU.xpath(doc, '//li[contains(@class, "oneSearchResult")]//h3/a'); | |
for (var i=0; i<rows.length; i++) { | |
var href = rows[i].href; | |
var title = ZU.trimInternal(rows[i].textContent); | |
if (!href || !title) continue; | |
if (checkOnly) return true; | |
found = true; | |
items[href] = title; | |
} | |
return found ? items : false; | |
} | |
function doWeb(doc, url) { | |
if (detectWeb(doc, url) == "multiple") { | |
Zotero.selectItems(getSearchResults(doc, false), function (items) { | |
if (!items) { | |
return true; | |
} | |
var articles = []; | |
for (var i in items) { | |
articles.push(i); | |
} | |
ZU.processDocuments(articles, scrape); | |
}); | |
} else { | |
scrape(doc, url); | |
} | |
} | |
function scrape(doc, url) { | |
var translator = Zotero.loadTranslator('web'); | |
// Embedded Metadata | |
translator.setTranslator('951c027d-74ac-47d4-a107-9c3069ab7b48'); | |
translator.setDocument(doc); | |
translator.setHandler('itemDone', function (obj, item) { | |
item.DOI = ZU.xpathText(doc, '//li[strong[contains(., "DOI")]]/a'); | |
item.tags = []; | |
var pdburl = ZU.xpathText(doc, '//ul/li/a[contains(., "PDB Format")]/@href'); | |
if (pdburl) { | |
item.attachments.push({ | |
url: pdburl, | |
title: "Protein Data Bank .pdb File", | |
mimeType: "chemical/x-pdb" | |
}); | |
} | |
item.complete(); | |
}); | |
translator.translate(); | |
} | |
/** BEGIN TEST CASES **/ | |
var testCases = [ | |
{ | |
"type": "web", | |
"url": "http://www.rcsb.org/pdb/explore/explore.do?structureId=1COW", | |
"items": [ | |
{ | |
"itemType": "journalArticle", | |
"title": "The structure of bovine F1-ATPase complexed with the antibiotic inhibitor aurovertin B.", | |
"creators": [ | |
{ | |
"firstName": "M. J.", | |
"lastName": "van Raaij", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "J. P.", | |
"lastName": "Abrahams", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "A. G.", | |
"lastName": "Leslie", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "J. E.", | |
"lastName": "Walker", | |
"creatorType": "author" | |
} | |
], | |
"date": "1996", | |
"DOI": "10.2210/pdb1cow/pdb", | |
"abstractNote": "1COW: The structure of bovine F1-ATPase complexed with the antibiotic inhibitor aurovertin B.", | |
"libraryCatalog": "www.rcsb.org", | |
"pages": "6913-6917", | |
"publicationTitle": "Proc.Natl.Acad.Sci.USA", | |
"url": "http://www.rcsb.org/pdb/explore/explore.do?structureId=1COW", | |
"volume": "93", | |
"attachments": [ | |
{ | |
"title": "Snapshot" | |
}, | |
{ | |
"title": "Protein Data Bank .pdb File", | |
"mimeType": "chemical/x-pdb" | |
} | |
], | |
"tags": [], | |
"notes": [], | |
"seeAlso": [] | |
} | |
] | |
}, | |
{ | |
"type": "web", | |
"url": "http://www.rcsb.org/pdb/explore/explore.do?structureId=1VHZ", | |
"items": [ | |
{ | |
"itemType": "journalArticle", | |
"title": "Structural analysis of a set of proteins resulting from a bacterial genomics project", | |
"creators": [ | |
{ | |
"firstName": "J.", | |
"lastName": "Badger", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "J. M.", | |
"lastName": "Sauder", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "J. M.", | |
"lastName": "Adams", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "S.", | |
"lastName": "Antonysamy", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "K.", | |
"lastName": "Bain", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "M. G.", | |
"lastName": "Bergseid", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "S. G.", | |
"lastName": "Buchanan", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "M. D.", | |
"lastName": "Buchanan", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "Y.", | |
"lastName": "Batiyenko", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "J. A.", | |
"lastName": "Christopher", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "S.", | |
"lastName": "Emtage", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "A.", | |
"lastName": "Eroshkina", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "I.", | |
"lastName": "Feil", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "E. B.", | |
"lastName": "Furlong", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "K. S.", | |
"lastName": "Gajiwala", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "X.", | |
"lastName": "Gao", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "D.", | |
"lastName": "He", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "J.", | |
"lastName": "Hendle", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "A.", | |
"lastName": "Huber", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "K.", | |
"lastName": "Hoda", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "P.", | |
"lastName": "Kearins", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "C.", | |
"lastName": "Kissinger", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "B.", | |
"lastName": "Laubert", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "H. A.", | |
"lastName": "Lewis", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "J.", | |
"lastName": "Lin", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "K.", | |
"lastName": "Loomis", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "D.", | |
"lastName": "Lorimer", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "G.", | |
"lastName": "Louie", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "M.", | |
"lastName": "Maletic", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "C. D.", | |
"lastName": "Marsh", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "I.", | |
"lastName": "Miller", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "J.", | |
"lastName": "Molinari", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "H. J.", | |
"lastName": "Muller-Dieckmann", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "J. M.", | |
"lastName": "Newman", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "B. W.", | |
"lastName": "Noland", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "B.", | |
"lastName": "Pagarigan", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "F.", | |
"lastName": "Park", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "T. S.", | |
"lastName": "Peat", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "K. W.", | |
"lastName": "Post", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "S.", | |
"lastName": "Radojicic", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "A.", | |
"lastName": "Ramos", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "R.", | |
"lastName": "Romero", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "M. E.", | |
"lastName": "Rutter", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "W. E.", | |
"lastName": "Sanderson", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "K. D.", | |
"lastName": "Schwinn", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "J.", | |
"lastName": "Tresser", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "J.", | |
"lastName": "Winhoven", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "T. A.", | |
"lastName": "Wright", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "L.", | |
"lastName": "Wu", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "J.", | |
"lastName": "Xu", | |
"creatorType": "author" | |
}, | |
{ | |
"firstName": "T. J.", | |
"lastName": "Harris", | |
"creatorType": "author" | |
} | |
], | |
"date": "2005", | |
"DOI": "10.2210/pdb1vhz/pdb", | |
"abstractNote": "1VHZ: Structural analysis of a set of proteins resulting from a bacterial genomics project", | |
"libraryCatalog": "www.rcsb.org", | |
"pages": "787-796", | |
"publicationTitle": "Proteins", | |
"url": "http://www.rcsb.org/pdb/explore/explore.do?structureId=1VHZ", | |
"volume": "60", | |
"attachments": [ | |
{ | |
"title": "Snapshot" | |
}, | |
{ | |
"title": "Protein Data Bank .pdb File", | |
"mimeType": "chemical/x-pdb" | |
} | |
], | |
"tags": [], | |
"notes": [], | |
"seeAlso": [] | |
} | |
] | |
} | |
] | |
/** END TEST CASES **/ |