344 lines
9.3 KiB
JavaScript
344 lines
9.3 KiB
JavaScript
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{
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"translatorID": "21f62926-4343-4518-b6f2-a284e650e64a",
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"label": "Bioconductor",
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"creator": "Qiang Hu",
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"target": "https?://(www\\.)?bioconductor\\.org/(packages/.*/bioc/html|help/search)/",
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"minVersion": "3.0",
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"maxVersion": "",
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"priority": 100,
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"inRepository": true,
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"translatorType": 4,
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"browserSupport": "gcsibv",
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"lastUpdated": "2019-09-17 16:47:07"
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}
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/*
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***** BEGIN LICENSE BLOCK *****
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Bioconductor Packages Translator
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Copyright © 2019 Qiang Hu
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This file is part of Zotero.
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Zotero is free software: you can redistribute it and/or modify
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it under the terms of the GNU Affero General Public License as published by
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the Free Software Foundation, either version 3 of the License, or
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(at your option) any later version.
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Zotero is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU Affero General Public License for more details.
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You should have received a copy of the GNU Affero General Public License
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along with Zotero. If not, see <http://www.gnu.org/licenses/>.
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***** END LICENSE BLOCK *****
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*/
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// attr()/text() v2
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// eslint-disable-next-line
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function attr(docOrElem,selector,attr,index){var elem=index?docOrElem.querySelectorAll(selector).item(index):docOrElem.querySelector(selector);return elem?elem.getAttribute(attr):null;}function text(docOrElem,selector,index){var elem=index?docOrElem.querySelectorAll(selector).item(index):docOrElem.querySelector(selector);return elem?elem.textContent:null;}
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function detectWeb(doc, url) {
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if (url.includes('/bioc/html/')) {
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return "computerProgram";
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}
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else if (url.includes('/search/index.html') && getSearchResults(doc, true)) {
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return "multiple";
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}
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else {
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return false;
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}
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}
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function getSearchResults(doc, checkOnly) {
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var items = {};
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var found = false;
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var rows = doc.querySelectorAll('dl>dt>a[href*="/bioc/html/"]');
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for (let i = 0; i < rows.length; i++) {
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let href = rows[i].href;
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let title = ZU.trimInternal(rows[i].textContent);
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if (!href || !title) continue;
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if (checkOnly) return true;
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found = true;
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items[href] = title;
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}
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return found ? items : false;
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}
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function doWeb(doc, url) {
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if (detectWeb(doc, url) == "multiple") {
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Zotero.selectItems(getSearchResults(doc, false), function (items) {
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if (!items) {
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return;
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}
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var articles = [];
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for (var i in items) {
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articles.push(i);
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}
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ZU.processDocuments(articles, scrape);
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});
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}
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else if (detectWeb(doc, url) == "computerProgram") {
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scrape(doc, url);
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}
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}
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function scrape(doc, url) {
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var item = new Zotero.Item('computerProgram');
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item.title = text(doc, '#PageContent > h1');
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var subtitle = text(doc, '#PageContent > div.do_not_rebase > h2');
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if (subtitle) {
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item.title += ": " + subtitle;
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}
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var doi = ZU.xpathText(doc, '//*[@id="PageContent"]/div[2]/a[contains(@href, "https://doi.org/")]');
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if (doi !== null) {
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item.extra = 'DOI: ' + doi;
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}
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var rows = doc.querySelectorAll('#PageContent > div.do_not_rebase > p');
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for (let i = 0; i < rows.length; i++) {
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if (ZU.trimInternal(rows[i].textContent).startsWith('Bioconductor version:')) {
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item.company = ZU.trimInternal(rows[i].textContent);
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item.abstractNote = ZU.trimInternal(rows[i + 1].textContent);
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}
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if (ZU.trimInternal(rows[i].textContent).startsWith('Author')) {
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var authorString = ZU.trimInternal(rows[i].textContent);
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var creators = authorString.replace(/Author:\s*/, '').replace(/\[.+?\]/g, '').replace(/\(.+?\)/g, '');
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creators = creators.split(/,|and\s*/);
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for (let i = 0; i < creators.length; i++) {
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item.creators.push(ZU.cleanAuthor(creators[i], 'programmer'));
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}
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}
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}
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item.versionNumber = ZU.xpathText(doc, '//table/tbody/tr/td[contains(text(), "Version")]/following-sibling::td');
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item.rights = ZU.xpathText(doc, '//table/tbody/tr/td[contains(text(), "License")]/following-sibling::td');
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item.url = ZU.xpathText(doc, '//table/tbody/tr/td[contains(text(), "Package Short Url")]/following-sibling::td') || url;
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var year = ZU.xpathText(doc, '//*[@id="SiteGlobalFooter"]/div/p[contains(text(), "Copyright")]');
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if (year) {
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item.date = year.match(/\d+/g)[1];
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}
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var tags = ZU.xpath(doc, '//td[contains(text(), "biocViews")]/following-sibling::td/a');
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for (let i = 0; i < tags.length; i++) {
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item.tags.push(tags[i].textContent);
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}
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item.complete();
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}
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/** BEGIN TEST CASES **/
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var testCases = [
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{
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"type": "web",
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"url": "https://bioconductor.org/help/search/index.html?q=SummarizedExperiment/",
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"items": "multiple"
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},
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{
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"type": "web",
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"url": "https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html",
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"items": [
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{
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"itemType": "computerProgram",
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"title": "SummarizedExperiment: SummarizedExperiment container",
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"creators": [
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{
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"firstName": "Martin",
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"lastName": "Morgan",
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"creatorType": "programmer"
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},
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{
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"firstName": "Valerie",
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"lastName": "Obenchain",
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"creatorType": "programmer"
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},
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{
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"firstName": "Jim",
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"lastName": "Hester",
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"creatorType": "programmer"
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},
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{
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"firstName": "Hervé",
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"lastName": "Pagès",
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"creatorType": "programmer"
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}
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],
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"date": "2019",
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"abstractNote": "The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.",
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"company": "Bioconductor version: Release (3.9)",
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"extra": "DOI: 10.18129/B9.bioc.SummarizedExperiment",
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"libraryCatalog": "Bioconductor",
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"rights": "Artistic-2.0",
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"shortTitle": "SummarizedExperiment",
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"url": "http://bioconductor.org/packages/SummarizedExperiment/",
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"versionNumber": "1.14.1",
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"attachments": [],
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"tags": [
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{
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"tag": "Annotation"
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},
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{
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"tag": "Coverage"
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},
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{
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"tag": "Genetics"
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},
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{
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"tag": "GenomeAnnotation"
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},
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{
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"tag": "Infrastructure"
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},
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{
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"tag": "Sequencing"
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},
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{
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"tag": "Software"
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}
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],
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"notes": [],
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"seeAlso": []
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}
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]
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},
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{
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"type": "web",
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"url": "https://bioconductor.org/packages/devel/bioc/html/SummarizedExperiment.html",
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"items": [
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{
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"itemType": "computerProgram",
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"title": "SummarizedExperiment: SummarizedExperiment container",
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"creators": [
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{
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"firstName": "Martin",
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"lastName": "Morgan",
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"creatorType": "programmer"
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},
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{
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"firstName": "Valerie",
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"lastName": "Obenchain",
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"creatorType": "programmer"
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},
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{
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"firstName": "Jim",
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"lastName": "Hester",
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"creatorType": "programmer"
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},
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{
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"firstName": "Hervé",
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"lastName": "Pagès",
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"creatorType": "programmer"
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}
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],
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"date": "2019",
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"abstractNote": "The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.",
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"company": "Bioconductor version: Development (3.10)",
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"extra": "DOI: 10.18129/B9.bioc.SummarizedExperiment",
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"libraryCatalog": "Bioconductor",
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"rights": "Artistic-2.0",
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"shortTitle": "SummarizedExperiment",
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"url": "http://bioconductor.org/packages/SummarizedExperiment/",
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"versionNumber": "1.15.9",
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"attachments": [],
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"tags": [
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{
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"tag": "Annotation"
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},
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{
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"tag": "Coverage"
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},
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{
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"tag": "Genetics"
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},
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{
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"tag": "GenomeAnnotation"
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},
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{
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"tag": "Infrastructure"
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},
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{
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"tag": "Sequencing"
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},
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{
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"tag": "Software"
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}
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],
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"notes": [],
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"seeAlso": []
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}
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]
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},
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{
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"type": "web",
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"url": "https://bioconductor.org/packages/3.2/bioc/html/SummarizedExperiment.html",
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"items": [
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{
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"itemType": "computerProgram",
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"title": "SummarizedExperiment: SummarizedExperiment container",
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"creators": [
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{
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"firstName": "Martin",
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"lastName": "Morgan",
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"creatorType": "programmer"
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},
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{
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"firstName": "Valerie",
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"lastName": "Obenchain",
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"creatorType": "programmer"
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},
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{
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"firstName": "Jim",
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"lastName": "Hester",
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"creatorType": "programmer"
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},
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{
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"firstName": "Hervé",
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"lastName": "Pagès",
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"creatorType": "programmer"
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}
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],
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"date": "2016",
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"abstractNote": "The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.",
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"company": "Bioconductor version: 3.2",
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"libraryCatalog": "Bioconductor",
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"rights": "Artistic-2.0",
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"shortTitle": "SummarizedExperiment",
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"url": "http://bioconductor.org/packages/SummarizedExperiment/",
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"versionNumber": "1.0.2",
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"attachments": [],
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"tags": [
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{
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"tag": "Annotation"
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},
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{
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"tag": "Coverage"
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},
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{
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"tag": "Genetics"
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},
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{
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"tag": "GenomeAnnotation"
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},
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{
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"tag": "Infrastructure"
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},
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{
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"tag": "Sequencing"
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},
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{
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||
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"tag": "Software"
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}
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],
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"notes": [],
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"seeAlso": []
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||
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}
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||
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]
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||
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}
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||
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]
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/** END TEST CASES **/
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