Java tutorial
/* Copyright (c) 2014, The Broad Institute All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of The Broad Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL The Broad Institute BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ /* * Copyright 2010 The Scripps Research Institute * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package bard.pubchem.xml; import java.io.IOException; import java.io.InputStream; import java.net.URL; import java.util.ArrayList; import java.util.Calendar; import java.util.Collection; import java.util.HashMap; import java.util.List; import java.util.Map; import javax.xml.parsers.ParserConfigurationException; import org.apache.commons.collections.list.GrowthList; import org.dom4j.Document; import org.dom4j.Node; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.xml.sax.SAXException; import bard.pubchem.PubChemException; import bard.pubchem.model.PCAssay; import bard.pubchem.model.PCAssayColumn; import bard.pubchem.model.PCAssayPanel; import bard.pubchem.model.PCAssayResult; import bard.pubchem.model.PCAssayXRef; import bard.pubchem.model.PCPlotLabel; import bard.pubchem.model.XRef; /** * @author Mark Southern * @author Stephanie Canny * * // Code Example: InputStream is = * PubChemFactory.getInstance().getXmlDescr(2551L); List<PCAssay> assays * = PubChemXMLParserFactory.getInstance().populateAssayFromXML(is, * true); * */ public class PubChemXMLParserFactory { private static final Logger log = LoggerFactory.getLogger(PubChemXMLParserFactory.class); protected static boolean DEBUGGING = false; private static PubChemXMLParserFactory instance; private static Map<String, String> targetType; private String separator = System.getProperty("line.separator"); private static void createTargetDBMap() { targetType = new HashMap<String, String>(); targetType.put("aid", "pcassay"); targetType.put("biosystem", "biosystems"); targetType.put("cid", "pccompound"); targetType.put("gene", "gene"); targetType.put("gi", "gi"); // Genbank general Id targetType.put("mesh", "mesh"); targetType.put("mim", "omim"); targetType.put("mmdb", "mmdb"); // 3d domains db not in einfo list of // databases! targetType.put("nucleotide", "nucleotide"); targetType.put("nucleotide-gi", "nucleotide"); targetType.put("pmid", "pubmed"); targetType.put("protein", "protein"); targetType.put("protein-gi", "protein"); targetType.put("regid", "regid"); // gene symbols, urls, aids. targetType.put("rn", "rn"); // Substance Registry, CAS numbers etc. targetType.put("rna", "nucleotide"); targetType.put("sid", "pcsubstance"); targetType.put("taxonomy", "taxonomy"); } public static PubChemXMLParserFactory getInstance() { if (instance == null) { synchronized (PubChemXMLParserFactory.class) { // 1 if (instance == null) { synchronized (PubChemXMLParserFactory.class) { // 3 // inst = new Singleton(); //4 instance = new PubChemXMLParserFactory(); createTargetDBMap(); } // instance = inst; //5 } } } return instance; } public PCAssay parsePublicAssayDescription(int aid) throws IOException, SAXException, ParserConfigurationException, PubChemException { String url = String.format("http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=%s&q=expdesc_xmldisplay", aid); InputStream is = new URL(url).openStream(); List<PCAssay> assays = populateAssaysFromXML(is, false); return assays.get(0); } public List<PCAssay> populateAssaysFromXML(InputStream inputStream, boolean includeResults) throws IOException, SAXException, ParserConfigurationException, PubChemException { Document doc = PubChemUtils.getDocument(inputStream); PubChemUtils.closeQuietly(inputStream); // SAXReader reader = new SAXReader(); // reader.addHandler("/PC-AssayContainer/PC-AssaySubmit/PC-AssaySubmit_data/PC-AssayResults", // new ElementHandler() { // public void onStart(ElementPath path) { // // } // // public void onEnd(ElementPath path) { // path.getCurrent().detach(); // } // }); // Document doc = reader.read(inputStream); return populateAssaysFromXMLDocument(doc, includeResults); } public List<PCAssay> populateAssaysFromXMLDocument(Document doc, boolean includeResults) throws PubChemException { List<PCAssay> assays = new ArrayList<PCAssay>(); // List<Node> assayNodes = // doc.selectNodes("/PC-AssayContainer/PC-AssaySubmit"); List<Node> assayNodes = doc.selectNodes("//PC-AssayDescription"); for (Node node : assayNodes) { PCAssay assay = populateAssayFromXMLNode(node); populateAssayResultsFromXML(assay, node); assays.add(assay); } return assays; } protected void populateAssayResultsFromXML(PCAssay assay, Node assayDescriptionNode) { List<Node> assayResultNodes = assayDescriptionNode .selectNodes("../../../PC-AssaySubmit_data/PC-AssayResults"); if (assayResultNodes.size() == 0) return; for (Node resultNode : assayResultNodes) { PCAssayResult result = new PCAssayResult(); String val = resultNode.selectSingleNode("PC-AssayResults_sid").valueOf("text()"); result.setSID(Long.parseLong(val)); val = resultNode.selectSingleNode("PC-AssayResults_outcome").valueOf("@value"); val = val.substring(0, 1).toUpperCase() + val.substring(1); result.setOutcome(val); val = resultNode.selectSingleNode("PC-AssayResults_rank").valueOf("text()"); result.setRankScore(Integer.parseInt(val)); List<Node> assayDataNodes = resultNode.selectNodes("PC-AssayResults_data/PC-AssayData"); List<String> all = GrowthList.decorate(new ArrayList<String>(assay.getColumns().size() - 2)); result.setAllValues(all); for (Node node : assayDataNodes) { val = node.valueOf("PC-AssayData_tid/text()"); int index = Integer.parseInt(val) - 1; val = node.selectSingleNode(".//*[starts-with(name(),'PC-AssayData_value_')]").getText(); all.set(index, val); } assay.getResults().add(result); } } protected PCAssay populateAssayFromXMLNode(Node topNode) throws PubChemException { // String assayDescPath = // "PC-AssaySubmit_assay/PC-AssaySubmit_assay_descr/PC-AssayDescription"; Node assayDescNode = null; if (topNode.getName().equals("PC-AssayDescription")) assayDescNode = topNode; else { assayDescNode = topNode.selectSingleNode(".//PC-AssayDescription"); } if (assayDescNode == null) throw new PubChemException( String.format("Cannot find PC-AssayDescription node in provided node %s", topNode.getPath())); Node node = assayDescNode.selectSingleNode("PC-AssayDescription_aid/PC-ID/PC-ID_id"); Integer aid = new Integer(node.getText()); try { PCAssay assay = new PCAssay(); if (aid > 0) assay.setAID(aid); node = assayDescNode.selectSingleNode("PC-AssayDescription_aid/PC-ID/PC-ID_version"); Integer version = new Integer(node.getText()); assay.setVersion(version); node = assayDescNode.selectSingleNode("PC-AssayDescription_revision"); Integer revision = new Integer(node.getText()); assay.setRevision(revision); Node trackingNode = assayDescNode .selectSingleNode("PC-AssayDescription_aid-source/PC-Source/PC-Source_db/PC-DBTracking"); node = trackingNode.selectSingleNode("PC-DBTracking_name"); assay.setSourceName(node.getText()); node = trackingNode.selectSingleNode("PC-DBTracking_source-id/Object-id/Object-id_str"); assay.setExtRegId(node.getText()); // hold until date node = trackingNode.selectSingleNode("PC-DBTracking_date"); if (node != null) { String year = node.selectSingleNode("Date/Date_std/Date-std/Date-std_year").getText(); String month = node.selectSingleNode("Date/Date_std/Date-std/Date-std_month").getText(); String day = node.selectSingleNode("Date/Date_std/Date-std/Date-std_day").getText(); if (DEBUGGING) log.info("year: " + year + " month: " + month + " day: " + day); Calendar calendar = Calendar.getInstance(); calendar.set(Integer.parseInt(year), Integer.parseInt(month) - 1, Integer.parseInt(day)); assay.setHoldUntilDate(calendar.getTime()); if (DEBUGGING) log.info(calendar.getTime().toString()); } node = assayDescNode.selectSingleNode("PC-AssayDescription_name"); assay.setName(node.getText()); List<Node> nodes = assayDescNode .selectNodes("PC-AssayDescription_description/PC-AssayDescription_description_E"); assay.setDescription(join(nodes, separator)); nodes = assayDescNode.selectNodes("PC-AssayDescription_protocol/PC-AssayDescription_protocol_E"); assay.setProtocol(join(nodes, separator)); nodes = assayDescNode.selectNodes("PC-AssayDescription_comment/PC-AssayDescription_comment_E"); assay.setComment(join(nodes, separator)); node = assayDescNode.selectSingleNode("PC-AssayDescription_activity-outcome-method"); if (node != null) assay.setActivityOutcomeMethod(node.valueOf("@value")); handlePlots(assay, assayDescNode); node = assayDescNode .selectSingleNode("PC-AssayDescription_grant-number/PC-AssayDescription_grant-number_E"); if (node != null) assay.setGrantNumber(node.getText()); node = assayDescNode.selectSingleNode("PC-AssayDescription_project-category"); if (node != null) assay.setProjectCategory(node.valueOf("@value")); assay.getAssayXRefs().removeAll(assay.getAssayXRefs()); nodes = assayDescNode.selectNodes("PC-AssayDescription_xref/PC-AnnotatedXRef"); handleXRefs(assay, null, nodes); nodes = assayDescNode.selectNodes("PC-AssayDescription_target/PC-AssayTargetInfo"); handleTargetXRefs(assay, null, nodes); handlePanels(assay, assayDescNode); handleColumns(assay, assayDescNode); handleComments(assay, assayDescNode); return assay; } catch (Exception ex) { throw new RuntimeException("Problem with AID " + aid, ex); } } protected void handlePlots(PCAssay assay, Node assayDescNode) { assay.getPlotLabels().clear(); List<Node> nodes = assayDescNode.selectNodes("PC-AssayDescription_dr/PC-AssayDRAttr"); for (Node node : nodes) { PCPlotLabel label = new PCPlotLabel(); label.setAssay(assay); label.setPlotLabel(Integer.parseInt(node.selectSingleNode("PC-AssayDRAttr_id").getText())); label.setTitle(node.selectSingleNode("PC-AssayDRAttr_descr").getText()); label.setConcentrationTitle(node.selectSingleNode("PC-AssayDRAttr_dn").getText()); label.setResponseTitle(node.selectSingleNode("PC-AssayDRAttr_rn").getText()); String test = nullSafeGet(node, "PC-AssayDRAttr_type", "text()"); label.setDerivedByEquation(!"".equals(test) & !"0".equals(test) ? true : false); assay.getPlotLabels().add(label); } } protected void handleComments(PCAssay assay, Node assayDescNode) { assay.getCategorizedComments().clear(); List<Node> nodes = assayDescNode .selectNodes("PC-AssayDescription_categorized-comment/PC-CategorizedComment"); for (Node commentNode : nodes) { String key = commentNode.selectSingleNode("PC-CategorizedComment_title").getText(); String value = join( commentNode.selectNodes("PC-CategorizedComment_comment/PC-CategorizedComment_comment_E"), separator); assay.getCategorizedComments().put(key, value); } } protected void handlePanels(PCAssay assay, Node assayDescNode) { Node node = assayDescNode.selectSingleNode("PC-AssayDescription_is-panel"); if (node == null) assay.setPanel(false); else assay.setPanel("true".equals(node.valueOf("@value"))); if (assay.isPanel()) { node = assayDescNode .selectSingleNode("PC-AssayDescription_panel-info/PC-AssayPanel/PC-AssayPanel_name"); assay.setPanelName(node.valueOf("text()")); node = assayDescNode .selectSingleNode("PC-AssayDescription_panel-info/PC-AssayPanel/PC-AssayPanel_descr"); assay.setPanelDescription(node == null ? "" : node.valueOf("text()")); } List<Node> nodes = assayDescNode.selectNodes( "PC-AssayDescription_panel-info/PC-AssayPanel/PC-AssayPanel_member/PC-AssayPanelMember"); for (Node n : nodes) { String mid = n.selectSingleNode("PC-AssayPanelMember_mid").getText(); Node node2 = n.selectSingleNode("PC-AssayPanelMember_name"); String name = node2 == null ? "" : node2.getText(); PCAssayPanel panel = new PCAssayPanel(); panel.setAssay(assay); assay.getPanels().add(panel); panel.setPanelNumber(Integer.parseInt(mid)); panel.setName(name); node2 = n.selectSingleNode("PC-AssayPanelMember_description"); panel.setDescription(node2 == null ? "" : node2.getText()); List<Node> nodes2 = n.selectNodes("PC-AssayPanelMember_protocol/PC-AssayPanelMember_protocol_E"); panel.setProtocol(join(nodes2, separator)); nodes2 = n.selectNodes("PC-AssayPanelMember_comment/PC-AssayPanelMember_comment_E"); panel.setComment(join(nodes2, separator)); List<Node> xrefNodes = n.selectNodes("PC-AssayPanelMember_xref/PC-AnnotatedXRef"); handleXRefs(assay, panel, xrefNodes); List<Node> targetNodes = n.selectNodes("PC-AssayPanelMember_target/PC-AssayTargetInfo"); handleTargetXRefs(assay, panel, targetNodes); } } private PCAssayColumn ensureColumn(PCAssay assay, int tid, String name, String type) { PCAssayColumn col; col = new PCAssayColumn(); col.setAssay(assay); col.setTID(tid); assay.getColumns().add(col); col.setName(name); col.setType(type); return col; } protected void handleColumns(PCAssay assay, Node assayDescNode) { Map<Integer, PCAssayColumn> map = new HashMap<Integer, PCAssayColumn>(); for (PCAssayColumn col : assay.getColumns()) map.put(col.getTID(), col); ensureColumn(assay, -1, "Outcome", "string"); ensureColumn(assay, 0, "Score", "float"); Map<Integer, PCAssayPanel> mapPanels = new HashMap<Integer, PCAssayPanel>(); for (PCAssayPanel panel : assay.getPanels()) mapPanels.put(panel.getPanelNumber(), panel); List<Node> nodes = assayDescNode.selectNodes("PC-AssayDescription_results/PC-ResultType"); for (Node n : nodes) { String tid = n.selectSingleNode("PC-ResultType_tid").getText(); String name = n.selectSingleNode("PC-ResultType_name").getText(); String type = n.selectSingleNode("PC-ResultType_type").valueOf("@value"); PCAssayColumn column = ensureColumn(assay, Integer.parseInt(tid), name, type); Node node = n.selectSingleNode("PC-ResultType_unit"); if (node != null) column.setUnit(node.valueOf("@value")); List<Node> descNodes = n.selectNodes("PC-ResultType_description/PC-ResultType_description_E"); column.setDescription(join(descNodes, separator)); if (DEBUGGING) log.info("Column description: " + join(descNodes, separator)); node = n.selectSingleNode("PC-ResultType_ac"); if (node != null) column.setActiveConcentration("true".equals(node.valueOf("@value"))); node = n.selectSingleNode("PC-ResultType_tc"); if (node != null) { Node node2 = node.selectSingleNode("PC-ConcentrationAttr/PC-ConcentrationAttr_dr-id"); if (node2 != null) { column.setCurvePlotLabel(Integer.parseInt(node2.getText())); } String testedConc = node.selectSingleNode("PC-ConcentrationAttr/PC-ConcentrationAttr_concentration") .getText(); column.setTestedConcentration(Double.parseDouble(testedConc)); String testedUnit = node.selectSingleNode("PC-ConcentrationAttr/PC-ConcentrationAttr_unit") .valueOf("@value"); column.setTestedConcentrationUnit(testedUnit); } node = n.selectSingleNode("PC-ResultType_panel-info/PC-AssayPanelTestResult"); if (node != null) { String panelId = node.selectSingleNode("PC-AssayPanelTestResult_mid").getText(); PCAssayPanel panel = mapPanels.get(Integer.parseInt(panelId)); column.setPanel(panel); String panelColumnType = node.selectSingleNode("PC-AssayPanelTestResult_readout-annot") .valueOf("@value"); column.setPanelReadoutType(panelColumnType); } } } protected void handleXRefs(PCAssay assay, PCAssayPanel panel, List<Node> nodes) { for (Node n : nodes) { Node node = n.selectSingleNode("PC-AnnotatedXRef_comment"); String comment = node == null ? "" : node.getText(); node = n.selectSingleNode("PC-AnnotatedXRef_xref/PC-XRefData/*"); String type = node.getName(); type = type.substring(type.lastIndexOf("_") + 1, type.length()); String database = targetType.containsKey(type) ? targetType.get(type) : type; String id = node.getText(); XRef xref = new XRef(); xref.setXRefId(id); xref.setDatabase(database); xref.setType(type); PCAssayXRef aXref = new PCAssayXRef(); aXref.setPanel(panel); aXref.setAssay(assay); aXref.setComment(comment); aXref.setXRef(xref); aXref.setTarget(false); assay.getAssayXRefs().add(aXref); } } private String nullSafeGet(Node node, String xpath, String expression) { Node node2 = node.selectSingleNode(xpath); if (null != node2) return node2.valueOf(expression); return ""; } protected void handleTargetXRefs(PCAssay assay, PCAssayPanel panel, List<Node> nodes) { for (Node n : nodes) { String name = n.selectSingleNode("PC-AssayTargetInfo_name").getText(); String id = n.selectSingleNode("PC-AssayTargetInfo_mol-id").getText(); String type = n.selectSingleNode("PC-AssayTargetInfo_molecule-type").valueOf("@value"); String database = targetType.containsKey(type) ? targetType.get(type) : type; Node taxonNode = n.selectSingleNode("PC-AssayTargetInfo_organism/BioSource/BioSource_org/Org-ref"); String taxonName = "", taxonCommon = "", taxon = ""; if (taxonNode != null) { taxonName = nullSafeGet(taxonNode, "Org-ref_taxname", "text()"); taxonCommon = nullSafeGet(taxonNode, "Org-ref_common", "text()"); String db = nullSafeGet(taxonNode, "Org-ref_db/Dbtag/Dbtag_db", "text()"); if (!"taxon".equals(db)) throw new RuntimeException("Non taxon BioSource Org-ref_db (was " + db + ")"); taxonNode = taxonNode.selectSingleNode("Org-ref_db/Dbtag/Dbtag_tag/Object-id/Object-id_id"); taxon = taxonNode.getText(); } XRef xref = new XRef(); xref.setXRefId(id); xref.setDatabase(database); xref.setType(type); xref.setName(name); PCAssayXRef aXref = new PCAssayXRef(); aXref.setTarget(true); aXref.setPanel(panel); aXref.setAssay(assay); aXref.setXRef(xref); if (!taxon.equals("")) { aXref.setTaxon(Long.parseLong(taxon)); aXref.setTaxonName(taxonName); aXref.setTaxonCommon(taxonCommon); } assay.getAssayXRefs().add(aXref); } } protected String join(Collection<Node> nodes, String separator) { StringBuffer sb = new StringBuffer(); int count = 0; for (Node node : nodes) { sb.append(node.getText()); if (count++ < nodes.size() - 1) sb.append(separator); } return sb.toString(); } }