/*************************************************************************
* *
* This file is part of the 20n/act project. *
* 20n/act enables DNA prediction for synthetic biology/bioengineering. *
* Copyright (C) 2017 20n Labs, Inc. *
* *
* Please direct all queries to act@20n.com. *
* *
* This program is free software: you can redistribute it and/or modify *
* it under the terms of the GNU General Public License as published by *
* the Free Software Foundation, either version 3 of the License, or *
* (at your option) any later version. *
* *
* This program 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 General Public License for more details. *
* *
* You should have received a copy of the GNU General Public License *
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
* *
*************************************************************************/
package act.installer.pubchem;
import act.server.MongoDB;
import act.shared.Chemical;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.CommandLineParser;
import org.apache.commons.cli.DefaultParser;
import org.apache.commons.cli.HelpFormatter;
import org.apache.commons.cli.Option;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.jaxen.JaxenException;
import org.jaxen.dom.DOMXPath;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.w3c.dom.Text;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.stream.XMLEventReader;
import javax.xml.stream.XMLInputFactory;
import javax.xml.stream.XMLStreamConstants;
import javax.xml.stream.XMLStreamException;
import javax.xml.stream.events.Characters;
import javax.xml.stream.events.XMLEvent;
import javax.xml.xpath.XPathExpressionException;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.stream.Collectors;
import java.util.zip.GZIPInputStream;
public class PubchemParser {
private static final Logger LOGGER = LogManager.getFormatterLogger(PubchemParser.class);
private static final String OPTION_DATA_DIRECTORY = "i";
private static final String OPTION_DB = "o";
private static final String GZIP_FILE_EXT = ".gz";
private static final String COMPOUND_DOC_TAG = "PC-Compound";
private static final int GZIP_BUFFER_SIZE = 1 << 27; // ~128MB of buffer space to help GZip really move.
private static final boolean ENABLE_XML_STREAM_TEXT_COALESCING = true;
public static final HelpFormatter HELP_FORMATTER = new HelpFormatter();
static {
HELP_FORMATTER.setWidth(100);
}
public static final String HELP_MESSAGE = "This class is used for parsing xml files and storing them in a db";
public static final List<Option.Builder> OPTION_BUILDERS = new ArrayList<Option.Builder>() {{
add(Option.builder(OPTION_DATA_DIRECTORY)
.argName("OPTION_DATA_DIRECTORY")
.desc("The data directory where the pubchem files live")
.hasArg()
.required()
.type(String.class)
);
add(Option.builder(OPTION_DB)
.argName("OPTION_DB")
.desc("The db to save the results in")
.hasArg()
.required()
.type(String.class)
);
add(Option.builder("h")
.argName("help")
.desc("Prints this help message")
.longOpt("help")
);
}};
/**
* Key terminologies for this file:
*
* a) An example of how an inchi is packaged in the XML document
*
<PC-InfoData>
<PC-InfoData_urn>
<PC-Urn>
<PC-Urn_label>InChI</PC-Urn_label>
<PC-Urn_name>Standard</PC-Urn_name>
<PC-Urn_datatype>
<PC-UrnDataType value="string">1</PC-UrnDataType>
</PC-Urn_datatype>
<PC-Urn_version>1.0.4</PC-Urn_version>
<PC-Urn_software>InChI</PC-Urn_software>
<PC-Urn_source>iupac.org</PC-Urn_source>
<PC-Urn_release>2012.11.26</PC-Urn_release>
</PC-Urn>
</PC-InfoData_urn>
<PC-InfoData_value>
<PC-InfoData_value_sval>InChI=1S/C12H17FO/c1-12(2,3)10-6-4-9(5-7-10)11(13)8-14/h4-7,11,14H,8H2,1-3H3</PC-InfoData_value_sval>
</PC-InfoData_value>
</PC-InfoData>
*
* In order to parse the inchi, we first detect the element <PC-Urn_label>InChI</PC-Urn_label>, since it tells us this
* node is an inchi node. The element PC-Urn_label is called a "ResourceName". The term "inchi", a value of the resource
* name node, is called a "ResourceValue". For element <PC-Urn_label>InChI</PC-Urn_label>, two xml events occurs in sequence:
* 1) START ELEMENT 2) CHARACTERS. We identify a ResourceName in (1) and ResourceValue in (2). In this case, we have two
* nodes of interest:
* a) <PC-Urn_label>InChI</PC-Urn_label>
* b) <PC-InfoData_value_sval>InChI=1S/C12H17FO/c1-12(2,3)10-6-4-9(5-7-10)11(13)8-14/h4-7,11,14H,8H2,1-3H3</PC-InfoData_value_sval>
*
* Once we detect the node as an inchi node from a), we can easily detect the ResourceName "PC-InfoData_value_sval" and
* store it's value for b). We call PC-Urn_label "PUBCHEM_KEY" since it is a key to the value of the inchi, whereas
* PC-InfoData_value_sval is the "PUBCHEM_VALUE" since it is the value to the inchi.
*/
private enum PC_XPATHS {
/* Structure: <feature name>_<level>_[_<sub-feature or structure>]_<type>
* [IUPAC_NAME]_[L1]_[NODES]: nodes in the original document (L1) that correspond to IUPAC name entries.
* [IUPAC_NAME]_[L2]_[VALUE]_[TEXT]: textual names in the IUPAC name sub-tree (L2).
*/
IUPAC_NAME_L1_NODES("/PC-Compound/PC-Compound_props/PC-InfoData[./PC-InfoData_urn/PC-Urn/PC-Urn_label/text()=\"IUPAC Name\"]"),
IUPAC_NAME_L2_TYPE_TEXT("/PC-InfoData/PC-InfoData_urn/PC-Urn/PC-Urn_name/text()"),
IUPAC_NAME_L2_VALUE_TEXT("/PC-InfoData/PC-InfoData_value/PC-InfoData_value_sval/text()"),
// TODO: ensure there is exactly one id_cid per compound.
PC_ID_L1_TEXT("/PC-Compound/PC-Compound_id/PC-CompoundType/PC-CompoundType_id/PC-CompoundType_id_cid/text()"),
INCHI_L1_NODES("/PC-Compound/PC-Compound_props/PC-InfoData[./PC-InfoData_urn/PC-Urn/PC-Urn_label/text()=\"InChI\"]"),
/* We could just use //PC-InfoData[./PC-InfoData_urn//PC-Urn_label/text()="InChI"]//PC-InfoData_value_sval/text()
* but we split the InChI parsing into two pieces in case there are multiple InChI entries (which would be insane).
*/
INCHI_L2_TEXT("/PC-InfoData/PC-InfoData_value/PC-InfoData_value_sval/text()"),
SMILES_L1_NODES("//PC-InfoData[./PC-InfoData_urn//PC-Urn_label/text()=\"SMILES\"]"),
SMILES_L2_TEXT("//PC-InfoData_value_sval/text()"),
;
private String path;
PC_XPATHS(String path) {
this.path = path;
}
public String getPath() {
return path;
}
DOMXPath compile() throws JaxenException {
return new DOMXPath(this.getPath());
}
}
private static final Set<String> TAGS_TO_INCLUDE = Collections.unmodifiableSet(new HashSet<String>() {{
add("PC-Compound_id");
add("PC-Compound_props");
}});
private final Map<PC_XPATHS, DOMXPath> xpaths = new HashMap<>(PC_XPATHS.values().length);
private MongoDB db;
private DocumentBuilder documentBuilder;
private XMLInputFactory xmlInputFactory;
public PubchemParser(MongoDB db) {
this.db = db;
}
/**
* Initializes a PubchemParser. Must be called before the PubchemParser can be used.
* @throws XPathExpressionException
* @throws ParserConfigurationException
*/
public void init() throws ParserConfigurationException, JaxenException {
// Would rather do this in its own block, but have to handle the XPath exception. :(
for (PC_XPATHS x : PC_XPATHS.values()) {
xpaths.put(x, x.compile());
}
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
documentBuilder = factory.newDocumentBuilder();
xmlInputFactory = XMLInputFactory.newInstance();
/* Configure the XMLInputFactory to return event streams that coalesce consecutive character events. Without this
* we can end up with malformed names and InChIs, as XPath will only fetch the first text node if there are several
* text children under one parent. */
xmlInputFactory.setProperty(XMLInputFactory.IS_COALESCING, ENABLE_XML_STREAM_TEXT_COALESCING);
if ((Boolean) xmlInputFactory.getProperty(XMLInputFactory.IS_COALESCING)) {
LOGGER.info("Successfully configured XML stream to coalesce character elements.");
} else {
LOGGER.error("Unable to configure XML stream to coalesce character elements.");
}
}
/**
* This function writes a chemical record to the DB.
* @param chemical Chemical to be written to the DB.
*/
private void writeChemicalToDB(Chemical chemical) {
Long id = db.getNextAvailableChemicalDBid();
db.submitToActChemicalDB(chemical, id);
}
/**
* Extracts compound features from a sub-document/sub-tree containing one PC-Compound element. Nodes that contain
* interesting features are found and their text extracted using XPath.
*
* @param d The document from which to extract features.
* @return A PubchemEntry object corresponding to features from one PC-Compound document.
* @throws XPathExpressionException
*/
private PubchemEntry extractPCCompoundFeatures(Document d) throws JaxenException {
Long id = Long.valueOf(xpaths.get(PC_XPATHS.PC_ID_L1_TEXT).stringValueOf(d));
PubchemEntry entry = new PubchemEntry(id);
// Jaxen's API is from a pre-generics age!
List<Node> nodes = (List<Node>) xpaths.get(PC_XPATHS.IUPAC_NAME_L1_NODES).selectNodes(d);
if (nodes.size() == 0) {
LOGGER.warn("No names available for compound %d", id);
}
for (Node n : nodes) {
/* In order to run XPath on a sub-document, we have to Extract the relevant nodes into their own document object.
* If we try to run evaluate on `n` instead of this new document, we'll get matching paths for the original
* document `d` but not for the nodes we're looking at right now. Very weird.
* TODO: remember this way of running XPath on documents the next time we need to write an XML parser. */
Document iupacNameDoc = documentBuilder.newDocument();
iupacNameDoc.adoptNode(n);
iupacNameDoc.appendChild(n);
String type = xpaths.get(PC_XPATHS.IUPAC_NAME_L2_TYPE_TEXT).stringValueOf(iupacNameDoc);
String value = xpaths.get(PC_XPATHS.IUPAC_NAME_L2_VALUE_TEXT).stringValueOf(iupacNameDoc);
entry.setNameByType(type, value);
}
// We really need an InChI for a chemical to make sense, so log errors if we can't find one.
boolean hasInChI = false;
nodes = xpaths.get(PC_XPATHS.INCHI_L1_NODES).selectNodes(d);
if (nodes.size() == 0) {
LOGGER.warn("Found chemical (%d) with no InChIs, hoping for SMILES instead", id);
} else if (nodes.size() > 1) {
LOGGER.error("Assumption violation: found chemical with multiple InChIs (%d), skipping", id);
return null;
} else {
hasInChI = true;
Node n = nodes.get(0);
Document inchiDoc = documentBuilder.newDocument();
inchiDoc.adoptNode(n);
inchiDoc.appendChild(n);
String value = xpaths.get(PC_XPATHS.INCHI_L2_TEXT).stringValueOf(inchiDoc);
entry.setInchi(value);
}
nodes = xpaths.get(PC_XPATHS.SMILES_L1_NODES).selectNodes(d);
if (nodes.size() == 0) {
if (hasInChI) {
LOGGER.warn("Found chemical (%d) with no SMILES, using only InChI");
} else {
LOGGER.warn("Found chemical (%d) with no InChI or SMILES, skipping");
return null;
}
} else {
for (Node n : nodes) {
Document smilesDoc = documentBuilder.newDocument();
smilesDoc.adoptNode(n);
smilesDoc.appendChild(n);
String smiles = xpaths.get(PC_XPATHS.SMILES_L2_TEXT).stringValueOf(smilesDoc);
entry.appendSmiles(smiles);
}
}
return entry;
}
/**
* Incrementally parses a stream of XML events from a PubChem file, extracting the next available PC-Compound entry
* as a Chemical object.
* @param eventReader The xml event reader we are parsing the XML from
* @return The constructed chemical
* @throws XMLStreamException
* @throws XPathExpressionException
*/
public Chemical extractNextChemicalFromXMLStream(XMLEventReader eventReader)
throws XMLStreamException, JaxenException {
Document bufferDoc = null;
Element currentElement = null;
StringBuilder textBuffer = null;
/* With help from
* http://stackoverflow.com/questions/7998733/loading-local-chunks-in-dom-while-parsing-a-large-xml-file-in-sax-java
*/
while (eventReader.hasNext()) {
XMLEvent event = eventReader.nextEvent();
switch (event.getEventType()) {
case XMLStreamConstants.START_ELEMENT:
String eventName = event.asStartElement().getName().getLocalPart();
if (COMPOUND_DOC_TAG.equals(eventName)) {
// Create a new document if we've found the start of a compound object.
bufferDoc = documentBuilder.newDocument();
currentElement = bufferDoc.createElement(eventName);
bufferDoc.appendChild(currentElement);
} else if (currentElement != null) { // Wait until we've found a compound entry to start slurping up data.
// Create a new child element and push down the current pointer when we find a new node.
Element newElement = bufferDoc.createElement(eventName);
currentElement.appendChild(newElement);
currentElement = newElement;
} // If we aren't in a PC-Compound tree, we just let the elements pass by.
break;
case XMLStreamConstants.CHARACTERS:
if (currentElement == null) { // Ignore this event if we're not in a PC-Compound tree.
continue;
}
Characters chars = event.asCharacters();
// Ignore only whitespace strings, which just inflate the size of the DOM. Text coalescing makes this safe.
if (chars.isWhiteSpace()) {
continue;
}
// Rely on the XMLEventStream to coalesce consecutive text events.
Text textNode = bufferDoc.createTextNode(chars.getData());
currentElement.appendChild(textNode);
break;
case XMLStreamConstants.END_ELEMENT:
if (currentElement == null) { // Ignore this event if we're not in a PC-Compound tree.
continue;
}
eventName = event.asEndElement().getName().getLocalPart();
Node parentNode = currentElement.getParentNode();
if (parentNode instanceof Element) {
currentElement = (Element) parentNode;
} else if (parentNode instanceof Document && eventName.equals(COMPOUND_DOC_TAG)) {
// We're back at the top of the node stack! Convert the buffered document into a Chemical.
PubchemEntry entry = extractPCCompoundFeatures(bufferDoc);
if (entry != null) {
return entry.asChemical();
} else {
// Skip this entry if we can't process it correctly by resetting the world and continuing on.
bufferDoc = null;
currentElement = null;
}
} else {
// This should not happen, but is here as a sanity check.
throw new RuntimeException(String.format("Parent of XML element %s is of type %d, not Element",
currentElement.getTagName(), parentNode.getNodeType()));
}
break;
// TODO: do we care about attributes or other XML structures?
}
}
// Return null when we run out of chemicals, just like readLine().
return null;
}
/**
* This function reads a given gzipped XML file, passes the xml event stream to a function to parse out the chemical,
* and writes the chemical to the db.
* @param file The input gzipped file that is being processed.
* @throws XMLStreamException
* @throws IOException
*/
public void openCompressedXMLFileAndWriteChemicals(File file)
throws XMLStreamException, JaxenException, IOException {
XMLEventReader eventReader = xmlInputFactory.createXMLEventReader(
new GZIPInputStream(new FileInputStream(file), GZIP_BUFFER_SIZE));
Chemical result;
while ((result = extractNextChemicalFromXMLStream(eventReader)) != null) {
writeChemicalToDB(result);
}
}
/**
* This function is the main driver of the class, which processes all the xml files of the pubchem dump.
* @throws XMLStreamException
* @throws IOException
*/
private void run(List<File> filesToProcess) throws XMLStreamException, JaxenException, IOException {
int counter = 1;
for (File file : filesToProcess) {
LOGGER.info("Processing file %d of %d", counter, filesToProcess.size());
LOGGER.info("File name is %s", file.getPath());
openCompressedXMLFileAndWriteChemicals(file);
counter++;
}
}
/**
* This function extracts gzipped xml files from a file directory.
* @param dataDirectory The directory of interest.
* @return A list of files of gzipped xml files.
* @throws XMLStreamException
* @throws IOException
*/
private static List<File> findGZippedFilesInDirectory(String dataDirectory) throws XMLStreamException, IOException {
File folder = new File(dataDirectory);
if (!folder.exists()) {
String msg = String.format("The folder %s does not exists", folder.getAbsolutePath());
LOGGER.error(msg);
throw new RuntimeException(msg);
}
List<File> result = Arrays.stream(folder.listFiles()).
filter(f -> f.getName().endsWith(GZIP_FILE_EXT)).collect(Collectors.toList());
// Sort files lexicographically for installer stability.
Collections.sort(result);
return result;
}
public static void main(String[] args) throws Exception {
// Parse the command line options
Options opts = new Options();
for (Option.Builder b : OPTION_BUILDERS) {
opts.addOption(b.build());
}
CommandLine cl = null;
try {
CommandLineParser parser = new DefaultParser();
cl = parser.parse(opts, args);
} catch (ParseException e) {
LOGGER.error("Argument parsing failed: %s\n", e.getMessage());
HELP_FORMATTER.printHelp(PubchemParser.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
System.exit(1);
}
if (cl.hasOption("help")) {
HELP_FORMATTER.printHelp(PubchemParser.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
return;
}
String dataDir = cl.getOptionValue(OPTION_DATA_DIRECTORY);
String dbName = cl.getOptionValue(OPTION_DB);
MongoDB db = new MongoDB("localhost", 27017, dbName);
PubchemParser pubchemParser = new PubchemParser(db);
pubchemParser.init();
pubchemParser.run(findGZippedFilesInDirectory(dataDir));
}
}