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Remove xpp3 dependency only used by PubChem readers.
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johnmay committed Dec 14, 2016
1 parent dcfa4d1 commit 170b6c9
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Showing 6 changed files with 172 additions and 171 deletions.
5 changes: 0 additions & 5 deletions storage/io/pom.xml
Expand Up @@ -18,11 +18,6 @@
<groupId>javax.vecmath</groupId>
<artifactId>vecmath</artifactId>
</dependency>
<dependency>
<groupId>xpp3</groupId>
<artifactId>xpp3</artifactId>
<version>1.1.4c</version>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
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Expand Up @@ -35,8 +35,10 @@
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat;
import org.openscience.cdk.io.pubchemxml.PubChemXMLHelper;
import org.xmlpull.v1.XmlPullParser;
import org.xmlpull.v1.XmlPullParserFactory;

import javax.xml.stream.XMLInputFactory;
import javax.xml.stream.XMLStreamReader;
import javax.xml.stream.events.XMLEvent;

/**
* Reads an object from ASN.1 XML formated input for PubChem Compound entries.
Expand All @@ -52,7 +54,7 @@
public class PCCompoundXMLReader extends DefaultChemObjectReader {

private Reader input;
private XmlPullParser parser;
private XMLStreamReader parser;
private PubChemXMLHelper parserHelper;
private IChemObjectBuilder builder;

Expand Down Expand Up @@ -83,12 +85,10 @@ public IResourceFormat getFormat() {
@Override
public void setReader(Reader input) throws CDKException {
try {
XmlPullParserFactory factory = XmlPullParserFactory.newInstance(
System.getProperty(XmlPullParserFactory.PROPERTY_NAME), null);
factory.setNamespaceAware(true);
parser = factory.newPullParser();
XMLInputFactory xmlfact = XMLInputFactory.newFactory();
xmlfact.setProperty(XMLInputFactory.IS_NAMESPACE_AWARE, true);
parser = xmlfact.createXMLStreamReader(input);
this.input = input;
parser.setInput(input);
} catch (Exception exception) {
throw new CDKException("Error while creating reader: " + exception.getMessage(), exception);
}
Expand Down Expand Up @@ -132,9 +132,9 @@ public void close() throws IOException {

private IAtomContainer readMolecule() throws Exception {
boolean foundCompound = false;
while (parser.next() != XmlPullParser.END_DOCUMENT) {
if (parser.getEventType() == XmlPullParser.START_TAG) {
if (parser.getName().equals("PC-Compound")) {
while (parser.next() != XMLEvent.END_DOCUMENT) {
if (parser.getEventType() == XMLEvent.START_ELEMENT) {
if (parser.getLocalName().equals("PC-Compound")) {
foundCompound = true;
break;
}
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Expand Up @@ -35,8 +35,10 @@
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat;
import org.openscience.cdk.io.pubchemxml.PubChemXMLHelper;
import org.xmlpull.v1.XmlPullParser;
import org.xmlpull.v1.XmlPullParserFactory;

import javax.xml.stream.XMLInputFactory;
import javax.xml.stream.XMLStreamReader;
import javax.xml.stream.events.XMLEvent;

/**
* Reads an object from ASN formated input for PubChem Compound entries. The following
Expand All @@ -52,7 +54,7 @@
public class PCSubstanceXMLReader extends DefaultChemObjectReader {

private Reader input;
private XmlPullParser parser;
private XMLStreamReader parser;
private PubChemXMLHelper parserHelper;
private IChemObjectBuilder builder;

Expand Down Expand Up @@ -83,12 +85,10 @@ public IResourceFormat getFormat() {
@Override
public void setReader(Reader input) throws CDKException {
try {
XmlPullParserFactory factory = XmlPullParserFactory.newInstance(
System.getProperty(XmlPullParserFactory.PROPERTY_NAME), null);
factory.setNamespaceAware(true);
parser = factory.newPullParser();
XMLInputFactory xmlfact = XMLInputFactory.newFactory();
xmlfact.setProperty(XMLInputFactory.IS_NAMESPACE_AWARE, true);
parser = xmlfact.createXMLStreamReader(input);
this.input = input;
parser.setInput(input);
} catch (Exception exception) {
throw new CDKException("Error while creating reader: " + exception.getMessage(), exception);
}
Expand Down Expand Up @@ -132,9 +132,9 @@ public void close() throws IOException {

private IAtomContainer readMolecule() throws Exception {
boolean foundCompound = false;
while (parser.next() != XmlPullParser.END_DOCUMENT) {
if (parser.getEventType() == XmlPullParser.START_TAG) {
if (parser.getName().equals("PC-Compound")) {
while (parser.next() != XMLEvent.END_DOCUMENT) {
if (parser.getEventType() == XMLEvent.START_ELEMENT) {
if (parser.getLocalName().equals("PC-Compound")) {
foundCompound = true;
break;
}
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Expand Up @@ -34,9 +34,11 @@
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat;
import org.openscience.cdk.io.pubchemxml.PubChemXMLHelper;
import org.xmlpull.v1.XmlPullParser;
import org.xmlpull.v1.XmlPullParserException;
import org.xmlpull.v1.XmlPullParserFactory;

import javax.xml.stream.XMLInputFactory;
import javax.xml.stream.XMLStreamException;
import javax.xml.stream.XMLStreamReader;
import javax.xml.stream.events.XMLEvent;

/**
* Iterating PubChem PCCompound ASN.1 XML reader.
Expand All @@ -56,9 +58,10 @@
public class IteratingPCCompoundXMLReader extends DefaultIteratingChemObjectReader<IAtomContainer> {

private Reader primarySource;
private XmlPullParser parser;
private XMLStreamReader parser;
private PubChemXMLHelper parserHelper;
private IChemObjectBuilder builder;
private final XMLInputFactory xmlfact;

private boolean nextAvailableIsKnown;
private boolean hasNext;
Expand All @@ -69,20 +72,19 @@ public class IteratingPCCompoundXMLReader extends DefaultIteratingChemObjectRead
*
* @param in The input stream
* @param builder The builder
* @throws org.xmlpull.v1.XmlPullParserException if there is an error isn setting up the XML parser
* @throws XMLStreamException if there is an error isn setting up the XML parser
*/
public IteratingPCCompoundXMLReader(Reader in, IChemObjectBuilder builder) throws IOException,
XmlPullParserException {
XMLStreamException {
this.builder = builder;
parserHelper = new PubChemXMLHelper(builder);

// initiate the pull parser
XmlPullParserFactory factory = XmlPullParserFactory.newInstance(
System.getProperty(XmlPullParserFactory.PROPERTY_NAME), null);
factory.setNamespaceAware(true);
parser = factory.newPullParser();
xmlfact = XMLInputFactory.newFactory();
xmlfact.setProperty(XMLInputFactory.IS_NAMESPACE_AWARE, true);

parser = xmlfact.createXMLStreamReader(in);
primarySource = in;
parser.setInput(primarySource);

nextMolecule = null;
nextAvailableIsKnown = false;
Expand Down Expand Up @@ -111,12 +113,12 @@ public boolean hasNext() {
hasNext = false;

try {
if (parser.next() == XmlPullParser.END_DOCUMENT) return false;
if (parser.next() == XMLEvent.END_DOCUMENT) return false;

while (parser.next() != XmlPullParser.END_DOCUMENT) {
if (parser.getEventType() == XmlPullParser.START_TAG) {
while (parser.next() != XMLEvent.END_DOCUMENT) {
if (parser.getEventType() == XMLEvent.START_ELEMENT) {
// System.out.println("start: '" + parser.getName() + "'");
if (parser.getName().equals("PC-Compound")) {
if (parser.getLocalName().equals("PC-Compound")) {
hasNext = true;
break;
}
Expand Down Expand Up @@ -163,8 +165,8 @@ public void remove() {
public void setReader(Reader reader) throws CDKException {
primarySource = reader;
try {
parser.setInput(primarySource);
} catch (XmlPullParserException e) {
parser = xmlfact.createXMLStreamReader(reader);
} catch (XMLStreamException e) {
throw new CDKException("Error while opening the input:" + e.getMessage(), e);
}
nextMolecule = null;
Expand Down
Expand Up @@ -35,9 +35,11 @@
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat;
import org.openscience.cdk.io.pubchemxml.PubChemXMLHelper;
import org.xmlpull.v1.XmlPullParser;
import org.xmlpull.v1.XmlPullParserException;
import org.xmlpull.v1.XmlPullParserFactory;

import javax.xml.stream.XMLInputFactory;
import javax.xml.stream.XMLStreamException;
import javax.xml.stream.XMLStreamReader;
import javax.xml.stream.events.XMLEvent;

/**
* Iterating PubChem PC-Substances ASN.1 XML reader.
Expand All @@ -55,8 +57,10 @@
public class IteratingPCSubstancesXMLReader extends DefaultIteratingChemObjectReader<IChemModel> {

private Reader primarySource;
private XmlPullParser parser;
private XMLStreamReader parser;
private PubChemXMLHelper parserHelper;
private final XMLInputFactory xmlfact;


private boolean nextAvailableIsKnown;
private boolean hasNext;
Expand All @@ -68,19 +72,17 @@ public class IteratingPCSubstancesXMLReader extends DefaultIteratingChemObjectRe
* @param in The input stream
* @param builder The builder
* @throws java.io.IOException if there is error in getting the {@link IsotopeFactory}
* @throws org.xmlpull.v1.XmlPullParserException if there is an error isn setting up the XML parser
* @throws XMLStreamException an error in reading XML
*/
public IteratingPCSubstancesXMLReader(Reader in, IChemObjectBuilder builder) throws IOException,
XmlPullParserException {
XMLStreamException {
parserHelper = new PubChemXMLHelper(builder);
xmlfact = XMLInputFactory.newFactory();

// initiate the pull parser
XmlPullParserFactory factory = XmlPullParserFactory.newInstance(
System.getProperty(XmlPullParserFactory.PROPERTY_NAME), null);
factory.setNamespaceAware(true);
parser = factory.newPullParser();
primarySource = in;
parser.setInput(primarySource);
xmlfact.setProperty(XMLInputFactory.IS_NAMESPACE_AWARE, true);
parser = xmlfact.createXMLStreamReader(in);
this.primarySource = in;

nextSubstance = null;
nextAvailableIsKnown = false;
Expand Down Expand Up @@ -109,11 +111,11 @@ public boolean hasNext() {
hasNext = false;

try {
if (parser.next() == XmlPullParser.END_DOCUMENT) return false;
if (parser.next() == XMLEvent.END_DOCUMENT) return false;

while (parser.next() != XmlPullParser.END_DOCUMENT) {
if (parser.getEventType() == XmlPullParser.START_TAG) {
if (PubChemXMLHelper.EL_PCSUBSTANCE.equals(parser.getName())) {
while (parser.next() != XMLEvent.END_DOCUMENT) {
if (parser.getEventType() == XMLEvent.START_ELEMENT) {
if (PubChemXMLHelper.EL_PCSUBSTANCE.equals(parser.getLocalName())) {
hasNext = true;
break;
}
Expand Down Expand Up @@ -162,8 +164,8 @@ public void remove() {
public void setReader(Reader reader) throws CDKException {
primarySource = reader;
try {
parser.setInput(primarySource);
} catch (XmlPullParserException e) {
parser = xmlfact.createXMLStreamReader(reader);
} catch (XMLStreamException e) {
throw new CDKException("Error while opening the input:" + e.getMessage(), e);
}
nextSubstance = null;
Expand Down

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