Author: kono
Date: 2011-06-02 11:42:17 -0700 (Thu, 02 Jun 2011)
New Revision: 25621
Modified:
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/OBONetworkReaderFactory.java
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/OBOReader.java
core3/table-import-impl/trunk/src/test/java/org/cytoscape/tableimport/internal/reader/ontology/OBOReaderTest.java
Log:
OBOReader supports most of the attributes in the file. Map attributes had been
removed.
Modified:
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/OBONetworkReaderFactory.java
===================================================================
---
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/OBONetworkReaderFactory.java
2011-06-02 18:30:39 UTC (rev 25620)
+++
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/OBONetworkReaderFactory.java
2011-06-02 18:42:17 UTC (rev 25621)
@@ -42,6 +42,6 @@
@Override
public TaskIterator getTaskIterator() {
- return new TaskIterator(new OBOReader(inputStream, "DAG",
cyNetworkViewFactory, cyNetworkFactory, eventHelper));
+ return new TaskIterator(new OBOReader(inputStream,
cyNetworkViewFactory, cyNetworkFactory, eventHelper));
}
}
\ No newline at end of file
Modified:
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/OBOReader.java
===================================================================
---
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/OBOReader.java
2011-06-02 18:30:39 UTC (rev 25620)
+++
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/OBOReader.java
2011-06-02 18:42:17 UTC (rev 25621)
@@ -1,19 +1,30 @@
package org.cytoscape.tableimport.internal.reader.ontology;
+import static
org.cytoscape.tableimport.internal.reader.ontology.OBOTags.ALT_ID;
+import static
org.cytoscape.tableimport.internal.reader.ontology.OBOTags.BROAD_SYNONYM;
+import static org.cytoscape.tableimport.internal.reader.ontology.OBOTags.DEF;
+import static
org.cytoscape.tableimport.internal.reader.ontology.OBOTags.DISJOINT_FROM;
+import static
org.cytoscape.tableimport.internal.reader.ontology.OBOTags.EXACT_SYNONYM;
+import static org.cytoscape.tableimport.internal.reader.ontology.OBOTags.ID;
+import static org.cytoscape.tableimport.internal.reader.ontology.OBOTags.IS_A;
+import static
org.cytoscape.tableimport.internal.reader.ontology.OBOTags.IS_OBSOLETE;
+import static org.cytoscape.tableimport.internal.reader.ontology.OBOTags.NAME;
+import static
org.cytoscape.tableimport.internal.reader.ontology.OBOTags.NARROW_SYNONYM;
+import static
org.cytoscape.tableimport.internal.reader.ontology.OBOTags.RELATED_SYNONYM;
+import static
org.cytoscape.tableimport.internal.reader.ontology.OBOTags.RELATIONSHIP;
+import static
org.cytoscape.tableimport.internal.reader.ontology.OBOTags.SUBSET;
+import static
org.cytoscape.tableimport.internal.reader.ontology.OBOTags.SYNONYM;
+import static org.cytoscape.tableimport.internal.reader.ontology.OBOTags.XREF;
+import static
org.cytoscape.tableimport.internal.reader.ontology.OBOTags.XREF_ANALOG;
+
import java.io.BufferedReader;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
-import java.net.URL;
import java.util.ArrayList;
import java.util.HashMap;
-import java.util.Iterator;
import java.util.List;
import java.util.Map;
-import java.util.Set;
-import java.util.TreeSet;
import org.cytoscape.event.CyEventHelper;
import org.cytoscape.io.read.CyNetworkReader;
@@ -23,9 +34,6 @@
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyTable;
import org.cytoscape.model.CyTableEntry;
-import org.cytoscape.tableimport.internal.reader.AbstractGraphReader;
-import org.cytoscape.tableimport.internal.reader.NetworkTableReader;
-import org.cytoscape.tableimport.internal.reader.TextTableReader;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.work.AbstractTask;
@@ -33,23 +41,19 @@
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-import static org.cytoscape.tableimport.internal.reader.ontology.OBOTags.*;
-
-
public class OBOReader extends AbstractTask implements CyNetworkReader {
private static final Logger logger =
LoggerFactory.getLogger(OBOReader.class);
private static final String[] COMPATIBLE_VERSIONS = { "1.2" };
- //
- private static final String ONTOLOGY_DAG_ROOT = "Ontology DAGs";
+
+ private static final String TERM_NAME = "term name";
- public static final String OBO_PREFIX = "ontology";
+ public static final String OBO_PREFIX = "obo.";
private static final String DEF_ORIGIN = "def_origin";
protected static final String TERM_TAG = "[Term]";
- private static final String DEF_ONTOLOGY_NAME = "Ontology DAG";
private List<String[]> interactionList;
-
+
private final CyNetworkViewFactory cyNetworkViewFactory;
private final CyNetworkFactory cyNetworkFactory;
private final CyEventHelper eventHelper;
@@ -58,147 +62,85 @@
private CyNetwork ontologyDAG;
private CyNetwork[] networks;
- private CyTable termAttributes;
- private CyTable networkAttributes;
-
private Map<String, String> header;
- private String name;
-
+
private final InputStream inputStream;
-
-
+
private final Map<String, CyNode> termID2nodeMap;
- public OBOReader(final InputStream oboStream, final String name, final
CyNetworkViewFactory cyNetworkViewFactory,
+ public OBOReader(final InputStream oboStream, final
CyNetworkViewFactory cyNetworkViewFactory,
final CyNetworkFactory cyNetworkFactory, final
CyEventHelper eventHelper) {
this.inputStream = oboStream;
- this.name = name;
this.cyNetworkFactory = cyNetworkFactory;
this.cyNetworkViewFactory = cyNetworkViewFactory;
this.eventHelper = eventHelper;
-
+
termID2nodeMap = new HashMap<String, CyNode>();
networks = new CyNetwork[1];
interactionList = new ArrayList<String[]>();
- // initialize();
}
-// private void initialize() {
-// interactionList = new ArrayList<String[]>();
-// header = new HashMap<String, String>();
-//
-// networkAttributes = Cytoscape.getNetworkAttributes();
-// termAttributes = Cytoscape.getNodeAttributes();
-//
-// if (name == null) {
-// name = DEF_ONTOLOGY_NAME;
-// }
-//
-// /*
-// * Ontology DAGs will be distinguished by this attribute.
-// */
-// networkAttributes.setAttribute(name, Ontology.IS_ONTOLOGY,
true);
-// networkAttributes.setUserVisible(Ontology.IS_ONTOLOGY, false);
-// networkAttributes.setUserEditable(Ontology.IS_ONTOLOGY, false);
-//
-// String rootID = Cytoscape.getOntologyRootID();
-//
-// if (rootID == null) {
-// Set<CyNetwork> networkSet = Cytoscape.getNetworkSet();
-//
-// for (CyNetwork net : networkSet) {
-// if (net.getTitle().equals(ONTOLOGY_DAG_ROOT)) {
-// rootID = net.getIdentifier();
-// }
-// }
-//
-// if (rootID == null) {
-// rootID =
Cytoscape.createNetwork(ONTOLOGY_DAG_ROOT, false).getIdentifier();
-// Cytoscape.setOntologyRootID(rootID);
-// }
-// }
-//
-// ontologyDAG = Cytoscape.createNetwork(name,
Cytoscape.getNetwork(rootID), false);
-// }
-
@Override
public void run(TaskMonitor tm) throws Exception {
-
+
BufferedReader bufRd = new BufferedReader(new
InputStreamReader(inputStream));
String line;
-
+
+ // Create new DAG
this.ontologyDAG = cyNetworkFactory.getInstance();
-
- // Phase 1: read header information
- header = new HashMap<String, String>();
- while ((line = bufRd.readLine()) != null) {
- if (line.startsWith(TERM_TAG))
- break;
- else if(line.startsWith("!"))
- continue;
- else if (line.trim().length() != 0)
- parseHeader(line);
+
+ try {
+ // Phase 1: read header information
+ header = new HashMap<String, String>();
+ while ((line = bufRd.readLine()) != null) {
+ if (line.startsWith(TERM_TAG))
+ break;
+ else if (line.startsWith("!"))
+ continue;
+ else if (line.trim().length() != 0)
+ parseHeader(line);
+ }
+ mapHeader();
+
+ // Phase 2: read actual contents
+ readEntry(bufRd);
+
+ } finally {
+ bufRd.close();
+ inputStream.close();
+
}
- mapHeader();
-
-
- // Phase 2: read actual contents
- readEntry(bufRd);
-
+
buildEdge();
-
-// while ((line = bufRd.readLine()) != null) {
-// // Read header
-// if (line.startsWith(TERM_TAG)) {
-// readEntry(bufRd);
-// }
-// }
-//
-// } finally {
-// if (bufRd != null) {
-// bufRd.close();
-// }
-// }
-// } finally {
-// if (inputStream != null) {
-// inputStream.close();
-// }
-// }
-//
-// buildDag();
-// setAttributeDescriptions();
-
-
- bufRd.close();
- inputStream.close();
- logger.debug("node Cont ===> " + this.termID2nodeMap.size());
networks[0] = this.ontologyDAG;
+
+ termID2nodeMap.clear();
+ logger.debug("Number of terms loaded = " +
this.termID2nodeMap.size());
}
-
+
private void parseHeader(final String line) {
final int colonInx = line.indexOf(':');
if (colonInx == -1)
return;
-
+
final String key = line.substring(0, colonInx).trim();
final String val = line.substring(colonInx + 1).trim();
header.put(key, val);
}
-
+
private void mapHeader() {
final CyTable networkTable =
this.ontologyDAG.getDefaultNetworkTable();
-
- for(String tag: header.keySet()) {
- if(networkTable.getColumn(tag) == null)
+
+ for (String tag : header.keySet()) {
+ if (networkTable.getColumn(tag) == null)
networkTable.createColumn(tag, String.class,
false);
-
+
networkTable.getRow(ontologyDAG.getSUID()).set(tag,
header.get(tag));
}
}
-
private void readEntry(final BufferedReader rd) throws IOException {
String id = "";
String line = null;
@@ -212,10 +154,8 @@
String[] synonymParts;
String[] entry;
String targetId;
- List<String> listAttr;
Map<String, String> synoMap;
-
CyNode termNode = null;
boolean termSection = true;
while ((line = rd.readLine()) != null) {
@@ -224,63 +164,70 @@
if (line.length() == 0 || line.startsWith("!"))
continue;
- //Tag?
- if(line.startsWith("[")) {
- logger.debug("tag found: " + line);
- if(line.startsWith(TERM_TAG) == false) {
+ // Tag?
+ if (line.startsWith("[")) {
+ if (line.startsWith(TERM_TAG) == false) {
termSection = false;
continue;
} else {
termSection = true;
}
}
-
- if(!termSection)
+
+ if (!termSection)
continue;
-
-
+
colonInx = line.indexOf(':');
- if (colonInx == -1)
+ if (colonInx == -1)
continue;
key = line.substring(0, colonInx).trim();
val = line.substring(colonInx + 1).trim();
- logger.debug(key + " = " + val);
if (key.equals(ID.toString())) {
// Create node for this term.
termNode = termID2nodeMap.get(val);
- if(termNode == null) {
+ if (termNode == null) {
termNode = this.ontologyDAG.addNode();
termNode.getCyRow().set(CyTableEntry.NAME, val);
termID2nodeMap.put(val, termNode);
id = val;
}
+ } else if (key.equals(NAME.toString())) {
+ // Name column is used in Cytoscape core, so
use different tag instead.
+ if
(termNode.getCyRow().getTable().getColumn(TERM_NAME) == null)
+
termNode.getCyRow().getTable().createColumn(TERM_NAME, String.class, true);
+ termNode.getCyRow().set(TERM_NAME, val);
+ } else if (key.equals(DEF.toString())) {
+ definitionParts = val.split("\"");
-// } else if (key.equals(DEF.toString())) {
-// definitionParts = val.split("\"");
-// termAttributes.setAttribute(id, OBO_PREFIX +
"." + key, definitionParts[1]);
-//
-// List<String> originList =
getReferences(val.substring(definitionParts[1].length() + 2));
-//
-// if (originList != null)
-// termAttributes.setListAttribute(id,
OBO_PREFIX + "." + DEF_ORIGIN, originList);
-// } else if (key.equals(EXACT_SYNONYM.toString()) ||
key.equals(RELATED_SYNONYM.toString())
-// || key.equals(BROAD_SYNONYM.toString())
|| key.equals(NARROW_SYNONYM.toString())
-// || key.equals(SYNONYM.toString())) {
-// synonymParts = val.split("\"");
-//
-// synoMap = termAttributes.getMapAttribute(id,
OBO_PREFIX + "." + OBOTags.SYNONYM.toString());
-//
-// if (synoMap == null)
-// synoMap = new HashMap<String, String>();
-//
-// if (key.equals(SYNONYM.toString())) {
-// synoMap.put(synonymParts[1],
synonymParts[2].trim());
-// } else
-// synoMap.put(synonymParts[1], key);
-//
-// termAttributes.setMapAttribute(id, OBO_PREFIX +
"." + SYNONYM.toString(), synoMap);
+ if
(termNode.getCyRow().getTable().getColumn(key) == null)
+
termNode.getCyRow().getTable().createColumn(key, String.class, true);
+ termNode.getCyRow().set(key,
definitionParts[1]);
+
+ final List<String> originList =
getReferences(val.substring(definitionParts[1].length() + 2));
+
+ if (originList != null) {
+ if
(termNode.getCyRow().getTable().getColumn(DEF_ORIGIN) == null)
+
termNode.getCyRow().getTable().createListColumn(DEF_ORIGIN, String.class, true);
+ termNode.getCyRow().set(DEF_ORIGIN,
originList);
+ }
+ } else if (key.equals(EXACT_SYNONYM.toString()) ||
key.equals(RELATED_SYNONYM.toString())
+ || key.equals(BROAD_SYNONYM.toString())
|| key.equals(NARROW_SYNONYM.toString())
+ || key.equals(SYNONYM.toString())) {
+ synonymParts = val.split("\"");
+
+ if
(termNode.getCyRow().getTable().getColumn(key) == null)
+
termNode.getCyRow().getTable().createListColumn(key, String.class, true);
+
+ List<String> listAttr =
termNode.getCyRow().getList(key, String.class);
+
+ if (listAttr == null)
+ listAttr = new ArrayList<String>();
+
+ listAttr.add(synonymParts[1]);
+
+ termNode.getCyRow().set(key, listAttr);
} else if (key.equals(RELATIONSHIP.toString())) {
entry = val.split(" ");
final String[] itr = new String[3];
@@ -288,13 +235,6 @@
itr[1] = entry[1];
itr[2] = entry[0];
interactionList.add(itr);
-
-// CyNode targetNode =
termID2nodeMap.get(entry[0]);
-// if(targetNode == null) {
-// targetNode = this.ontologyDAG.addNode();
-// termID2nodeMap.put(val, targetNode);
-// }
-// ontologyDAG.addEdge(termNode, targetNode, true);
} else if (key.equals(IS_A.toString())) {
int colonidx = val.indexOf('!');
@@ -304,98 +244,76 @@
else
targetId = val.substring(0,
colonidx).trim();
-
final String[] itr = new String[3];
itr[0] = id;
itr[1] = targetId;
itr[2] = "is_a";
interactionList.add(itr);
-
-// CyNode targetNode =
termID2nodeMap.get(targetId);
-// if(targetNode == null) {
-// targetNode = ontologyDAG.addNode();
-// termID2nodeMap.put(val, targetNode);
-// }
-// ontologyDAG.addEdge(termNode, targetNode, true);
-// target = Cytoscape.getCyNode(targetId, true);
-// ontologyDAG.addNode(target);
-//
-// final String[] itr = new String[3];
-// itr[0] = id;
-// itr[1] = targetId;
-// itr[2] = "is_a";
-// interactionList.add(itr);
-// } else if (key.equals(IS_OBSOLETE.toString())) {
-// termAttributes.setAttribute(id, OBO_PREFIX +
"." + key, Boolean.parseBoolean(val));
-// } else if (key.equals(XREF.toString()) ||
key.equals(XREF_ANALOG.toString())
-// || key.equals(ALT_ID.toString()) ||
key.equals(SUBSET.toString())
-// ||
key.equals(DISJOINT_FROM.toString())) {
-// listAttr = termAttributes.getListAttribute(id,
OBO_PREFIX + "." + key);
-//
-// if (listAttr == null)
-// listAttr = new ArrayList<String>();
-//
-// if (val != null) {
-// if
(key.equals(DISJOINT_FROM.toString())) {
-//
listAttr.add(val.split("!")[0].trim());
-// } else
-// listAttr.add(val);
-// }
-//
-// termAttributes.setListAttribute(id, OBO_PREFIX
+ "." + key, listAttr);
-// } else
-// termAttributes.setAttribute(id, OBO_PREFIX +
"." + key, val);
+ } else if (key.equals(IS_OBSOLETE.toString())) {
+ if
(termNode.getCyRow().getTable().getColumn(key) == null)
+
termNode.getCyRow().getTable().createColumn(key, Boolean.class, true);
+ try {
+ termNode.getCyRow().set(key,
Boolean.parseBoolean(val));
+ } catch(Exception e) {
+ // Ignore invalid entries.
+ continue;
+ }
+ } else if (key.equals(XREF.toString()) ||
key.equals(XREF_ANALOG.toString())
+ || key.equals(ALT_ID.toString()) ||
key.equals(SUBSET.toString())
+ ||
key.equals(DISJOINT_FROM.toString())) {
+
+ if
(termNode.getCyRow().getTable().getColumn(key) == null)
+
termNode.getCyRow().getTable().createListColumn(key, String.class, true);
+
+ List<String> listAttr =
termNode.getCyRow().getList(key, String.class);
+ if (listAttr == null)
+ listAttr = new ArrayList<String>();
+
+ if (val != null) {
+ if
(key.equals(DISJOINT_FROM.toString())) {
+
listAttr.add(val.split("!")[0].trim());
+ } else
+ listAttr.add(val);
+ }
+ termNode.getCyRow().set(key, listAttr);
+ } else {
+ // Others will be stored as a string attr.
+ if
(termNode.getCyRow().getTable().getColumn(key) == null)
+
termNode.getCyRow().getTable().createColumn(key, String.class, true);
+ termNode.getCyRow().set(key, val);
}
}
}
-
+
private void buildEdge() {
- for(String[] entry: this.interactionList) {
- CyEdge edge =
ontologyDAG.addEdge(termID2nodeMap.get(entry[0]), termID2nodeMap.get(entry[1])
, true);
- // add attr
+ for (String[] entry : this.interactionList) {
+ CyEdge edge =
ontologyDAG.addEdge(termID2nodeMap.get(entry[0]), termID2nodeMap.get(entry[1]),
true);
+ edge.getCyRow().set(CyEdge.INTERACTION, entry[2]);
}
-
+ interactionList.clear();
}
-
-
-// private List<String> getReferences(String list) {
-// String trimed = list.trim();
-// trimed = trimed.substring(trimed.indexOf("[") + 1,
trimed.indexOf("]"));
-//
-// if (trimed.length() == 0) {
-// return null;
-// } else {
-// List<String> entries = new ArrayList<String>();
-//
-// for (String entry : trimed.split(",")) {
-// entries.add(entry.trim());
-// }
-//
-// return entries;
-// }
-// }
-//
-// private void setAttributeDescriptions() {
-// String[] attrNames = termAttributes.getAttributeNames();
-// Set<String> attrNameSet = new TreeSet<String>();
-//
-// for (String name : attrNames) {
-// attrNameSet.add(name);
-// }
-//
-// for (OBOTags tags : OBOTags.values()) {
-// if (attrNameSet.contains(OBOTags.getPrefix() + "." +
tags.toString())) {
-//
termAttributes.setAttributeDescription(OBOTags.getPrefix() + "." +
tags.toString(),
-// tags.getDescription());
-// }
-// }
-// }
+ private List<String> getReferences(String list) {
+ String trimed = list.trim();
+ trimed = trimed.substring(trimed.indexOf("[") + 1,
trimed.indexOf("]"));
+ if (trimed.length() == 0) {
+ return null;
+ } else {
+ List<String> entries = new ArrayList<String>();
+
+ for (String entry : trimed.split(",")) {
+ entries.add(entry.trim());
+ }
+
+ return entries;
+ }
+ }
+
@Override
public CyNetworkView buildCyNetworkView(CyNetwork arg0) {
- // TODO Auto-generated method stub
- return null;
+ final CyNetworkView view =
cyNetworkViewFactory.getNetworkView(ontologyDAG);
+ return view;
}
@Override
Modified:
core3/table-import-impl/trunk/src/test/java/org/cytoscape/tableimport/internal/reader/ontology/OBOReaderTest.java
===================================================================
---
core3/table-import-impl/trunk/src/test/java/org/cytoscape/tableimport/internal/reader/ontology/OBOReaderTest.java
2011-06-02 18:30:39 UTC (rev 25620)
+++
core3/table-import-impl/trunk/src/test/java/org/cytoscape/tableimport/internal/reader/ontology/OBOReaderTest.java
2011-06-02 18:42:17 UTC (rev 25621)
@@ -62,7 +62,7 @@
}
private CyNetwork testFile(File file) throws Exception {
- final OBOReader reader = new
OBOReader(file.toURI().toURL().openStream(), "yeast slim", cyNetworkViewFactory,
+ final OBOReader reader = new
OBOReader(file.toURI().toURL().openStream(), cyNetworkViewFactory,
cyNetworkFactory, eventHelper);
reader.run(null);
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