Author: rodche
Date: 2012-01-31 16:28:50 -0800 (Tue, 31 Jan 2012)
New Revision: 28172
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxFilter.java
Log:
Modified the BioPaxFilter in the biopax-impl (CyFileFilter) to enable import
BioPAX networks from URLs as well (i.e., using the panel button rather than
using File...Import...network...from public db menu and UI). e.g., directly a
web service that returns BioPAX data stream.
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxFilter.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxFilter.java
2012-01-31 23:04:52 UTC (rev 28171)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxFilter.java
2012-02-01 00:28:50 UTC (rev 28172)
@@ -36,12 +36,8 @@
import java.io.InputStream;
import java.io.InputStreamReader;
import java.net.URI;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.Set;
-import org.cytoscape.io.CyFileFilter;
+import org.cytoscape.io.BasicCyFileFilter;
import org.cytoscape.io.DataCategory;
import org.cytoscape.io.util.StreamUtil;
@@ -50,29 +46,23 @@
* BioPax Filer class. Extends CyFileFilter for integration into the
Cytoscape ImportHandler
* framework.
*
- * @author Ethan Cerami.
+ * @author Ethan Cerami; (refactored by) Jason Montojo and Igor Rodchenkov
*/
-public class BioPaxFilter implements CyFileFilter {
+public class BioPaxFilter extends BasicCyFileFilter {
private static final String BIOPAX_XML_NAMESPACE = "www.biopax.org";
private static final int DEFAULT_LINES_TO_CHECK = 20;
/**
- * Filter Description.
- */
- private static String description = "BioPAX files";
-
- private final StreamUtil streamUtil;
- private final Set<String> extensions;
- private final Set<String> contentTypes;
-
- /**
* Constructor.
*/
public BioPaxFilter(StreamUtil streamUtil) {
- this.streamUtil = streamUtil;
- extensions = new HashSet<String>(Arrays.asList(new String[] {
"xml", "owl", "rdf" }));
- contentTypes = new HashSet<String>(Arrays.asList(new String[] {
"text/xml", "application/rdf+xml" }));
+ super(
+ new String[] { "xml", "owl", "rdf" },
+ new String[] { "text/xml",
"application/rdf+xml", "application/xml" },
+ "BioPAX data",
+ DataCategory.NETWORK,
+ streamUtil);
}
/**
@@ -89,78 +79,35 @@
*/
@Override
public boolean accepts(InputStream stream, DataCategory category) {
- if (category != DataCategory.NETWORK) {
+ if (category != this.category)
return false;
- }
- // Second test: file header must contain the biopax
declaration
+ // file/stream header must contain the biopax declaration
try {
- return checkHeader(stream);
+ BufferedReader reader = new BufferedReader(new
InputStreamReader(stream));
+ int linesToCheck = DEFAULT_LINES_TO_CHECK;
+ while (linesToCheck > 0) {
+ String line = reader.readLine();
+ if (line != null &&
line.contains(BIOPAX_XML_NAMESPACE)) {
+ return true;
+ }
+ linesToCheck--;
+ }
+ return false;
} catch (IOException e) {
}
return false;
}
-
- private boolean checkHeader(InputStream stream) throws IOException {
- BufferedReader reader = new BufferedReader(new
InputStreamReader(stream));
- int linesToCheck = DEFAULT_LINES_TO_CHECK;
- while (linesToCheck > 0) {
- String line = reader.readLine();
- if (line != null &&
line.contains(BIOPAX_XML_NAMESPACE)) {
- return true;
- }
- linesToCheck--;
- }
- return false;
- }
-
@Override
- public boolean accepts(URI uri, DataCategory category) {
- if (category != DataCategory.NETWORK) {
- return false;
- }
-
- String path = uri.getPath();
- boolean firstPass = false;
-
- // First test: file must end with one of the registered file
extensions.
- for (String extension : extensions) {
- if (path.endsWith(extension)) {
- firstPass = true;
- }
- }
-
- if (!firstPass) {
- return false;
- }
-
+ public boolean accepts(URI uri, DataCategory category) {
try {
- return accepts(streamUtil.getInputStream(uri.toURL()),
category);
+ return super.accepts(uri, category) &&
accepts(streamUtil.getInputStream(uri.toURL()), category);
} catch (IOException e) {
return false;
}
}
-
- @Override
- public Set<String> getContentTypes() {
- return Collections.unmodifiableSet(contentTypes);
- }
-
- @Override
- public DataCategory getDataCategory() {
- return DataCategory.NETWORK;
- }
-
- @Override
- public String getDescription() {
- return description;
- }
-
- @Override
- public Set<String> getExtensions() {
- return Collections.unmodifiableSet(extensions);
- }
+
}
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