[MOBY-guts] biomoby commit
Eddie Kawas
kawas at pub.open-bio.org
Thu Apr 28 18:39:40 UTC 2005
kawas
Thu Apr 28 14:39:40 EDT 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources
In directory pub.open-bio.org:/tmp/cvs-serv10633/org/biomoby/client/ui/graphical/servlet/jresources
Modified Files:
RESOURCE.java
Log Message:
added a backup to getTypes() that kicks in if mysql connections, etc dont work.
Eddie
moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources RESOURCE.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources/RESOURCE.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources/RESOURCE.java 2005/04/07 16:42:29 1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources/RESOURCE.java 2005/04/28 18:39:40 1.2
@@ -1,8 +1,11 @@
package org.biomoby.client.ui.graphical.servlet.jresources;
+import java.io.BufferedReader;
import java.io.IOException;
+import java.io.InputStreamReader;
import java.io.PrintWriter;
import java.io.StringWriter;
+import java.net.URL;
import java.util.Map;
import java.util.Properties;
import java.util.regex.Matcher;
@@ -156,7 +159,9 @@
private static boolean RUN_MAIN = false;
- /* (non-Javadoc)
+ /*
+ * (non-Javadoc)
+ *
* @see javax.servlet.GenericServlet#init()
*/
public final void init() throws ServletException {
@@ -186,12 +191,14 @@
try {
model = getObjects(model);
} catch (MobyException e) {
- response.sendError(HttpServletResponse.SC_BAD_REQUEST, "Could not get Objects");
+ response.sendError(HttpServletResponse.SC_BAD_REQUEST,
+ "Could not get Objects");
e.printStackTrace();
return;
}
if (model == null) {
- response.sendError(HttpServletResponse.SC_BAD_REQUEST, "Cound not create model");
+ response.sendError(HttpServletResponse.SC_BAD_REQUEST,
+ "Cound not create model");
return;
}
response.setContentType("application/rdf+xml");
@@ -205,12 +212,14 @@
try {
model = getNamespaces(model);
} catch (MobyException e) {
- response.sendError(HttpServletResponse.SC_BAD_REQUEST, "Could not get Namespaces");
+ response.sendError(HttpServletResponse.SC_BAD_REQUEST,
+ "Could not get Namespaces");
e.printStackTrace();
return;
}
if (model == null) {
- response.sendError(HttpServletResponse.SC_BAD_REQUEST, "Cound not create model");
+ response.sendError(HttpServletResponse.SC_BAD_REQUEST,
+ "Cound not create model");
return;
}
response.setContentType("application/rdf+xml");
@@ -224,12 +233,14 @@
try {
model = getServices(model);
} catch (MobyException e) {
- response.sendError(HttpServletResponse.SC_BAD_REQUEST, "Could not get Services");
+ response.sendError(HttpServletResponse.SC_BAD_REQUEST,
+ "Could not get Services");
e.printStackTrace();
return;
}
if (model == null) {
- response.sendError(HttpServletResponse.SC_BAD_REQUEST, "Cound not create model");
+ response.sendError(HttpServletResponse.SC_BAD_REQUEST,
+ "Cound not create model");
return;
}
response.setContentType("application/rdf+xml");
@@ -243,12 +254,14 @@
try {
model = getServiceInstances(model);
} catch (Exception e) {
- response.sendError(HttpServletResponse.SC_BAD_REQUEST, "Could not get ServiceInstances");
+ response.sendError(HttpServletResponse.SC_BAD_REQUEST,
+ "Could not get ServiceInstances");
e.printStackTrace();
return;
}
if (model == null) {
- response.sendError(HttpServletResponse.SC_BAD_REQUEST, "Cound not create model");
+ response.sendError(HttpServletResponse.SC_BAD_REQUEST,
+ "Cound not create model");
return;
}
response.setContentType("application/rdf+xml");
@@ -262,12 +275,14 @@
try {
model = getAll(model);
} catch (Exception e) {
- response.sendError(HttpServletResponse.SC_BAD_REQUEST, "Could not get All");
+ response.sendError(HttpServletResponse.SC_BAD_REQUEST,
+ "Could not get All");
e.printStackTrace();
return;
}
if (model == null) {
- response.sendError(HttpServletResponse.SC_BAD_REQUEST, "Cound not create model");
+ response.sendError(HttpServletResponse.SC_BAD_REQUEST,
+ "Cound not create model");
return;
}
response.setContentType("application/rdf+xml");
@@ -279,7 +294,7 @@
return;
}
} else {
- //response.sendError(HttpServletResponse.SC_NOT_FOUND);
+ // response.sendError(HttpServletResponse.SC_NOT_FOUND);
out.println(RESOURCE.Four0FourError);
return;
}
@@ -291,7 +306,7 @@
*
* @param model
* @return
- * @throws MobyException
+ * @throws MobyException
*/
private final Model getAll(Model model) throws Exception {
model = getObjects(model);
@@ -326,7 +341,8 @@
e.printStackTrace();
}
if (central == null || services == null)
- throw new MobyException("Could not retrieve useful information from CentralDigestImpl().getServices(String)");
+ throw new MobyException(
+ "Could not retrieve useful information from CentralDigestImpl().getServices(String)");
for (int i = 0; i < services.length; i++) {
MobyData[] primaryInputs = services[i].getPrimaryInputs(); // consumes
MobyData[] secondaryInputs = services[i].getSecondaryInputs(); // consumes
@@ -413,7 +429,7 @@
}
}
if (innerBag != null && innerBag.size() > 0) {
- //TODO
+ // TODO
consumeBag.add(innerBag);
}
// iterate through items adding them to the bag
@@ -554,7 +570,7 @@
MobyNamespace mns = ns[k];
_li.addProperty(Predicates.namespace_type, model
.createResource(NS + mns.getName()));
- //.addProperty(RDF.type, RDFS.Class));
+ // .addProperty(RDF.type, RDFS.Class));
}
}
return _li;
@@ -565,7 +581,7 @@
*
* @param model
* @return
- * @throws MobyException
+ * @throws MobyException
*/
private final Model getServices(Model model) throws MobyException {
@@ -602,7 +618,7 @@
*
* @param model
* @return
- * @throws MobyException
+ * @throws MobyException
*/
private final Model getNamespaces(Model model) throws MobyException {
String str = getTypes("Namespaces");
@@ -632,7 +648,7 @@
* <b>PRE: </b> <p><b>POST: </b> <p>
*
* @param model
- * @throws MobyException
+ * @throws MobyException
*/
private final Model getObjects(Model model) throws MobyException {
String str = getTypes("Objects");
@@ -667,7 +683,7 @@
m = Pattern.compile(".*:isa$", Pattern.CASE_INSENSITIVE).matcher(
pred);
if (m.matches()) {
- //System.out.println("is " +pred);
+ // System.out.println("is " +pred);
_addSubClass(model, _subject, OBJ, obj);
}
m = Pattern.compile(".*:hasa$", Pattern.CASE_INSENSITIVE).matcher(
@@ -774,21 +790,61 @@
private final String getTypes(String type) throws MobyException {
if (type.equalsIgnoreCase("objects")) {
- return new JObjects().getObjects();
+ try {
+ return new JObjects().getObjects();
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ // resort to a secondary method for retrieval of JObjects
+ return getURL("http://mobycentral.cbr.nrc.ca:8090/types/Objects");
} else if (type.equalsIgnoreCase("services")) {
- return new JServices().getServices();
+ try {
+ return new JServices().getServices();
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ // resort to a secondary method for retrieval of JServices
+ return getURL("http://mobycentral.cbr.nrc.ca:8090/types/Services");
} else if (type.equalsIgnoreCase("namespaces")) {
- return new JNamespaces().getNamespaces();
+ try {
+ return new JNamespaces().getNamespaces();
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ // resort to a secondary method for retrieval of JNamespaces
+ return getURL("http://mobycentral.cbr.nrc.ca:8090/types/Namespaces");
}
return "";
}
+ /*
+ *
+ */
+ private String getURL(String url) {
+ StringBuffer sb = new StringBuffer();
+ try {
+ URL _url = new URL(url);
+ BufferedReader in = new BufferedReader(new InputStreamReader(_url
+ .openStream()));
+ String inputLine;
+ while ((inputLine = in.readLine()) != null)
+ sb.append(inputLine+"\n");
+ in.close();
+ } catch (Exception e) {
+ e.printStackTrace();
+ System.err.println("Could not retrieve contents of URL.");
+ }
+ return sb.toString();
+ }
+
protected final void doPost(HttpServletRequest request,
HttpServletResponse response) throws ServletException, IOException {
response.sendError(HttpServletResponse.SC_METHOD_NOT_ALLOWED);
}
- /* (non-Javadoc)
+ /*
+ * (non-Javadoc)
+ *
* @see javax.servlet.GenericServlet#getServletInfo()
*/
public final String getServletInfo() {
@@ -863,8 +919,9 @@
}
return "";
}
+
public static void main(String[] args) throws MobyException {
- System.out.println(new RESOURCE().getRESOURCES("ServiceInstances"));
+ System.out.println(new RESOURCE().getRESOURCES("Objects"));
}
}
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