package ext.edu.ucsf.rbvi.strucviz2;
+ import jalview.ws.HttpClientUtils;
+
import java.awt.Color;
+ import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
+ import java.io.InputStream;
+ import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
+ import org.apache.http.NameValuePair;
+ import org.apache.http.message.BasicNameValuePair;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
*/
public class ChimeraManager
{
- private static final boolean debug = true;
++ private static final boolean debug = false;
+
+ /*
+ * true: use REST API (recommended), false: use stdout/stdin (deprecated)
+ */
++ // TODO remove once definitely happy with using REST
+ private static final boolean USE_REST = true;
+
- // Port number for Chimera REST service
- private int restPort;
++ private int chimeraRestPort;
private Process chimera;
- private ListenerThreads chimeraListenerThreads;
+ private ListenerThreads chimeraListenerThread;
private Map<Integer, ChimeraModel> currentModelsMap;
{
this.structureManager = structureManager;
chimera = null;
- chimeraListenerThreads = null;
+ chimeraListenerThread = null;
currentModelsMap = new HashMap<Integer, ChimeraModel>();
}
{
chimera = null;
currentModelsMap.clear();
- chimeraListenerThreads = null;
- if (!USE_REST)
++ if (USE_REST)
++ {
++ this.chimeraRestPort = 0;
++ }
++ else
+ {
+ chimeraListenerThread.requestStop();
+ chimeraListenerThread = null;
+ }
structureManager.clearOnChimeraExit();
}
List<String> args = new ArrayList<String>();
args.add(chimeraPath);
args.add("--start");
- args.add("ReadStdin");
+ args.add(USE_REST ? "RESTServer" : "ReadStdin");
ProcessBuilder pb = new ProcessBuilder(args);
chimera = pb.start();
error = "";
workingPath = chimeraPath;
- logger.info("Strarting " + chimeraPath);
+ logger.info("Starting " + chimeraPath + " with "
+ + (USE_REST ? "REST API" : "stdin/stdout"));
break;
} catch (Exception e)
{
// If no error, then Chimera was launched successfully
if (error.length() == 0)
{
- // Initialize the listener threads
- chimeraListenerThreads = new ListenerThreads(chimera,
- structureManager);
- chimeraListenerThreads.start();
+ if (USE_REST)
+ {
- this.restPort = getPortNumber();
++ this.chimeraRestPort = getPortNumber();
++ System.out.println("Chimera REST API on port " + chimeraRestPort);
+ }
+ else
+ {
+ // Initialize the listener threads
+ chimeraListenerThread = new ListenerThreads(chimera,
+ structureManager);
+ chimeraListenerThread.start();
+ }
// structureManager.initChimTable();
structureManager.setChimeraPathProperty(workingPath);
// TODO: [Optional] Check Chimera version and show a warning if below 1.8
}
/**
+ * Read and return the port number returned in the reply to --start RESTServer
+ */
+ private int getPortNumber()
+ {
+ int port = 0;
+ InputStream readChan = chimera.getInputStream();
+ BufferedReader lineReader = new BufferedReader(new InputStreamReader(
+ readChan));
+ String response = null;
+ try
+ {
+ // expect: REST server on host 127.0.0.1 port port_number
+ response = lineReader.readLine();
+ String [] tokens = response.split(" ");
+ if (tokens.length == 7 && "port".equals(tokens[5])) {
+ port = Integer.parseInt(tokens[6]);
- logger.info("Chimera REST service listening on port " + restPort);
++ logger.info("Chimera REST service listening on port "
++ + chimeraRestPort);
+ }
+ } catch (Exception e)
+ {
+ logger.error("Failed to get REST port number from " + response + ": "
+ + e.getMessage());
+ } finally
+ {
+ try
+ {
+ lineReader.close();
+ } catch (IOException e2)
+ {
+ }
+ }
+ return port;
+ }
+
+ /**
* Determine the color that Chimera is using for this model.
*
* @param model
*/
public List<String> sendChimeraCommand(String command, boolean reply)
{
- if (!isChimeraLaunched())
+ if (!isChimeraLaunched() || command == null
+ || "".equals(command.trim()))
{
return null;
}
;
}
busy = true;
+ long startTime = System.currentTimeMillis();
try
{
- chimeraListenerThreads.clearResponse(command);
- String text = command.concat("\n");
- // System.out.println("send command to chimera: " + text);
- try
+ if (USE_REST)
{
- // send the command
- chimera.getOutputStream().write(text.getBytes());
- chimera.getOutputStream().flush();
- } catch (IOException e)
- {
- // logger.info("Unable to execute command: " + text);
- // logger.info("Exiting...");
- logger.warn("Unable to execute command: " + text);
- logger.warn("Exiting...");
- clearOnChimeraExit();
- // busy = false;
- return null;
+ return sendRestCommand(command);
}
- if (!reply)
+ else
{
- // busy = false;
- return null;
+ return sendStdinCommand(command, reply);
}
} finally
{
busy = false;
+ if (debug)
+ {
+ System.out.println("Chimera command took "
+ + (System.currentTimeMillis() - startTime) + "ms: "
+ + command);
+ }
+
+ }
+ }
+
+ /**
+ * Sends the command to Chimera's REST API, and returns any response lines.
+ *
+ * @param command
+ * @return
+ */
+ protected List<String> sendRestCommand(String command)
+ {
+ // TODO start a separate thread to do this so we don't block?
- String restUrl = "http://127.0.0.1:" + this.restPort + "/run";
++ String restUrl = "http://127.0.0.1:" + this.chimeraRestPort + "/run";
+ List<NameValuePair> commands = new ArrayList<NameValuePair>(1);
+ commands.add(new BasicNameValuePair("command", command));
+
+ List<String> reply = new ArrayList<String>();
+ BufferedReader response = null;
+ try {
+ response = HttpClientUtils.doHttpUrlPost(restUrl,
+ commands);
+ String line = "";
+ while ((line = response.readLine()) != null) {
+ reply.add(line);
+ }
+ } catch (Exception e)
+ {
+ logger.error("REST call " + command + " failed: " + e.getMessage());
+ } finally
+ {
+ if (response != null)
+ {
+ try
+ {
+ response.close();
+ } catch (IOException e)
+ {
+ }
+ }
+ }
+ return reply;
+ }
+
+ /**
+ * Send a command to stdin of Chimera process, and optionally read any
+ * responses.
+ *
+ * @param command
+ * @param readReply
+ * @return
+ */
+ protected List<String> sendStdinCommand(String command, boolean readReply)
+ {
+ chimeraListenerThread.clearResponse(command);
+ String text = command.concat("\n");
+ try
+ {
+ // send the command
+ chimera.getOutputStream().write(text.getBytes());
+ chimera.getOutputStream().flush();
+ } catch (IOException e)
+ {
+ // logger.info("Unable to execute command: " + text);
+ // logger.info("Exiting...");
+ logger.warn("Unable to execute command: " + text);
+ logger.warn("Exiting...");
+ clearOnChimeraExit();
+ return null;
+ }
+ if (!readReply)
+ {
+ return null;
}
+ List<String> rsp = chimeraListenerThread.getResponse(command);
+ return rsp;
}
public StructureManager getStructureManager()
git://source.jalview.org / jalview.git / commitdiff