X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fext%2Fedu%2Fucsf%2Frbvi%2Fstrucviz2%2FChimeraManager.java;h=668039bb55da8d604f53f7225218657b0c563984;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=fdcf34f69169c33205209e742eaca60f115164fb;hpb=e39a32e4af4800fd0a72bf810dc13b5e2514c409;p=jalview.git diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java index fdcf34f..668039b 100644 --- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java +++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java @@ -1,13 +1,47 @@ +/* vim: set ts=2: */ +/** + * Copyright (c) 2006 The Regents of the University of California. + * All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions + * are met: + * 1. Redistributions of source code must retain the above copyright + * notice, this list of conditions, and the following disclaimer. + * 2. Redistributions in binary form must reproduce the above + * copyright notice, this list of conditions, and the following + * disclaimer in the documentation and/or other materials provided + * with the distribution. + * 3. Redistributions must acknowledge that this software was + * originally developed by the UCSF Computer Graphics Laboratory + * under support by the NIH National Center for Research Resources, + * grant P41-RR01081. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY + * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR + * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE + * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR + * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT + * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR + * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, + * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE + * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, + * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + */ 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.io.UnsupportedEncodingException; +import java.net.URLEncoder; +import java.nio.charset.StandardCharsets; +import java.nio.file.Paths; import java.util.ArrayList; import java.util.Collection; import java.util.HashMap; @@ -21,6 +55,7 @@ import org.slf4j.LoggerFactory; import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType; import ext.edu.ucsf.rbvi.strucviz2.port.ListenerThreads; +import jalview.ws.HttpClientUtils; /** * This object maintains the Chimera communication information. @@ -51,7 +86,7 @@ public class ChimeraManager this.structureManager = structureManager; chimera = null; chimeraListenerThread = null; - currentModelsMap = new HashMap(); + currentModelsMap = new HashMap<>(); } @@ -66,7 +101,7 @@ public class ChimeraManager public List getChimeraModels(String modelName, ModelType modelType) { - List models = new ArrayList(); + List models = new ArrayList<>(); for (ChimeraModel model : currentModelsMap.values()) { if (modelName.equals(model.getModelName()) @@ -80,7 +115,7 @@ public class ChimeraManager public Map> getChimeraModelsMap() { - Map> models = new HashMap>(); + Map> models = new HashMap<>(); for (ChimeraModel model : currentModelsMap.values()) { String modelName = model.getModelName(); @@ -142,10 +177,11 @@ public class ChimeraManager return hasChimeraModel(modelNubmer, 0); } - public boolean hasChimeraModel(Integer modelNubmer, Integer subModelNumber) + public boolean hasChimeraModel(Integer modelNubmer, + Integer subModelNumber) { - return currentModelsMap.containsKey(ChimUtils.makeModelKey(modelNubmer, - subModelNumber)); + return currentModelsMap.containsKey( + ChimUtils.makeModelKey(modelNubmer, subModelNumber)); } public void addChimeraModel(Integer modelNumber, Integer subModelNumber, @@ -155,7 +191,8 @@ public class ChimeraManager ChimUtils.makeModelKey(modelNumber, subModelNumber), model); } - public void removeChimeraModel(Integer modelNumber, Integer subModelNumber) + public void removeChimeraModel(Integer modelNumber, + Integer subModelNumber) { int modelKey = ChimUtils.makeModelKey(modelNumber, subModelNumber); if (currentModelsMap.containsKey(modelKey)) @@ -210,9 +247,8 @@ public class ChimeraManager if (!modelList.contains(newModel)) { newModel.setModelName(modelName); - sendChimeraCommand( - "setattr M name " + modelName + " #" - + newModel.getModelNumber(), false); + sendChimeraCommand("setattr M name " + modelName + " #" + + newModel.getModelNumber(), false); modelList.add(newModel); } } @@ -221,7 +257,7 @@ public class ChimeraManager for (ChimeraModel chimeraModel : modelList) { // get model color - Color modelColor = getModelColor(chimeraModel); + Color modelColor = isChimeraX() ? null : getModelColor(chimeraModel); if (modelColor != null) { chimeraModel.setModelColor(modelColor); @@ -232,7 +268,7 @@ public class ChimeraManager // chimeraSend("repr stick "+newModel.toSpec()); // Create the information we need for the navigator - if (type != ModelType.SMILES) + if (type != ModelType.SMILES && !isChimeraX()) { addResidues(chimeraModel); } @@ -282,8 +318,8 @@ public class ChimeraManager { sendChimeraCommand("close " + model.toSpec(), false); // currentModelNamesMap.remove(model.getModelName()); - currentModelsMap.remove(ChimUtils.makeModelKey( - model.getModelNumber(), model.getSubModelNumber())); + currentModelsMap.remove(ChimUtils.makeModelKey(model.getModelNumber(), + model.getSubModelNumber())); // selectionList.remove(chimeraModel); } else @@ -296,12 +332,14 @@ public class ChimeraManager public void startListening() { - sendChimeraCommand("listen start models; listen start selection", false); + sendChimeraCommand("listen start models; listen start selection", + false); } public void stopListening() { - sendChimeraCommand("listen stop models ; listen stop selection ", false); + String command = "listen stop models ; listen stop selection "; + sendChimeraCommand(command, false); } /** @@ -311,9 +349,17 @@ public class ChimeraManager */ public void startListening(String uri) { - sendChimeraCommand("listen start models url " + uri - + ";listen start select prefix SelectionChanged url " + uri, - false); + /* + * listen for model changes + */ + String command = "listen start models url " + uri; + sendChimeraCommand(command, false); + + /* + * listen for selection changes + */ + command = "listen start select prefix SelectionChanged url " + uri; + sendChimeraCommand(command, false); } /** @@ -348,6 +394,8 @@ public class ChimeraManager sendChimeraCommand("stop really", false); try { + // TODO is this too violent? could it force close the process + // before it has done an orderly shutdown? chimera.destroy(); } catch (Exception ex) { @@ -359,7 +407,7 @@ public class ChimeraManager public Map getSelectedModels() { - Map selectedModelsMap = new HashMap(); + Map selectedModelsMap = new HashMap<>(); List chimeraReply = sendChimeraCommand( "list selection level molecule", true); if (chimeraReply != null) @@ -384,15 +432,24 @@ public class ChimeraManager */ public List getSelectedResidueSpecs() { - List selectedResidues = new ArrayList(); - List chimeraReply = sendChimeraCommand( - "list selection level residue", true); + List selectedResidues = new ArrayList<>(); + + String command = "list selection level residue"; + List chimeraReply = sendChimeraCommand(command, true); if (chimeraReply != null) { + /* + * expect 0, 1 or more lines of the format either + * Chimera: + * residue id #0:43.A type GLY + * ChimeraX: + * residue id /A:89 name THR index 88 + * We are only interested in the atomspec (third token of the reply) + */ for (String inputLine : chimeraReply) { String[] inputLineParts = inputLine.split("\\s+"); - if (inputLineParts.length == 5) + if (inputLineParts.length >= 5) { selectedResidues.add(inputLineParts[2]); } @@ -432,15 +489,22 @@ public class ChimeraManager // TODO: [Optional] Handle smiles names in a better way in Chimera? public List getModelList() { - List modelList = new ArrayList(); - List list = sendChimeraCommand("list models type molecule", - true); + List modelList = new ArrayList<>(); + String command = "list models type " + + (isChimeraX() ? "AtomicStructure" : "molecule"); + List list = sendChimeraCommand(command, true); if (list != null) { for (String modelLine : list) { - ChimeraModel chimeraModel = new ChimeraModel(modelLine); - modelList.add(chimeraModel); + try + { + ChimeraModel chimeraModel = new ChimeraModel(modelLine); + modelList.add(chimeraModel); + } catch (NullPointerException e) + { + // hack for now + } } } return modelList; @@ -455,7 +519,7 @@ public class ChimeraManager */ public List getPresets() { - ArrayList presetList = new ArrayList(); + ArrayList presetList = new ArrayList<>(); List output = sendChimeraCommand("preset list", true); if (output != null) { @@ -511,22 +575,23 @@ public class ChimeraManager // iterate over possible paths for starting Chimera for (String chimeraPath : chimeraPaths) { - File path = new File(chimeraPath); - // uncomment the next line to simulate Chimera not installed - // path = new File(chimeraPath + "x"); - if (!path.canExecute()) - { - error += "File '" + path + "' does not exist.\n"; - continue; - } try { - List args = new ArrayList(); + // ensure symbolic links are resolved + chimeraPath = Paths.get(chimeraPath).toRealPath().toString(); + File path = new File(chimeraPath); + // uncomment the next line to simulate Chimera not installed + // path = new File(chimeraPath + "x"); + if (!path.canExecute()) + { + error += "File '" + path + "' does not exist.\n"; + continue; + } + List args = new ArrayList<>(); args.add(chimeraPath); // shows Chimera output window but suppresses REST responses: // args.add("--debug"); - args.add("--start"); - args.add("RESTServer"); + addLaunchArguments(args); ProcessBuilder pb = new ProcessBuilder(args); chimera = pb.start(); error = ""; @@ -534,7 +599,7 @@ public class ChimeraManager break; } catch (Exception e) { - // Chimera could not be started + // Chimera could not be started using this path error += e.getMessage(); } } @@ -542,8 +607,8 @@ public class ChimeraManager if (error.length() == 0) { this.chimeraRestPort = getPortNumber(); - System.out.println("Chimera REST API started on port " - + chimeraRestPort); + System.out.println( + "Chimera REST API started on port " + chimeraRestPort); // structureManager.initChimTable(); structureManager.setChimeraPathProperty(workingPath); // TODO: [Optional] Check Chimera version and show a warning if below 1.8 @@ -558,14 +623,27 @@ public class ChimeraManager } /** + * Adds command-line arguments to start the REST server + *

+ * Method extracted for Jalview to allow override in ChimeraXManager + * + * @param args + */ + protected void addLaunchArguments(List args) + { + args.add("--start"); + args.add("RESTServer"); + } + + /** * 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)); + BufferedReader lineReader = new BufferedReader( + new InputStreamReader(readChan)); StringBuilder responses = new StringBuilder(); try { @@ -574,21 +652,29 @@ public class ChimeraManager { responses.append("\n" + response); // expect: REST server on host 127.0.0.1 port port_number + // ChimeraX is the same except "REST server started on host..." if (response.startsWith("REST server")) { String[] tokens = response.split(" "); - if (tokens.length == 7 && "port".equals(tokens[5])) + for (int i = 0; i < tokens.length - 1; i++) { - port = Integer.parseInt(tokens[6]); - break; + if ("port".equals(tokens[i])) + { + port = Integer.parseInt(tokens[i + 1]); + break; + } } } + if (port > 0) + { + break; // hack for hanging readLine() + } response = lineReader.readLine(); } } catch (Exception e) { - logger.error("Failed to get REST port number from " + responses - + ": " + e.getMessage()); + logger.error("Failed to get REST port number from " + responses + ": " + + e.getMessage()); } finally { try @@ -600,11 +686,12 @@ public class ChimeraManager } if (port == 0) { - System.err - .println("Failed to start Chimera with REST service, response was: " + System.err.println( + "Failed to start Chimera with REST service, response was: " + responses); } - logger.info("Chimera REST service listening on port " + chimeraRestPort); + logger.info( + "Chimera REST service listening on port " + chimeraRestPort); return port; } @@ -660,8 +747,9 @@ public class ChimeraManager public List getAttrList() { - List attributes = new ArrayList(); - final List reply = sendChimeraCommand("list resattr", true); + List attributes = new ArrayList<>(); + String command = (isChimeraX() ? "info " : "list ") + "resattr"; + final List reply = sendChimeraCommand(command, true); if (reply != null) { for (String inputLine : reply) @@ -679,7 +767,7 @@ public class ChimeraManager public Map getAttrValues(String aCommand, ChimeraModel model) { - Map values = new HashMap(); + Map values = new HashMap<>(); final List reply = sendChimeraCommand("list residue spec " + model.toSpec() + " attribute " + aCommand, true); if (reply != null) @@ -689,8 +777,8 @@ public class ChimeraManager String[] lineParts = inputLine.split("\\s"); if (lineParts.length == 5) { - ChimeraResidue residue = ChimUtils - .getResidue(lineParts[2], model); + ChimeraResidue residue = ChimUtils.getResidue(lineParts[2], + model); String value = lineParts[4]; if (residue != null) { @@ -733,18 +821,27 @@ public class ChimeraManager */ public List sendChimeraCommand(String command, boolean reply) { - // System.out.println("chimeradebug>> " + command); + if (debug) + { + System.out.println("chimeradebug>> " + command); + } if (!isChimeraLaunched() || command == null || "".equals(command.trim())) { return null; } - // TODO do we need a maximum wait time before aborting? - while (busy) + /* + * set a maximum wait time before trying anyway + * to avoid hanging indefinitely + */ + int waited = 0; + int pause = 25; + while (busy && waited < 1001) { try { - Thread.sleep(25); + Thread.sleep(pause); + waited += pause; } catch (InterruptedException q) { } @@ -766,7 +863,6 @@ public class ChimeraManager + (System.currentTimeMillis() - startTime) + "ms: " + command); } - } } @@ -779,15 +875,31 @@ public class ChimeraManager protected List sendRestCommand(String command) { String restUrl = "http://127.0.0.1:" + this.chimeraRestPort + "/run"; - List commands = new ArrayList(1); + List commands = new ArrayList<>(1); + String method = getHttpRequestMethod(); + if ("GET".equals(method)) + { + try + { + command = URLEncoder.encode(command, StandardCharsets.UTF_8.name()); + } catch (UnsupportedEncodingException e) + { + command = command.replace(" ", "+").replace("#", "%23") + .replace("|", "%7C").replace(";", "%3B") + .replace(":", "%3A"); + } + } commands.add(new BasicNameValuePair("command", command)); - List reply = new ArrayList(); + List reply = new ArrayList<>(); BufferedReader response = null; try { - response = HttpClientUtils.doHttpUrlPost(restUrl, commands, CONNECTION_TIMEOUT_MS, - REST_REPLY_TIMEOUT_MS); + response = "GET".equals(method) + ? HttpClientUtils.doHttpGet(restUrl, commands, + CONNECTION_TIMEOUT_MS, REST_REPLY_TIMEOUT_MS) + : HttpClientUtils.doHttpUrlPost(restUrl, commands, + CONNECTION_TIMEOUT_MS, REST_REPLY_TIMEOUT_MS); String line = ""; while ((line = response.readLine()) != null) { @@ -812,6 +924,17 @@ public class ChimeraManager } /** + * Returns "POST" as the HTTP request method to use for REST service calls to + * Chimera + * + * @return + */ + protected String getHttpRequestMethod() + { + return "POST"; + } + + /** * Send a command to stdin of Chimera process, and optionally read any * responses. * @@ -854,4 +977,14 @@ public class ChimeraManager { return busy; } + + public Process getChimeraProcess() + { + return chimera; + } + + public boolean isChimeraX() + { + return false; + } }