X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fext%2Fedu%2Fucsf%2Frbvi%2Fstrucviz2%2FChimeraManager.java;h=ea48cb6283aaf9868f93ac40d7a49530b5f81372;hb=4994aa94fd62af0058f2db96f0ea6c4ca1abe80b;hp=7cc72cff5d198e41f5d7f3358a69a3e0fd36c042;hpb=946d983b176eeda08ae0af13aff6cd1c9e017806;p=jalview.git diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java index 7cc72cf..ea48cb6 100644 --- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java +++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java @@ -1,13 +1,44 @@ +/* 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.nio.file.Paths; import java.util.ArrayList; import java.util.Collection; import java.util.HashMap; @@ -21,12 +52,17 @@ 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. */ public class ChimeraManager { + private static final int REST_REPLY_TIMEOUT_MS = 15000; + + private static final int CONNECTION_TIMEOUT_MS = 100; + private static final boolean debug = false; private int chimeraRestPort; @@ -47,7 +83,7 @@ public class ChimeraManager this.structureManager = structureManager; chimera = null; chimeraListenerThread = null; - currentModelsMap = new HashMap(); + currentModelsMap = new HashMap<>(); } @@ -62,7 +98,7 @@ 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()) @@ -76,7 +112,7 @@ public class ChimeraManager public Map> getChimeraModelsMap() { - Map> models = new HashMap>(); + Map> models = new HashMap<>(); for (ChimeraModel model : currentModelsMap.values()) { String modelName = model.getModelName(); @@ -178,6 +214,7 @@ public class ChimeraManager { logger.info("chimera open " + modelPath); // stopListening(); + List modelList = getModelList(); List response = null; // TODO: [Optional] Handle modbase models if (type == ModelType.MODBASE_MODEL) @@ -197,76 +234,29 @@ public class ChimeraManager logger.warn("Could not open " + modelPath); return null; } - List models = new ArrayList(); - int[] modelNumbers = null; - if (type == ModelType.PDB_MODEL) - { - for (String line : response) - { - if (line.startsWith("#")) - { - modelNumbers = ChimUtils.parseOpenedModelNumber(line); - if (modelNumbers != null) - { - int modelNumber = ChimUtils.makeModelKey(modelNumbers[0], - modelNumbers[1]); - if (currentModelsMap.containsKey(modelNumber)) - { - continue; - } - ChimeraModel newModel = new ChimeraModel(modelName, type, - modelNumbers[0], modelNumbers[1]); - currentModelsMap.put(modelNumber, newModel); - models.add(newModel); - - // - // patch for Jalview - set model name in Chimera - // TODO: find a variant that works for sub-models - sendChimeraCommand("setattr M name " + modelName + " #" - + modelNumbers[0], false); - // end patch for Jalview - - modelNumbers = null; - } - } - } - } - else + + // patch for Jalview - set model name in Chimera + // TODO: find a variant that works for sub-models + for (ChimeraModel newModel : getModelList()) { - // TODO: [Optional] Open smiles from file would fail. Do we need it? - // If parsing fails, iterate over all open models to get the right one - List openModels = getModelList(); - for (ChimeraModel openModel : openModels) + if (!modelList.contains(newModel)) { - String openModelName = openModel.getModelName(); - if (openModelName.endsWith("...")) - { - openModelName = openModelName.substring(0, - openModelName.length() - 3); - } - if (modelPath.startsWith(openModelName)) - { - openModel.setModelName(modelPath); - int modelNumber = ChimUtils - .makeModelKey(openModel.getModelNumber(), - openModel.getSubModelNumber()); - if (!currentModelsMap.containsKey(modelNumber)) - { - currentModelsMap.put(modelNumber, openModel); - models.add(openModel); - } - } + newModel.setModelName(modelName); + sendChimeraCommand( + "setattr M name " + modelName + " #" + + newModel.getModelNumber(), false); + modelList.add(newModel); } } // assign color and residues to open models - for (ChimeraModel newModel : models) + for (ChimeraModel chimeraModel : modelList) { // get model color - Color modelColor = getModelColor(newModel); + Color modelColor = isChimeraX() ? null : getModelColor(chimeraModel); if (modelColor != null) { - newModel.setModelColor(modelColor); + chimeraModel.setModelColor(modelColor); } // Get our properties (default color scheme, etc.) @@ -274,15 +264,15 @@ 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(newModel); + addResidues(chimeraModel); } } sendChimeraCommand("focus", false); // startListening(); // see ChimeraListener - return models; + return modelList; } /** @@ -302,13 +292,12 @@ public class ChimeraManager // TODO: [Optional] Convert path to name in a better way if (modelPath.lastIndexOf(File.separator) > 0) { - modelName = modelPath.substring(modelPath - .lastIndexOf(File.separator) + 1); + modelName = modelPath + .substring(modelPath.lastIndexOf(File.separator) + 1); } else if (modelPath.lastIndexOf("/") > 0) { - modelName = modelPath - .substring(modelPath.lastIndexOf("/") + 1); + modelName = modelPath.substring(modelPath.lastIndexOf("/") + 1); } return modelName; } @@ -344,7 +333,8 @@ public class ChimeraManager public void stopListening() { - sendChimeraCommand("listen stop models ; listen stop selection ", false); + String command = "listen stop models ; listen stop selection "; + sendChimeraCommand(command, false); } /** @@ -354,8 +344,17 @@ 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); } /** @@ -379,7 +378,7 @@ public class ChimeraManager { chimera = null; currentModelsMap.clear(); - this.chimeraRestPort = 0; + this.chimeraRestPort = 0; structureManager.clearOnChimeraExit(); } @@ -390,6 +389,8 @@ 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) { @@ -401,7 +402,7 @@ 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) @@ -426,15 +427,24 @@ 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]); } @@ -474,15 +484,22 @@ 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; @@ -497,7 +514,7 @@ public class ChimeraManager */ public List getPresets() { - ArrayList presetList = new ArrayList(); + ArrayList presetList = new ArrayList<>(); List output = sendChimeraCommand("preset list", true); if (output != null) { @@ -553,22 +570,23 @@ 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 = ""; @@ -576,7 +594,7 @@ public class ChimeraManager break; } catch (Exception e) { - // Chimera could not be started + // Chimera could not be started using this path error += e.getMessage(); } } @@ -600,6 +618,18 @@ 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() @@ -616,22 +646,29 @@ 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()); + + ": " + e.getMessage()); } finally { try @@ -703,8 +740,9 @@ 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) @@ -722,7 +760,7 @@ 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) @@ -776,7 +814,7 @@ public class ChimeraManager */ public List sendChimeraCommand(String command, boolean reply) { -// System.out.println("chimeradebug>> " + command); + System.out.println("chimeradebug>> " + command); if (!isChimeraLaunched() || command == null || "".equals(command.trim())) { @@ -822,21 +860,32 @@ 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)) + { + command = command.replace(" ", "+").replace("#", "%23") + .replace("|", "%7C").replace(";", "%3B"); + } commands.add(new BasicNameValuePair("command", command)); - List reply = new ArrayList(); + List reply = new ArrayList<>(); BufferedReader response = null; - try { - response = HttpClientUtils - .doHttpUrlPost(restUrl, commands, 100, 5000); + try + { + 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) { + while ((line = response.readLine()) != null) + { reply.add(line); } } catch (Exception e) { - logger.error("REST call " + command + " failed: " + e.getMessage()); + logger.error("REST call '" + command + "' failed: " + e.getMessage()); } finally { if (response != null) @@ -853,6 +902,15 @@ 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. * @@ -895,4 +953,14 @@ public class ChimeraManager { return busy; } + + public Process getChimeraProcess() + { + return chimera; + } + + public boolean isChimeraX() + { + return false; + } }