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  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package jalview.ws.jws1

File Discoverer.java

 

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45% of files have more coverage

Code metrics

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Classes

Class Line # Actions
Discoverer 36 106 39 96
0.384615438.5%
 

Contributing tests

This file is covered by 92 tests. .

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1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
7    * Jalview is free software: you can redistribute it and/or
8    * modify it under the terms of the GNU General Public License
9    * as published by the Free Software Foundation, either version 3
10    * of the License, or (at your option) any later version.
11    *
12    * Jalview is distributed in the hope that it will be useful, but
13    * WITHOUT ANY WARRANTY; without even the implied warranty
14    * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15    * PURPOSE. See the GNU General Public License for more details.
16    *
17    * You should have received a copy of the GNU General Public License
18    * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19    * The Jalview Authors are detailed in the 'AUTHORS' file.
20    */
21    package jalview.ws.jws1;
22   
23    import jalview.gui.JvOptionPane;
24    import jalview.util.MessageManager;
25   
26    import java.util.Hashtable;
27    import java.util.StringTokenizer;
28    import java.util.Vector;
29   
30    import ext.vamsas.IRegistry;
31    import ext.vamsas.IRegistryServiceLocator;
32    import ext.vamsas.RegistryServiceSoapBindingStub;
33    import ext.vamsas.ServiceHandle;
34    import ext.vamsas.ServiceHandles;
35   
 
36    public class Discoverer implements Runnable
37    {
38    ext.vamsas.IRegistry registry; // the root registry service.
39   
40    private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
41    this);
42   
43    /**
44    * change listeners are notified of "services" property changes
45    *
46    * @param listener
47    * to be added that consumes new services Hashtable object.
48    */
 
49  1 toggle public void addPropertyChangeListener(
50    java.beans.PropertyChangeListener listener)
51    {
52  1 changeSupport.addPropertyChangeListener(listener);
53    }
54   
55    /**
56    *
57    *
58    * @param listener
59    * to be removed
60    */
 
61  0 toggle public void removePropertyChangeListener(
62    java.beans.PropertyChangeListener listener)
63    {
64  0 changeSupport.removePropertyChangeListener(listener);
65    }
66   
67    /**
68    * Property change listener firing routine
69    *
70    * @param prop
71    * services
72    * @param oldvalue
73    * old services hash
74    * @param newvalue
75    * new services hash
76    */
 
77  0 toggle public void firePropertyChange(String prop, Object oldvalue,
78    Object newvalue)
79    {
80  0 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
81    }
82   
83    /**
84    * Initializes the server field with a valid service implementation.
85    *
86    * @return true if service was located.
87    */
 
88  0 toggle private IRegistry locateWebService(java.net.URL WsURL)
89    {
90  0 IRegistryServiceLocator loc = new IRegistryServiceLocator(); // Default
91  0 IRegistry server = null;
92  0 try
93    {
94  0 server = loc.getRegistryService(WsURL);
95  0 ((RegistryServiceSoapBindingStub) server).setTimeout(60000); // One
96    // minute
97    // timeout
98    } catch (Exception ex)
99    {
100  0 jalview.bin.Cache.log.error(
101    "Serious! Service location failed\nfor URL :" + WsURL + "\n",
102    ex);
103   
104  0 return null;
105    }
106   
107  0 loc.getEngine().setOption("axis", "1");
108   
109  0 return server;
110    }
111   
112    static private java.net.URL RootServiceURL = null;
113   
114    static public Vector ServiceURLList = null;
115   
116    static private boolean reallyDiscoverServices = true;
117   
118    public static java.util.Hashtable services = null; // vectors of services
119   
120    // stored by
121    // abstractServiceType
122    // string
123   
124    public static java.util.Vector serviceList = null; // flat list of services
125   
 
126  0 toggle static private Vector getDiscoveryURLS()
127    {
128  0 Vector urls = new Vector();
129  0 String RootServiceURLs = jalview.bin.Cache.getDefault("DISCOVERY_URLS",
130    "http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry");
131   
132  0 try
133    {
134  0 StringTokenizer st = new StringTokenizer(RootServiceURLs, ",");
135  0 while (st.hasMoreElements())
136    {
137  0 String url = null;
138  0 try
139    {
140  0 java.net.URL u = new java.net.URL(url = st.nextToken());
141  0 if (!urls.contains(u))
142    {
143  0 urls.add(u);
144    }
145    else
146    {
147  0 jalview.bin.Cache.log
148    .info("Ignoring duplicate url in DISCOVERY_URLS list");
149    }
150    } catch (Exception ex)
151    {
152  0 jalview.bin.Cache.log
153    .warn("Problem whilst trying to make a URL from '"
154  0 + ((url != null) ? url : "<null>") + "'");
155  0 jalview.bin.Cache.log.warn(
156    "This was probably due to a malformed comma separated list"
157    + " in the DISCOVERY_URLS entry of $(HOME)/.jalview_properties)");
158  0 jalview.bin.Cache.log.debug("Exception was ", ex);
159    }
160    }
161    } catch (Exception ex)
162    {
163  0 jalview.bin.Cache.log.warn(
164    "Error parsing comma separated list of urls in DISCOVERY_URLS.",
165    ex);
166    }
167  0 if (urls.size() > 0)
168    {
169  0 return urls;
170    }
171  0 return null;
172    }
173   
174    /**
175    * fetch new services or reset to hardwired defaults depending on preferences.
176    */
 
177  11 toggle static public void doDiscovery()
178    {
179  11 jalview.bin.Cache.log
180    .debug("(Re)-Initialising the discovery URL list.");
181  11 try
182    {
183  11 reallyDiscoverServices = jalview.bin.Cache
184    .getDefault("DISCOVERY_START", false);
185  11 if (reallyDiscoverServices)
186    {
187  0 ServiceURLList = getDiscoveryURLS();
188    }
189    else
190    {
191  11 jalview.bin.Cache.log.debug("Setting default services");
192  11 services = new Hashtable();
193    // Muscle, Clustal and JPred.
194  11 ServiceHandle[] defServices = { new ServiceHandle("MsaWS",
195    "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment "
196    + "with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.",
197    "http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS",
198    MessageManager.getString(
199    "label.muscle_multiple_protein_sequence_alignment")),
200    new ServiceHandle("MsaWS",
201    "Katoh, K., K. Kuma, K., Toh, H., and Miyata, T. (2005) "
202    + "\"MAFFT version 5: improvement in accuracy of multiple sequence alignment.\""
203    + " Nucleic Acids Research, 33 511-518",
204    "http://www.compbio.dundee.ac.uk/JalviewWS/services/MafftWS",
205    MessageManager.getString(
206    "label.mafft_multiple_sequence_alignment")),
207    new ServiceHandle("MsaWS",
208    "Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"
209    + " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."
210    + " Nucleic Acids Research, 22 4673-4680",
211    "http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS",
212    MessageManager.getString(
213    "label.clustalw_multiple_sequence_alignment")),
214    new ServiceHandle("SecStrPred",
215    "Drozdetskiy A, Cole C, Procter J & Barton GJ. (2015)\nJPred4: a protein secondary structure prediction server"
216    + "\nNucleic Acids Research, Web Server issue (first published 15th April 2015)"
217    + "\ndoi://10.1093/nar/gkv332",
218    "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred",
219    "JPred Secondary Structure Prediction") };
220  11 services = new Hashtable();
221  11 serviceList = new Vector();
222  11 buildServiceLists(defServices, serviceList, services);
223    }
224   
225    } catch (Exception e)
226    {
227  0 System.err.println(
228    "jalview.rootRegistry is not a proper url!\nWas set to "
229    + RootServiceURL + "\n" + e);
230    }
231   
232    }
233   
234    // TODO: JBPNote : make this discover more services based on list of
235    // discovery service urls, break cyclic references to the same url and
236    // duplicate service entries (same endpoint *and* same interface)
 
237  0 toggle private ServiceHandle[] getServices(java.net.URL location)
238    {
239  0 ServiceHandles shs = null;
240  0 try
241    {
242  0 jalview.bin.Cache.log.debug("Discovering services using " + location);
243  0 shs = locateWebService(location).getServices();
244    } catch (org.apache.axis.AxisFault f)
245    {
246    // JBPNote - should do this a better way!
247  0 if (f.getFaultReason().indexOf("(407)") > -1)
248    {
249  0 if (jalview.gui.Desktop.desktop != null)
250    {
251  0 JvOptionPane.showMessageDialog(jalview.gui.Desktop.desktop,
252    MessageManager.getString("label.set_proxy_settings"),
253    MessageManager
254    .getString("label.proxy_authorization_failed"),
255    JvOptionPane.WARNING_MESSAGE);
256    }
257    }
258    else
259    {
260  0 jalview.bin.Cache.log.warn("No Discovery service at " + location);
261  0 jalview.bin.Cache.log.debug("Axis Fault", f);
262    }
263    } catch (Exception e)
264    {
265  0 jalview.bin.Cache.log.warn("No Discovery service at " + location);
266  0 jalview.bin.Cache.log.debug("Discovery Service General Exception", e);
267    }
268  0 if ((shs != null) && shs.getServices().length > 0)
269    {
270  0 return shs.getServices();
271    }
272  0 return null;
273    }
274   
275    /**
276    * Adds a list of services to the service catalog and categorised catalog
277    * returns true if ServiceURLList was modified with a new DiscoveryService URL
278    *
279    * @param sh
280    * ServiceHandle[]
281    * @param cat
282    * Vector
283    * @param sscat
284    * Hashtable
285    * @return boolean
286    */
 
287  11 toggle static private boolean buildServiceLists(ServiceHandle[] sh, Vector cat,
288    Hashtable sscat)
289    {
290  11 boolean seenNewDiscovery = false;
291  55 for (int i = 0, j = sh.length; i < j; i++)
292    {
293  44 if (!cat.contains(sh[i]))
294    {
295  44 jalview.bin.Cache.log.debug("A " + sh[i].getAbstractName()
296    + " service called " + sh[i].getName() + " exists at "
297    + sh[i].getEndpointURL() + "\n");
298  44 if (!sscat.containsKey(sh[i].getAbstractName()))
299    {
300  22 sscat.put(sh[i].getAbstractName(), cat = new Vector());
301    }
302    else
303    {
304  22 cat = (Vector) sscat.get(sh[i].getAbstractName());
305    }
306  44 cat.add(sh[i]);
307  44 if (sh[i].getAbstractName().equals("Registry"))
308    {
309  0 for (int s = 0, sUrls = ServiceURLList.size(); s < sUrls; s++)
310    {
311  0 java.net.URL disc_serv = null;
312  0 try
313    {
314  0 disc_serv = new java.net.URL(sh[i].getEndpointURL());
315  0 if (!ServiceURLList.contains(disc_serv))
316    {
317  0 jalview.bin.Cache.log.debug(
318    "Adding new discovery service at " + disc_serv);
319  0 ServiceURLList.add(disc_serv);
320  0 seenNewDiscovery = true;
321    }
322    } catch (Exception e)
323    {
324  0 jalview.bin.Cache.log
325    .debug("Ignoring bad discovery service URL "
326    + sh[i].getEndpointURL(), e);
327    }
328    }
329    }
330    }
331    }
332  11 return seenNewDiscovery;
333    }
334   
 
335  11 toggle public void discoverServices()
336    {
337  11 Hashtable sscat = new Hashtable();
338  11 Vector cat = new Vector();
339  11 ServiceHandle sh[] = null;
340  11 int s_url = 0;
341  11 if (ServiceURLList == null)
342    {
343  11 jalview.bin.Cache.log
344    .debug("No service endpoints to use for service discovery.");
345  11 return;
346    }
347  0 while (s_url < ServiceURLList.size())
348    {
349  0 if ((sh = getServices(
350    (java.net.URL) ServiceURLList.get(s_url))) != null)
351    {
352   
353  0 buildServiceLists(sh, cat, sscat);
354    }
355    else
356    {
357  0 jalview.bin.Cache.log.warn("No services at "
358    + (ServiceURLList.get(s_url))
359    + " - check DISCOVERY_URLS property in .jalview_properties");
360    }
361  0 s_url++;
362    }
363    // TODO: decide on correct semantics for services list - PropertyChange
364    // provides a way of passing the new object around
365    // so no need to access original discovery thread.
366    // Curent decision is to change properties then notify listeners with old
367    // and new values.
368  0 Hashtable oldServices = services;
369    // Vector oldServicelist = serviceList;
370  0 services = sscat;
371  0 serviceList = cat;
372  0 changeSupport.firePropertyChange("services", oldServices, services);
373    }
374   
375    /**
376    * creates a new thread to call discoverServices()
377    */
 
378  11 toggle @Override
379    public void run()
380    {
381  11 final Discoverer discoverer = this;
382  11 Thread discoverThread = new Thread()
383    {
 
384  11 toggle @Override
385    public void run()
386    {
387  11 discoverer.doDiscovery();
388  11 discoverer.discoverServices();
389    }
390    };
391  11 discoverThread.start();
392    }
393   
394    /**
395    * binding service abstract name to handler class
396    */
397    private static Hashtable serviceClientBindings;
398   
 
399  1110 toggle public static WS1Client getServiceClient(ServiceHandle sh)
400    {
401  1110 if (serviceClientBindings == null)
402    {
403    // get a list from Config or create below
404  1 serviceClientBindings = new Hashtable();
405  1 serviceClientBindings.put("MsaWS", new MsaWSClient());
406  1 serviceClientBindings.put("SecStrPred", new JPredClient());
407  1 serviceClientBindings.put("SeqSearch", new SeqSearchWSClient());
408    }
409  1110 WS1Client instance = (WS1Client) serviceClientBindings
410    .get(sh.getAbstractName());
411  1110 if (instance == null)
412    {
413  0 System.err.println(
414    "WARNING - POSSIBLE IMPLEMENTATION ERROR - cannot find WSClient implementation for "
415    + sh.getAbstractName());
416    }
417    else
418    {
419  1110 instance.serviceHandle = sh;
420    }
421  1110 return instance;
422    }
423    /**
424    * notes on discovery service 1. need to allow multiple discovery source urls.
425    * 2. user interface to add/control list of urls in preferences notes on
426    * wsclient discovery 1. need a classpath property with list of additional
427    * plugin directories 2. optional config to cite specific bindings between
428    * class name and Abstract service name. 3. precedence for automatic discovery
429    * by using getAbstractName for WSClient - user added plugins override default
430    * plugins ? notes on wsclient gui code for gui attachment now moved to
431    * wsclient implementation. Needs more abstraction but approach seems to work.
432    * is it possible to 'generalise' the data retrieval calls further ? current
433    * methods are very specific (gatherForMSA or gatherForSeqOrMsaSecStrPred),
434    * new methods for conservation (group or alignment), treecalc (aligned
435    * profile), seqannot (sequences selected from dataset, annotation back to
436    * dataset).
437    *
438    */
439    }
  • Report generated by OpenClover v 4.2.1 on Wed Oct 31 2018 15:15:54 GMT using coverage data from Wed Oct 31 2018 15:15:47 GMT.
  • Clover free edition.