Changeset 1306:96b1f04ce4d2 in orange-bioinformatics

Timestamp:

01/10/11 17:56:46 (2 years ago)

Author:

ales_erjavec <ales.erjavec@…>

Branch:

default

Convert:

de2bcb362c9847f78c92e2df032c207df4d4e4bc

Message:

 

Files:

• obiBioMart.py (modified) (9 diffs)
• widgets/OWBioMart.py (modified) (8 diffs)

obiBioMart.py

@@ -31 +31 @@
 import itertools
 
+import warnings
+
 import orngEnviron
 
@@ -180 +182 @@
                 raise StopIteration
             except Exception, ex:
-                print >> sys.stderr, "An error occured during iteration:\n"
-                traceback.print_exc(file=sys.stderr)
+                warnings.warn("An error occured during iteration:\n%s" % str(ex), UserWarning, stacklevel=2)
+#                print >> sys.stderr, "An error occured during iteration:\n"
+#                traceback.print_exc(file=sys.stderr)
     return list(_iter(generator))
 
@@ -190 +193 @@
     DEFAULT_CACHE = shelve.open(os.path.join(orngEnviron.bufferDir, "BioMartCache.pck"))
 except Exception, ex:
-    import warnings
     warnings.warn("Could not open Bio Mart cache! %s" % str(ex))
     DEFAULT_CACHE = {}
@@ -200 +202 @@
     elif response.strip().startswith("Problem retrieving datasets"):
         raise BioMartError(response)
+    elif response.startswith("non-BioMart die():"):
+        raise BioMartServerError(response)
 
 
@@ -215 +219 @@
         self.address = address if address is not None else DEFAULT_ADDRESS
         self.cache = cache if cache is not None else DEFAULT_CACHE
+        self.errorCache = {}
         
     def request_url(self, **kwargs):
         url = self.address + "?" + "&".join("%s=%s" % item for item in kwargs.items() if item[0] != "POST")
+#        print url
         return url.replace(" ", "%20")
     
     def request(self, **kwargs):
         url = self.request_url(**kwargs)
+        if url in self.errorCache:
+            raise self.errorCache[url]
         if str(url) not in self.cache:
-            response = urllib2.urlopen(url).read()
-            checkBioMartServerError(response)
+            try:
+                response = urllib2.urlopen(url).read()
+                checkBioMartServerError(response)
+            except Exception, ex:
+                self.errorCache[url] = ex
+                raise ex
+            
             self.cache[str(url)] = response
             if hasattr(self.cache, "sync"):
@@ -476 +489 @@
         self.visible = visible
         self.__dict__.update(kwargs.items())
-        self.connection = BioMartConnection("http://" + self.host + ":" + self.port + self.path) if connection is None \
-                            or (kwargs.get("redirect", None) == "1" and BioMartConnection.FOLLOW_REDIRECTS) else connection
+        
+        if connection is None:
+            connection = BioMartConnection()
+            
+        if kwargs.get("redirect", None) == "1" and BioMartConnection.FOLLOW_REDIRECTS:
+            redirect = BioMartConnection("http://" + self.host + ":" + self.port + self.path, cache=connection.cache)
+            try:
+                registry = redirect.registry()
+                connection = redirect
+            except urllib2.HTTPError, ex:
+                warnings.warn("'%s' is not responding!, using the default original connection. %s" % (redirect.address, str(ex)))
+            
+        self.connection = connection
+        
+#        self.connection = BioMartConnection("http://" + self.host + ":" + self.port + self.path) if connection is None \
+#                            or (kwargs.get("redirect", None) == "1" and BioMartConnection.FOLLOW_REDIRECTS) else connection
 
     @cached    
@@ -487 +514 @@
         except BioMartError, ex:
             if self.virtualSchema == "default":
-                print >> sys.stderr, "error", ex
                 datasets = self.connection.datasets(mart=self.name).read()
             else:
@@ -840 +866 @@
         
         dataset = self.registry.dataset(pointerDataset)
+        
         conf = dataset.configuration()
         desc = list(conf.elements(getter, internalName=name))
@@ -845 +872 @@
             return dataset, desc[0]
         else:
-            import warnings
             warnings.warn("Could not resolve pointer '%s' in '%s'" % (name, pointerDataset), UserWarning, stacklevel=2)
             return None, None

widgets/OWBioMart.py

@@ -717 +717 @@
                      callback = self.clearCache)
         
+        
         self.martsCombo = OWGUI.comboBox(self.controlArea, self, "selectedDatabase", "Database",
                                          callback=self.setSelectedMart,
@@ -779 +780 @@
         self.connect(self.myThread, SIGNAL("finished()"), lambda :sys.stderr.write("Thread finished\n"))
         
+        self.error(0)
         self.setEnabled(False)
         self.get_registry_async = OWConcurrent.createTask(self._get_registry,
@@ -812 +814 @@
         assert(QThread.currentThread() is self.thread())
         if str(status).lower() != "ok":
-            print "AsyncCall failed with message:", status
+            print >> sys.stderr, "AsyncCall failed with message:", status
+            self.error(0, status)
         self.setEnabled(True)
             
@@ -826 +829 @@
     def setSelectedMart(self):
         self.mart = self.marts[self.selectedDatabase]
+        self.error(0)
         self.setEnabled(False)
         self.get_datasets_async = OWConcurrent.createTask(self.mart.datasets,
@@ -842 +846 @@
     def setSelectedDataset(self):
         self.dataset = self.datasets[self.selectedDataset]
-        self.setEnabled(False)
+        self.error(0)
         
         def get_configuration(dataset):
@@ -851 +855 @@
             response = stream.read()
             return response
+        
+        self.setEnabled(False)
         
         self.get_configuration_async = OWConcurrent.createTask(get_configuration, (self.dataset,),
@@ -981 +987 @@
                 query.add_filter(filter, value)
         
-        print query.xml_query()
+#        print query.xml_query()
+        self.error(0)
         self.setEnabled(False)
         self.run_query_async = OWConcurrent.createTask(query.get_example_table,
@@ -1035 +1042 @@
     def clearCache(self):
         obiBioMart.DEFAULT_CACHE.clear()
+        self.registry.connection.errorCache.clear()
     
 if __name__ == "__main__":