Patch 1: Adds a dataframe feature for a query

intermine/decorators.py

@@ -1,19 +1,19 @@
-from functools import wraps
-from intermine.errors import ServiceError
-
-def requires_version(required):
-
-    error_fmt = "Service must be at version %s, but is at %s"
-
-    def decorator(f):
-
-        @wraps(f)
-        def wrapper(self, *args, **kwargs):
-            if self.version < required:
-                raise ServiceError(error_fmt % (required, self.version))
-            return f(self, *args, **kwargs)
-
-        return wrapper
-
-    return decorator
-
+from functools import wraps
+from intermine.errors import ServiceError
+
+
+def requires_version(required):
+
+    error_fmt = "Service must be at version %s, but is at %s"
+
+    def decorator(f):
+
+        @wraps(f)
+        def wrapper(self, *args, **kwargs):
+            if self.version < required:
+                raise ServiceError(error_fmt % (required, self.version))
+            return f(self, *args, **kwargs)
+
+        return wrapper
+
+    return decorator

intermine/errors.py

@@ -1,12 +1,15 @@
-from intermine.util import ReadableException
-
-class UnimplementedError(Exception):
-    pass
-
-class ServiceError(ReadableException):
-    """Errors in the creation and use of the Service object"""
-    pass
-
-class WebserviceError(IOError):
-    """Errors from interaction with the webservice"""
-    pass
+from intermine.util import ReadableException
+
+
+class UnimplementedError(Exception):
+    pass
+
+
+class ServiceError(ReadableException):
+    """Errors in the creation and use of the Service object"""
+    pass
+
+
+class WebserviceError(IOError):
+    """Errors from interaction with the webservice"""
+    pass

intermine/idresolution.py

@@ -1,91 +1,94 @@
-import weakref
-import time
-
-# Use core json for 2.6+, simplejson for <=2.5
-try:
-    import json
-except ImportError:
-    import simplejson as json
-
-def get_json(service, path, key):
-    text = service.opener.read(service.root + path)
-    data = json.loads(text)
-    if data['error'] is not None:
-        raise Exception(data['error'])
-    if key not in data:
-        raise Exception(key + " not returned from " + path)
-    return data[key]
-
-ONE_MINUTE = 60
-
-COMPLETED = set(["SUCCESS", "ERROR"])
-
-class Job(object):
-    """
-    A Representation of an Identifier Resolution Job
-    ================================================
-
-    Users can submit requests to resolve sets of IDs to
-    objects in the data-store. These jobs begin in a PENDING
-    state, and transition through RUNNING to either SUCCESS
-    or ERROR.
-
-    Upon completion, the results of the job may be fetched, and the
-    job may be deleted on the server.
-    """
-
-    INITIAL_DECAY = 1.25
-    INITIAL_BACKOFF = 0.05
-    MAX_BACKOFF = ONE_MINUTE
-
-    def __init__(self, service, uid):
-        self.service = weakref.proxy(service)
-        self.uid = uid
-        self.status = None
-        self.backoff = Job.INITIAL_BACKOFF
-        self.decay = Job.INITIAL_DECAY
-        self.max_backoff = Job.MAX_BACKOFF
-        if self.uid is None:
-            raise Exception("No uid found")
-
-    def poll(self):
-        """
-        Check to see if the job has been completed, updating the
-        status of the job in the process.
-
-        @return: Boolean Whether or not the job is complete.
-        """
-        if self.status not in COMPLETED:
-            backoff = self.backoff
-            self.backoff = min(self.max_backoff, backoff * self.decay)
-            time.sleep(backoff)
-            self.status = self.fetch_status()
-        return self.status in COMPLETED
-
-    def fetch_status(self):
-        """
-        Retrieve the results of this completed job from the server.
-
-        @rtype: dict
-        """
-        return get_json(self.service, "/ids/{0}/status".format(self.uid), "status")
-
-    def delete(self):
-        """
-        Delete the job from the server.
-
-        The job should not be used again once this method has been invoked.
-        """
-        path = "/ids/" + self.uid
-        response = self.service.opener.delete(self.service.root + path)
-        response_data = json.loads(response)
-        if response_data['error'] is not None:
-            raise Exception(response_data['error'])
-
-    def fetch_results(self):
-        """
-        Retrieve the current status of this job from the server.
-
-        @rtype String
-        """
-        return get_json(self.service, "/ids/{0}/result".format(self.uid), "results")
+import weakref
+import time
+
+# Use core json for 2.6+, simplejson for <=2.5
+try:
+    import json
+except ImportError:
+    import simplejson as json
+
+
+def get_json(service, path, key):
+    text = service.opener.read(service.root + path)
+    data = json.loads(text)
+    if data['error'] is not None:
+        raise Exception(data['error'])
+    if key not in data:
+        raise Exception(key + " not returned from " + path)
+    return data[key]
+
+
+ONE_MINUTE = 60
+
+COMPLETED = set(["SUCCESS", "ERROR"])
+
+
+class Job(object):
+    """
+    A Representation of an Identifier Resolution Job
+    ================================================
+
+    Users can submit requests to resolve sets of IDs to
+    objects in the data-store. These jobs begin in a PENDING
+    state, and transition through RUNNING to either SUCCESS
+    or ERROR.
+
+    Upon completion, the results of the job may be fetched, and the
+    job may be deleted on the server.
+    """
+
+    INITIAL_DECAY = 1.25
+    INITIAL_BACKOFF = 0.05
+    MAX_BACKOFF = ONE_MINUTE
+
+    def __init__(self, service, uid):
+        self.service = weakref.proxy(service)
+        self.uid = uid
+        self.status = None
+        self.backoff = Job.INITIAL_BACKOFF
+        self.decay = Job.INITIAL_DECAY
+        self.max_backoff = Job.MAX_BACKOFF
+        if self.uid is None:
+            raise Exception("No uid found")
+
+    def poll(self):
+        """
+        Check to see if the job has been completed, updating the
+        status of the job in the process.
+
+        @return: Boolean Whether or not the job is complete.
+        """
+        if self.status not in COMPLETED:
+            backoff = self.backoff
+            self.backoff = min(self.max_backoff, backoff * self.decay)
+            time.sleep(backoff)
+            self.status = self.fetch_status()
+        return self.status in COMPLETED
+
+    def fetch_status(self):
+        """
+        Retrieve the results of this completed job from the server.
+
+        @rtype: dict
+        """
+        return get_json(self.service, "/ids/{0}/status".format(self.uid), "status")
+
+    def delete(self):
+        """
+        Delete the job from the server.
+
+        The job should not be used again once this method has been invoked.
+        """
+        path = "/ids/" + self.uid
+        response = self.service.opener.delete(self.service.root + path)
+        response_data = json.loads(response)
+        if response_data['error'] is not None:
+            raise Exception(response_data['error'])
+
+    def fetch_results(self):
+        """
+        Retrieve the current status of this job from the server.
+
+        @rtype String
+        """
+        return get_json(self.service, "/ids/{0}/result".format(self.uid), "results")