Removing support for Python 2. Fix for retrieving job results.

tmtabor · tmtabor · commit 8296a0a412e0 · 2017-12-05T13:23:06.000-05:00
diff --git a/README.md b/README.md
@@ -4,23 +4,25 @@
 
 # GenePattern Python Library
 
-This is a Python library for working with GenePattern programmatically. Calls from this library execute the GenePattern REST API.
+This is a Python library for working with GenePattern programmatically. Behind the scenes, calls from this library execute the GenePattern REST API.
 
-## Supported Versions
+## Supported Python Versions
 
-This library supports Python 2.7 and Python 3.4+. The bundled data submodule `gp.data` requires [pandas](http://pandas.pydata.org/) and Python 3, although the rest of the module does not.
+This library requires Python 3.4+. The bundled data submodule `gp.data` also requires [pandas](http://pandas.pydata.org/), although the rest of the module does not.
+
+**Python 2 Support:** Support for Python 2 was removed in version 1.4.0. Python 2 users should use version 1.3.1.
 
 ## Installing
 
 It is recommended to install this library from PIP. Simply execute the command below:
 
-> sudo pip install genepattern-python
+> pip install genepattern-python
 
 ## Upgrading
 
 To upgrade to the latest version of the library, execute the command below:
 
-> sudo pip install genepattern-python --upgrade
+> pip install genepattern-python --upgrade
 
 ## Tutorial
 
diff --git a/gp/__init__.py b/gp/__init__.py
@@ -1,12 +1,12 @@
 __authors__ = ['Thorin Tabor', 'Chet Birger']
 __copyright__ = 'Copyright 2014-2017, Regents of the University of California & Broad Institute'
-__version__ = '1.3.2'
+__version__ = '1.4.0'
 __status__ = 'Production'
 
 """
 GenePattern Python Client
 
-Compatible with Python 2.7 and Python 3.4+
+Compatible with Python 3.4+
 """
 
 from .core import GPException, GPFile, GPJob, GPJobSpec, GPResource, GPServer, GPTask, GPTaskParam
diff --git a/gp/core.py b/gp/core.py
@@ -4,14 +4,8 @@
 import json
 import time
 from contextlib import closing
-
-# Imports requiring compatibility between Python 2 and Python 3
-if sys.version_info.major == 2:
-    import urllib2
-    import urllib as parse
-elif sys.version_info.major == 3:
-    from urllib import request as urllib2
-    import urllib.parse as parse
+import urllib.request
+import urllib.parse
 
 
 class GPServer(object):
@@ -26,28 +20,8 @@ def __init__(self, url, username, password):
         self.url = url
         self.username = username
         self.password = password
-        self.auth_header = None
         self.last_job = None
 
-        # Handle Basic Auth differences in Python 2 vs. Python 3
-        if sys.version_info.major == 2:
-            auth_string = base64.encodestring('%s:%s' % (self.username, self.password))[:-1]
-            self.auth_header = "Basic %s" % auth_string
-        elif sys.version_info.major == 3:
-            password_mgr = urllib2.HTTPPasswordMgrWithDefaultRealm()
-            password_mgr.add_password(None, url, username, password)
-            handler = urllib2.HTTPBasicAuthHandler(password_mgr)
-            opener = urllib2.build_opener(handler)
-            urllib2.install_opener(opener)
-
-            # auth_string = '%s:%s' % (self.username, self.password)
-            # if sys.version_info.major == 3:  # Required for Python 3
-            #     auth_string = bytes(auth_string, 'ascii')
-            # auth_string = base64.encodestring(auth_string)[:-1]
-            # self.auth_header = "Basic %s" % auth_string
-        else:
-            raise GPException('Version of Python not supported')
-
     def __str__(self):
         return self.url + ' ' + self.username + ' ' + self.password
 
@@ -57,7 +31,7 @@ def authorization_header(self):
         with GenePattern. This string is included in the header of subsequent
         requests sent to GenePattern.
         """
-        return self.auth_header
+        return 'Basic %s' % base64.b64encode(bytes(self.username + ':' + self.password, 'ascii')).decode('ascii')
 
     def upload_file(self, file_name, file_path):
         """
@@ -67,23 +41,21 @@ def upload_file(self, file_name, file_path):
         will be named filename.
 
         Args:
-            filename: The name that the uploaded file will be called on the server.
-            filepath: The path of the local file to upload.
-            server_data: GPServer object used to make the server call.
+            :param file_name: The name that the uploaded file will be called on the server.
+            :param file_path: The path of the local file to upload.
 
         Returns:
-            A GPFile object that wraps the URI of the uploaded file, or None if the
-            upload fails.
+            :return: A GPFile object that wraps the URI of the uploaded file, or None if the upload fails.
         """
 
-        request = urllib2.Request(self.url + '/rest/v1/data/upload/job_input?name=' + file_name)
+        request = urllib.request.Request(self.url + '/rest/v1/data/upload/job_input?name=' + file_name)
         if self.authorization_header() is not None:
             request.add_header('Authorization', self.authorization_header())
         request.add_header('User-Agent', 'GenePatternRest')
         data = open(file_path, 'rb').read()
 
         try:
-            response = urllib2.urlopen(request, data)
+            response = urllib.request.urlopen(request, data)
         except IOError:
             print("authentication failed")
             return None
@@ -103,11 +75,9 @@ def run_job(self, job_spec, wait_until_done=True):
         polling the server, but can also run asynchronously.
 
         Args:
-            jobspec: A GPJobSpec object that contains the data defining the job to be
-                run.
-            server_data: GPServer object used to make the server call.
-            waitUntilDone: Whether to wait until the job is finished before
-                returning.
+            :param job_spec: A GPJobSpec object that contains the data defining the job to be run.
+            :param wait_until_done: Whether to wait until the job is finished before returning.
+            :return:
 
         Returns:
             a GPJob object that refers to the running job on the server.  If called
@@ -120,12 +90,12 @@ def run_job(self, job_spec, wait_until_done=True):
         json_string = json.dumps({'lsid': job_spec.lsid, 'params': job_spec.params, 'tags': ['GenePattern Python Client']})
         if sys.version_info.major == 3:  # Handle conversion to bytes for Python 3
             json_string = bytes(json_string, 'utf-8')
-        request = urllib2.Request(self.url + '/rest/v1/jobs')
+        request = urllib.request.Request(self.url + '/rest/v1/jobs')
         if self.authorization_header() is not None:
             request.add_header('Authorization', self.authorization_header())
         request.add_header('Content-Type', 'application/json')
         request.add_header('User-Agent', 'GenePatternRest')
-        response = urllib2.urlopen(request, json_string)
+        response = urllib.request.urlopen(request, json_string)
         if response.getcode() != 201:
             print(" job POST failed, status code = %i" % response.getcode())
             return None
@@ -143,11 +113,11 @@ def get_task_list(self):
         each representing one of the modules installed on the server. Useful
         for determining which are available on the server.
         """
-        request = urllib2.Request(self.url + '/rest/v1/tasks/all.json')
+        request = urllib.request.Request(self.url + '/rest/v1/tasks/all.json')
         if self.authorization_header() is not None:
             request.add_header('Authorization', self.authorization_header())
         request.add_header('User-Agent', 'GenePatternRest')
-        response = urllib2.urlopen(request)
+        response = urllib.request.urlopen(request)
         response_string = response.read().decode('utf-8')
         category_and_tasks = json.loads(response_string)
         raw_list = category_and_tasks['all_modules']
@@ -157,7 +127,8 @@ def get_task_list(self):
             task_list.append(task)
         return task_list
 
-    def wait_until_complete(self, job_list):
+    @staticmethod
+    def wait_until_complete(job_list):
         """
         Args: Accepts a list of GPJob objects
 
@@ -188,11 +159,13 @@ def get_recent_jobs(self, n_jobs=10):
         """
 
         # Query the server for the list of jobs
-        request = urllib2.Request(self.url + '/rest/v1/jobs/?pageSize=' + str(n_jobs) + '&userId=' + str(parse.quote(self.username)) + '&orderBy=-dateSubmitted')
+        request = urllib.request.Request(self.url + '/rest/v1/jobs/?pageSize=' +
+                                         str(n_jobs) + '&userId=' + str(urllib.parse.quote(self.username)) +
+                                         '&orderBy=-dateSubmitted')
         if self.authorization_header() is not None:
             request.add_header('Authorization', self.authorization_header())
         request.add_header('User-Agent', 'GenePatternRest')
-        response = urllib2.urlopen(request)
+        response = urllib.request.urlopen(request)
         response_string = response.read().decode('utf-8')
         response_json = json.loads(response_string)
 
@@ -207,6 +180,7 @@ def get_recent_jobs(self, n_jobs=10):
 
         return job_list
 
+
 class GPResource(object):
     """
     Base class for resources on a Gene Pattern server.
@@ -246,11 +220,11 @@ def open(self):
 
             * getcode() - return the HTTP status code of the response
         """
-        request = urllib2.Request(self.uri)
+        request = urllib.request.Request(self.uri)
         if self.server_data.authorization_header() is not None:
             request.add_header('Authorization', self.server_data.authorization_header())
         request.add_header('User-Agent', 'GenePatternRest')
-        return urllib2.urlopen(request)
+        return urllib.request.urlopen(request)
 
     def read(self):
         """
@@ -270,7 +244,7 @@ def get_name(self):
         """
         Returns the file name of the output file
         """
-        return parse.unquote(self.get_url().split('/')[-1])
+        return urllib.parse.unquote(self.get_url().split('/')[-1])
 
 
 class GPJob(GPResource):
@@ -314,11 +288,11 @@ def get_info(self):
             * URL of Output Files
             * Number of Output Files
         """
-        request = urllib2.Request(self.server_data.url + "/rest/v1/jobs/" + self.uri)
+        request = urllib.request.Request(self.server_data.url + "/rest/v1/jobs/" + self.uri)
         if self.server_data.authorization_header() is not None:
             request.add_header('Authorization', self.server_data.authorization_header())
         request.add_header('User-Agent', 'GenePatternRest')
-        response = urllib2.urlopen(request)
+        response = urllib.request.urlopen(request)
 
         self.json = response.read().decode('utf-8')
         self.info = json.loads(self.json)
@@ -574,18 +548,12 @@ def param_load(self):
         Queries the server for the parameter information and other metadata associated with
         this task
         """
-        # Differences between Python 2 and Python 3
-        escaped_uri = self.uri
-        if sys.version_info.major == 2:
-            escaped_uri = urllib.quote(self.uri)
-        elif sys.version_info.major == 3:
-            escaped_uri = urllib.parse.quote(self.uri)
-
-        request = urllib2.Request(self.server_data.url + '/rest/v1/tasks/' + escaped_uri)
+        escaped_uri = urllib.parse.quote(self.uri)
+        request = urllib.request.Request(self.server_data.url + '/rest/v1/tasks/' + escaped_uri)
         if self.server_data.authorization_header() is not None:
             request.add_header('Authorization', self.server_data.authorization_header())
         request.add_header('User-Agent', 'GenePatternRest')
-        response = urllib2.urlopen(request)
+        response = urllib.request.urlopen(request)
         self.json = response.read().decode('utf-8')
         self.dto = json.loads(self.json)
 
@@ -812,11 +780,11 @@ def get_choices(self):
             print(self.get_choice_status())
             print("choice status not initialized")
 
-            request = urllib2.Request(self.get_choice_href())
+            request = urllib.request.Request(self.get_choice_href())
             if self.task.server_data.authorization_header() is not None:
                 request.add_header('Authorization', self.task.server_data.authorization_header())
             request.add_header('User-Agent', 'GenePatternRest')
-            response = urllib2.urlopen(request)
+            response = urllib.request.urlopen(request)
             self.dto[self.name]['choiceInfo'] = json.loads(response.read().decode('utf-8'))
         return self.dto[self.name]['choiceInfo']['choices']
 
@@ -843,7 +811,8 @@ def get_alt_description(self):
         else:
             return None
 
-    def _is_string_true(self, test):
+    @staticmethod
+    def _is_string_true(test):
         """
         Determines whether a string value is "True" for the purposes of GenePattern's
         parameter parsing
@@ -861,4 +830,4 @@ def __init__(self, value):
         self.value = value
 
     def __str__(self):
-        return repr(self.value)
+        return repr(self.value)
diff --git a/gp/modules.py b/gp/modules.py
@@ -3,7 +3,7 @@
 
 Tools for converting Python scripts into GenePattern server modules
 
-Compatible with Python 2.7 and Python 3.4+
+Compatible with Python 3.4+
 """
 import getpass
 import json
@@ -21,7 +21,7 @@
 
 __authors__ = ['Thorin Tabor']
 __version__ = '0.2.0'
-__status__ = 'Beta'
+__status__ = 'Alpha'
 
 
 class StringEnum(str, Enum):
