Merge 72130c8 into 7802d45

.travis.yml

@@ -7,21 +7,21 @@ python:
     - '3.5'
 
 install:
-    - sudo apt-get update
-
-    - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
-    - bash miniconda.sh -b -p $HOME/miniconda
-    - export PATH="$HOME/miniconda/bin:$PATH"
-    - hash -r
-    - conda config --set always_yes yes --set changeps1 no
-    - conda update -q conda
+    # - sudo apt-get update
+    - pip install -r requirements.txt
+    # - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+    # - bash miniconda.sh -b -p $HOME/miniconda
+    # - export PATH="$HOME/miniconda/bin:$PATH"
+    # - hash -r
+    # - conda config --set always_yes yes --set changeps1 no
+    # - conda update -q conda
 
     # Useful for debugging any issues with conda.
-    - conda info -a
+    # - conda info -a
 
     # Create conda environment.
-    - conda create -q -n test python=$TRAVIS_PYTHON_VERSION
-    - source activate test
+    # - conda create -q -n test python=$TRAVIS_PYTHON_VERSION
+    # - source activate test
 
     # Install with test dependencies.
     - pip install .[dev]

src/pybiomart/dataset.py

@@ -6,7 +6,6 @@
 from future.utils import native_str
 
 from io import StringIO
-from xml.etree import ElementTree
 
 import pandas as pd
 
@@ -15,6 +14,12 @@
 
 # pylint: enable=import-error
 
+# xml 
+try:
+    from xml.etree import cElementTree as ET
+except ImportError:
+    from xml.etree import ElementTree as ET
+
 class Dataset(ServerBase):
     """Class representing a biomart dataset.
 
@@ -148,7 +153,7 @@ def _fetch_configuration(self):
                                    'check the dataset name and schema.')
 
         # Get filters and attributes from xml.
-        xml = ElementTree.fromstring(response.content)
+        xml = ET.fromstring(response.content)
 
         filters = {f.name: f for f in self._filters_from_xml(xml)}
         attributes = {a.name: a for a in self._attributes_from_xml(xml)}
@@ -159,8 +164,19 @@ def _fetch_configuration(self):
     def _filters_from_xml(xml):
         for node in xml.iter('FilterDescription'):
             attrib = node.attrib
+            # remove the id_list and boolean_list type
+            if attrib.get('type', 'None') in ['id_list', 'boolean_list']:
+                continue
+            if attrib.get('type') is None:
+                yield Filter(name=attrib['pointerFilter'], type='text')
+                continue
             yield Filter(
-                name=attrib['internalName'], type=attrib.get('type', ''))
+                name=attrib['internalName'], type=attrib['type'])
+        # tag:Option with type
+        # python2.7 iter() takes no keyword arguments
+        for node in xml.iter('Option'):
+            if node.attrib.get('type'):
+                yield Filter(name=node.attrib['internalName'], type=node.attrib['type'])
 
     @staticmethod
     def _attributes_from_xml(xml):
@@ -224,15 +240,15 @@ def query(self,
         # </Query>
 
         # Setup query element.
-        root = ElementTree.Element('Query')
+        root = ET.Element('Query')
         root.set('virtualSchemaName', self._virtual_schema)
         root.set('formatter', 'TSV')
         root.set('header', '1')
         root.set('uniqueRows', native_str(int(only_unique)))
         root.set('datasetConfigVersion', '0.6')
 
         # Add dataset element.
-        dataset = ElementTree.SubElement(root, 'Dataset')
+        dataset = ET.SubElement(root, 'Dataset')
         dataset.set('name', self.name)
         dataset.set('interface', 'default')
 
@@ -262,7 +278,7 @@ def query(self,
                         'for a list of valid filters.'.format(name))
 
         # Fetch response.
-        response = self.get(query=ElementTree.tostring(root))
+        response = self.get(query=ET.tostring(root))
 
         # Raise exception if an error occurred.
         if 'Query ERROR' in response.text:
@@ -287,13 +303,13 @@ def query(self,
 
     @staticmethod
     def _add_attr_node(root, attr):
-        attr_el = ElementTree.SubElement(root, 'Attribute')
+        attr_el = ET.SubElement(root, 'Attribute')
         attr_el.set('name', attr.name)
 
     @staticmethod
     def _add_filter_node(root, filter_, value):
         """Adds filter xml node to root."""
-        filter_el = ElementTree.SubElement(root, 'Filter')
+        filter_el = ET.SubElement(root, 'Filter')
         filter_el.set('name', filter_.name)
 
         # Set filter value depending on type.