Version 1.0.1 with updates to VisitAtribute.

CHANGES

@@ -1,3 +1,11 @@
+cutlass 1.0.1
+
+  * Support for mother_child, and time_during_pregnancy properties
+    in VisitAttribute.
+  * Minor pylint issues correct with VisitAttribute class.
+
+ - Victor <[email protected]>  Fri, 26 Jan 2018 17:00:00 -0400
+
 cutlass 1.0.0
 
   * Added serology, host_epigenetics_raw_seq_set and host_variant_call nodes,

MANIFEST.in

@@ -1,27 +1,44 @@
 include cutlass/__init__.py
-include cutlass/iHMPSession.py
+include cutlass/AbundanceMatrix.py
+include cutlass/Annotation.py
 include cutlass/Base.py
 include cutlass/ClusteredSeqSet.py
-include cutlass/HostSeqSet.py
+include cutlass/Cytokine.py
+include cutlass/dependency.py
+include cutlass/DiseaseMeta.py
+include cutlass/HostAssayPrep.py
+include cutlass/HostEpigeneticsRawSeqSet.py
+include cutlass/HostSeqPrep.py
 include cutlass/HostTranscriptomicsRawSeqSet.py
+include cutlass/HostVariantCall.py
+include cutlass/HostWgsRawSeqSet.py
+include cutlass/iHMPSession.py
 include cutlass/Lipidome.py
 include cutlass/Metabolome.py
+include cutlass/MicrobiomeAssayPrep.py
 include cutlass/MicrobTranscriptomicsRawSeqSet.py
+include cutlass/mimarks.py
+include cutlass/mims.py
+include cutlass/mixs.py
 include cutlass/Project.py
-include cutlass/Study.py
-include cutlass/Subject.py
+include cutlass/Proteome.py
+include cutlass/ProteomeNonPride.py
 include cutlass/Sample.py
+include cutlass/SampleAttribute.py
+include cutlass/Serology.py
 include cutlass/SixteenSDnaPrep.py
 include cutlass/SixteenSRawSeqSet.py
 include cutlass/SixteenSTrimmedSeqSet.py
+include cutlass/Study.py
+include cutlass/Subject.py
+include cutlass/SubjectAttribute.py
+include cutlass/Util.py
+include cutlass/ViralSeqSet.py
 include cutlass/Visit.py
 include cutlass/VisitAttribute.py
-include cutlass/ViralSeqSet.py
+include cutlass/WgsAssembledSeqSet.py
 include cutlass/WgsDnaPrep.py
 include cutlass/WgsRawSeqSet.py
-include cutlass/mimarks.py
-include cutlass/mims.py
-include cutlass/mixs.py
 include cutlass/aspera/__init__.py
 include cutlass/aspera/aspera.py
 recursive-include tests *.py

cutlass/Util.py

@@ -8,6 +8,8 @@
 import sys
 import inspect
 
+# pylint: disable=C0123,C0111
+
 DATE_FORMAT = '%Y-%m-%d'
 PYTHON_MIN_VERSION = (2, 7, 0)
 PYTHON_MAX_VERSION = (3, 0, 0)

cutlass/VisitAttribute.py

@@ -8,7 +8,7 @@
 from cutlass.Base import Base
 from cutlass.Util import *
 
-# pylint: disable=W0703, C1801, R0912
+# pylint: disable=W0703, W0201, W0212, C1801, R0912
 
 # Create a module logger named after the module
 module_logger = logging.getLogger(__name__)
@@ -28,8 +28,10 @@ class VisitAttribute(Base):
 
     __dict = {
         'comment': [str, None],
+        'mother_child': [str, None],
         'survey_id': [str, None],
         'study': [str, None],
+        'time_during_pregnancy': [str, None],
 
         # These are the disease metadata fields
         'disease_comment': ["DiseaseMeta.comment", None],
@@ -192,10 +194,10 @@ class VisitAttribute(Base):
         'dinner_food':       [str, "dietary_log_today"],
         'dinner_amt':        [str, "dietary_log_today"],
         'other_food_intake': [str, "dietary_log_today"]
-        # pylint: enable=C0326
     }
 
     @staticmethod
+    # pylint: disable=W0211,W0613
     def _getx(self, propname, *args):
         if propname in self.__dict:
             propType = self.__dict[propname][0]
@@ -212,11 +214,13 @@ def _getx(self, propname, *args):
         return value
 
     @staticmethod
+    # pylint: disable=W0211
     def _setx(self, value, n):
         self._d[n] = value
 
     @staticmethod
     def _bindRead(name):
+        # pylint: disable=C0111
         def getXXXX(self, *args):
             return VisitAttribute._getx(self, name, *args)
 
@@ -225,6 +229,7 @@ def getXXXX(self, *args):
 
     @staticmethod
     def _bindWrite(name, t):
+        # pylint: disable=C0111
         def setXXXX(self, val):
             func = VisitAttribute._setx
 
@@ -246,7 +251,14 @@ def setXXXX(self, val):
         setXXXX.__name__ = name
         return setXXXX
 
-    def __init__(self):
+    def __init__(self, *args, **kwargs):
+        """
+        Constructor for the VisitAttribute class. This initializes the fields
+        specific to the VisitAttribute class, and inherits from the Base class.
+
+        Args:
+            None
+        """
         self.logger = logging.getLogger(self.__module__ + '.' + self.__class__.__name__)
 
         self.logger.addHandler(logging.NullHandler())
@@ -272,6 +284,8 @@ def __init__(self):
             x = property(VisitAttribute._bindRead(propname), VisitAttribute._bindWrite(propname, t))
             setattr(self.__class__, propname, x)
 
+        super(VisitAttribute, self).__init__(*args, **kwargs)
+
     def __setattr__(self, name, value):
         if name == "_d":
             self.__dict__[name] = value
@@ -345,8 +359,8 @@ def load_visit_attr(attrib_data):
 
             # Handle any special cases that we need too.
             if (section == "excercise" or
-               (propname.startswith('breakfast') or propname.startswith('lunch') or
-                propname.startswith('dinner'))):
+                    (propname.startswith('breakfast') or propname.startswith('lunch') or
+                     propname.startswith('dinner'))):
                 (propbase, propkey) = propname.split('_', 1)
 
                 propval = attrib_metadata.get(section, {}).get(propbase, {}).get(propkey)
@@ -369,8 +383,10 @@ def load_visit_attr(attrib_data):
 
             disease_props = dict(('disease_%s' % key, value) for key, value in
                                  attrib_data['meta']['disease']['study_disease'].iteritems())
+
             # This will have a double "disease" on it so we need to correct it.
-            disease_props['disease_ontology_id'] = disease_props.pop('disease_disease_ontology_id')
+            disease_props['disease_ontology_id'] = \
+                disease_props.pop('disease_disease_ontology_id')
 
             map(lambda key: setattr(attrib, key, disease_props.get(key)), disease_props.keys())
 

examples/visit_attribute.py

@@ -29,12 +29,14 @@ def set_logging():
 va.comment = "test comment"
 va.survey_id = "test survey id"
 va.study = "prediabetes"
+va.mother_child = "mother"
+va.time_during_pregnancy = "first_trimester"
 va.add_tag("test")
 va.add_tag("visit_attr")
-va.links = {"associated_with":  ["610a4911a5ca67de12cdc1e4b400f121"]}
+va.links = {"associated_with": ["610a4911a5ca67de12cdc1e4b400f121"]}
 
-va.disease_study_status = "test disease status"
-va.disease_name = "test disease name"
+va.disease_study_status = "affected"
+va.disease_name = "obesity"
 va.disease_description = "test disease description"
 va.disease_nci_id = "NCI id"
 va.disease_mesh_id = "MESH id"

setup.py

@@ -3,7 +3,7 @@
 
 # Utility function to read files. Used for the long_description.
 def read(fname):
-    """Reads the description of the package from the README.md file. """
+    """ Reads the description of the package from the README.md file. """
     return open(os.path.join(os.path.dirname(__file__), fname)).read()
 
 def get_version():

tests/test_visit_attr.py

@@ -74,6 +74,24 @@ def testComment(self):
 
         self.util.stringTypeTest(self, attr, "comment")
 
+        self.util.stringPropertyTest(self, attr, "comment")
+
+    def testMotherChild(self):
+        """ Test the mother_child property. """
+        attr = self.session.create_visit_attr()
+
+        self.util.stringTypeTest(self, attr, "mother_child")
+
+        self.util.stringPropertyTest(self, attr, "mother_child")
+
+    def testTimeDuringPregnancy(self):
+        """ Test the time_during_pregnancy property. """
+        attr = self.session.create_visit_attr()
+
+        self.util.stringTypeTest(self, attr, "time_during_pregnancy")
+
+        self.util.stringPropertyTest(self, attr, "time_during_pregnancy")
+
     def testClinicalPatientAge(self):
         """ Test the age property. """
         attr = self.session.create_visit_attr()