preg_term and ga_at_delivery support.

Author: victor73

CHANGES

@@ -1,3 +1,9 @@
+cutlass 1.0.3
+
+  * Support for preg_term and ga_at_delivery fields in SubjectAttribute.
+
+ - Victor <victor73@github.com>  Wed, 21 Feb 2018 16:00:00 -0400
+
 cutlass 1.0.2
 
   * Support for subproject in VisitAttribute, SubjectAttribute and

cutlass/DiseaseMeta.py

@@ -1,6 +1,6 @@
 import json
 import logging
-from Util import *
+from Util import enforce_string
 
 class DiseaseMeta(object):
     def __init__(self):

cutlass/HostAssayPrep.py

@@ -7,9 +7,9 @@
 from itertools import count
 from cutlass.iHMPSession import iHMPSession
 from cutlass.Base import Base
-from cutlass.Util import *
+from cutlass.Util import enforce_int, enforce_string
 
-# pylint: disable=C0302, W0703, R0192
+# pylint: disable=C0302, W0703
 
 # Create a module logger named after the module
 module_logger = logging.getLogger(__name__)

cutlass/SubjectAttribute.py

@@ -56,6 +56,7 @@ def __init__(self, *args, **kwargs):
         self._education = None
         self._family_history = None
         self._father = None
+        self._ga_at_delivery = None
         self._gallbladder = None
         self._hyperlipidemia = None
         self._hypertension = None
@@ -68,6 +69,7 @@ def __init__(self, *args, **kwargs):
         self._osa = None
         self._pancreatitis = None
         self._postmenopausal = None
+        self._preg_term = None
         self._pvd = None
         self._rx = None
         self._siblings = None
@@ -399,6 +401,33 @@ def father(self, father):
 
         self._father = father
 
+    @property
+    def ga_at_delivery(self):
+        """
+        str: Gestational age at delivery, in weeks. There are three
+        possible values: "<37wk", ">37wk" and "unknown".
+        """
+        self.logger.debug("In 'ga_at_delivery' getter.")
+
+        return self._ga_at_delivery
+
+    @ga_at_delivery.setter
+    @enforce_string
+    def ga_at_delivery(self, ga_at_delivery):
+        """
+        The setter for the gestational age at delivery.
+
+        Args:
+            ga_at_delivery (str): "<37wk", ">37wk", or "unknown".
+
+        Returns:
+            None
+        """
+
+        self.logger.debug("In 'ga_at_delivery' setter.")
+
+        self._ga_at_delivery = ga_at_delivery
+
     @property
     def gallbladder(self):
         """
@@ -412,7 +441,7 @@ def gallbladder(self):
     @enforce_string
     def gallbladder(self, gallbladder):
         """
-        The setter for the gallbladder disaese data.
+        The setter for the gallbladder disease data.
 
         Args:
             gallbladder (str): Yes/No, duration, clarification.
@@ -713,6 +742,32 @@ def postmenopausal(self, postmenopausal):
 
         self._postmenopausal = postmenopausal
 
+    @property
+    def preg_term(self):
+        """
+        str: Status of pregnancy ("preterm": <37wk, "full term": >= 37wk, or "NA").
+        """
+        self.logger.debug("In 'preg_term' getter.")
+
+        return self._preg_term
+
+    @preg_term.setter
+    @enforce_string
+    def preg_term(self, preg_term):
+        """
+        The setter for the status of pregnancy.
+
+        Args:
+            preg_term (str): The status of pregnancy.
+
+        Returns:
+            None
+        """
+
+        self.logger.debug("In 'preg_term' setter.")
+
+        self._preg_term = preg_term
+
     @property
     def pvd(self):
         """
@@ -1030,55 +1085,59 @@ def _get_raw_doc(self):
             doc['meta']['chf'] = self._chf
 
         if self._comment is not None:
-            self.logger.debug(__name__ + " object has comment set.")
+            self.logger.debug("%s object has comment set.", __name__)
             doc['meta']['comment'] = self._comment
 
         if self._contact is not None:
-            self.logger.debug(__name__ + " object has contact set.")
+            self.logger.debug("%s object has contact set.", __name__)
             doc['meta']['contact'] = self._contact
 
         if self._diabetes is not None:
-            self.logger.debug(__name__ + " object has diabetes set.")
+            self.logger.debug("%s object has diabetes set.", __name__)
             doc['meta']['diabetes'] = self._diabetes
 
         if self._education is not None:
-            self.logger.debug(__name__ + " object has education set.")
+            self.logger.debug("%s object has education set.", __name__)
             doc['meta']['education'] = self._education
 
         if self._family_history is not None:
-            self.logger.debug(__name__ + " object has family_history set.")
+            self.logger.debug("%s object has family_history set.", __name__)
             doc['meta']['family_history'] = self._family_history
 
         if self._father is not None:
-            self.logger.debug(__name__ + " object has father set.")
+            self.logger.debug("%s object has father set.", __name__)
             doc['meta']['father'] = self._father
 
+        if self._ga_at_delivery is not None:
+            self.logger.debug("%s object has ga_at_delivery set.", __name__)
+            doc['meta']['ga_at_delivery'] = self._ga_at_delivery
+
         if self._gallbladder is not None:
-            self.logger.debug(__name__ + " object has gallbladder set.")
+            self.logger.debug("%s object has gallbladder set.", __name__)
             doc['meta']['gallbladder'] = self._gallbladder
 
         if self._hyperlipidemia is not None:
-            self.logger.debug(__name__ + " object has hyperlipidemia set.")
+            self.logger.debug("%s object has hyperlipidemia set.", __name__)
             doc['meta']['hyperlipidemia'] = self._hyperlipidemia
 
         if self._hypertension is not None:
-            self.logger.debug(__name__ + " object has hypertension set.")
+            self.logger.debug("%s object has hypertension set.", __name__)
             doc['meta']['hypertension'] = self._hypertension
 
         if self._illicit_drug is not None:
-            self.logger.debug(__name__ + " object has illicit_drug set.")
+            self.logger.debug("%s object has illicit_drug set.", __name__)
             doc['meta']['illicit_drug'] = self._illicit_drug
 
         if self._kidney is not None:
-            self.logger.debug(__name__ + " object has kidney set.")
+            self.logger.debug("%s object has kidney set.", __name__)
             doc['meta']['kidney'] = self._kidney
 
         if self._liver is not None:
-            self.logger.debug(__name__ + " object has liver set.")
+            self.logger.debug("%s object has liver set.", __name__)
             doc['meta']['liver'] = self._liver
 
         if self._lmp is not None:
-            self.logger.debug(__name__ + " object has lmp set.")
+            self.logger.debug("%s object has lmp set.", __name__)
             doc['meta']['lmp'] = self._lmp
 
         if self._mother is not None:
@@ -1101,6 +1160,10 @@ def _get_raw_doc(self):
             self.logger.debug("%s object has postmenopausal set.", __name__)
             doc['meta']['postmenopausal'] = self._postmenopausal
 
+        if self._preg_term is not None:
+            self.logger.debug("%s object has preg_term set.", __name__)
+            doc['meta']['preg_term'] = self._preg_term
+
         if self._pvd is not None:
             self.logger.debug("%s object has pvd set.", __name__)
             doc['meta']['pvd'] = self._pvd
@@ -1286,6 +1349,9 @@ def load_subject_attr(attrib_data):
         if 'father' in attrib_data['meta']:
             attrib.father = attrib_data['meta']['father']
 
+        if 'ga_at_delivery' in attrib_data['meta']:
+            attrib.ga_at_delivery = attrib_data['meta']['ga_at_delivery']
+
         if 'gallbladder' in attrib_data['meta']:
             attrib.gallbladder = attrib_data['meta']['gallbladder']
 
@@ -1322,6 +1388,9 @@ def load_subject_attr(attrib_data):
         if 'postmenopausal' in attrib_data['meta']:
             attrib.postmenopausal = attrib_data['meta']['postmenopausal']
 
+        if 'preg_term' in attrib_data['meta']:
+            attrib.preg_term = attrib_data['meta']['preg_term']
+
         if 'pvd' in attrib_data['meta']:
             attrib.pvd = attrib_data['meta']['pvd']
 

tests/test_subject_attr.py

@@ -270,6 +270,15 @@ def testFather(self):
 
         self.util.stringPropertyTest(self, subj_attr, "father")
 
+    # ga_at_delivery
+    def testGaAtDelivery(self):
+        """ Test the ga_at_delivery property. """
+        subj_attr = self.session.create_subject_attr()
+
+        self.util.stringTypeTest(self, subj_attr, "ga_at_delivery")
+
+        self.util.stringPropertyTest(self, subj_attr, "ga_at_delivery")
+
     # gallbladder
     def testGallbladder(self):
         """ Test the gallbladder property. """
@@ -376,6 +385,15 @@ def testPostmenopausal(self):
 
         self.util.stringPropertyTest(self, subj_attr, "postmenopausal")
 
+    # preg_term
+    def testPregTerm(self):
+        """ Test the preg_term property. """
+        subj_attr = self.session.create_subject_attr()
+
+        self.util.stringTypeTest(self, subj_attr, "preg_term")
+
+        self.util.stringPropertyTest(self, subj_attr, "preg_term")
+
     # pvd (peripheral vascular disease)
     def testPVD(self):
         """ Test the pvd (peripheral vascular disease) property. """
@@ -455,6 +473,7 @@ def testLoadSaveDeleteSubjectAttribute(self):
         subj_attr.education = "Yes, high school"
         subj_attr.family_history = "Yes, cancer"
         subj_attr.father = "Dad"
+        subj_attr.ga_at_delivery = "<37wk"
         subj_attr.gallbladder = "Yes, 2 years"
         subj_attr.hyperlipidemia = "Yes, 3 years"
         subj_attr.hypertension = "Yes, 4 years"
@@ -467,6 +486,7 @@ def testLoadSaveDeleteSubjectAttribute(self):
         subj_attr.osa = "Yes, 6 years"
         subj_attr.pancreatitis = "Yes, 7 years"
         subj_attr.postmenopausal = "N/A"
+        subj_attr.preg_term = "preterm"
         subj_attr.pvd = "Yes, 8 years"
         subj_attr.rx = "None"
         subj_attr.siblings = "Brother and sister"
@@ -505,6 +525,10 @@ def testLoadSaveDeleteSubjectAttribute(self):
                          "SubjectAttribute comment not saved & loaded successfully")
         self.assertEqual(subj_attr.contact, subj_attr_loaded.contact,
                          "SubjectAttribute contact not saved & loaded successfully")
+        self.assertEqual(subj_attr.ga_at_delivery, subj_attr_loaded.ga_at_delivery,
+                         "SubjectAttribute ga_at_delivery not saved & loaded successfully")
+        self.assertEqual(subj_attr.preg_term, subj_attr_loaded.preg_term,
+                         "SubjectAttribute preg_term not saved & loaded successfully")
         self.assertEqual(subj_attr.subproject, subj_attr_loaded.subproject,
                          "SubjectAttribute subproject not saved & loaded successfully")
         self.assertEqual(subj_attr.tags[0], subj_attr_loaded.tags[0],