Merge pull request #78 from mdsol/feature/add_protocol_deviation

Feature/add protocol deviation

rwslib/__init__.py

@@ -2,9 +2,9 @@
 
 __title__ = 'rwslib'
 __author__ = 'Ian Sparks (isparks@mdsol.com)'
-__version__ = '1.1.7'
+__version__ = '1.1.8'
 __license__ = 'MIT'
-__copyright__ = 'Copyright 2016 Medidata Solutions Inc'
+__copyright__ = 'Copyright 2017 Medidata Solutions Inc'
 
 
 import requests

rwslib/builder_constants.py

@@ -235,6 +235,11 @@ class LogicalRecordPositionType(enum.Enum):
     MinBySubject = 'MinBySubject'
 
 
+class ProtocolDeviationStatus(enum.Enum):
+    Open = "Open"
+    Removed = "Removed"
+
+
 LOGICAL_RECORD_POSITIONS = [
     LogicalRecordPositionType.MaxBySubject,
     LogicalRecordPositionType.MaxBySubject,

rwslib/builders.py

@@ -160,6 +160,7 @@ class UserRef(ODMElement):
     """
     Reference to a :class:`User`
     """
+
     def __init__(self, oid):
         """
         :param str oid: OID for referenced :class:`User`
@@ -178,6 +179,7 @@ class LocationRef(ODMElement):
     """
     Reference to a :class:`Location`
     """
+
     def __init__(self, oid):
         """
         :param str oid: OID for referenced :class:`Location`
@@ -196,6 +198,7 @@ class SignatureRef(ODMElement):
     """
     Reference to a Signature
     """
+
     def __init__(self, oid):
         """
         :param str oid: OID for referenced :class:`Signature`
@@ -214,6 +217,7 @@ class ReasonForChange(ODMElement):
     """
     A user-supplied reason for a data change.
     """
+
     def __init__(self, reason):
         """
         :param str reason: Supplied Reason for change
@@ -234,6 +238,7 @@ class DateTimeStamp(ODMElement):
     The date/time that the data entry, modification, or signature was performed.
     This applies to the initial occurrence of the action, not to subsequent transfers between computer systems.
     """
+
     def __init__(self, date_time):
         #: specified DateTime for event
         self.date_time = date_time
@@ -260,6 +265,7 @@ class Signature(ODMElement):
     the date and time of signing,
     and (in the case of a digital signature) an encrypted hash of the included data.
     """
+
     def __init__(self, signature_id=None, user_ref=None, location_ref=None, signature_ref=None, date_time_stamp=None):
         #: Unique ID for Signature
         """
@@ -420,7 +426,7 @@ def build(self, builder):
 
         if self.seqnum is None:
             # SeqNum is not optional (and defaulted)
-            raise ValueError("SeqNum is not set.") # pragma: no cover
+            raise ValueError("SeqNum is not set.")  # pragma: no cover
         params["SeqNum"] = self.seqnum
 
         if self.annotation_id is not None:
@@ -562,6 +568,7 @@ class FlagType(ODMElement):
 
     .. note:: FlagType is not supported by Rave
     """
+
     def __init__(self, flag_type, codelist_oid=None):
         """
         :param flag_type: Type for :class:`Flag`
@@ -600,6 +607,7 @@ class FlagValue(ODMElement):
 
     .. note::  FlagValue is not supported by Rave
     """
+
     def __init__(self, flag_value, codelist_oid=None):
         """
         :param flag_value: Value for :class:`Flag`
@@ -729,6 +737,8 @@ def __init__(self, itemoid, value, specify_value=None, transaction_type=None, lo
         self.annotations = []
         #: the corresponding :class:`MeasurementUnitRef` for the DataPoint
         self.measurement_unit_ref = None
+        #: the list of :class:`MdsolProtocolDeviation` references on the DataPoint - *Rave Specific Attribute*
+        self.deviations = []
 
     def build(self, builder):
         """
@@ -765,21 +775,26 @@ def build(self, builder):
         if self.measurement_unit_ref is not None:
             self.measurement_unit_ref.build(builder)
 
-        for query in self.queries:
+        for query in self.queries:  # type: MdsolQuery
             query.build(builder)
 
-        for annotation in self.annotations:
+        for deviation in self.deviations:  # type: MdsolProtocolDeviation
+            deviation.build(builder)
+
+        for annotation in self.annotations:  # type: Annotation
             annotation.build(builder)
 
         builder.end("ItemData")
 
     def __lshift__(self, other):
-        if not isinstance(other, (MeasurementUnitRef, AuditRecord, MdsolQuery, Annotation)):
-            raise ValueError("ItemData object can only receive MeasurementUnitRef, AuditRecord, Annotation"
-                             " or MdsolQuery objects")
+        if not isinstance(other, (MeasurementUnitRef, AuditRecord, MdsolQuery, Annotation,
+                                  MdsolProtocolDeviation)):
+            raise ValueError("ItemData object can only receive MeasurementUnitRef, AuditRecord, Annotation,"
+                             "MdsolProtocolDeviation or MdsolQuery objects")
         self.set_single_attribute(other, MeasurementUnitRef, 'measurement_unit_ref')
         self.set_single_attribute(other, AuditRecord, 'audit_record')
         self.set_list_attribute(other, MdsolQuery, 'queries')
+        self.set_list_attribute(other, MdsolProtocolDeviation, 'deviations')
         self.set_list_attribute(other, Annotation, 'annotations')
         return other
 
@@ -873,9 +888,9 @@ def __init__(self, formoid, transaction_type=None, form_repeat_key=None):
         self.form_repeat_key = form_repeat_key
         self.itemgroups = []
         #: :class:`Signature` for FormData
-        self.signature = None
+        self.signature = None  # type: Signature
         #: Collection of :class:`Annotation` for FormData - *Not supported by Rave*
-        self.annotations = []
+        self.annotations = []  # type: list(Annotation)
 
     def __lshift__(self, other):
         """Override << operator"""
@@ -1209,6 +1224,7 @@ class Symbol(ODMElement):
     """
     A human-readable name for a :class:`MeasurementUnit`.
     """
+
     def __init__(self):
         #: Collection of :class:`TranslatedText`
         self.translations = []
@@ -1327,6 +1343,7 @@ class StudyEventRef(ODMElement):
     The :class:`StudyEventRef` within a :class:`Protocol` must not have duplicate StudyEventOIDs nor
     duplicate OrderNumbers.
     """
+
     def __init__(self, oid, order_number, mandatory):
         """
         :param oid: :class:`StudyEventDef` OID
@@ -1380,6 +1397,7 @@ class FormRef(ODMElement):
     The list of :class:`FormRef` identifies the types of forms that are allowed to occur within this type of study
     event. The :class:`FormRef` within a single :class:`StudyEventDef` must not have duplicate FormOIDs nor OrderNumbers.
     """
+
     def __init__(self, oid, order_number, mandatory):
         """
         :param str oid: Set the :class:`FormDef` OID for the :class:`FormRef`
@@ -1723,6 +1741,7 @@ class MdsolAttribute(ODMElement):
 
     .. note:: This is  Medidata Rave Specific Element
     """
+
     def __init__(self, namespace, name, value, transaction_type='Insert'):
         #: Namespace for the Attribute
         self.namespace = namespace
@@ -1750,6 +1769,7 @@ class ItemRef(ODMElement):
     A reference to an :class:`ItemDef` as it occurs within a specific :class:`ItemGroupDef`.
     The list of ItemRefs identifies the types of items that are allowed to occur within this type of item group.
     """
+
     def __init__(self, oid, order_number=None, mandatory=False, key_sequence=None,
                  imputation_method_oid=None, role=None, role_codelist_oid=None):
         """
@@ -1814,6 +1834,7 @@ class ItemGroupDef(ODMElement):
     """
     An ItemGroupDef describes a type of item group that can occur within a Study.
     """
+
     def __init__(self, oid, name, repeating=False, is_reference_data=False, sas_dataset_name=None,
                  domain=None, origin=None, role=None, purpose=None, comment=None):
         """
@@ -1898,6 +1919,7 @@ class Question(ODMElement):
     """
     A label shown to a human user when prompted to provide data for an item on paper or on a screen.
     """
+
     def __init__(self):
         #: Collection of :class:`Translation` for the Question
         self.translations = []
@@ -1926,6 +1948,7 @@ class MeasurementUnitRef(ODMElement):
     """
     A reference to a measurement unit definition (:class:`MeasurementUnit`).
     """
+
     def __init__(self, oid, order_number=None):
         """
         :param str oid: :class:`MeasurementUnit` OID
@@ -2208,9 +2231,9 @@ def __init__(self, comparator, soft_hard):
         self.comparator = comparator
         self._soft_hard = None
         self.soft_hard = soft_hard
-        #! :class:`CheckValue` for RangeCheck
+        # ! :class:`CheckValue` for RangeCheck
         self.check_value = None
-        #! :class:`MeasurementUnitRef` for RangeCheck
+        # ! :class:`MeasurementUnitRef` for RangeCheck
         self.measurement_unit_ref = None
 
     @property
@@ -2532,6 +2555,7 @@ class Decode(ODMElement):
     """
     The displayed value relating to the CodedValue
     """
+
     def __init__(self):
         #: Collection of :class:`Translation` for the Decode
         self.translations = []
@@ -2556,6 +2580,7 @@ class CodeListItem(ODMElement):
     Defines an individual member value of a :class:`CodeList` including display format.
     The actual value is given, along with a set of print/display-forms.
     """
+
     def __init__(self, coded_value, order_number=None, specify=False):
         """
         :param str coded_value: Coded Value for CodeListItem
@@ -3058,6 +3083,73 @@ def __lshift__(self, other):
         self.set_list_attribute(other, MdsolCheckAction, 'check_actions')
 
 
+class MdsolProtocolDeviation(TransactionalElement):
+    """
+    Extension for Protocol Deviations in Rave
+    
+    .. note:: This is a Medidata Rave Specific Extension
+    .. note:: This primarily exists as a mechanism for use by the Clinical Audit Record Service, but it is useful 
+        to define for the builders
+    """
+    ALLOWED_TRANSACTION_TYPES = ["Insert"]
+
+    def __init__(self, value, status, repeat_key=1, code=None, klass=None, transaction_type=None):
+        """
+        :param str value: Value for the Protocol Deviation 
+        :param rwslib.builder_constants.ProtocolDeviationStatus status: 
+        :param int repeat_key: RepeatKey for the Protocol Deviation
+        :param basestring code: Protocol Deviation Code
+        :param basestring klass: Protocol Deviation Class 
+        :param transaction_type: Transaction Type for the Protocol Deviation
+        """
+        super(MdsolProtocolDeviation, self).__init__(transaction_type=transaction_type)
+        self._status = None
+        self._repeat_key = None
+        self.status = status
+        self.value = value
+        self.repeat_key = repeat_key
+        self.code = code
+        self.pdclass = klass
+
+    @property
+    def repeat_key(self):
+        return self._repeat_key
+
+    @repeat_key.setter
+    def repeat_key(self, value):
+        if isinstance(value, int):
+            self._repeat_key = value
+        else:
+            raise ValueError("RepeatKey should be an integer, not {}".format(value))
+
+    @property
+    def status(self):
+        return self._status
+
+    @status.setter
+    def status(self, value):
+        if isinstance(value, ProtocolDeviationStatus):
+            self._status = value
+        else:
+            raise ValueError("Status {} is not a valid ProtocolDeviationStatus".format(value))
+
+    def build(self, builder):
+        """Build XML by appending to builder"""
+        params = dict(Value=self.value,
+                      Status=self.status.value,
+                      ProtocolDeviationRepeatKey=self.repeat_key
+                      )
+
+        if self.code:
+            params['Code'] = self.code
+        if self.pdclass:
+            params['Class'] = self.pdclass
+        if self.transaction_type:
+            params['TransactionType'] = self.transaction_type
+        builder.start('mdsol:ProtocolDeviation', params)
+        builder.end('mdsol:ProtocolDeviation')
+
+
 class MdsolDerivationDef(ODMElement):
     """
     Extension for Rave derivations

rwslib/tests/common.py

@@ -0,0 +1,16 @@
+# -*- coding: utf-8 -*-
+
+__author__ = 'glow'
+
+from xml.etree import cElementTree as ET
+
+
+def obj_to_doc(obj, *args, **kwargs):
+    """Convert an object to am XML document object
+    :rtype: xml.etree.ElementTree.Element
+    """
+    builder = ET.TreeBuilder()
+    obj.build(builder, *args, **kwargs)
+    return builder.close()
+
+

rwslib/tests/test_builders.py

@@ -1,15 +1,11 @@
+# -*- coding: utf-8 -*-
+
 __author__ = 'isparks'
 
 import unittest
 from rwslib.builders import *
 from xml.etree import cElementTree as ET
-
-
-def obj_to_doc(obj, *args, **kwargs):
-    """Convert an object to am XML document object"""
-    builder = ET.TreeBuilder()
-    obj.build(builder, *args, **kwargs)
-    return builder.close()
+from rwslib.tests.common import obj_to_doc
 
 
 class TestBoolToTrueFalse(unittest.TestCase):
@@ -193,38 +189,6 @@ def test_no_datetime_stamp(self):
             self.assertIn("DateTimeStamp", err.exception.message)
 
 
-class TestMdsolQuery(unittest.TestCase):
-    """Test extension MdsolQuery"""
-
-    def get_tested(self):
-        return MdsolQuery(status=QueryStatusType.Open, value="Data missing", query_repeat_key=123,
-                          recipient="Site from System", requires_response=True)
-
-    def test_basic(self):
-        tested = self.get_tested()
-        self.assertEqual("Data missing", tested.value)
-        self.assertEqual(123, tested.query_repeat_key)
-        self.assertEqual(QueryStatusType.Open, tested.status)
-        self.assertEqual("Site from System", tested.recipient)
-        self.assertEqual(True, tested.requires_response)
-
-    def test_builder(self):
-        tested = self.get_tested()
-        tested.response = "Done"
-        doc = obj_to_doc(tested)
-        self.assertEqual("mdsol:Query", doc.tag)
-        self.assertEqual("Yes", doc.attrib['RequiresResponse'])
-        self.assertEqual("Site from System", doc.attrib['Recipient'])
-        self.assertEqual("123", doc.attrib['QueryRepeatKey'])
-        self.assertEqual("Data missing", doc.attrib['Value'])
-        self.assertEqual("Done", doc.attrib['Response'])
-
-    def test_invalid_status_value(self):
-        """Status must come from QueryStatusType"""
-        with self.assertRaises(AttributeError):
-            MdsolQuery(status='A test')
-
-
 class TestSignatureRef(unittest.TestCase):
     def test_creates_expected_element(self):
         """We get the Signature Ref element"""
@@ -1306,5 +1270,7 @@ def test_str_well_formed(self):
         self.assertEqual(doc.attrib["Description"], self.tested.description)
 
 
+
+
 if __name__ == '__main__':
     unittest.main()