Merge pull request #81 from mdsol/develop

Merge Develop to Master

Author: iansparks

.travis.yml

@@ -5,8 +5,20 @@ python:
   - "3.4"
   - "3.5"
   - "3.6"
-  - "pypy"
+
 # command to install dependencies
 install: "python setup.py install"
 # command to run tests
-script: "python setup.py test"
+script: "python setup.py test"
+
+# Automated Deployment to PyPI on tag
+deploy:
+  provider: pypi
+  user: glow-mdsol
+  password:
+    secure: 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
+  on:
+    tags: true
+    python: "3.6"
+  distributions: "sdist bdist_wheel"
+

docs/source/classes.rst

@@ -17,31 +17,54 @@ Note: Any Class with the Prefix **Mdsol** represents a Medidata Rave specific ex
     :members:
     :undoc-members:
 
+.. autoclass:: ActionType
+.. autoclass:: Address
+.. autoclass:: AdminData
+.. autoclass:: Alias
 .. autoclass:: Annotation
+.. autoclass:: Annotations
 .. autoclass:: AuditRecord
 .. autoclass:: BasicDefinitions
 .. autoclass:: CheckValue
+.. autoclass:: City
 .. autoclass:: ClinicalData
 .. autoclass:: CodeList
 .. autoclass:: CodeListItem
 .. autoclass:: CodeListRef
 .. autoclass:: Comment
+.. autoclass:: ControlType
+.. autoclass:: Country
+.. autoclass:: DataType
 .. autoclass:: DateTimeStamp
 .. autoclass:: Decode
+.. autoclass:: DisplayName
+.. autoclass:: Email
+.. autoclass:: FirstName
 .. autoclass:: Flag
 .. autoclass:: FlagType
 .. autoclass:: FlagValue
 .. autoclass:: FormData
 .. autoclass:: FormDef
 .. autoclass:: FormRef
+.. autoclass:: FullName
 .. autoclass:: GlobalVariables
+.. autoclass:: GranularityType
 .. autoclass:: ItemData
 .. autoclass:: ItemDef
 .. autoclass:: ItemGroupData
 .. autoclass:: ItemGroupDef
 .. autoclass:: ItemGroupRef
 .. autoclass:: ItemRef
+.. autoclass:: LastName
+.. autoclass:: LastUpdateMixin
+.. autoclass:: Location
 .. autoclass:: LocationRef
+.. autoclass:: LocationType
+.. autoclass:: LogicalRecordPositionType
+.. autoclass:: LoginName
+.. autoclass:: MODMAttribute
+.. autoclass:: MODMExtensionRegistry
+.. autoclass:: MODMMixin
 .. autoclass:: MdsolAttribute
 .. autoclass:: MdsolCheckAction
 .. autoclass:: MdsolCheckStep
@@ -55,20 +78,37 @@ Note: Any Class with the Prefix **Mdsol** represents a Medidata Rave specific ex
 .. autoclass:: MdsolHelpText
 .. autoclass:: MdsolLabelDef
 .. autoclass:: MdsolLabelRef
+.. autoclass:: MdsolProtocolDeviation
 .. autoclass:: MdsolQuery
 .. autoclass:: MdsolReviewGroup
 .. autoclass:: MdsolViewRestriction
 .. autoclass:: MeasurementUnit
 .. autoclass:: MeasurementUnitRef
 .. autoclass:: MetaDataVersion
+.. autoclass:: MetaDataVersionRef
+.. autoclass:: MilestoneMixin
 .. autoclass:: ODM
 .. autoclass:: ODMElement
+.. autoclass:: Organization
+.. autoclass:: OtherText
+.. autoclass:: Phone
+.. autoclass:: PostalCode
 .. autoclass:: Protocol
+.. autoclass:: ProtocolDeviationStatus
+.. autoclass:: QueryStatusType
 .. autoclass:: Question
 .. autoclass:: RangeCheck
+.. autoclass:: RangeCheckComparatorType
+.. autoclass:: RangeCheckType
 .. autoclass:: ReasonForChange
 .. autoclass:: Signature
 .. autoclass:: SignatureRef
+.. autoclass:: SimpleChildElement
+.. autoclass:: SiteRef
+.. autoclass:: SourceID
+.. autoclass:: StateProv
+.. autoclass:: StepType
+.. autoclass:: StreetName
 .. autoclass:: Study
 .. autoclass:: StudyEventData
 .. autoclass:: StudyEventDef
@@ -77,7 +117,9 @@ Note: Any Class with the Prefix **Mdsol** represents a Medidata Rave specific ex
 .. autoclass:: Symbol
 .. autoclass:: TransactionalElement
 .. autoclass:: TranslatedText
+.. autoclass:: User
 .. autoclass:: UserRef
+.. autoclass:: UserType
 
 rwslib.rws_requests
 ===================

docs/source/conf.py

@@ -19,7 +19,7 @@
 
 parentdir = os.path.split(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))[0]
 sys.path.insert(0,str(parentdir))
-import rwslib
+
 from rwslib import __version__, __copyright__
 
 # -- General configuration -----------------------------------------------------

rwslib/__init__.py

@@ -2,7 +2,7 @@
 
 __title__ = 'rwslib'
 __author__ = 'Ian Sparks ([email protected])'
-__version__ = '1.1.8'
+__version__ = '1.2.0'
 __license__ = 'MIT'
 __copyright__ = 'Copyright 2017 Medidata Solutions Inc'
 
@@ -74,6 +74,7 @@ def send_request(self, request_object, timeout=None, retries=1, **kwargs):
         full_url = make_url(self.base_url, request_object.url_path())
         if request_object.requires_authorization:
             kwargs['auth'] = self.auth
+            # TODO: Look at different connect and read timeouts?
             kwargs['timeout'] = timeout
             kwargs.update(request_object.args())
 
@@ -93,7 +94,15 @@ def send_request(self, request_object, timeout=None, retries=1, **kwargs):
                   "POST": session.post}[request_object.method]
 
         start_time = time.time()
-        r = action(full_url, **kwargs)
+
+        try:
+            r = action(full_url, **kwargs)
+        except (requests.exceptions.ConnectTimeout, requests.exceptions.ReadTimeout) as exc:
+            if isinstance(exc, (requests.exceptions.ConnectTimeout,)):
+                raise RWSException("Server Connection Timeout", "Connection timeout for {}".format(full_url))
+            elif isinstance(exc, (requests.exceptions.ReadTimeout,)):
+                raise RWSException("Server Read Timeout", "Read timeout for {}".format(full_url))
+
         self.request_time = time.time() - start_time
         self.last_result = r #see also r.elapsed for timedelta object.
 

rwslib/builders/README.md

@@ -0,0 +1,13 @@
+# builders
+
+This package assists in the building of CDISC ODM (with Medidata Extensions where applicable)
+
+## Organisation
+The package is broken down by the logical arrangement of the ODM document itself.
+
+* [common.py](common.py) - common elements, functions that are reused across the module
+* [core.py](core.py) -  the ODM parent element
+* [metadata.py](metadata.py) - metadata elements, starting with the Study Element
+* [clinicaldata.py](clinicaldata.py) - clinical data elements, starting with the ClinicalData Element
+* [admindata.py](admindata.py) - Administrative Data elements, starting with the AdminData Element
+* [constants.py](constants.py) - Constants such as enumerated lists of options for Type elements (as an example)

rwslib/builders/__init__.py

@@ -0,0 +1,27 @@
+# -*- coding: utf-8 -*-
+
+__author__ = 'glow'
+
+# Common elements
+from rwslib.builders.common import ODMElement, TransactionalElement
+
+# Constants
+from rwslib.builders.constants import *
+
+# Core
+from rwslib.builders.core import *
+
+# Metadata
+from rwslib.builders.metadata import *
+
+# ClinicalData
+from rwslib.builders.clinicaldata import *
+
+# AdminData
+from rwslib.builders.admindata import *
+
+# ReferenceData
+#from rwslib.builders.referencedata import *
+
+# MODM
+from rwslib.builders.modm import *