Merge pull request #71 from mdsol/develop

Merge release 1.1.5 for pushing to pypi

.gitignore

@@ -4,9 +4,17 @@
 #Distribution folder
 dist/
 rwslib.egg-info/
+build
 
 # sphinx build folder
 docs/build
 
 # coverage
 htmlcov
+
+# tox
+.tox
+.eggs
+
+# coverage
+.coverage

.travis.yml

@@ -0,0 +1,11 @@
+language: python
+python:
+  - "2.7"
+  - "3.3"
+  - "3.4"
+  - "3.5"
+  - "pypy"
+# command to install dependencies
+install: "python setup.py install"
+# command to run tests
+script: "python setup.py test"

AUTHORS.rst

@@ -7,4 +7,4 @@ Authors
 - Geoff Low <glow@mdsol.com>
 - Andrew Newbigging <anewbigging@mdsol.com>
 - Oli Quinet <https://github.com/Oli76>
-
+- Daniel Smoczyk <https://github.com/dPeS>

docs/source/classes.rst

@@ -21,6 +21,7 @@ Class Reference
 .. autoclass:: StudyDatasetRequest
 .. autoclass:: SubjectDatasetRequest
 .. autoclass:: VersionDatasetRequest
+.. autoclass:: ConfigurableDatasetRequest
 
 .. module:: rwslib.rwsobjects
 

docs/source/getting_started.rst

@@ -54,7 +54,7 @@ RWSConnection ``send_request`` method::
     >>> rws = RWSConnection('innovate')
     >>> from rwslib.rws_requests import VersionRequest
     >>> rws.send_request(VersionRequest())
-    1.8.0
+    u'1.8.0'
 
 The result you get back from send_request will depend on the request type since Request objects have the chance to
 process the text values returned from Rave. ``VersionRequest()`` returns a string value but other request types may
@@ -174,15 +174,15 @@ were sent, what URL was called etc.
     >>> rws = RWSConnection('innovate')
     >>> #Get the rave version from rws
     >>> rws.send_request(VersionRequest())
-    1.8.0
+    u'1.8.0'
     >>> rws.last_result.url
     https://innovate.mdsol.com/RaveWebServices/version
     >>> rws.last_result.status_code
     200
     >>> rws.last_result.headers['content-type']
     text/plain; charset=utf-8
     >>> rws.last_result.text
-    1.8.0
+    u'1.8.0'
 
 ``last_result`` is a `Requests <http://docs.python-requests.org/>`_ object. Please see that library for more
 information on all the properties that can be returned there.
@@ -202,7 +202,7 @@ in it's ``request_time`` attribute.
     >>> rws = RWSConnection('innovate')
     >>> #Get the rave version from rws
     >>> rws.send_request(VersionRequest())
-    1.8.0
+    u'1.8.0'
     >>> #Get the elapsed time in seconds to process the previous request
     >>> rws.request_time
     0.760736942291

docs/source/index.rst

@@ -23,9 +23,9 @@ Contents:
    using_builders
    biostats_gateway
    odm_adapter
+   rwscmd
    classes
 
-
 Indices and tables
 ==================
 

docs/source/rws_requests.rst

@@ -36,7 +36,7 @@ Example::
     >>> from rwslib.rws_requests import VersionRequest
     >>> r = RWSConnection('innovate', 'username', 'password')  #Authorization optional
     >>> r.send_request(VersionRequest())
-    1.8.0
+    u'1.15.0'
 
 
 .. _buildversion_request:
@@ -57,10 +57,31 @@ Example::
     >>> from rwslib.rws_requests import BuildVersionRequest
     >>> r = RWSConnection('innovate', 'username', 'password')  #Authorization optional
     >>> r.send_request(BuildVersionRequest())
-    5.6.5.12
+    u'5.6.5.213'
 
 
 
+.. _codename_request:
+.. index:: CodeNameRequest
+
+CodeNameRequest()
+-----------------
+
+Returns the text result of calling::
+
+    https://{ host }/RaveWebServices/version/codename
+
+Returns a 200 response code and the internal code name of the RWS version.
+
+Example::
+
+    >>> from rwslib import RWSConnection
+    >>> from rwslib.rws_requests import CodeNameRequest
+    >>> r = RWSConnection('innovate')  #Authorization optional
+    >>> r.send_request(CodeNameRequest())
+    u'Uakari'
+
+
 .. _diagnostics_request:
 .. index:: DiagnosticsRequest
 
@@ -69,7 +90,7 @@ DiagnosticsRequest()
 
 Returns the text result of calling::
 
-    https://{ host }/RaveWebServices/version/build
+    https://{ host }/RaveWebServices/diagnostics
 
 Returns a 200 response code and the text *OK* if RWS self-checks pass.
 
@@ -79,8 +100,29 @@ Example::
     >>> from rwslib.rws_requests import DiagnosticsRequest
     >>> r = RWSConnection('innovate', 'username', 'password')  #Authorization optional
     >>> r.send_request(DiagnosticsRequest())
-    OK
+    u'OK'
+
+
+.. _twohundred_request:
+.. index:: TwoHundredRequest
+
+TowHundredRequest()
+-------------------
+
+Returns the html result of calling::
+
+    https://{ host }/RaveWebServices/twohundred
+
+Returns a 200 response code and a html document that contains information about the MAuth configuration of Rave
+Web Services on this url.
 
+Example::
+
+    >>> from rwslib import RWSConnection
+    >>> from rwslib.rws_requests import TwoHundredRequest
+    >>> r = RWSConnection('innovate') #Authorization optional
+    >>> r.send_request(TwoHundredRequest())
+    u'<!DOCTYPE html>\r\n<html>\r\n<head><script.....
 
 
 .. _cacheflush_request:
@@ -114,3 +156,37 @@ Example::
     >>> response.istransactionsucessful
     True
 
+
+.. _configurabledatasetrequest_request:
+.. index:: ConfigurableDatasetRequest
+
+ConfigurableDatasetRequest()
+----------------------------
+
+Authorization is required for this method call.
+
+Returns the text result of calling::
+
+    https://{ host }/RaveWebServices/datasets/{dataset_name}(.{dataset_format})?{params}
+
+
+Sends a Configurable Dataset request to RWS.  The `dataset_format` argument is optional and is only required if the
+corresponding configurable dataset requires it.  The primary use case of this is as an abstract class that the user
+can subclass for their particular Configurable Dataset; the implemented class could such as validation of the
+requested `dataset_format` against the list of formats accepted by the configurable dataset or by overloading the
+`result` method to parse the raw response content (e.g. return a pre-parsed JSON response or a `csv.reader`).
+Returns a :class:`rwsobjects.RWSResponse` object:
+
+Example::
+
+    >>> from rwslib import RWSConnection
+    >>> from rwslib.rws_requests import ConfigurableDatasetRequest
+    >>> r = RWSConnection('innovate', 'username', 'password')  #Authorization REQUIRED
+    >>> response = r.send_request(ConfigurableDatasetRequest('SomeRequest', dataset_format='csv', params=dict(start='2012-02-01')))
+    >>> response.text
+    DataPageID,DataPointID,LastUpdated
+    1234,4321,2012-12-01T12:33:00
+    4334,1234,2012-12-02T12:33:00
+    ...
+
+

docs/source/rwscmd.rst

@@ -0,0 +1,56 @@
+.. _rwscmd:
+
+rwscmd
+******
+
+rwscmd is a command-line tool providing convenient access to Rave WebServices, via rwslib.
+
+Usage
+-----
+
+.. code-block:: shell
+
+    rwscmd [OPTIONS] URL COMMAND [ARGS]
+    Options:
+      -u, --username TEXT           Rave login
+      -p, --password TEXT           Rave password
+      --virtual_dir TEXT            RWS virtual directory, defaults to RaveWebServices
+      --raw / --list                Display raw xml response from RWS or human-readable list, defaults to list
+      -v, --verbose / -s, --silent
+      -o, --output FILENAME         Write output to file
+      --help                        Show this message and exit.
+
+    Commands:
+     autofill  Request enterable data for a subject,...
+     data      List EDC data for [STUDY] [ENV] [SUBJECT]
+     direct    Make direct call to RWS, bypassing rwslib
+     metadata  List metadata for [PROJECT] [VERSION]
+     post      Post ODM clinical data
+     version   Display RWS version
+
+Examples
+--------
+
+.. code-block:: shell
+
+    $ rwscmd innovate version
+        Username: anewbigging
+        Password:
+        1.15.0
+
+    $ export RWSCMD_USERNAME=anewbigging
+    $ export RWSCMD_PASSWORD=*********
+
+    $ rwscmd innovate version
+        1.15.0
+
+    $ rwscmd innovate data
+        ATN01(Prod)
+        Medidata(Prod)
+        Mediflex(Prod)
+        Mediflex(Dev)
+
+    $ rwscmd innovate data Mediflex Prod
+        0004-bbc-003
+        001 aaa
+        001 ADS

docs/source/using_builders.rst

@@ -132,7 +132,8 @@ following example creates the same document as above::
 The builder creates a number of ODM properties including CreationDateTime, FileOID (a random identifier), FileType and
 all namespace declarations.
 
-## Metadata Builders
+Metadata Builders
+-----------------
 
 Builders also exist for creating Metadata ODM files::
 

requirements.txt

@@ -1,7 +1,9 @@
-lxml>=3.4.4
+lxml
 requests
 httpretty
 tox
 six
 enum34
-mock
+mock
+click
+fake-factory

rwslib/__init__.py

@@ -2,7 +2,7 @@
 
 __title__ = 'rwslib'
 __author__ = 'Ian Sparks (isparks@mdsol.com)'
-__version__ = '1.1.4'
+__version__ = '1.1.5'
 __license__ = 'MIT'
 __copyright__ = 'Copyright 2016 Medidata Solutions Inc'
 

rwslib/builders.py

@@ -90,6 +90,12 @@ def add(self, *args):
             self << child
         return self
 
+    def __str__(self):
+        """Return string representation"""
+        builder = ET.TreeBuilder()
+        self.build(builder)
+        return ET.tostring(builder.close(),encoding='utf-8').decode('utf-8')
+
     def set_single_attribute(self, other, trigger_klass, property_name):
         """Used to set guard the setting of an attribute which is singular and can't be set twice"""
 
@@ -1365,7 +1371,8 @@ class ItemDef(ODMElement):
     VALID_DATATYPES = [DataType.Text, DataType.Integer, DataType.Float, DataType.Date,
                        DataType.DateTime, DataType.Time]
 
-    def __init__(self, oid, name, datatype, length,
+    def __init__(self, oid, name, datatype,
+                 length=None,
                  significant_digits=None,
                  sas_field_name=None,
                  sds_var_name=None,
@@ -1404,6 +1411,13 @@ def __init__(self, oid, name, datatype, length,
             if not isinstance(control_type, ControlType):
                 raise AttributeError("{0} is not a valid Control Type".format(control_type))
 
+        if length is None:
+            if datatype in [DataType.DateTime, DataType.Time, DataType.Date]:
+                # Default this
+                length = len(date_time_format)
+            else:
+                raise AttributeError('length must be set for all datatypes except Date/Time types')
+
         self.datatype = datatype
         self.length = length
         self.significant_digits = significant_digits

rwslib/extras/audit_event/README.md

@@ -45,15 +45,18 @@ The _context_ object passed contains all the data pulled from the audit record.
             transaction_type
             instance_name
             instance_overdue
+            instance_id
         form
             oid
             repeat_key
             transaction_type
             datapage_name
+            datapage_id
         itemgroup
             oid
             repeat_key
-            transaction_type  
+            transaction_type
+            record_id  
         item
             oid 
             value