Merge branch 'develop' into main

Author: ufl-taeber

Makefile

@@ -0,0 +1,7 @@
+build: egg
+egg:
+	python setup.py bdist_egg
+
+clean:
+	rm -rf dist/ build/ nacculator.egg-info/
+	find . -name '*.pyc' | xargs rm

README

@@ -1,4 +1,4 @@
-								   NACCulator
+                                   NACCulator
 
 Converts a CSV data file exported from REDCap into the NACC's UDS3 fixed-width
 format.
@@ -9,30 +9,30 @@ FILES
 This is not exhaustive, but here is an explanation of some important files.
 
 nacc/:
-	Top-level Python package for all things NACC.
+    Top-level Python package for all things NACC.
 
 nacc/redcap2nacc.py:
-	converts a CSV data file exported from REDCap into NACC's UDS3 fixed-width
-	format
+    converts a CSV data file exported from REDCap into NACC's UDS3 fixed-width
+    format
 
 nacc/uds3/blanks.py:
-	specialized library for "Blanking Rules"
+    specialized library for "Blanking Rules"
 
 nacc/uds3/ivp/forms.py:
-	UDS3 IVP forms represented as Python classes
+    UDS3 IVP forms represented as Python classes
 
 tools/generator.py:
-	generates Python objects based on NACC Data Element Dictionaries in CSV
+    generates Python objects based on NACC Data Element Dictionaries in CSV
 
 
 HOWTO Convert from REDCap to NACC
 ---------------------------------
 
-	$ pip install nacculator
-	$ redcap2nacc < data.csv > data.nacc
+    $ pip install nacculator
+    $ redcap2nacc < data.csv > data.nacc
 
 Manually:
-	$ PYTHONPATH=. ./nacc/redcap2nacc.py data.csv > data.nacc
+    $ PYTHONPATH=. ./nacc/redcap2nacc.py data.csv > data.nacc
 
 Note: output is written to STDOUT; errors are written to STDERR; input can be
       STDIN or the first argument passed to redcap2nacc.
@@ -41,11 +41,11 @@ HOWTO Generate New Forms
 ------------------------
 
 Note: executing generator.py from within tools is an important step as the
-	  script assumes any corrected DEDs are stored under a folder in the
-	  current working directory called 'corrected'.
+      script assumes any corrected DEDs are stored under a folder in the
+      current working directory called 'corrected'.
 
 Warning: read the warnings in the current ../nacc/uds3/ivp/forms.py first.
 
-	$ cd tools
-	$ PYTHONPATH=.. ./generator.py uds3/ded/csv/ > ../nacc/uds3/ivp/forms.py
-	$ edit ../nacc/uds3/ivp/forms
+    $ cd tools
+    $ PYTHONPATH=.. ./generator.py uds3/ded/csv/ > ../nacc/uds3/ivp/forms.py
+    $ edit ../nacc/uds3/ivp/forms

nacc/redcap2nacc.py

@@ -10,14 +10,14 @@
 import re
 import sys
 
-from nacc.uds3 import ivp
-from nacc.uds3.ivp import forms as ivp_forms
 from nacc.uds3 import blanks
+from nacc.uds3.ivp import forms as ivp_forms
+from nacc.uds3.ivp import packet as ivp_packet
 
 
 def udsv3_ivp_from_redcap_csv(record):
     """ Converts REDCap CSV data into a packet (list of IVP Form objects) """
-    packet = ivp.Packet()
+    packet = ivp_packet.Packet()
 
     # Set up us the forms
     a1 = ivp_forms.FormA1()

nacc/uds3/ivp/__init__.py

@@ -1,40 +0,0 @@
-###############################################################################
-# Copyright 2015-2016 University of Florida. All rights reserved.
-# This file is part of UF CTS-IT's NACCulator project.
-# Use of this source code is governed by the license found in the LICENSE file.
-###############################################################################
-
-class Packet(list):
-    """
-    A collection of UDS Forms
-
-    This class is makes it convenient to access a field, which are all uniquely
-    named, regardless of which form they are in with the exception of A4D.
-    """
-
-    def __init__(self):
-        self._cache = dict()
-
-    def __getitem__(self, key):
-        """
-        Searches through each form in the packet for the field, `key`
-
-        Note: you cannot access fields in A4D in this manner since there is no
-        guarantee there will only be one; a KeyError will be raised.
-
-        Example:
-            packet['RESTTRL'] is equivalent to:
-            packet.__getitem__('RESTTRL')
-        """
-        if key in self._cache:
-            return self._cache[key]
-
-        for form in self:
-            if key in form.fields:
-                if "A4D" in str(form.__class__):
-                    raise KeyError("Form A4D is unsupported")
-                self._cache[key] = form.fields[key]
-                return self._cache[key]
-
-        raise KeyError(key)
-

nacc/uds3/ivp/packet.py

@@ -0,0 +1,40 @@
+###############################################################################
+# Copyright 2015-2016 University of Florida. All rights reserved.
+# This file is part of UF CTS-IT's NACCulator project.
+# Use of this source code is governed by the license found in the LICENSE file.
+###############################################################################
+
+class Packet(list):
+    """
+    A collection of UDS Forms
+
+    This class is makes it convenient to access a field, which are all uniquely
+    named, regardless of which form they are in with the exception of A4D.
+    """
+
+    def __init__(self):
+        self._cache = dict()
+
+    def __getitem__(self, key):
+        """
+        Searches through each form in the packet for the field, `key`
+
+        Note: you cannot access fields in A4D in this manner since there is no
+        guarantee there will only be one; a KeyError will be raised.
+
+        Example:
+            packet['RESTTRL'] is equivalent to:
+            packet.__getitem__('RESTTRL')
+        """
+        if key in self._cache:
+            return self._cache[key]
+
+        for form in self:
+            if key in form.fields:
+                if "A4D" in str(form.__class__):
+                    raise KeyError("Form A4D is unsupported")
+                self._cache[key] = form.fields[key]
+                return self._cache[key]
+
+        raise KeyError(key)
+

setup.py

@@ -6,21 +6,25 @@
 
 from setuptools import setup
 
+VERSION="0.1.1"
+
 setup(
-    name="NACCulator",
-    version="0.1.0",
+    name="nacculator",
+    version=VERSION,
+    author="Taeber Rapczak",
+    author_email="taeber@ufl.edu",
+    maintainer="UF CTS-IT",
+    maintainer_email="ctsit@ctsi.ufl.edu",
+    url="https://github.com/ctsit/nacculator",
+    license=open('LICENSE').read(),
+    description="CSV to NACC's UDS3 format converter",
+    keywords=["REDCap", "NACC", "UDS", "Clinical data"],
+    download_url="https://github.com/ctsit/nacculator/releases/tag/" + VERSION,
+
     packages=["nacc"],
     entry_points={
         "console_scripts": [
             "redcap2nacc = nacc.redcap2nacc:main"
         ]
-    },
-    author="Taeber Rapczak",
-    author_email="taeber@ufl.edu",
-    description="CSV to NACC's UDS3 format converter",
-    license="BSD 2-Clause",
-
-    url='https://github.com/ctsit/nacculator',
-    download_url='https://github.com/ctsit/nacculator/releases/tag/0.1.0',
-    keywords=['REDCap', 'NACC', 'UDS', 'Clinical data'],
+    }
 )

tools/generator.py

@@ -1,12 +1,11 @@
 #!/usr/bin/env python
+# coding=ascii
 ###############################################################################
 # Copyright 2015-2016 University of Florida. All rights reserved.
 # This file is part of UF CTS-IT's NACCulator project.
 # Use of this source code is governed by the license found in the LICENSE file.
 ###############################################################################
 
-# coding=ascii
-
 import csv
 import os
 import re