Merge pull request #3 from Sage-Bionetworks/develop

Add license, setup, some function name/parameter modifications

LICENSE.txt

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) [2017] [Phil Snyder]
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -58,7 +58,7 @@ Welcome, AnnotatorAdmin!
 In [4]: p = annotator.Pipeline(syn, meta="syn7654321")
  [####################]100.00%   1/1   Done...
 In [5]: # Copy the default annotations (assay, study, etc.) as they appear above to your clipboard
-In [6]: cols = annotator.utils.convertClipboardToDict(" - ")
+In [6]: cols = annotator.utils.clipboardToDict(" - ")
 In [7]: for c in ['specimenID', 'individualID', 'assayTarget', 'cellType']:
             cols[c] = None
 In [8]: p.createFileView(name="EpiDiff_CHiPSeq", parent="syn0000000", scope="syn1234567", addCols=cols)
@@ -126,7 +126,7 @@ Remember, we still have to add a file format column and transform the values in
 In [12]: p.addFileFormatCol()
 In [13]: p.substituteColumnValues('cellType', {'Pos':'NeuN+', 'Neg':'NeuN-'})
 ```
-The `addFileFormatCol` method defaults to a preprogrammed regex and uses column 'name' in the data view. But we can use a more flexible approach by using `annotator.utils.makeColFromRegex` if necessary.
+The `addFileFormatCol` method defaults to a preprogrammed regex and uses column 'name' in the data view. But we can use a more flexible approach by using `annotator.utils.colFromRegex` if necessary.
 
 If everything looks good, we can go ahead and push our changes back up to Synapse.
 

annotator/Pipeline.py

@@ -395,7 +395,7 @@ def _parseView(self, view, sortCols, isMeta=False):
         if isinstance(view, str):
             return utils.synread(self.syn, view, sortCols)
         elif isinstance(view, list) and meta:
-            return utils.combineSynapseTabulars(self.syn, view)
+            return utils.combineSynapseTabulars(self.syn, view, axis=1)
         elif isinstance(view, pd.DataFrame):
             if sortCols:
                 view = view.sort_index(1)

annotator/utils.py

@@ -39,7 +39,7 @@ def _synread(synId, f, syn_, sortCols):
     else:
         return d
 
-def convertClipboardToDict(sep):
+def clipboardToDict(sep):
     """ Parse two-column delimited clipboard contents to a dictionary.
 
     Parameters
@@ -149,8 +149,8 @@ def makeColumns(obj, asSynapseCols=True):
     elif isinstance(obj, dict): return _colsFromDict(obj, asSynapseCols)
     elif isinstance(obj, list): return _colsFromList(obj, asSynapseCols)
 
-def combineSynapseTabulars(syn, tabulars):
-    """ Concatenate tabular files column-wise.
+def combineSynapseTabulars(syn, tabulars, axis=0):
+    """ Concatenate tabular files.
 
     Parameters
     ----------
@@ -163,7 +163,7 @@ def combineSynapseTabulars(syn, tabulars):
     pandas.DataFrame
     """
     tabulars = synread(syn, tabulars)
-    return pd.concat(tabulars, axis=1, ignore_index=True).sort_index(1)
+    return pd.concat(tabulars, axis=axis, ignore_index=True).sort_index(1)
 
 def inferValues(df, col, referenceCols):
     """ Fill in values for indices which match on `referenceCols`
@@ -206,7 +206,7 @@ def substituteColumnValues(referenceList, mod):
             type(referenceList)))
     return referenceList
 
-def makeColFromRegex(referenceList, regex):
+def colFromRegex(referenceList, regex):
     """ Return a list created by mapping a regular expression to another list.
     The regular expression must contain at least one capture group.
 

setup.py

@@ -0,0 +1,14 @@
+from setuptools import setup, find_packages
+
+setup(
+    name='annotator',
+    version='0.1',
+    description='A Synapse annotations automation tool.',
+    url='https://github.com/Sage-Bionetworks/annotator',
+    author='Phil Snyder',
+    author_email='phil.snyder@sagebase.org',
+    license='MIT',
+    packages=find_packages(),
+    install_requires=[
+        'pandas',
+        'synapseclient'])