Merge pull request #5 from thehyve/dev

Get latest fixes and Py3 support from Dev

arborist/__init__.py

@@ -1,4 +1,4 @@
-
+#!/usr/bin/env python3
 import os
 import sys
 from collections import OrderedDict
@@ -11,13 +11,13 @@
 import urllib
 from markupsafe import Markup
 
-from functions.params import Clinical_params, Expression_params, get_study_id
-from functions.exceptions import HyveException, HyveIOException
-from functions.clinical import columns_to_tree, json_to_columns, getchildren, \
+from .functions.params import Clinical_params, Expression_params, get_study_id
+from .functions.exceptions import HyveException, HyveIOException
+from .functions.clinical import columns_to_tree, json_to_columns, getchildren, \
                                get_datafiles, get_column_map_file, \
                                add_to_column_file, get_word_map
-from functions.feedback import get_feedback_dict, merge_feedback_dicts
-from functions.highdim import subject_sample_to_tree, get_subject_sample_map
+from .functions.feedback import get_feedback_dict, merge_feedback_dicts
+from .functions.highdim import subject_sample_to_tree, get_subject_sample_map
 
 STUDIES_FOLDER = 'studies'
 ALLOWED_EXTENSIONS = set(['txt', 'tsv'])
@@ -55,13 +55,20 @@ def add_slash_if_not_windows(url_path):
     return url_path
 
 
+def replace_back_with_forward_slash(string):
+    string = string.replace('\\', '/')
+    return string
+
+
 class FolderPathConverter(BaseConverter):
     def __init__(self, url_map):
         super(FolderPathConverter, self).__init__(url_map)
         self.regex = '.*'
 
     def to_python(self, value):
-        return add_slash_if_not_windows(value)
+        value = add_slash_if_not_windows(value)
+        value = replace_back_with_forward_slash(value)
+        return value
 
     def to_url(self, value):
         return value
@@ -80,7 +87,10 @@ def urlencode_filter(s):
     if type(s) == 'Markup':
         s = s.unescape()
     s = s.encode('utf8')
-    s = urllib.quote_plus(s)
+    if sys.version_info.major == 2:
+        s = urllib.quote_plus(s)
+    else:
+        s = urllib.parse.quote_plus(s)
     return Markup(s)
 
 
@@ -379,7 +389,7 @@ def save_columnsfile(studiesfolder, study):
 
     columnsfile = get_column_map_file(studiesfolder, study)
     if columnsfile is not None:
-        columnmappingfile = open(columnsfile, 'wb')
+        columnmappingfile = open(columnsfile, 'w')
         columnmappingfile.write(tree)
         columnmappingfile.close()
 

arborist/functions/clinical.py

@@ -1,8 +1,8 @@
 import csv
 import os
 
-from feedback import get_feedback_dict
-from params import Clinical_params
+from .feedback import get_feedback_dict
+from .params import Clinical_params
 
 
 outoftree = 'OUT OF TREE'
@@ -26,6 +26,16 @@
                   'New Data Value']
 
 
+def columns_not_present(line, column_list):
+    """Return True if one or more of column_list are not present"""
+    if len(line) == 0:
+        return False
+    for column in column_list:
+        if line[column] == '':
+            return False
+    return True
+
+
 def columns_to_tree(filename):
     with open(filename, 'rU') as csvfile:
         csvreader = csv.reader(csvfile, delimiter='\t', quotechar='"')
@@ -36,8 +46,7 @@ def columns_to_tree(filename):
 
         for line in csvreader:
             # Skip lines without filename, column number or data label
-            if line[filenamecolumn] != '' and line[columnnumbercolumn] != '' \
-                                          and line[datalabelcolumn] != '':
+            if columns_not_present(line, [filenamecolumn, columnnumbercolumn, datalabelcolumn]):
                 # If categorycode is empty this is a special concept that is
                 # not in the tree
                 # Eg SUBJ_ID, STUDY_ID, OMIT or DATA LABEL
@@ -192,7 +201,8 @@ def get_datafiles(columnfilename):
         csvreader = csv.reader(csvfile, delimiter='\t', quotechar='"')
         next(csvreader)
         for line in csvreader:
-            datafiles.add(line[filenamecolumn])
+            if len(line) > 0:
+                datafiles.add(line[filenamecolumn])
 
     return datafiles
 
@@ -210,7 +220,7 @@ def get_column_map_file(studiesfolder, study):
 def add_to_column_file(datafilename, columnmappingfilename):
     with open(datafilename, 'rU') as csvfile:
         csvreader = csv.reader(csvfile, delimiter='\t', quotechar='"')
-        headerline = csvreader.next()
+        headerline = next(csvreader)
         with open(columnmappingfilename, "a") as columnmappingfile:
             i = 1
             for header in headerline:

arborist/functions/feedback.py

@@ -1,4 +1,4 @@
-from exceptions import HyveException
+from .exceptions import HyveException
 feedback_categories = ['errors', 'warnings', 'infos']
 
 

arborist/functions/highdim.py

@@ -1,7 +1,7 @@
 import csv
 import os
 
-from params import Expression_params
+from .params import Expression_params
 
 subject_sample_map_headers = ['STUDY_ID', 'SITE_ID', 'SUBJECT_ID', 'SAMPLE_ID',
                               'PLATFORM', 'TISSUETYPE', 'ATTR1', 'ATTR2',

arborist/functions/params.py

@@ -1,7 +1,7 @@
 import os
 
-from exceptions import HyveException, HyveIOException
-from feedback import get_feedback_dict, merge_feedback_dicts
+from .exceptions import HyveException, HyveIOException
+from .feedback import get_feedback_dict, merge_feedback_dicts
 
 
 class Params(object):

docs/building_on_windows.md

@@ -3,3 +3,6 @@ To build the code into a packaged executable for Windows you can use py2exe. To
 
 ## Tips
 * Building is recommended when having installed 32bit Python (Windows version should not matter). Building on 64bit Python as not been tested. Furthermore, the executable would not be able to run on 32 bit Windows while not providing any benefits to the user.
+
+## Known issues
+* The current version of py2exe (0.9.2.2) does not support python3.5.  Building should work for python3.3 and python3.4.

runserver.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 from arborist import app
 import socket
 import argparse