Move CSV files into a specific directory

Author: pafonta

nat/additionsToOntologies.csv nat/data/additionsToOntologies.csvnat/additionsToOntologies.csv renamed to nat/data/additionsToOntologies.csv

@@ -2,16 +2,15 @@
 
 __author__ = "Christian O'Reilly"
 
-import os
 import csv
 from io import StringIO
+
 import pandas as pd
 
+from nat.utils import data_path
 from .tag import RequiredTag
 
 
-
-
 class ParameterTypeTree:
 
     def __init__(self, value):
@@ -89,7 +88,7 @@ def addChildren(tree, df):
     def getParamTypeDF(fileName = None):
 
         if fileName is None:
-            fileName = os.path.join(os.path.dirname(__file__), "modelingDictionary.csv")
+            fileName = data_path("modelingDictionary.csv")
 
         df = pd.read_csv(fileName, skip_blank_lines=True, comment="#",
                          delimiter=";", quotechar='"',
@@ -103,7 +102,7 @@ def getParamTypeDF(fileName = None):
 def getParameterTypes(fileName = None):
 
     if fileName is None:
-        fileName = os.path.join(os.path.dirname(__file__), "modelingDictionary.csv")
+        fileName = data_path("modelingDictionary.csv")
 
     with open(fileName, 'r') as f:
         lines = f.readlines()

nat/modelingDictionary.csv nat/data/modelingDictionary.csvnat/modelingDictionary.csv renamed to nat/data/modelingDictionary.csv

@@ -12,7 +12,7 @@
 import numpy as np
 from quantities import Quantity
 
-from nat import utils
+from nat.utils import data_directory
 from .ageResolver import AgeResolver
 from .aggregators import SampleAggregator
 from .annotationSearch import ParameterGetter
@@ -63,7 +63,7 @@ def copy(self):
     def setZoteroLib(self, library_id, library_type, api_key):
         # FIXME Delayed refactoring.
         if library_id is not None and library_type is not None and api_key is not None:
-            work_dir = utils.working_directory()
+            work_dir = data_directory()
             self.zotWrap = ZoteroWrap(library_id, library_type, api_key, work_dir)
             # TODO Implement an offline mode. Catch PyZoteroError.
             self.zotWrap.initialize()

nat/modelingDictionary_relationships.csv …ata/modelingDictionary_relationships.csvnat/modelingDictionary_relationships.csv renamed to nat/data/modelingDictionary_relationships.csv nat/modelingDictionary_relationships.csv renamed to nat/data/modelingDictionary_relationships.csv

@@ -3,18 +3,19 @@
 __author__ = 'oreilly'
 __email__  = 'christian.oreilly@epfl.ch'
 
+import os
+import pickle
 
-from .tagUtilities import nlx2ks
-from .tag import RequiredTag
-from .modelingParameter import ParameterTypeTree
-#from .scigraph_client import Graph
-from .ontoDic import OntoDic
+import numpy as np
+import pandas as pd
 import requests
 
-import os
-import pandas as pd
-import numpy as np
-import pickle
+from nat.utils import data_path
+from .modelingParameter import ParameterTypeTree
+# from .scigraph_client import Graph
+from .ontoDic import OntoDic
+from .tag import RequiredTag
+from .tagUtilities import nlx2ks
 
 rootIDs = {}
 
@@ -33,7 +34,7 @@ def flatten_list(l):
 
 def getBBPChildren(root_id, df=None, childrenDic=None):
     if df is None:
-        csvFileName = os.path.join(os.path.dirname(__file__), './additionsToOntologies.csv')
+        csvFileName = data_path("additionsToOntologies.csv")
 
         df = pd.read_csv(csvFileName, skip_blank_lines=True, comment="#", 
                          delimiter=";", names=["id", "label", "definition", "superCategory", "synonyms"])    
@@ -173,7 +174,7 @@ def addSuppTerms(dic):
 
 
 def appendAdditions(treeData, dicData):
-    csvFileName = os.path.join(os.path.dirname(__file__), './additionsToOntologies.csv')
+    csvFileName = data_path("additionsToOntologies.csv")
 
     df = pd.read_csv(csvFileName, skip_blank_lines=True, comment="#", 
                      delimiter=";", names=["id", "label", "definition", "superCategory", "synonyms"])

nat/modelingParameter.py

@@ -6,18 +6,22 @@
 """
 
 import os
-import sys
 from copy import copy
 from glob import glob
 from os.path import basename
 
 
-def working_directory():
-    """Return the working directory according to it being bundled/frozen."""
-    if getattr(sys, 'frozen', False):
-        return os.path.dirname(sys.executable)
-    else:
-        return os.path.dirname(__file__)
+def data_directory():
+    """Return the absolute path to the directory containing the package data."""
+    package_directory = os.path.abspath(os.path.dirname(__file__))
+    return os.path.join(package_directory, "data")
+
+
+def data_path(filename):
+    """Return the absolute path to a file in the directory containing the package data."""
+    return os.path.join(data_directory(), filename)
+
+
 
 # See http://www.w3schools.com/tags/ref_urlencode.asp for list of encoders
 
@@ -91,7 +95,7 @@ def test_ID_conversion():
     library_type = "group"
     api_key = "4D3rDZsAVBd139alqoVZBKOO"
     library_id = "427244"
-    work_dir = working_directory()
+    work_dir = data_directory()
     zot_wrap = ZoteroWrap(library_id, library_type, api_key, work_dir)
     # TODO Implement an offline mode. Catch PyZoteroError.
     zot_wrap.initialize()