Merge branch 'master' of https://github.com/zsloan/genenetwork2 into zsloan

3 files changed, 181 insertions, 16 deletions

diff --git a/wqflask/utility/chunks.py b/wqflask/utility/chunks.py
new file mode 100644
index 00000000..9565fb96
--- /dev/null
+++ b/wqflask/utility/chunks.py
@@ -0,0 +1,96 @@
+from __future__ import absolute_import, print_function, division
+
+import math
+import time
+
+
+def divide_into_chunks(the_list, number_chunks):
+    """Divides a list into approximately number_chunks smaller lists
+    
+    >>> divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 3)
+    [[1, 2, 7], [3, 22, 8], [5, 22, 333]]
+    >>> divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 4)                                                                                                                                                     
+    [[1, 2, 7], [3, 22, 8], [5, 22, 333]]
+    >>> divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 5)                                                                                                                                                     
+    [[1, 2], [7, 3], [22, 8], [5, 22], [333]]
+    >>>
+    
+    """
+    length = len(the_list)
+
+    if length == 0:
+        return [[]]
+    
+    if length <= number_chunks:
+        number_chunks = length
+
+    chunksize = int(math.ceil(length / number_chunks))
+
+    chunks = []
+    for counter in range(0, length, chunksize):
+        chunks.append(the_list[counter:counter+chunksize])
+
+    return chunks
+
+def _confirm_chunk(original, result):
+    all_chunked = []
+    for chunk in result:
+        all_chunked.extend(chunk)
+    print("length of all chunked:", len(all_chunked))
+    assert original == all_chunked, "You didn't chunk right"
+
+
+def _chunk_test(divide_func):
+    import random
+    random.seed(7)
+
+    number_exact = 0
+    total_amount_off = 0
+
+    for test in range(1, 1001):
+        print("\n\ntest:", test)
+        number_chunks = random.randint(1, 20)
+        number_elements = random.randint(0, 100)
+        the_list = list(range(1, number_elements))
+        result = divide_func(the_list, number_chunks)
+
+        print("Dividing list of length {} into approximately {} chunks - got {} chunks".format(
+            len(the_list), number_chunks, len(result)))
+        print("result:", result)
+
+        _confirm_chunk(the_list, result)
+
+        amount_off = abs(number_chunks - len(result))
+        if amount_off == 0:
+            number_exact += 1
+        else:
+            total_amount_off += amount_off
+
+
+        print("\n{} exact out of {}    [Total amount off: {}]".format(number_exact,
+                                                                      test,
+                                                                      total_amount_off))
+    assert number_exact == 558
+    assert total_amount_off == 1580
+    return number_exact, total_amount_off
+
+
+def _main():
+    info = dict()
+    #funcs = (("sam", sam_divide_into_chunks), ("zach", zach_divide_into_chunks))
+    funcs = (("only one", divide_into_chunks),)
+    for name, func in funcs:
+        start = time.time()
+        number_exact, total_amount_off = _chunk_test(func)
+        took = time.time() - start
+        info[name] = dict(number_exact=number_exact,
+                          total_amount_off=total_amount_off,
+                          took=took)
+
+    print("info is:", info)
+
+if __name__ == '__main__':
+    _main()
+    print("\nConfirming doctests...")
+    import doctest
+    doctest.testmod()
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
new file mode 100644
index 00000000..760ded7c
--- /dev/null
+++ b/wqflask/utility/tools.py
@@ -0,0 +1,84 @@
+# Tools/paths finder resolves external paths from settings and/or environment
+# variables
+#
+# Currently supported:
+#
+#   PYLMM_PATH finds the root of the git repository of the pylmm_gn2 tool 
+
+import os
+import sys
+from wqflask import app
+
+def get_setting(id,default,guess,get_valid_path):
+    """
+    Resolve a setting from the environment or the global settings in app.config
+    """
+    # ---- Check whether environment exists
+    path = get_valid_path(os.environ.get(id))
+    # ---- Check whether setting exists
+    setting = app.config.get(id)
+    if not path:
+        path = get_valid_path(setting)
+    # ---- Check whether default exists
+    if not path:
+        path = get_valid_path(default)
+    # ---- Guess directory
+    if not path:
+        if not setting:
+            setting = guess
+        path = get_valid_path(guess)
+    if not path:
+        raise Exception(id+' '+setting+' path unknown or faulty (update settings.py?). '+id+' should point to the root of the git repository')
+
+    return path
+
+def pylmm_command(default=None):
+    """
+    Return the path to the repository and the python command to call
+    """
+    def get_valid_path(path):
+        """Test for a valid repository"""
+        if path:
+            sys.stderr.write("Trying PYLMM_PATH in "+path+"\n")
+        if path and os.path.isfile(path+'/pylmm_gn2/lmm.py'):
+            return path
+        else:
+            None
+
+    guess = os.environ.get('HOME')+'/pylmm_gn2'
+    path = get_setting('PYLMM_PATH',default,guess,get_valid_path)
+    pylmm_command = 'python '+path+'/pylmm_gn2/lmm.py'
+    return path,pylmm_command
+
+def plink_command(default=None):
+    """
+    Return the path to the repository and the python command to call
+    """
+    def get_valid_path(path):
+        """Test for a valid repository"""
+        if path:
+            sys.stderr.write("Trying PLINK_PATH in "+path+"\n")
+        if path and os.path.isfile(path+'/plink'):
+            return path
+        else:
+            None
+
+    guess = os.environ.get('HOME')+'/plink'
+    path = get_setting('PLINK_PATH',default,guess,get_valid_path)
+    plink_command = path+'/plink'
+    return path,plink_command
+
+def gemma_command(default=None):
+    def get_valid_path(path):
+        """Test for a valid repository"""
+        if path:
+            sys.stderr.write("Trying PLINK_PATH in "+path+"\n")
+        if path and os.path.isfile(path+'/plink'):
+            return path
+        else:
+            None
+
+    guess = os.environ.get('HOME')+'/plink'
+    path = get_setting('PLINK_PATH',default,guess,get_valid_path)
+    gemma_command = path+'/gemma'
+    return path, gemma_command
\ No newline at end of file
diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py
index 4d7981d9..f842dde0 100755
--- a/wqflask/utility/webqtlUtil.py
+++ b/wqflask/utility/webqtlUtil.py
@@ -43,6 +43,7 @@ ParInfo ={
 'BXH':['BHF1', 'HBF1',  'C57BL/6J', 'C3H/HeJ'],
 'AKXD':['AKF1', 'KAF1', 'AKR/J', 'DBA/2J'],
 'BXD':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
+'C57BL-6JxC57BL-6NJF2':['', '', 'C57BL/6J', 'C57BL/6NJ'],
 'BXD300':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
 'B6BTBRF2':['B6BTBRF1', 'BTBRB6F1', 'C57BL/6J', 'BTBRT<+>tf/J'],
 'BHHBF2':['B6HF2','HB6F2','C57BL/6J','C3H/HeJ'],
@@ -880,22 +881,6 @@ def cmpGenoPos(A,B):
     except:
         return 0
 
-#XZhou: Must use "BINARY" to enable case sensitive comparison.
-def authUser(name,password,db, encrypt=None):
-    try:
-        if encrypt:
-            query = 'SELECT privilege, id,name,password, grpName FROM User WHERE name= BINARY \'%s\' and password= BINARY \'%s\'' % (name,password)
-        else:
-            query = 'SELECT privilege, id,name,password, grpName FROM User WHERE name= BINARY \'%s\' and password= BINARY SHA(\'%s\')' % (name,password)
-        db.execute(query)
-        records = db.fetchone()
-        if not records:
-            raise ValueError
-        return records#(privilege,id,name,password,grpName)
-    except:
-        return (None, None, None, None, None)
-
-
 def hasAccessToConfidentialPhenotypeTrait(privilege, userName, authorized_users):
     access_to_confidential_phenotype_trait = 0
     if webqtlConfig.USERDICT[privilege] > webqtlConfig.USERDICT['user']: