Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing

7 files changed, 69 insertions, 121 deletions

diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index cce8435d..9bc84d22 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -35,8 +35,6 @@ import sys, os
 from numarray import linear_algebra as la
 from numarray import ones, array, dot, swapaxes
 
-import reaper
-
 import webqtlUtil
 import corestats
 from base import webqtlConfig
diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index f9028f32..ed7462d1 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -6,7 +6,7 @@ import requests
 from base import data_set, webqtlConfig
 
 from utility import hmac
-from utility.redis_tools import get_redis_conn, get_resource_info, get_resource_id
+from utility.redis_tools import get_redis_conn, get_resource_info, get_resource_id, add_resource
 Redis = get_redis_conn()
 
 from flask import Flask, g, redirect, url_for
@@ -16,13 +16,7 @@ logger = logging.getLogger(__name__ )
 
 def check_resource_availability(dataset, trait_id=None):
 
-    #ZS: Check if super-user - we should probably come up with some way to integrate this into the proxy
-    if g.user_session.user_id in Redis.smembers("super_users"):
-       return webqtlConfig.SUPER_PRIVILEGES
-
-    response = None
-
-    #At least for now assume temporary entered traits are accessible#At least for now assume temporary entered traits are accessible
+    #At least for now assume temporary entered traits are accessible
     if type(dataset) == str:
         return webqtlConfig.DEFAULT_PRIVILEGES
     if dataset.type == "Temp":
@@ -33,9 +27,13 @@ def check_resource_availability(dataset, trait_id=None):
     if resource_id:
         resource_info = get_resource_info(resource_id)
         if not resource_info:
-            return webqtlConfig.DEFAULT_PRIVILEGES
-    else:
-        return response #ZS: Need to substitute in something that creates the resource in Redis later
+            resource_info = add_new_resource(dataset, trait_id)
+
+    #ZS: Check if super-user - we should probably come up with some way to integrate this into the proxy
+    if g.user_session.user_id in Redis.smembers("super_users"):
+       return webqtlConfig.SUPER_PRIVILEGES
+
+    response = None
 
     the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
     try:
@@ -43,10 +41,43 @@ def check_resource_availability(dataset, trait_id=None):
     except:
         response = resource_info['default_mask']
 
-    if response:
-        return response
-    else: #ZS: No idea how this would happen, but just in case
-        return False
+    return response
+
+def add_new_resource(dataset, trait_id=None):
+    resource_ob = {
+        'owner_id'    : webqtlConfig.DEFAULT_OWNER_ID,
+        'default_mask': webqtlConfig.DEFAULT_PRIVILEGES,
+        'group_masks' : {}
+    }
+
+    if dataset.type == "Publish":
+        resource_ob['name'] = get_group_code(dataset) + "_" + str(trait_id)
+        resource_ob['data'] = {
+            'dataset': dataset.id,
+            'trait'  : trait_id
+        }
+        resource_ob['type'] = 'dataset-publish'
+    elif dataset.type == "Geno":
+        resource_ob['name'] = dataset.name
+        resource_ob['data'] = {
+            'dataset': dataset.id
+        }
+        resource_ob['type'] = 'dataset-geno'
+    else:
+        resource_ob['name'] = dataset.name
+        resource_ob['data'] = {
+            'dataset': dataset.id
+        }
+        resource_ob['type'] = 'dataset-probeset'
+
+    resource_info = add_resource(resource_ob, update=False)
+
+    return resource_info
+
+def get_group_code(dataset):
+    results = g.db.execute("SELECT InbredSetCode from InbredSet where Name='{}'".format(dataset.group.name)).fetchone()
+
+    return results[0]
 
 def check_admin(resource_id=None):
     the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
diff --git a/wqflask/utility/chunks.py b/wqflask/utility/chunks.py
index b0e33c08..d91b9bf4 100644
--- a/wqflask/utility/chunks.py
+++ b/wqflask/utility/chunks.py
@@ -31,66 +31,3 @@ def divide_into_chunks(the_list, number_chunks):
         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/corr_result_helpers.py b/wqflask/utility/corr_result_helpers.py
index b543c589..ea3ababf 100644
--- a/wqflask/utility/corr_result_helpers.py
+++ b/wqflask/utility/corr_result_helpers.py
@@ -14,15 +14,11 @@ def normalize_values(a_values, b_values):
     min_length = min(len(a_values), len(b_values))
     a_new = []
     b_new = []
-    for counter in range(min_length):
-        if (a_values[counter] or a_values[counter] == 0) and (b_values[counter] or b_values[counter] == 0):
-            a_new.append(a_values[counter])
-            b_new.append(b_values[counter])
-
-    num_overlap = len(a_new)
-    assert num_overlap == len(b_new), "Lengths should be the same"
-
-    return a_new, b_new, num_overlap
+    for a, b in zip(a_values, b_values):
+        if not (a == None or b == None):
+            a_new.append(a)
+            b_new.append(b)
+    return a_new, b_new, len(a_new)
 
 
 def common_keys(a_samples, b_samples):
@@ -37,20 +33,10 @@ def common_keys(a_samples, b_samples):
 
 def normalize_values_with_samples(a_samples, b_samples):
     common_samples = common_keys(a_samples, b_samples)
-
     a_new = {}
     b_new = {}
     for sample in common_samples:
         a_new[sample] = a_samples[sample]
         b_new[sample] = b_samples[sample]
 
-    num_overlap = len(a_new)
-    assert num_overlap == len(b_new), "Lengths should be the same"
-
-    return a_new, b_new, num_overlap
-
-
-
-if __name__ == '__main__':
-    import doctest
-    doctest.testmod()
\ No newline at end of file
+    return a_new, b_new, len(a_new)
diff --git a/wqflask/utility/formatting.py b/wqflask/utility/formatting.py
index e53dda22..1da3e9b7 100644
--- a/wqflask/utility/formatting.py
+++ b/wqflask/utility/formatting.py
@@ -28,21 +28,20 @@ def numify(number, singular=None, plural=None):
     '12,334 hippopotami'
 
     """
-    num_repr = {1 : "one",
-                2 : "two",
-                3 : "three",
-                4 : "four",
-                5 : "five",
-                6 : "six",
-                7 : "seven",
-                8 : "eight",
-                9 : "nine",
-                10 : "ten",
-                11 : "eleven",
-                12 : "twelve"}
-
-    #Below line commented out cause doesn't work in Python 2.4
-    #assert all((singular, plural)) or not any((singular, plural)), "Need to pass two words or none"
+    num_repr = {0: "zero",
+                1: "one",
+                2: "two",
+                3: "three",
+                4: "four",
+                5: "five",
+                6: "six",
+                7: "seven",
+                8: "eight",
+                9: "nine",
+                10: "ten",
+                11: "eleven",
+                12: "twelve"}
+
     if number == 1:
         word = singular
     else:
diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py
index 6c912a23..1377a564 100644
--- a/wqflask/utility/redis_tools.py
+++ b/wqflask/utility/redis_tools.py
@@ -264,17 +264,14 @@ def get_resources():
     return resource_list
 
 def get_resource_id(dataset, trait_id=None):
+    resource_id = False
     if dataset.type == "Publish":
         if trait_id:
             resource_id = hmac.hmac_creation("{}:{}:{}".format('dataset-publish', dataset.id, trait_id))
-        else:
-            return False
     elif dataset.type == "ProbeSet":
         resource_id = hmac.hmac_creation("{}:{}".format('dataset-probeset', dataset.id))
     elif dataset.type == "Geno":
         resource_id = hmac.hmac_creation("{}:{}".format('dataset-geno', dataset.id))
-    else:
-        return False
 
     return resource_id
 
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 89d88516..77db5d53 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -270,8 +270,8 @@ if ORCID_CLIENT_ID != 'UNKNOWN' and ORCID_CLIENT_SECRET:
                       ORCID_CLIENT_ID+"&client_secret="+ORCID_CLIENT_SECRET
     ORCID_TOKEN_URL = get_setting('ORCID_TOKEN_URL')
 
-# ELASTICSEARCH_HOST = get_setting('ELASTICSEARCH_HOST')
-# ELASTICSEARCH_PORT = get_setting('ELASTICSEARCH_PORT')
+ELASTICSEARCH_HOST = get_setting('ELASTICSEARCH_HOST')
+ELASTICSEARCH_PORT = get_setting('ELASTICSEARCH_PORT')
 # import utility.elasticsearch_tools as es
 # es.test_elasticsearch_connection()