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-rw-r--r--wqflask/utility/Plot.py2
-rw-r--r--wqflask/utility/authentication_tools.py61
-rw-r--r--wqflask/utility/chunks.py63
-rw-r--r--wqflask/utility/corr_result_helpers.py26
-rw-r--r--wqflask/utility/formatting.py29
-rw-r--r--wqflask/utility/redis_tools.py5
-rw-r--r--wqflask/utility/tools.py4
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()
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-29 19:43:24 +0000