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authorPjotr Prins2020-07-25 08:24:33 +0100
committerPjotr Prins2020-07-25 08:24:33 +0100
commit9f8beacddb71aac9905c896b9d81caf45b4735a0 (patch)
tree1f3ea2b1bdb6835a6c172b739e6872bf59af6181 /wqflask
parentc249ba2ef7d691227da8864838dfc97db68d4084 (diff)
parentf66da35a09cbb8da13cfb142cbe3ff208404970b (diff)
downloadgenenetwork2-9f8beacddb71aac9905c896b9d81caf45b4735a0.tar.gz
Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/.coveragerc28
-rw-r--r--wqflask/base/GeneralObject.py77
-rw-r--r--wqflask/base/data_set.py307
-rw-r--r--wqflask/base/trait.py19
-rw-r--r--wqflask/cfg/default_settings.py1
-rw-r--r--wqflask/mock/es_double.py15
-rw-r--r--wqflask/tests/__init__.py (renamed from wqflask/cfg/__init__.py)0
-rw-r--r--wqflask/tests/base/__init__.py (renamed from wqflask/mock/__init__.py)0
-rw-r--r--wqflask/tests/base/test_data_set.py35
-rw-r--r--wqflask/tests/base/test_general_object.py41
-rw-r--r--wqflask/tests/utility/__init__.py0
-rw-r--r--wqflask/tests/utility/test_chunks.py19
-rw-r--r--wqflask/tests/utility/test_corestats.py55
-rw-r--r--wqflask/tests/utility/test_corr_result_helpers.py32
-rw-r--r--wqflask/tests/utility/test_formatting.py33
-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
-rw-r--r--wqflask/wqflask/__init__.py3
-rw-r--r--wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py2
-rw-r--r--wqflask/wqflask/correlation/show_corr_results.py2
-rw-r--r--wqflask/wqflask/correlation_matrix/show_corr_matrix.py2
-rw-r--r--wqflask/wqflask/export_traits.py119
-rw-r--r--wqflask/wqflask/heatmap/heatmap.py2
-rw-r--r--wqflask/wqflask/network_graph/network_graph.py2
-rw-r--r--wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js9
-rw-r--r--wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js5
-rw-r--r--wqflask/wqflask/static/new/javascript/get_traits_from_collection.js48
-rw-r--r--wqflask/wqflask/static/new/javascript/search_results.js16
-rw-r--r--wqflask/wqflask/templates/base.html8
-rw-r--r--wqflask/wqflask/templates/correlation_page.html6
-rw-r--r--wqflask/wqflask/templates/gsearch_gene.html5
-rw-r--r--wqflask/wqflask/templates/gsearch_pheno.html5
-rw-r--r--wqflask/wqflask/templates/mapping_results.html1
-rw-r--r--wqflask/wqflask/templates/search_result_page.html18
-rw-r--r--wqflask/wqflask/templates/show_trait.html5
-rw-r--r--wqflask/wqflask/templates/show_trait_calculate_correlations.html2
-rw-r--r--wqflask/wqflask/templates/show_trait_details.html2
-rwxr-xr-xwqflask/wqflask/templates/show_trait_mapping_tools.html10
-rw-r--r--wqflask/wqflask/templates/snp_browser.html4
-rw-r--r--wqflask/wqflask/views.py28
45 files changed, 720 insertions, 436 deletions
diff --git a/wqflask/.coveragerc b/wqflask/.coveragerc
new file mode 100644
index 00000000..939e51b9
--- /dev/null
+++ b/wqflask/.coveragerc
@@ -0,0 +1,28 @@
+[run]
+branch = True
+
+[report]
+omit =
+ */site-packages/*
+ tests/*
+# Regexes for lines to exclude from consideration
+exclude_lines =
+# Have to re-enable the standard pragma
+ pragma: no cover
+
+ # Don't complain about missing debug-only code:
+ def __repr__
+ if self\.debug
+
+ # Don't complain if tests don't hit defensive assertion code:
+ raise AssertionError
+ raise NotImplementedError
+
+ # Don't complain if non-runnable code isn't run:
+ if 0:
+ if __name__ == .__main__.:
+
+ignore_errors = False
+
+[html]
+directory = coverage_html_report \ No newline at end of file
diff --git a/wqflask/base/GeneralObject.py b/wqflask/base/GeneralObject.py
index 02a1ef06..0fccaab3 100644
--- a/wqflask/base/GeneralObject.py
+++ b/wqflask/base/GeneralObject.py
@@ -25,44 +25,41 @@
# Last updated by GeneNetwork Core Team 2010/10/20
class GeneralObject:
- """
- Base class to define an Object.
- a = [Spam(1, 4), Spam(9, 3), Spam(4,6)]
- a.sort(lambda x, y: cmp(x.eggs, y.eggs))
- """
+ """
+ Base class to define an Object.
+ a = [Spam(1, 4), Spam(9, 3), Spam(4,6)]
+ a.sort(lambda x, y: cmp(x.eggs, y.eggs))
+ """
- def __init__(self, *args, **kw):
- self.contents = list(args)
- for name, value in kw.items():
- setattr(self, name, value)
-
- def __setitem__(self, key, value):
- setattr(self, key, value)
-
- def __getitem__(self, key):
- return getattr(self, key)
-
- def __getattr__(self, key):
- if key in self.__dict__.keys():
- return self.__dict__[key]
- else:
- return eval("self.__dict__.%s" % key)
-
- def __len__(self):
- return len(self.__dict__) - 1
-
- def __str__(self):
- s = ''
- for key in self.__dict__.keys():
- if key != 'contents':
- s += '%s = %s\n' % (key,self.__dict__[key])
- return s
-
- def __repr__(self):
- s = ''
- for key in self.__dict__.keys():
- s += '%s = %s\n' % (key,self.__dict__[key])
- return s
-
- def __cmp__(self,other):
- return len(self.__dict__.keys()).__cmp__(len(other.__dict__.keys())) \ No newline at end of file
+ def __init__(self, *args, **kw):
+ self.contents = list(args)
+ for name, value in kw.items():
+ setattr(self, name, value)
+
+ def __setitem__(self, key, value):
+ setattr(self, key, value)
+
+ def __getitem__(self, key):
+ return getattr(self, key)
+
+ def __getattr__(self, key):
+ return eval("self.__dict__.%s" % key)
+
+ def __len__(self):
+ return len(self.__dict__) - 1
+
+ def __str__(self):
+ s = ''
+ for key in self.__dict__.keys():
+ if key != 'contents':
+ s += '%s = %s\n' % (key, self.__dict__[key])
+ return s
+
+ def __repr__(self):
+ s = ''
+ for key in self.__dict__.keys():
+ s += '%s = %s\n' % (key, self.__dict__[key])
+ return s
+
+ def __cmp__(self, other):
+ return len(self.__dict__.keys()).__cmp__(len(other.__dict__.keys()))
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 2272b6ee..5d562871 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -19,6 +19,23 @@
# This module is used by GeneNetwork project (www.genenetwork.org)
from __future__ import absolute_import, print_function, division
+from db.call import fetchall, fetchone, fetch1
+from utility.logger import getLogger
+from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists, GN2_BASE_URL
+from db.gn_server import menu_main
+from pprint import pformat as pf
+from MySQLdb import escape_string as escape
+from maintenance import get_group_samplelists
+from utility.tools import locate, locate_ignore_error, flat_files
+from utility import gen_geno_ob
+from utility import chunks
+from utility.benchmark import Bench
+from utility import webqtlUtil
+from db import webqtlDatabaseFunction
+from base import species
+from base import webqtlConfig
+import reaper
+from flask import Flask, g
import os
import math
import string
@@ -32,39 +49,17 @@ import cPickle as pickle
import itertools
from redis import Redis
-Redis = Redis()
-
-from flask import Flask, g
-
-import reaper
-
-from base import webqtlConfig
-from base import species
-from db import webqtlDatabaseFunction
-from utility import webqtlUtil
-from utility.benchmark import Bench
-from utility import chunks
-from utility import gen_geno_ob
-from utility.tools import locate, locate_ignore_error, flat_files
-
-from wqflask.api import gen_menu
-
-from maintenance import get_group_samplelists
-from MySQLdb import escape_string as escape
-from pprint import pformat as pf
-from db.gn_server import menu_main
-from db.call import fetchall,fetchone,fetch1
+r = Redis()
-from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists, GN2_BASE_URL
-from utility.logger import getLogger
-logger = getLogger(__name__ )
+logger = getLogger(__name__)
# Used by create_database to instantiate objects
# Each subclass will add to this
DS_NAME_MAP = {}
-def create_dataset(dataset_name, dataset_type = None, get_samplelist = True, group_name = None):
+
+def create_dataset(dataset_name, dataset_type=None, get_samplelist=True, group_name=None):
if dataset_name == "Temp":
dataset_type = "Temp"
@@ -78,9 +73,10 @@ def create_dataset(dataset_name, dataset_type = None, get_samplelist = True, gro
else:
return dataset_class(dataset_name, get_samplelist)
-class Dataset_Types(object):
- def __init__(self):
+class DatasetType:
+
+ def __init__(self, redis_instance):
"""Create a dictionary of samples where the value is set to Geno,
Publish or ProbeSet. E.g.
@@ -95,14 +91,15 @@ Publish or ProbeSet. E.g.
'B139_K_1206_R': 'ProbeSet' ...
"""
+ self.redis_instance = redis_instance
self.datasets = {}
-
- data = Redis.get("dataset_structure")
+ data = redis_instance.get("dataset_structure")
if data:
self.datasets = json.loads(data)
- else: #ZS: I don't think this should ever run unless Redis is emptied
+ else: # ZS: I don't think this should ever run unless Redis is emptied
try:
- data = json.loads(requests.get(GN2_BASE_URL + "/api/v_pre1/gen_dropdown", timeout = 5).content)
+ data = json.loads(requests.get(
+ GN2_BASE_URL + "/api/v_pre1/gen_dropdown", timeout=5).content)
for species in data['datasets']:
for group in data['datasets'][species]:
for dataset_type in data['datasets'][species][group]:
@@ -118,10 +115,10 @@ Publish or ProbeSet. E.g.
except:
pass
- Redis.set("dataset_structure", json.dumps(self.datasets))
+ redis_instance.set("dataset_structure", json.dumps(self.datasets))
# Set LOG_LEVEL_DEBUG=5 to see the following:
- logger.debugf(5, "datasets",self.datasets)
+ logger.debugf(5, "datasets", self.datasets)
def __call__(self, name):
if name not in self.datasets:
@@ -137,7 +134,7 @@ Publish or ProbeSet. E.g.
results = g.db.execute(mrna_expr_query).fetchall()
if len(results):
self.datasets[name] = "ProbeSet"
- Redis.set("dataset_structure", json.dumps(self.datasets))
+ redis_instance.set("dataset_structure", json.dumps(self.datasets))
return self.datasets[name]
group_name = name.replace("Publish", "")
@@ -151,10 +148,10 @@ Publish or ProbeSet. E.g.
results = g.db.execute(pheno_query).fetchall()
if len(results):
self.datasets[name] = "Publish"
- Redis.set("dataset_structure", json.dumps(self.datasets))
+ redis_instance.set("dataset_structure", json.dumps(self.datasets))
return self.datasets[name]
- #ZS: For when there isn't an InfoFiles ID; not sure if this and the preceding query are both necessary
+ # ZS: For when there isn't an InfoFiles ID; not sure if this and the preceding query are both necessary
other_pheno_query = """SELECT PublishFreeze.Name
FROM PublishFreeze, InbredSet
WHERE InbredSet.Name = '{}' AND
@@ -163,10 +160,10 @@ Publish or ProbeSet. E.g.
results = g.db.execute(other_pheno_query).fetchall()
if len(results):
self.datasets[name] = "Publish"
- Redis.set("dataset_structure", json.dumps(self.datasets))
+ redis_instance.set("dataset_structure", json.dumps(self.datasets))
return self.datasets[name]
- geno_query = """
+ geno_query = """
SELECT
GenoFreeze.Id
FROM
@@ -178,21 +175,23 @@ Publish or ProbeSet. E.g.
results = g.db.execute(geno_query).fetchall()
if len(results):
self.datasets[name] = "Geno"
- Redis.set("dataset_structure", json.dumps(self.datasets))
+ self.redis_instance.set("dataset_structure", json.dumps(self.datasets))
return self.datasets[name]
- #ZS: It shouldn't ever reach this
+ # ZS: It shouldn't ever reach this
return None
else:
return self.datasets[name]
+
# Do the intensive work at startup one time only
-Dataset_Getter = Dataset_Types()
+Dataset_Getter = DatasetType(r)
+
def create_datasets_list():
if USE_REDIS:
key = "all_datasets"
- result = Redis.get(key)
+ result = r.get(key)
if result:
logger.debug("Redis cache hit")
@@ -208,16 +207,16 @@ def create_datasets_list():
for dataset_type in type_dict:
query = "SELECT Name FROM {}".format(type_dict[dataset_type])
for result in fetchall(query):
- #The query at the beginning of this function isn't
- #necessary here, but still would rather just reuse
- #it logger.debug("type: {}\tname:
- #{}".format(dataset_type, result.Name))
+ # The query at the beginning of this function isn't
+ # necessary here, but still would rather just reuse
+ # it logger.debug("type: {}\tname:
+ # {}".format(dataset_type, result.Name))
dataset = create_dataset(result.Name, dataset_type)
datasets.append(dataset)
if USE_REDIS:
- Redis.set(key, pickle.dumps(datasets, pickle.HIGHEST_PROTOCOL))
- Redis.expire(key, 60*60)
+ r.set(key, pickle.dumps(datasets, pickle.HIGHEST_PROTOCOL))
+ r.expire(key, 60*60)
return datasets
@@ -238,8 +237,9 @@ def mescape(*items):
class Markers(object):
"""Todo: Build in cacheing so it saves us reading the same file more than once"""
+
def __init__(self, name):
- json_data_fh = open(locate(name + ".json",'genotype/json'))
+ json_data_fh = open(locate(name + ".json", 'genotype/json'))
markers = []
with open("%s/%s_snps.txt" % (flat_files('genotype/bimbam'), name), 'r') as bimbam_fh:
@@ -271,7 +271,7 @@ class Markers(object):
if type(p_values) is list:
# THIS IS only needed for the case when we are limiting the number of p-values calculated
- #if len(self.markers) > len(p_values):
+ # if len(self.markers) > len(p_values):
# self.markers = self.markers[:len(p_values)]
for marker, p_value in itertools.izip(self.markers, p_values):
@@ -283,7 +283,7 @@ class Markers(object):
marker['lrs_value'] = 0
else:
marker['lod_score'] = -math.log10(marker['p_value'])
- #Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values
+ # Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values
marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61
elif type(p_values) is dict:
filtered_markers = []
@@ -298,18 +298,20 @@ class Markers(object):
marker['lrs_value'] = 0
else:
marker['lod_score'] = -math.log10(marker['p_value'])
- #Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values
- marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61
+ # Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values
+ marker['lrs_value'] = - \
+ math.log10(marker['p_value']) * 4.61
filtered_markers.append(marker)
- #else:
+ # else:
#logger.debug("marker {} NOT in p_values".format(i))
- #self.markers.remove(marker)
+ # self.markers.remove(marker)
#del self.markers[i]
self.markers = filtered_markers
+
class HumanMarkers(Markers):
- def __init__(self, name, specified_markers = []):
+ def __init__(self, name, specified_markers=[]):
marker_data_fh = open(flat_files('mapping') + '/' + name + '.bim')
self.markers = []
for line in marker_data_fh:
@@ -332,7 +334,6 @@ class HumanMarkers(Markers):
#logger.debug("markers is: ", pf(self.markers))
-
def add_pvalues(self, p_values):
super(HumanMarkers, self).add_pvalues(p_values)
@@ -345,12 +346,15 @@ class DatasetGroup(object):
has multiple datasets associated with it.
"""
+
def __init__(self, dataset, name=None):
"""This sets self.group and self.group_id"""
if name == None:
- self.name, self.id, self.genetic_type = fetchone(dataset.query_for_group)
+ self.name, self.id, self.genetic_type = fetchone(
+ dataset.query_for_group)
else:
- self.name, self.id, self.genetic_type = fetchone("SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType FROM InbredSet where Name='%s'" % name)
+ self.name, self.id, self.genetic_type = fetchone(
+ "SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType FROM InbredSet where Name='%s'" % name)
if self.name == 'BXD300':
self.name = "BXD"
@@ -369,7 +373,8 @@ class DatasetGroup(object):
def get_mapping_methods(self):
- mapping_id = g.db.execute("select MappingMethodId from InbredSet where Name= '%s'" % self.name).fetchone()[0]
+ mapping_id = g.db.execute(
+ "select MappingMethodId from InbredSet where Name= '%s'" % self.name).fetchone()[0]
if mapping_id == "1":
mapping_names = ["GEMMA", "QTLReaper", "R/qtl"]
elif mapping_id == "2":
@@ -426,22 +431,23 @@ class DatasetGroup(object):
result = None
key = "samplelist:v3:" + self.name
if USE_REDIS:
- result = Redis.get(key)
+ result = r.get(key)
if result is not None:
self.samplelist = json.loads(result)
else:
logger.debug("Cache not hit")
- genotype_fn = locate_ignore_error(self.name+".geno",'genotype')
+ genotype_fn = locate_ignore_error(self.name+".geno", 'genotype')
if genotype_fn:
- self.samplelist = get_group_samplelists.get_samplelist("geno", genotype_fn)
+ self.samplelist = get_group_samplelists.get_samplelist(
+ "geno", genotype_fn)
else:
self.samplelist = None
if USE_REDIS:
- Redis.set(key, json.dumps(self.samplelist))
- Redis.expire(key, 60*5)
+ r.set(key, json.dumps(self.samplelist))
+ r.expire(key, 60*5)
def all_samples_ordered(self):
result = []
@@ -451,15 +457,16 @@ class DatasetGroup(object):
def read_genotype_file(self, use_reaper=False):
'''Read genotype from .geno file instead of database'''
- #genotype_1 is Dataset Object without parents and f1
- #genotype_2 is Dataset Object with parents and f1 (not for intercross)
+ # genotype_1 is Dataset Object without parents and f1
+ # genotype_2 is Dataset Object with parents and f1 (not for intercross)
#genotype_1 = reaper.Dataset()
# reaper barfs on unicode filenames, so here we ensure it's a string
if self.genofile:
- if "RData" in self.genofile: #ZS: This is a temporary fix; I need to change the way the JSON files that point to multiple genotype files are structured to point to other file types like RData
- full_filename = str(locate(self.genofile.split(".")[0] + ".geno", 'genotype'))
+ if "RData" in self.genofile: # ZS: This is a temporary fix; I need to change the way the JSON files that point to multiple genotype files are structured to point to other file types like RData
+ full_filename = str(
+ locate(self.genofile.split(".")[0] + ".geno", 'genotype'))
else:
full_filename = str(locate(self.genofile, 'genotype'))
else:
@@ -472,11 +479,12 @@ class DatasetGroup(object):
genotype_1 = gen_geno_ob.genotype(full_filename)
if genotype_1.type == "group" and self.parlist:
- genotype_2 = genotype_1.add(Mat=self.parlist[0], Pat=self.parlist[1]) #, F1=_f1)
+ genotype_2 = genotype_1.add(
+ Mat=self.parlist[0], Pat=self.parlist[1]) # , F1=_f1)
else:
genotype_2 = genotype_1
- #determine default genotype object
+ # determine default genotype object
if self.incparentsf1 and genotype_1.type != "intercross":
genotype = genotype_2
else:
@@ -487,7 +495,8 @@ class DatasetGroup(object):
return genotype
-def datasets(group_name, this_group = None):
+
+def datasets(group_name, this_group=None):
key = "group_dataset_menu:v2:" + group_name
dataset_menu = []
the_results = fetchall('''
@@ -510,12 +519,13 @@ def datasets(group_name, this_group = None):
and InbredSet.Name like %s
ORDER BY Tissue.Name, ProbeSetFreeze.OrderList DESC)
''' % (group_name,
- group_name,
- "'" + group_name + "'"))
+ group_name,
+ "'" + group_name + "'"))
sorted_results = sorted(the_results, key=lambda kv: kv[0])
- pheno_inserted = False #ZS: This is kind of awkward, but need to ensure Phenotypes show up before Genotypes in dropdown
+ # ZS: This is kind of awkward, but need to ensure Phenotypes show up before Genotypes in dropdown
+ pheno_inserted = False
geno_inserted = False
for dataset_item in sorted_results:
tissue_name = dataset_item[0]
@@ -523,13 +533,16 @@ def datasets(group_name, this_group = None):
dataset_short = dataset_item[2]
if tissue_name in ['#PublishFreeze', '#GenoFreeze']:
if tissue_name == '#PublishFreeze' and (dataset_short == group_name + 'Publish'):
- dataset_menu.insert(0, dict(tissue=None, datasets=[(dataset, dataset_short)]))
+ dataset_menu.insert(
+ 0, dict(tissue=None, datasets=[(dataset, dataset_short)]))
pheno_inserted = True
elif pheno_inserted and tissue_name == '#GenoFreeze':
- dataset_menu.insert(1, dict(tissue=None, datasets=[(dataset, dataset_short)]))
+ dataset_menu.insert(
+ 1, dict(tissue=None, datasets=[(dataset, dataset_short)]))
geno_inserted = True
else:
- dataset_menu.append(dict(tissue=None, datasets=[(dataset, dataset_short)]))
+ dataset_menu.append(
+ dict(tissue=None, datasets=[(dataset, dataset_short)]))
else:
tissue_already_exists = False
for i, tissue_dict in enumerate(dataset_menu):
@@ -542,11 +555,11 @@ def datasets(group_name, this_group = None):
dataset_menu[i]['datasets'].append((dataset, dataset_short))
else:
dataset_menu.append(dict(tissue=tissue_name,
- datasets=[(dataset, dataset_short)]))
+ datasets=[(dataset, dataset_short)]))
if USE_REDIS:
- Redis.set(key, pickle.dumps(dataset_menu, pickle.HIGHEST_PROTOCOL))
- Redis.expire(key, 60*5)
+ r.set(key, pickle.dumps(dataset_menu, pickle.HIGHEST_PROTOCOL))
+ r.expire(key, 60*5)
if this_group != None:
this_group._datasets = dataset_menu
@@ -554,6 +567,7 @@ def datasets(group_name, this_group = None):
else:
return dataset_menu
+
class DataSet(object):
"""
DataSet class defines a dataset in webqtl, can be either Microarray,
@@ -561,7 +575,7 @@ class DataSet(object):
"""
- def __init__(self, name, get_samplelist = True, group_name = None):
+ def __init__(self, name, get_samplelist=True, group_name=None):
assert name, "Need a name"
self.name = name
@@ -569,22 +583,23 @@ class DataSet(object):
self.shortname = None
self.fullname = None
self.type = None
- self.data_scale = None #ZS: For example log2
+ self.data_scale = None # ZS: For example log2
self.setup()
- if self.type == "Temp": #Need to supply group name as input if temp trait
- self.group = DatasetGroup(self, name=group_name) # sets self.group and self.group_id and gets genotype
+ if self.type == "Temp": # Need to supply group name as input if temp trait
+ # sets self.group and self.group_id and gets genotype
+ self.group = DatasetGroup(self, name=group_name)
else:
self.check_confidentiality()
self.retrieve_other_names()
- self.group = DatasetGroup(self) # sets self.group and self.group_id and gets genotype
+ # sets self.group and self.group_id and gets genotype
+ self.group = DatasetGroup(self)
self.accession_id = self.get_accession_id()
if get_samplelist == True:
- self.group.get_samplelist()
+ self.group.get_samplelist()
self.species = species.TheSpecies(self)
-
def get_desc(self):
"""Gets overridden later, at least for Temp...used by trait's get_given_name"""
return None
@@ -644,8 +659,9 @@ class DataSet(object):
WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id
AND ProbeFreeze.TissueId = Tissue.Id
AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFreeze.ShortName = '%s')
- """ % (query_args),"/dataset/"+self.name+".json",
- lambda r: (r["id"],r["name"],r["full_name"],r["short_name"],r["data_scale"],r["tissue"])
+ """ % (query_args), "/dataset/"+self.name+".json",
+ lambda r: (r["id"], r["name"], r["full_name"],
+ r["short_name"], r["data_scale"], r["tissue"])
)
else:
query_args = tuple(escape(x) for x in (
@@ -662,7 +678,8 @@ class DataSet(object):
""" % (query_args))
except TypeError:
- logger.debug("Dataset {} is not yet available in GeneNetwork.".format(self.name))
+ logger.debug(
+ "Dataset {} is not yet available in GeneNetwork.".format(self.name))
pass
def get_trait_data(self, sample_list=None):
@@ -720,7 +737,7 @@ class DataSet(object):
and {}.Id = {}XRef.{}Id
order by {}.Id
""".format(*mescape(self.type, self.type, self.type, self.name,
- dataset_type, self.type, dataset_type, dataset_type))
+ dataset_type, self.type, dataset_type, dataset_type))
else:
query += """
WHERE {}XRef.{}FreezeId = {}Freeze.Id
@@ -728,7 +745,7 @@ class DataSet(object):
and {}.Id = {}XRef.{}Id
order by {}.Id
""".format(*mescape(self.type, self.type, self.type, self.type,
- self.name, dataset_type, self.type, self.type, dataset_type))
+ self.name, dataset_type, self.type, self.type, dataset_type))
#logger.debug("trait data query: ", query)
@@ -748,6 +765,7 @@ class DataSet(object):
self.trait_data[trait_name] += (
trait_sample_data[chunk_counter][trait_counter][data_start_pos:])
+
class PhenotypeDataSet(DataSet):
DS_NAME_MAP['Publish'] = 'PhenotypeDataSet'
@@ -757,16 +775,16 @@ class PhenotypeDataSet(DataSet):
# Fields in the database table
self.search_fields = ['Phenotype.Post_publication_description',
- 'Phenotype.Pre_publication_description',
- 'Phenotype.Pre_publication_abbreviation',
- 'Phenotype.Post_publication_abbreviation',
- 'PublishXRef.mean',
- 'Phenotype.Lab_code',
- 'Publication.PubMed_ID',
- 'Publication.Abstract',
- 'Publication.Title',
- 'Publication.Authors',
- 'PublishXRef.Id']
+ 'Phenotype.Pre_publication_description',
+ 'Phenotype.Pre_publication_abbreviation',
+ 'Phenotype.Post_publication_abbreviation',
+ 'PublishXRef.mean',
+ 'Phenotype.Lab_code',
+ 'Publication.PubMed_ID',
+ 'Publication.Abstract',
+ 'Publication.Title',
+ 'Publication.Authors',
+ 'PublishXRef.Id']
# Figure out what display_fields is
self.display_fields = ['name', 'group_code',
@@ -788,13 +806,13 @@ class PhenotypeDataSet(DataSet):
# Fields displayed in the search results table header
self.header_fields = ['Index',
- 'Record',
- 'Description',
- 'Authors',
- 'Year',
- 'Max LRS',
- 'Max LRS Location',
- 'Additive Effect']
+ 'Record',
+ 'Description',
+ 'Authors',
+ 'Year',
+ 'Max LRS',
+ 'Max LRS Location',
+ 'Additive Effect']
self.type = 'Publish'
@@ -812,7 +830,7 @@ class PhenotypeDataSet(DataSet):
# (Urgently?) Need to write this
pass
- def get_trait_info(self, trait_list, species = ''):
+ def get_trait_info(self, trait_list, species=''):
for this_trait in trait_list:
if not this_trait.haveinfo:
@@ -820,9 +838,9 @@ class PhenotypeDataSet(DataSet):
description = this_trait.post_publication_description
- #If the dataset is confidential and the user has access to confidential
- #phenotype traits, then display the pre-publication description instead
- #of the post-publication description
+ # If the dataset is confidential and the user has access to confidential
+ # phenotype traits, then display the pre-publication description instead
+ # of the post-publication description
if this_trait.confidential:
this_trait.description_display = ""
continue # for now, because no authorization features
@@ -847,7 +865,7 @@ class PhenotypeDataSet(DataSet):
if this_trait.pubmed_id:
this_trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % this_trait.pubmed_id
- #LRS and its location
+ # LRS and its location
this_trait.LRS_score_repr = "N/A"
this_trait.LRS_location_repr = "N/A"
@@ -867,7 +885,8 @@ class PhenotypeDataSet(DataSet):
LRS_Mb = result[1]
this_trait.LRS_score_repr = LRS_score_repr = '%3.1f' % this_trait.lrs
- this_trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (LRS_Chr, float(LRS_Mb))
+ this_trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (
+ LRS_Chr, float(LRS_Mb))
def retrieve_sample_data(self, trait):
query = """
@@ -934,12 +953,13 @@ class GenotypeDataSet(DataSet):
this_trait.retrieveInfo()
if this_trait.chr and this_trait.mb:
- this_trait.location_repr = 'Chr%s: %.6f' % (this_trait.chr, float(this_trait.mb) )
+ this_trait.location_repr = 'Chr%s: %.6f' % (
+ this_trait.chr, float(this_trait.mb))
def retrieve_sample_data(self, trait):
query = """
SELECT
- Strain.Name, GenoData.value, GenoSE.error, GenoData.Id, Strain.Name2
+ Strain.Name, GenoData.value, GenoSE.error, "N/A", Strain.Name2
FROM
(GenoData, GenoFreeze, Strain, Geno, GenoXRef)
left join GenoSE on
@@ -1003,14 +1023,14 @@ class MrnaAssayDataSet(DataSet):
# Fields displayed in the search results table header
self.header_fields = ['Index',
- 'Record',
- 'Symbol',
- 'Description',
- 'Location',
- 'Mean',
- 'Max LRS',
- 'Max LRS Location',
- 'Additive Effect']
+ 'Record',
+ 'Symbol',
+ 'Description',
+ 'Location',
+ 'Mean',
+ 'Max LRS',
+ 'Max LRS Location',
+ 'Additive Effect']
# Todo: Obsolete or rename this field
self.type = 'ProbeSet'
@@ -1026,7 +1046,6 @@ class MrnaAssayDataSet(DataSet):
ProbeSetFreeze.Name = "%s"
''' % escape(self.name)
-
def check_confidentiality(self):
return geno_mrna_confidentiality(self)
@@ -1044,10 +1063,12 @@ class MrnaAssayDataSet(DataSet):
if not this_trait.symbol:
this_trait.symbol = "N/A"
- #XZ, 12/08/2008: description
- #XZ, 06/05/2009: Rob asked to add probe target description
- description_string = unicode(str(this_trait.description).strip(codecs.BOM_UTF8), 'utf-8')
- target_string = unicode(str(this_trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
+ # XZ, 12/08/2008: description
+ # XZ, 06/05/2009: Rob asked to add probe target description
+ description_string = unicode(
+ str(this_trait.description).strip(codecs.BOM_UTF8), 'utf-8')
+ target_string = unicode(
+ str(this_trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
if len(description_string) > 1 and description_string != 'None':
description_display = description_string
@@ -1062,11 +1083,12 @@ class MrnaAssayDataSet(DataSet):
this_trait.description_display = description_display
if this_trait.chr and this_trait.mb:
- this_trait.location_repr = 'Chr%s: %.6f' % (this_trait.chr, float(this_trait.mb))
+ this_trait.location_repr = 'Chr%s: %.6f' % (
+ this_trait.chr, float(this_trait.mb))
- #Get mean expression value
+ # Get mean expression value
query = (
- """select ProbeSetXRef.mean from ProbeSetXRef, ProbeSet
+ """select ProbeSetXRef.mean from ProbeSetXRef, ProbeSet
where ProbeSetXRef.ProbeSetFreezeId = %s and
ProbeSet.Id = ProbeSetXRef.ProbeSetId and
ProbeSet.Name = '%s'
@@ -1082,11 +1104,11 @@ class MrnaAssayDataSet(DataSet):
if mean:
this_trait.mean = "%2.3f" % mean
- #LRS and its location
+ # LRS and its location
this_trait.LRS_score_repr = 'N/A'
this_trait.LRS_location_repr = 'N/A'
- #Max LRS and its Locus location
+ # Max LRS and its Locus location
if this_trait.lrs and this_trait.locus:
query = """
select Geno.Chr, Geno.Mb from Geno, Species
@@ -1100,18 +1122,22 @@ class MrnaAssayDataSet(DataSet):
if result:
lrs_chr, lrs_mb = result
this_trait.LRS_score_repr = '%3.1f' % this_trait.lrs
- this_trait.LRS_location_repr = 'Chr%s: %.6f' % (lrs_chr, float(lrs_mb))
+ this_trait.LRS_location_repr = 'Chr%s: %.6f' % (
+ lrs_chr, float(lrs_mb))
return trait_list
def retrieve_sample_data(self, trait):
query = """
SELECT
- Strain.Name, ProbeSetData.value, ProbeSetSE.error, ProbeSetData.Id, Strain.Name2
+ Strain.Name, ProbeSetData.value, ProbeSetSE.error, NStrain.count, Strain.Name2
FROM
(ProbeSetData, ProbeSetFreeze, Strain, ProbeSet, ProbeSetXRef)
left join ProbeSetSE on
(ProbeSetSE.DataId = ProbeSetData.Id AND ProbeSetSE.StrainId = ProbeSetData.StrainId)
+ left join NStrain on
+ (NStrain.DataId = ProbeSetData.Id AND
+ NStrain.StrainId = ProbeSetData.StrainId)
WHERE
ProbeSet.Name = '%s' AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
@@ -1161,7 +1187,6 @@ class TempDataSet(DataSet):
self.fullname = 'Temporary Storage'
self.shortname = 'Temp'
-
@staticmethod
def handle_pca(desc):
if 'PCA' in desc:
@@ -1202,7 +1227,7 @@ def geno_mrna_confidentiality(ob):
#logger.debug("dataset_table [%s]: %s" % (type(dataset_table), dataset_table))
query = '''SELECT Id, Name, FullName, confidentiality,
- AuthorisedUsers FROM %s WHERE Name = "%s"''' % (dataset_table,ob.name)
+ AuthorisedUsers FROM %s WHERE Name = "%s"''' % (dataset_table, ob.name)
logger.sql(query)
result = g.db.execute(query)
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 8e11c11d..7666348e 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -152,7 +152,7 @@ class GeneralTrait(object):
'''Return a text formatted alias'''
alias = 'Not available'
- if self.alias:
+ if getattr(self, "alias", None):
alias = string.replace(self.alias, ";", " ")
alias = string.join(string.split(alias), ", ")
@@ -395,20 +395,24 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
query = """
SELECT
PublishXRef.Id, InbredSet.InbredSetCode, Publication.PubMed_ID,
- Phenotype.Pre_publication_description, Phenotype.Post_publication_description, Phenotype.Original_description,
- Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, PublishXRef.mean,
+ CAST(Phenotype.Pre_publication_description AS BINARY),
+ CAST(Phenotype.Post_publication_description AS BINARY),
+ CAST(Phenotype.Original_description AS BINARY),
+ CAST(Phenotype.Pre_publication_abbreviation AS BINARY),
+ CAST(Phenotype.Post_publication_abbreviation AS BINARY), PublishXRef.mean,
Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users,
- Publication.Authors, Publication.Title, Publication.Abstract,
- Publication.Journal, Publication.Volume, Publication.Pages,
+ CAST(Publication.Authors AS BINARY), CAST(Publication.Title AS BINARY), CAST(Publication.Abstract AS BINARY),
+ CAST(Publication.Journal AS BINARY), Publication.Volume, Publication.Pages,
Publication.Month, Publication.Year, PublishXRef.Sequence,
Phenotype.Units, PublishXRef.comments
FROM
- PublishXRef, Publication, Phenotype, PublishFreeze
+ PublishXRef, Publication, Phenotype, PublishFreeze, InbredSet
WHERE
PublishXRef.Id = %s AND
Phenotype.Id = PublishXRef.PhenotypeId AND
Publication.Id = PublishXRef.PublicationId AND
PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
+ PublishXRef.InbredSetId = InbredSet.Id AND
PublishFreeze.Id = %s
""" % (trait.name, dataset.id)
@@ -462,9 +466,6 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
trait.haveinfo = True
for i, field in enumerate(dataset.display_fields):
holder = trait_info[i]
- # if isinstance(trait_info[i], basestring):
- # holder = unicode(holder.strip(codecs.BOM_UTF8), 'utf-8', "ignore")
-
setattr(trait, field, holder)
if dataset.type == 'Publish':
diff --git a/wqflask/cfg/default_settings.py b/wqflask/cfg/default_settings.py
deleted file mode 100644
index 5af61d5a..00000000
--- a/wqflask/cfg/default_settings.py
+++ /dev/null
@@ -1 +0,0 @@
-# no longer in use
diff --git a/wqflask/mock/es_double.py b/wqflask/mock/es_double.py
deleted file mode 100644
index 6ef8a1b9..00000000
--- a/wqflask/mock/es_double.py
+++ /dev/null
@@ -1,15 +0,0 @@
-class ESDouble(object):
- def __init__(self):
- self.items = {}
-
- def ping(self):
- return true
-
- def create(self, index, doc_type, body, id):
- self.items["index"] = {doc_type: {"id": id, "_source": data}}
-
- def search(self, index, doc_type, body):
- return {
- "hits": {
- "hits": self.items[index][doc_type][body]
- }}
diff --git a/wqflask/cfg/__init__.py b/wqflask/tests/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/cfg/__init__.py
+++ b/wqflask/tests/__init__.py
diff --git a/wqflask/mock/__init__.py b/wqflask/tests/base/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/mock/__init__.py
+++ b/wqflask/tests/base/__init__.py
diff --git a/wqflask/tests/base/test_data_set.py b/wqflask/tests/base/test_data_set.py
new file mode 100644
index 00000000..44a54c7e
--- /dev/null
+++ b/wqflask/tests/base/test_data_set.py
@@ -0,0 +1,35 @@
+import unittest
+import mock
+
+from wqflask import app
+
+from base.data_set import DatasetType
+
+
+class TestDataSetTypes(unittest.TestCase):
+ def setUp(self):
+ self.app_context = app.app_context()
+ self.app_context.push()
+
+ def tearDown(self):
+ self.app_context.pop()
+
+ @mock.patch('base.data_set.g')
+ def test_data_set_type(self, db_mock):
+ with app.app_context():
+ db_mock.get = mock.Mock()
+ r = mock.Mock()
+ r.get.return_value = """
+ {
+ "AD-cases-controls-MyersGeno": "Geno",
+ "AD-cases-controls-MyersPublish": "Publish",
+ "AKXDGeno": "Geno",
+ "AXBXAGeno": "Geno",
+ "AXBXAPublish": "Publish",
+ "Aging-Brain-UCIPublish": "Publish",
+ "All Phenotypes": "Publish",
+ "B139_K_1206_M": "ProbeSet",
+ "B139_K_1206_R": "ProbeSet"
+ }
+ """
+ self.assertEqual(DatasetType(r)("All Phenotypes"), "Publish")
diff --git a/wqflask/tests/base/test_general_object.py b/wqflask/tests/base/test_general_object.py
new file mode 100644
index 00000000..c7701021
--- /dev/null
+++ b/wqflask/tests/base/test_general_object.py
@@ -0,0 +1,41 @@
+import unittest
+
+from base.GeneralObject import GeneralObject
+
+
+class TestGeneralObjectTests(unittest.TestCase):
+ """
+ Test the GeneralObject base class
+ """
+
+ def test_object_contents(self):
+ """Test whether base contents are stored properly"""
+ test_obj = GeneralObject("a", "b", "c")
+ self.assertEqual("abc", ''.join(test_obj.contents))
+ self.assertEqual(len(test_obj), 0)
+
+ def test_object_dict(self):
+ """Test whether the base class is printed properly"""
+ test_obj = GeneralObject("a", name="test", value=1)
+ self.assertEqual(str(test_obj), "value = 1\nname = test\n")
+ self.assertEqual(
+ repr(test_obj), "value = 1\nname = test\ncontents = ['a']\n")
+ self.assertEqual(len(test_obj), 2)
+ self.assertEqual(test_obj["value"], 1)
+ test_obj["test"] = 1
+ self.assertEqual(test_obj["test"], 1)
+
+ def test_get_attribute(self):
+ "Test that getattr works"
+ test_obj = GeneralObject("a", name="test", value=1)
+ self.assertEqual(getattr(test_obj, "value", None), 1)
+ self.assertEqual(getattr(test_obj, "non-existent", None), None)
+
+ def test_object_comparisons(self):
+ "Test that 2 objects of the same length are equal"
+ test_obj1 = GeneralObject("a", name="test", value=1)
+ test_obj2 = GeneralObject("b", name="test2", value=2)
+ test_obj3 = GeneralObject("a", name="test", x=1, y=2)
+ self.assertTrue(test_obj1 == test_obj2 )
+ self.assertFalse(test_obj1 == test_obj3 )
+
diff --git a/wqflask/tests/utility/__init__.py b/wqflask/tests/utility/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/tests/utility/__init__.py
diff --git a/wqflask/tests/utility/test_chunks.py b/wqflask/tests/utility/test_chunks.py
new file mode 100644
index 00000000..8d90a1ec
--- /dev/null
+++ b/wqflask/tests/utility/test_chunks.py
@@ -0,0 +1,19 @@
+"""Test chunking"""
+
+import unittest
+
+from utility.chunks import divide_into_chunks
+
+
+class TestChunks(unittest.TestCase):
+ "Test Utility method for chunking"
+ def test_divide_into_chunks(self):
+ "Check that a list is chunked correctly"
+ self.assertEqual(divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 3),
+ [[1, 2, 7], [3, 22, 8], [5, 22, 333]])
+ self.assertEqual(divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 4),
+ [[1, 2, 7], [3, 22, 8], [5, 22, 333]])
+ self.assertEqual(divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 5),
+ [[1, 2], [7, 3], [22, 8], [5, 22], [333]])
+ self.assertEqual(divide_into_chunks([], 5),
+ [[]])
diff --git a/wqflask/tests/utility/test_corestats.py b/wqflask/tests/utility/test_corestats.py
new file mode 100644
index 00000000..cf91a248
--- /dev/null
+++ b/wqflask/tests/utility/test_corestats.py
@@ -0,0 +1,55 @@
+"""Test Core Stats"""
+
+import unittest
+
+from utility.corestats import Stats
+
+
+class TestChunks(unittest.TestCase):
+ "Test Utility method for chunking"
+
+ def setUp(self):
+ self.stat_test = Stats((x for x in range(1, 11)))
+
+ def test_stats_sum(self):
+ """ Test sequence sum """
+ self.assertEqual(self.stat_test.sum(), 55)
+ self.stat_test = Stats([])
+ self.assertEqual(self.stat_test.sum(), None)
+
+ def test_stats_count(self):
+ """ Test sequence count """
+ self.assertEqual(self.stat_test.count(), 10)
+ self.stat_test = Stats([])
+ self.assertEqual(self.stat_test.count(), 0)
+
+ def test_stats_min(self):
+ """ Test min value in sequence"""
+ self.assertEqual(self.stat_test.min(), 1)
+ self.stat_test = Stats([])
+ self.assertEqual(self.stat_test.min(), None)
+
+ def test_stats_max(self):
+ """ Test max value in sequence """
+ self.assertEqual(self.stat_test.max(), 10)
+ self.stat_test = Stats([])
+ self.assertEqual(self.stat_test.max(), None)
+
+ def test_stats_avg(self):
+ """ Test avg of sequence """
+ self.assertEqual(self.stat_test.avg(), 5.5)
+ self.stat_test = Stats([])
+ self.assertEqual(self.stat_test.avg(), None)
+
+ def test_stats_stdev(self):
+ """ Test standard deviation of sequence """
+ self.assertEqual(self.stat_test.stdev(), 3.0276503540974917)
+ self.stat_test = Stats([])
+ self.assertEqual(self.stat_test.stdev(), None)
+
+ def test_stats_percentile(self):
+ """ Test percentile of sequence """
+ self.assertEqual(self.stat_test.percentile(20), 3.0)
+ self.assertEqual(self.stat_test.percentile(101), None)
+ self.stat_test = Stats([])
+ self.assertEqual(self.stat_test.percentile(20), None)
diff --git a/wqflask/tests/utility/test_corr_result_helpers.py b/wqflask/tests/utility/test_corr_result_helpers.py
new file mode 100644
index 00000000..e196fbdf
--- /dev/null
+++ b/wqflask/tests/utility/test_corr_result_helpers.py
@@ -0,0 +1,32 @@
+""" Test correlation helper methods """
+
+import unittest
+from utility.corr_result_helpers import normalize_values, common_keys, normalize_values_with_samples
+
+
+class TestCorrelationHelpers(unittest.TestCase):
+ """Test methods for normalising lists"""
+
+ def test_normalize_values(self):
+ """Test that a list is normalised correctly"""
+ self.assertEqual(
+ normalize_values([2.3, None, None, 3.2, 4.1, 5], [
+ 3.4, 7.2, 1.3, None, 6.2, 4.1]),
+ ([2.3, 4.1, 5], [3.4, 6.2, 4.1], 3)
+ )
+
+ def test_common_keys(self):
+ """Test that common keys are returned as a list"""
+ a = dict(BXD1=9.113, BXD2=9.825, BXD14=8.985, BXD15=9.300)
+ b = dict(BXD1=9.723, BXD3=9.825, BXD14=9.124, BXD16=9.300)
+ self.assertEqual(sorted(common_keys(a, b)), ['BXD1', 'BXD14'])
+
+ def test_normalize_values_with_samples(self):
+ """Test that a sample(dict) is normalised correctly"""
+ self.assertEqual(
+ normalize_values_with_samples(
+ dict(BXD1=9.113, BXD2=9.825, BXD14=8.985,
+ BXD15=9.300, BXD20=9.300),
+ dict(BXD1=9.723, BXD3=9.825, BXD14=9.124, BXD16=9.300)),
+ (({'BXD1': 9.113, 'BXD14': 8.985}, {'BXD1': 9.723, 'BXD14': 9.124}, 2))
+ )
diff --git a/wqflask/tests/utility/test_formatting.py b/wqflask/tests/utility/test_formatting.py
new file mode 100644
index 00000000..9d3033d1
--- /dev/null
+++ b/wqflask/tests/utility/test_formatting.py
@@ -0,0 +1,33 @@
+import unittest
+from utility.formatting import numify, commify
+
+
+class TestFormatting(unittest.TestCase):
+ """Test formatting numbers by numifying or commifying"""
+
+ def test_numify(self):
+ "Test that a number is correctly converted to a English readable string"
+ self.assertEqual(numify(1, 'item', 'items'),
+ 'one item')
+ self.assertEqual(numify(2, 'book'), 'two')
+ self.assertEqual(numify(2, 'book', 'books'), 'two books')
+ self.assertEqual(numify(0, 'book', 'books'), 'zero books')
+ self.assertEqual(numify(0), 'zero')
+ self.assertEqual(numify(5), 'five')
+ self.assertEqual(numify(14, 'book', 'books'), '14 books')
+ self.assertEqual(numify(999, 'book', 'books'), '999 books')
+ self.assertEqual(numify(1000000, 'book', 'books'), '1,000,000 books')
+ self.assertEqual(numify(1956), '1956')
+
+ def test_commify(self):
+ "Test that commas are added correctly"
+ self.assertEqual(commify(1), '1')
+ self.assertEqual(commify(123), '123')
+ self.assertEqual(commify(1234), '1234')
+ self.assertEqual(commify(12345), '12,345')
+ self.assertEqual(commify(1234567890), '1,234,567,890')
+ self.assertEqual(commify(123.0), '123.0')
+ self.assertEqual(commify(1234.5), '1234.5')
+ self.assertEqual(commify(1234.56789), '1234.56789')
+ self.assertEqual(commify(123456.789), '123,456.789')
+ self.assertEqual(commify(None), None)
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()
diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py
index 62e98b36..d729aef5 100644
--- a/wqflask/wqflask/__init__.py
+++ b/wqflask/wqflask/__init__.py
@@ -12,7 +12,6 @@ logging.basicConfig(level=logging.INFO)
app = Flask(__name__)
-app.config.from_object('cfg.default_settings') # Get the defaults from cfg.default_settings
app.config.from_envvar('GN2_SETTINGS') # See http://flask.pocoo.org/docs/config/#configuring-from-files
# Note no longer use the badly named WQFLASK_OVERRIDES (nyi)
@@ -22,4 +21,4 @@ app.jinja_env.globals.update(
)
from wqflask.api import router
-import wqflask.views \ No newline at end of file
+import wqflask.views
diff --git a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
index 5d74dc9d..09d6b9cc 100644
--- a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
+++ b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
@@ -35,8 +35,6 @@ import resource
from pprint import pformat as pf
-import reaper
-
from base.trait import create_trait
from base import data_set
from utility import webqtlUtil, helper_functions, corr_result_helpers
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index bc2912f2..de7a1c0c 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -42,8 +42,6 @@ utils = importr("utils")
from pprint import pformat as pf
-import reaper
-
from base import webqtlConfig
from utility.THCell import THCell
from utility.TDCell import TDCell
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index 2b9467d1..0ac94139 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -41,8 +41,6 @@ import rpy2.robjects as robjects
from pprint import pformat as pf
-import reaper
-
from utility.redis_tools import get_redis_conn
Redis = get_redis_conn()
THIRTY_DAYS = 60 * 60 * 24 * 30
diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py
index 2d96c05a..3272c03d 100644
--- a/wqflask/wqflask/export_traits.py
+++ b/wqflask/wqflask/export_traits.py
@@ -4,24 +4,30 @@ import csv
import xlsxwriter
import StringIO
import datetime
+import itertools
+
+from zipfile import ZipFile, ZIP_DEFLATED
import simplejson as json
+from base.trait import create_trait, retrieve_trait_info
+
from pprint import pformat as pf
+from utility.logger import getLogger
+logger = getLogger(__name__ )
+
def export_search_results_csv(targs):
table_data = json.loads(targs['export_data'])
- table_headers = table_data['headers']
table_rows = table_data['rows']
- buff = StringIO.StringIO()
- writer = csv.writer(buff)
-
+ now = datetime.datetime.now()
+ time_str = now.strftime('%H:%M_%d%B%Y')
if 'file_name' in targs:
- file_name = targs['file_name']
+ zip_file_name = targs['file_name'] + "_export_" + time_str
else:
- file_name = "table_export.csv"
+ zip_file_name = "export_" + time_str
metadata = []
@@ -40,19 +46,98 @@ def export_search_results_csv(targs):
if targs['filter_term'] != "None":
metadata.append(["Search Filter Terms: " + targs['filter_term']])
metadata.append(["Exported Row Number: " + str(len(table_rows))])
+ metadata.append(["Funding for The GeneNetwork: NIAAA (U01AA13499, U24AA13513), NIDA, NIMH, and NIAAA (P20-DA21131), NCI MMHCC (U01CA105417), and NCRR (U01NR 105417)"])
+ metadata.append([])
+
+ trait_list = []
+ for trait in table_rows:
+ trait_name, dataset_name, _hash = trait.split(":")
+ trait_ob = create_trait(name=trait_name, dataset_name=dataset_name)
+ trait_ob = retrieve_trait_info(trait_ob, trait_ob.dataset, get_qtl_info=True)
+ trait_list.append(trait_ob)
+
+ table_headers = ['Species', 'Group', 'Dataset', 'Record ID', 'Symbol', 'Description', 'ProbeTarget', 'PubMed_ID', 'Chr', 'Mb', 'Alias', 'Gene_ID', 'Homologene_ID', 'UniGene_ID', 'Strand_Probe', 'Probe_set_specificity', 'Probe_set_BLAT_score', 'Probe_set_BLAT_Mb_start', 'Probe_set_BLAT_Mb_end', 'QTL_Chr', 'QTL_Mb', 'Locus_at_Peak', 'Max_LRS', 'P_value_of_MAX', 'Mean_Expression']
+
+ traits_by_group = sort_traits_by_group(trait_list)
+
+ file_list = []
+ for group in traits_by_group.keys():
+ group_traits = traits_by_group[group]
+ buff = StringIO.StringIO()
+ writer = csv.writer(buff)
+ csv_rows = []
+
+ sample_headers = []
+ for sample in group_traits[0].dataset.group.samplelist:
+ sample_headers.append(sample)
+ sample_headers.append(sample + "_SE")
+
+ full_headers = table_headers + sample_headers
+
+ for metadata_row in metadata:
+ writer.writerow(metadata_row)
+
+ csv_rows.append(full_headers)
+
+ for trait in group_traits:
+ if getattr(trait, "symbol", None):
+ trait_symbol = getattr(trait, "symbol")
+ elif getattr(trait, "abbreviation", None):
+ trait_symbol = getattr(trait, "abbreviation")
+ else:
+ trait_symbol = "N/A"
+ row_contents = [
+ trait.dataset.group.species,
+ trait.dataset.group.name,
+ trait.dataset.name,
+ trait.name,
+ trait_symbol,
+ getattr(trait, "description_display", "N/A"),
+ getattr(trait, "probe_target_description", "N/A"),
+ getattr(trait, "pubmed_id", "N/A"),
+ getattr(trait, "chr", "N/A"),
+ getattr(trait, "mb", "N/A"),
+ trait.alias_fmt,
+ getattr(trait, "geneid", "N/A"),
+ getattr(trait, "homologeneid", "N/A"),
+ getattr(trait, "unigeneid", "N/A"),
+ getattr(trait, "strand_probe", "N/A"),
+ getattr(trait, "probe_set_specificity", "N/A"),
+ getattr(trait, "probe_set_blat_score", "N/A"),
+ getattr(trait, "probe_set_blat_mb_start", "N/A"),
+ getattr(trait, "probe_set_blat_mb_end", "N/A"),
+ getattr(trait, "locus_chr", "N/A"),
+ getattr(trait, "locus_mb", "N/A"),
+ getattr(trait, "locus", "N/A"),
+ getattr(trait, "lrs", "N/A"),
+ getattr(trait, "pvalue", "N/A"),
+ getattr(trait, "mean", "N/A")
+ ]
+
+ for sample in trait.dataset.group.samplelist:
+ if sample in trait.data:
+ row_contents += [trait.data[sample].value, trait.data[sample].variance]
+ else:
+ row_contents += ["x", "x"]
+
+ csv_rows.append(row_contents)
+
+ csv_rows = map(list, itertools.izip_longest(*[row for row in csv_rows]))
+ writer.writerows(csv_rows)
+ csv_data = buff.getvalue()
+ buff.close()
- for metadata_row in metadata:
- writer.writerow(metadata_row)
+ file_name = group + "_traits.csv"
+ file_list.append([file_name, csv_data])
- writer.writerow([])
+ return file_list
- writer.writerow(table_headers)
- for trait_info in table_rows:
- writer.writerow(trait_info)
+def sort_traits_by_group(trait_list=[]):
+ traits_by_group = {}
+ for trait in trait_list:
+ if trait.dataset.group.name not in traits_by_group.keys():
+ traits_by_group[trait.dataset.group.name] = []
- writer.writerow([])
- writer.writerow(["Funding for The GeneNetwork: NIAAA (U01AA13499, U24AA13513), NIDA, NIMH, and NIAAA (P20-DA21131), NCI MMHCC (U01CA105417), and NCRR (U01NR 105417)"])
- csv_data = buff.getvalue()
- buff.close()
+ traits_by_group[trait.dataset.group.name].append(trait)
- return csv_data, file_name \ No newline at end of file
+ return traits_by_group \ No newline at end of file
diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py
index e82aa0ef..5098a184 100644
--- a/wqflask/wqflask/heatmap/heatmap.py
+++ b/wqflask/wqflask/heatmap/heatmap.py
@@ -19,8 +19,6 @@ import numpy as np
from pprint import pformat as pf
-import reaper
-
from base.trait import GeneralTrait
from base import data_set
from base import species
diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py
index f41f3017..f61c40b4 100644
--- a/wqflask/wqflask/network_graph/network_graph.py
+++ b/wqflask/wqflask/network_graph/network_graph.py
@@ -40,8 +40,6 @@ import rpy2.robjects as robjects
from pprint import pformat as pf
-import reaper
-
from utility.THCell import THCell
from utility.TDCell import TDCell
from base.trait import create_trait
diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js
index d172907a..48ffd731 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js
+++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js
@@ -81,11 +81,17 @@ redo_dropdown = function(dropdown, items) {
this_opt_group.append($("<option />").val(item[0]).text(item[1]));
} else if (current_family != "" && item[2] == current_family){
this_opt_group.append($("<option />").val(item[0]).text(item[1]));
+ if (_i == group_family_list.length - 1){
+ _results.push(dropdown.append(this_opt_group))
+ }
} else if (current_family != "" && item[2] != current_family && item[2] != "None"){
current_family = item[2]
_results.push(dropdown.append(this_opt_group))
this_opt_group = $("<optgroup label=\"" + current_family + "\">")
this_opt_group.append($("<option />").val(item[0]).text(item[1]));
+ if (_i == group_family_list.length - 1){
+ _results.push(dropdown.append(this_opt_group))
+ }
} else if (current_family != "" && this_opt_group != null && item[2] == "None"){
_results.push(dropdown.append(this_opt_group))
current_family = ""
@@ -109,6 +115,9 @@ redo_dropdown = function(dropdown, items) {
current_family = item[2]
this_opt_group = $("<optgroup label=\"" + item[2] + "\">")
this_opt_group.append($("<option />").val(item[0]).text(item[1]));
+ if (_i == type_family_list.length - 1){
+ _results.push(dropdown.append(this_opt_group))
+ }
} else if (current_family != "" && item[2] == current_family){
this_opt_group.append($("<option />").val(item[0]).text(item[1]));
if (_i == type_family_list.length - 1){
diff --git a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js
index 956e0467..1bae8773 100644
--- a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js
+++ b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js
@@ -337,14 +337,13 @@ function getdata() {
continue
}
+ sizev = 10;
+ datav = 0;
if (size_cofactor_vals.length > 0){
if (cofactor_samples.indexOf(js_data.indIDs[j])) {
datav = size_cofactor_vals[j]
sizev = map1to2(datamin, datamax, sizemin, sizemax, datav);
}
- } else {
- datav = 0;
- sizev = 10;
}
x_values.push(js_data.data[0][j])
diff --git a/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js
index 6f03b98f..4ec62157 100644
--- a/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js
+++ b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js
@@ -41,29 +41,31 @@ $('#trait_table').dataTable( {
"orderClasses": true
} );
-$('#collection_table').dataTable( {
- "createdRow": function ( row, data, index ) {
- if ($('td', row).eq(2).text().length > 40) {
- $('td', row).eq(2).text($('td', row).eq(2).text().substring(0, 40));
- $('td', row).eq(2).text($('td', row).eq(2).text() + '...')
- }
- if ($('td', row).eq(4).text().length > 50) {
- $('td', row).eq(4).text($('td', row).eq(4).text().substring(0, 50));
- $('td', row).eq(4).text($('td', row).eq(4).text() + '...')
- }
- },
- "columnDefs": [ {
- "targets": 0,
- "orderable": false
- } ],
- "order": [[1, "asc" ]],
- "sDom": "ZRtr",
- "iDisplayLength": -1,
- "autoWidth": true,
- "bSortClasses": false,
- "paging": false,
- "orderClasses": true
-} );
+if ( ! $.fn.DataTable.isDataTable( '#collection_table' ) ) {
+ $('#collection_table').dataTable( {
+ "createdRow": function ( row, data, index ) {
+ if ($('td', row).eq(2).text().length > 40) {
+ $('td', row).eq(2).text($('td', row).eq(2).text().substring(0, 40));
+ $('td', row).eq(2).text($('td', row).eq(2).text() + '...')
+ }
+ if ($('td', row).eq(4).text().length > 50) {
+ $('td', row).eq(4).text($('td', row).eq(4).text().substring(0, 50));
+ $('td', row).eq(4).text($('td', row).eq(4).text() + '...')
+ }
+ },
+ "columnDefs": [ {
+ "targets": 0,
+ "orderable": false
+ } ],
+ "order": [[1, "asc" ]],
+ "sDom": "ZRtr",
+ "iDisplayLength": -1,
+ "autoWidth": true,
+ "bSortClasses": false,
+ "paging": false,
+ "orderClasses": true
+ } );
+}
collection_click = function() {
var this_collection_url;
diff --git a/wqflask/wqflask/static/new/javascript/search_results.js b/wqflask/wqflask/static/new/javascript/search_results.js
index 39aae113..b3ed06fc 100644
--- a/wqflask/wqflask/static/new/javascript/search_results.js
+++ b/wqflask/wqflask/static/new/javascript/search_results.js
@@ -161,23 +161,11 @@ $(function() {
trait_table.find('tbody tr').each(function (i, tr) {
if (trait_table.find('input[name="searchResult"]:checked').length > 0) {
if ($(this).find('input[name="searchResult"]').is(':checked')){
- this_row = [];
- $(tr).find('td').each(function(j, td){
- if ($(td).data('export')){
- this_row.push($(td).data('export'));
- }
- });
- rows.push(this_row);
+ rows.push($(this).find('input[name="searchResult"]:checked').val())
}
}
else {
- this_row = [];
- $(tr).find('td').each(function(j, td){
- if ($(td).data('export')){
- this_row.push($(td).data('export'));
- }
- });
- rows.push(this_row);
+ rows.push($(this).find('input[name="searchResult"]').val())
}
});
table_dict['rows'] = rows;
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 262d9ee5..50562200 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -69,7 +69,7 @@
<li><a href="https://systems-genetics.org/">Systems Genetics PheWAS</a></li>
<li><a href="http://ucscbrowser.genenetwork.org/">Genome Browser</a></li>
<li><a href="http://power.genenetwork.org">BXD Power Calculator</a></li>
- <li><a href="httP://datafiles.genenetwork.org">Interplanetary File System</a></li>
+ <li><a href="http://datafiles.genenetwork.org">Interplanetary File System</a></li>
</ul>
</li>
{% if g.user_session %}
@@ -96,7 +96,11 @@
</li>
{% if g.user_session.logged_in %}
<li class="">
- <a id="manage_groups" title="Manage Groups" href="/groups/manage">Manage Groups</a>
+ <a href="/edit_account_settings" class="dropdow-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">User Account Settings<span class="caret"></a>
+ <ul class="dropdown-menu">
+ <li><a id="manage_user" title="User Options" href="/user/manage">User Options</a></li>
+ <li><a id="manage_groups" title="Manage Groups" href="/groups/manage">Manage Groups</a></li>
+ </ul>
</li>
{% endif %}
{% endif %}
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 3d750bea..df3e43f1 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -200,7 +200,7 @@
{% endblock %}
{% block js %}
- <!--<script type="text/javascript" src="/static/new/js_external/md5.min.js"></script>-->
+ <script type="text/javascript" src="/static/new/js_external/md5.min.js"></script>
<script type="text/javascript" src="/static/new/javascript/search_results.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
@@ -427,10 +427,6 @@
{ "type": "natural" },
{ "type": "natural" }
],
- "createdRow": function ( row, data, index ) {
- $('td', row).eq(4).text(decodeURIComponent(escape($('td', row).eq(4).text())));
- $('td', row).eq(5).text(decodeURIComponent(escape($('td', row).eq(5).text())));
- },
"order": [[9, "asc" ]],
"sDom": "Btir",
"iDisplayLength": -1,
diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html
index 8c261eec..62ef1a7b 100644
--- a/wqflask/wqflask/templates/gsearch_gene.html
+++ b/wqflask/wqflask/templates/gsearch_gene.html
@@ -249,10 +249,11 @@
}
],
'order': [[1, "asc" ]],
- 'sDom': "tir",
+ 'sDom': "pitirp",
'autoWidth': true,
+ 'iDisplayLength': 500,
'deferRender': true,
- 'paging': false,
+ 'paging': true,
'orderClasses': true,
'processing': true,
'language': {
diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html
index 04b45659..f5058158 100644
--- a/wqflask/wqflask/templates/gsearch_pheno.html
+++ b/wqflask/wqflask/templates/gsearch_pheno.html
@@ -250,10 +250,11 @@
}
],
'order': [[1, "asc" ]],
- 'sDom': "tir",
+ 'sDom': "pitirp",
'autoWidth': false,
'deferRender': true,
- 'paging': false,
+ 'iDisplayLength': 500,
+ 'paging': true,
'orderClasses': true,
'processing': true,
'language': {
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 132d5249..81803deb 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -333,6 +333,7 @@
{% block js %}
<script type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script>
+ <script type="text/javascript" src="/static/new/js_external/md5.min.js"></script>
<script type="text/javascript" src="/static/new/js_external/underscore-min.js"></script>
<script type="text/javascript" src="/static/new/js_external/underscore.string.min.js"></script>
<script type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 3dfae3dd..1f76ea82 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -377,11 +377,12 @@
} else{
author_string = data.authors
}
- try {
- return decodeURIComponent(escape(author_string))
- } catch(err){
- return author_string
- }
+ return author_string
+ // try {
+ // return decodeURIComponent(escape(author_string))
+ // } catch(err){
+ // return author_string
+ // }
}
},
{
@@ -441,12 +442,13 @@
postfixButtons: [ 'colvisRestore' ]
}
],
- 'sDom': "Bitir",
+ 'sDom': "Bpitirp",
{% else %}
- 'sDom': "itir",
+ 'sDom': "pitirp",
{% endif %}
+ 'iDisplayLength': 500,
'deferRender': true,
- 'paging': false,
+ 'paging': true,
'orderClasses': true,
'processing': true,
'language': {
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 7380d198..acee6724 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -21,8 +21,7 @@
{% endif %}
</div>
- <form method="post" action="" target="_blank" name="trait_page" id="trait_data_form"
- class="form-horizontal">
+ <form method="post" action="" target="_blank" name="trait_page" id="trait_data_form" class="form-horizontal">
<div id="hidden_inputs">
<input type="hidden" name="trait_hmac" value="{{ data_hmac('{}:{}'.format(this_trait.name, dataset.name)) }}">
{% for key in hddn %}
@@ -74,7 +73,7 @@
<div class="panel-body">
{% include 'show_trait_transform_and_filter.html' %}
</div>
- <div id="transform_alert_placeholder"><div id="transform_alert" style="display: none;"class="alert alert-success outlier-alert"><a class="close" data-dismiss="alert">�</a><span>Because there are some values between 0 and 1, log2 and log10 transforms will add 1 to each value.</span></div></div>
+ <div id="transform_alert_placeholder"><div id="transform_alert" style="display: none;"class="alert alert-success outlier-alert"><a href="#" class="close" data-dismiss="alert">�</a><span>Because there are some values between 0 and 1, log2 and log10 transforms will add 1 to each value.</span></div></div>
</div>
</div>
<div class="panel panel-default">
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index a9b371b8..1378b91b 100644
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -78,7 +78,7 @@
<div class="form-group">
<label class="col-xs-2 control-label">Min Expr</label>
<div class="col-xs-3 controls">
- <input name="min_expr" value="" type="text" class="form-control" style="width: 50px;">
+ <input name="min_expr" value="" type="text" class="form-control" style="width: 70px;">
</div>
</div>
<div class="form-group">
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 965c0340..58353f05 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -234,7 +234,7 @@
<button type="button" class="btn btn-default" title="Write or review comments about this gene">GeneWiki</button>
</a>
{% if dataset.group.species == "mouse" or dataset.group.species == "rat" %}
- <a href="./snp_browser?first_run=true&species={{ dataset.group.species }}&gene_name={{ this_trait.symbol }}&limit_strains=on">
+ <a href="/snp_browser?first_run=true&species={{ dataset.group.species }}&gene_name={{ this_trait.symbol }}&limit_strains=on">
<button type="button" class="btn btn-default" title="View SNPs and Indels">SNPs</button>
</a>
{% endif %}
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 4d51adff..27040045 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -90,7 +90,7 @@
<div class="mapping_method_fields form-group">
<label class="col-xs-3 control-label"></label>
<div style="margin-left:20px;" class="col-xs-6">
- <input type="button" id="gemma_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression" value="Compute">
+ <button id="gemma_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression" value="Compute">Compute</button>
</div>
</div>
</div>
@@ -99,7 +99,7 @@
<div class="tab-pane" id="interval_mapping">
<div style="margin-top: 20px" class="form-horizontal">
<div class="mapping_method_fields form-group">
- <label for="reaper_version" style="text-align: right;" class="col-xs-3 control-label">Version<sup><a title="'New' is the new qtlreaper implementation written in RUST by Christian Fischer. 'Original' corresponds to the original version written in C.">?</a></sup></label>
+ <label for="reaper_version" style="text-align: right;" class="col-xs-3 control-label">Version<sup><a href="https://github.com/chfi/rust-qtlreaper" target="_blank" title="'New' is the new qtlreaper implementation written in RUST by Christian Fischer. 'Original' corresponds to the original version written in C.">?</a></sup></label>
<div style="margin-left:20px;" class="col-xs-3 controls">
<select name="reaper_version" class="form-control" style="width: 80px;">
<option value="new">New</option>
@@ -224,7 +224,7 @@
<div class="mapping_method_fields form-group">
<label class="col-xs-3 control-label"></label>
<div style="margin-left:20px;" class="col-xs-6">
- <input type="button" id="interval_mapping_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping" value="Compute">
+ <button id="interval_mapping_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping" value="Compute">Compute</button>
</div>
</div>
</div>
@@ -387,7 +387,7 @@
<div class="mapping_method_fields form-group">
<label class="col-xs-3 control-label"></label>
<div style="margin-left:20px;" class="col-xs-6">
- <input type="button" id="rqtl_geno_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression" value="Compute">
+ <button id="rqtl_geno_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression" value="Compute">Compute</button>
</div>
</div>
</div>
@@ -422,4 +422,4 @@
{% else %}
Mapping options are disabled for data not matched with genotypes.
{% endif %}
-</div>
+</div> \ No newline at end of file
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index 88cb4d31..4537cd06 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -406,8 +406,8 @@
],
{% endif %}
'order': [[1, "asc" ]],
- 'sDom': "rti",
- 'iDisplayLength': -1,
+ 'sDom': "rtip",
+ 'iDisplayLength': 500,
'processing': true,
'language': {
'loadingRecords': '&nbsp;',
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 131345d3..57183eed 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -11,24 +11,24 @@ import datetime # for errors
import time # for errors
import sys
import csv
+import simplejson as json
+import yaml
import xlsxwriter
import StringIO # Todo: Use cStringIO?
+from zipfile import ZipFile, ZIP_DEFLATED
+
import gc
import numpy as np
-
import cPickle as pickle
import uuid
-import simplejson as json
-import yaml
-
import flask
import base64
import array
import sqlalchemy
from wqflask import app
-from flask import g, Response, request, make_response, render_template, send_from_directory, jsonify, redirect, url_for
+from flask import g, Response, request, make_response, render_template, send_from_directory, jsonify, redirect, url_for, send_file
from wqflask import group_manager
from wqflask import resource_manager
from wqflask import search_results
@@ -421,11 +421,21 @@ def export_traits_csv():
logger.info("In export_traits_csv")
logger.info("request.form:", request.form)
logger.info(request.url)
- csv_data, file_name = export_traits.export_search_results_csv(request.form)
+ file_list = export_traits.export_search_results_csv(request.form)
- return Response(csv_data,
- mimetype='text/csv',
- headers={"Content-Disposition":"attachment;filename=" + file_name + ".csv"})
+ if len(file_list) > 1:
+ memory_file = StringIO.StringIO()
+ with ZipFile(memory_file, mode='w', compression=ZIP_DEFLATED) as zf:
+ for the_file in file_list:
+ zf.writestr(the_file[0], the_file[1])
+
+ memory_file.seek(0)
+
+ return send_file(memory_file, attachment_filename=filename + ".zip", as_attachment=True)
+ else:
+ return Response(file_list[0][1],
+ mimetype='text/csv',
+ headers={"Content-Disposition":"attachment;filename=" + file_list[0][0]})
@app.route('/export_perm_data', methods=('POST',))
def export_perm_data():