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authorBonfaceKilz2021-04-30 12:26:19 +0300
committerBonfaceKilz2021-04-30 13:45:15 +0300
commit406eb27859cca232a562c722cbbd37aca2e3be84 (patch)
treeba3fba783e33cc56c535b68bd64d757bc6cde608 /wqflask
parentc7e661b8ff9f70955418fbc4527378904beb0cf4 (diff)
downloadgenenetwork2-406eb27859cca232a562c722cbbd37aca2e3be84.tar.gz
autopep8: Fix E301,E302,E303,E304,E305,E306
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/base/data_set.py1
-rw-r--r--wqflask/base/mrna_assay_tissue_data.py1
-rw-r--r--wqflask/base/species.py3
-rw-r--r--wqflask/base/webqtlCaseData.py3
-rw-r--r--wqflask/db/call.py4
-rw-r--r--wqflask/db/gn_server.py1
-rw-r--r--wqflask/db/webqtlDatabaseFunction.py1
-rw-r--r--wqflask/maintenance/convert_dryad_to_bimbam.py3
-rw-r--r--wqflask/maintenance/convert_geno_to_bimbam.py4
-rw-r--r--wqflask/maintenance/gen_select_dataset.py5
-rw-r--r--wqflask/maintenance/generate_kinship_from_bimbam.py1
-rw-r--r--wqflask/maintenance/generate_probesetfreeze_file.py7
-rw-r--r--wqflask/maintenance/geno_to_json.py6
-rw-r--r--wqflask/maintenance/get_group_samplelists.py3
-rw-r--r--wqflask/maintenance/print_benchmark.py4
-rw-r--r--wqflask/maintenance/quantile_normalize.py6
-rw-r--r--wqflask/maintenance/set_resource_defaults.py7
-rw-r--r--wqflask/run_gunicorn.py2
-rw-r--r--wqflask/tests/unit/base/test_webqtl_case_data.py1
-rw-r--r--wqflask/tests/unit/utility/test_authentication_tools.py1
-rw-r--r--wqflask/tests/unit/utility/test_chunks.py1
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py2
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py3
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py2
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py2
-rw-r--r--wqflask/tests/unit/wqflask/test_collect.py2
-rw-r--r--wqflask/tests/wqflask/show_trait/test_show_trait.py1
-rw-r--r--wqflask/utility/Plot.py13
-rw-r--r--wqflask/utility/__init__.py2
-rw-r--r--wqflask/utility/after.py1
-rw-r--r--wqflask/utility/authentication_tools.py1
-rw-r--r--wqflask/utility/benchmark.py1
-rw-r--r--wqflask/utility/corestats.py2
-rw-r--r--wqflask/utility/elasticsearch_tools.py7
-rw-r--r--wqflask/utility/external.py1
-rw-r--r--wqflask/utility/gen_geno_ob.py3
-rw-r--r--wqflask/utility/genofile_parser.py1
-rw-r--r--wqflask/utility/logger.py3
-rw-r--r--wqflask/utility/pillow_utils.py4
-rw-r--r--wqflask/utility/startup_config.py1
-rw-r--r--wqflask/utility/svg.py67
-rw-r--r--wqflask/utility/temp_data.py1
-rw-r--r--wqflask/utility/tools.py25
-rw-r--r--wqflask/utility/type_checking.py5
-rw-r--r--wqflask/utility/webqtlUtil.py5
-rw-r--r--wqflask/wqflask/__init__.py1
-rw-r--r--wqflask/wqflask/api/correlation.py7
-rw-r--r--wqflask/wqflask/api/mapping.py2
-rw-r--r--wqflask/wqflask/api/router.py20
-rw-r--r--wqflask/wqflask/collect.py8
-rw-r--r--wqflask/wqflask/correlation/corr_scatter_plot.py1
-rw-r--r--wqflask/wqflask/correlation/show_corr_results.py4
-rw-r--r--wqflask/wqflask/correlation_matrix/show_corr_matrix.py3
-rw-r--r--wqflask/wqflask/ctl/ctl_analysis.py1
-rw-r--r--wqflask/wqflask/database.py2
-rw-r--r--wqflask/wqflask/db_info.py1
-rw-r--r--wqflask/wqflask/do_search.py21
-rw-r--r--wqflask/wqflask/docs.py2
-rw-r--r--wqflask/wqflask/export_traits.py2
-rw-r--r--wqflask/wqflask/external_tools/send_to_bnw.py1
-rw-r--r--wqflask/wqflask/external_tools/send_to_geneweaver.py3
-rw-r--r--wqflask/wqflask/external_tools/send_to_webgestalt.py3
-rw-r--r--wqflask/wqflask/group_manager.py9
-rw-r--r--wqflask/wqflask/gsearch.py1
-rw-r--r--wqflask/wqflask/heatmap/heatmap.py3
-rw-r--r--wqflask/wqflask/interval_analyst/GeneUtil.py2
-rw-r--r--wqflask/wqflask/marker_regression/display_mapping_results.py9
-rw-r--r--wqflask/wqflask/marker_regression/plink_mapping.py9
-rw-r--r--wqflask/wqflask/marker_regression/qtlreaper_mapping.py5
-rw-r--r--wqflask/wqflask/marker_regression/rqtl_mapping.py15
-rw-r--r--wqflask/wqflask/marker_regression/run_mapping.py9
-rw-r--r--wqflask/wqflask/model.py7
-rw-r--r--wqflask/wqflask/network_graph/network_graph.py1
-rw-r--r--wqflask/wqflask/news.py1
-rw-r--r--wqflask/wqflask/parser.py1
-rw-r--r--wqflask/wqflask/pbkdf2.py2
-rw-r--r--wqflask/wqflask/resource_manager.py7
-rw-r--r--wqflask/wqflask/search_results.py4
-rw-r--r--wqflask/wqflask/send_mail.py3
-rw-r--r--wqflask/wqflask/server_side.py1
-rw-r--r--wqflask/wqflask/show_trait/SampleList.py1
-rw-r--r--wqflask/wqflask/show_trait/export_trait_data.py3
-rw-r--r--wqflask/wqflask/snp_browser/snp_browser.py9
-rw-r--r--wqflask/wqflask/submit_bnw.py1
-rw-r--r--wqflask/wqflask/update_search_results.py1
-rw-r--r--wqflask/wqflask/user_login.py21
-rw-r--r--wqflask/wqflask/user_manager.py38
-rw-r--r--wqflask/wqflask/user_session.py6
88 files changed, 435 insertions, 36 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 55ab45f5..c14808d6 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -311,7 +311,6 @@ class HumanMarkers(Markers):
marker['Mb'] = float(splat[3]) / 1000000
self.markers.append(marker)
-
def add_pvalues(self, p_values):
super(HumanMarkers, self).add_pvalues(p_values)
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index f3264b3d..cbc05738 100644
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ b/wqflask/base/mrna_assay_tissue_data.py
@@ -11,6 +11,7 @@ from utility.db_tools import escape
from utility.logger import getLogger
logger = getLogger(__name__)
+
class MrnaAssayTissueData:
def __init__(self, gene_symbols=None):
diff --git a/wqflask/base/species.py b/wqflask/base/species.py
index cf764d72..44f133b5 100644
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -6,6 +6,7 @@ from flask import Flask, g
from utility.logger import getLogger
logger = getLogger(__name__)
+
class TheSpecies:
def __init__(self, dataset=None, species_name=None):
if species_name != None:
@@ -15,6 +16,7 @@ class TheSpecies:
self.dataset = dataset
self.chromosomes = Chromosomes(dataset=self.dataset)
+
class IndChromosome:
def __init__(self, name, length):
self.name = name
@@ -25,6 +27,7 @@ class IndChromosome:
"""Chromosome length in megabases"""
return self.length / 1000000
+
class Chromosomes:
def __init__(self, dataset=None, species=None):
self.chromosomes = collections.OrderedDict()
diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py
index aa55470f..2d07ab9d 100644
--- a/wqflask/base/webqtlCaseData.py
+++ b/wqflask/base/webqtlCaseData.py
@@ -28,6 +28,7 @@ import utility.tools
utility.tools.show_settings()
+
class webqtlCaseData:
"""one case data in one trait"""
@@ -78,4 +79,4 @@ class webqtlCaseData:
def display_num_cases(self):
if self.num_cases is not None:
return "%s" % self.num_cases
- return "x" \ No newline at end of file
+ return "x"
diff --git a/wqflask/db/call.py b/wqflask/db/call.py
index 555878ad..9412b376 100644
--- a/wqflask/db/call.py
+++ b/wqflask/db/call.py
@@ -16,6 +16,7 @@ logger = getLogger(__name__)
# from inspect import stack
+
def fetch1(query, path=None, func=None):
"""Fetch one result as a Tuple using either a SQL query or the URI
path to GN_SERVER (when USE_GN_SERVER is True). Apply func to
@@ -35,6 +36,7 @@ GN_SERVER result when set (which should return a Tuple)
else:
return fetchone(query)
+
def fetchone(query):
"""Return tuple containing one row by calling SQL directly (the
original fetchone, but with logging)
@@ -46,6 +48,7 @@ original fetchone, but with logging)
return res.fetchone()
return logger.sql(query, helper)
+
def fetchall(query):
"""Return row iterator by calling SQL directly (the
original fetchall, but with logging)
@@ -57,6 +60,7 @@ original fetchall, but with logging)
return res.fetchall()
return logger.sql(query, helper)
+
def gn_server(path):
"""Return JSON record by calling GN_SERVER
diff --git a/wqflask/db/gn_server.py b/wqflask/db/gn_server.py
index 6c7383d0..f9b01658 100644
--- a/wqflask/db/gn_server.py
+++ b/wqflask/db/gn_server.py
@@ -5,5 +5,6 @@ from db.call import gn_server
from utility.logger import getLogger
logger = getLogger(__name__)
+
def menu_main():
return gn_server("/int/menu/main.json")
diff --git a/wqflask/db/webqtlDatabaseFunction.py b/wqflask/db/webqtlDatabaseFunction.py
index 18ade405..50ac06fd 100644
--- a/wqflask/db/webqtlDatabaseFunction.py
+++ b/wqflask/db/webqtlDatabaseFunction.py
@@ -31,6 +31,7 @@ logger = getLogger(__name__)
# function: connect to database and return cursor instance
###########################################################################
+
def retrieve_species(group):
"""Get the species of a group (e.g. returns string "mouse" on "BXD"
diff --git a/wqflask/maintenance/convert_dryad_to_bimbam.py b/wqflask/maintenance/convert_dryad_to_bimbam.py
index 8eab66e8..e417c280 100644
--- a/wqflask/maintenance/convert_dryad_to_bimbam.py
+++ b/wqflask/maintenance/convert_dryad_to_bimbam.py
@@ -55,15 +55,18 @@ def read_dryad_file(filename):
#
# return geno_rows
+
def write_bimbam_files(geno_rows):
with open('/home/zas1024/cfw_data/CFW_geno.txt', 'w') as geno_fh:
for row in geno_rows:
geno_fh.write(", ".join(row) + "\n")
+
def convert_dryad_to_bimbam(filename):
geno_file_rows = read_dryad_file(filename)
write_bimbam_files(geno_file_rows)
+
if __name__ == "__main__":
input_filename = "/home/zas1024/cfw_data/" + sys.argv[1] + ".txt"
convert_dryad_to_bimbam(input_filename)
diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py
index dc01cbb3..5b2369c9 100644
--- a/wqflask/maintenance/convert_geno_to_bimbam.py
+++ b/wqflask/maintenance/convert_geno_to_bimbam.py
@@ -20,8 +20,10 @@ import simplejson as json
from pprint import pformat as pf
+
class EmptyConfigurations(Exception): pass
+
class Marker:
def __init__(self):
self.name = None
@@ -30,6 +32,7 @@ class Marker:
self.Mb = None
self.genotypes = []
+
class ConvertGenoFile:
def __init__(self, input_file, output_files):
@@ -178,6 +181,7 @@ class ConvertGenoFile:
print(" Row is:", convertob.latest_row_value)
break
+
if __name__ == "__main__":
Old_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype"""
New_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype/bimbam"""
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index f480d63f..583a06e1 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -55,6 +55,7 @@ from pprint import pformat as pf
#conn = Engine.connect()
+
def parse_db_uri():
"""Converts a database URI to the db name, host name, user name, and password"""
@@ -143,6 +144,7 @@ def phenotypes_exist(group_name):
else:
return False
+
def genotypes_exist(group_name):
#print("group_name:", group_name)
Cursor.execute("""select Name from GenoFreeze
@@ -156,6 +158,7 @@ def genotypes_exist(group_name):
else:
return False
+
def build_types(species, group):
"""Fetches tissues
@@ -184,6 +187,7 @@ def build_types(species, group):
return results
+
def get_datasets(types):
"""Build datasets list"""
datasets = {}
@@ -308,6 +312,7 @@ def _test_it():
datasets = build_datasets("Mouse", "BXD", "Hippocampus")
#print("build_datasets:", pf(datasets))
+
if __name__ == '__main__':
Conn = MySQLdb.Connect(**parse_db_uri())
Cursor = Conn.cursor()
diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py
index 664e9e48..7cc60c9e 100644
--- a/wqflask/maintenance/generate_kinship_from_bimbam.py
+++ b/wqflask/maintenance/generate_kinship_from_bimbam.py
@@ -13,6 +13,7 @@ sys.path.append("..")
import os
import glob
+
class GenerateKinshipMatrices:
def __init__(self, group_name, geno_file, pheno_file):
self.group_name = group_name
diff --git a/wqflask/maintenance/generate_probesetfreeze_file.py b/wqflask/maintenance/generate_probesetfreeze_file.py
index b1e41e9a..bd9c2ab4 100644
--- a/wqflask/maintenance/generate_probesetfreeze_file.py
+++ b/wqflask/maintenance/generate_probesetfreeze_file.py
@@ -23,10 +23,12 @@ def get_cursor():
cursor = con.cursor()
return cursor
+
def show_progress(process, counter):
if counter % 1000 == 0:
print("{}: {}".format(process, counter))
+
def get_strains(cursor):
cursor.execute("""select Strain.Name
from Strain, StrainXRef, InbredSet
@@ -42,6 +44,7 @@ def get_strains(cursor):
return strains
+
def get_probeset_vals(cursor, dataset_name):
cursor.execute(""" select ProbeSet.Id, ProbeSet.Name
from ProbeSetXRef,
@@ -77,6 +80,7 @@ def get_probeset_vals(cursor, dataset_name):
return probeset_vals
+
def trim_strains(strains, probeset_vals):
trimmed_strains = []
#print("probeset_vals is:", pf(probeset_vals))
@@ -89,6 +93,7 @@ def trim_strains(strains, probeset_vals):
print("trimmed_strains:", pf(trimmed_strains))
return trimmed_strains
+
def write_data_matrix_file(strains, probeset_vals, filename):
with open(filename, "wb") as fh:
csv_writer = csv.writer(fh, delimiter=",", quoting=csv.QUOTE_ALL)
@@ -103,6 +108,7 @@ def write_data_matrix_file(strains, probeset_vals, filename):
csv_writer.writerow(row_data)
show_progress("Writing", counter)
+
def main():
filename = os.path.expanduser("~/gene/wqflask/maintenance/" +
"ProbeSetFreezeId_210_FullName_Eye_AXBXA_Illumina_V6.2" +
@@ -117,5 +123,6 @@ def main():
trimmed_strains = trim_strains(strains, probeset_vals)
write_data_matrix_file(trimmed_strains, probeset_vals, filename)
+
if __name__ == '__main__':
main()
diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py
index fa0dcebd..ad3f2b72 100644
--- a/wqflask/maintenance/geno_to_json.py
+++ b/wqflask/maintenance/geno_to_json.py
@@ -25,10 +25,10 @@ from pprint import pformat as pf
#from utility.tools import flat_files
+
class EmptyConfigurations(Exception): pass
-
class Marker:
def __init__(self):
self.name = None
@@ -37,6 +37,7 @@ class Marker:
self.Mb = None
self.genotypes = []
+
class ConvertGenoFile:
def __init__(self, input_file, output_file):
@@ -78,7 +79,6 @@ class ConvertGenoFile:
# elif self.file_type == "snps":
# self.process_snps_file()
-
def process_csv(self):
for row_count, row in enumerate(self.process_rows()):
row_items = row.split("\t")
@@ -121,7 +121,6 @@ class ConvertGenoFile:
# self.output_fh.write("\n")
-
def process_rows(self):
for self.latest_row_pos, row in enumerate(self.input_fh):
# if self.input_file.endswith(".geno.gz"):
@@ -182,7 +181,6 @@ class ConvertGenoFile:
# convertob = ConvertGenoFile(input_file, output_file)
-
if __name__ == "__main__":
Old_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype"""
New_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype/json"""
diff --git a/wqflask/maintenance/get_group_samplelists.py b/wqflask/maintenance/get_group_samplelists.py
index 3f9d0278..0a450d3f 100644
--- a/wqflask/maintenance/get_group_samplelists.py
+++ b/wqflask/maintenance/get_group_samplelists.py
@@ -4,12 +4,14 @@ import gzip
from base import webqtlConfig
+
def get_samplelist(file_type, geno_file):
if file_type == "geno":
return get_samplelist_from_geno(geno_file)
elif file_type == "plink":
return get_samplelist_from_plink(geno_file)
+
def get_samplelist_from_geno(genofilename):
if os.path.isfile(genofilename + '.gz'):
genofilename += '.gz'
@@ -33,6 +35,7 @@ def get_samplelist_from_geno(genofilename):
samplelist = headers[3:]
return samplelist
+
def get_samplelist_from_plink(genofilename):
genofile = open(genofilename)
diff --git a/wqflask/maintenance/print_benchmark.py b/wqflask/maintenance/print_benchmark.py
index a1046c86..9d12da8a 100644
--- a/wqflask/maintenance/print_benchmark.py
+++ b/wqflask/maintenance/print_benchmark.py
@@ -15,15 +15,18 @@ class TheCounter:
self.time_took = time.time() - start_time
TheCounter.Counters[self.__class__.__name__] = self.time_took
+
class PrintAll(TheCounter):
def print_it(self, counter):
print(counter)
+
class PrintSome(TheCounter):
def print_it(self, counter):
if counter % 1000 == 0:
print(counter)
+
class PrintNone(TheCounter):
def print_it(self, counter):
pass
@@ -37,5 +40,6 @@ def new_main():
print(pf(TheCounter.Counters))
+
if __name__ == '__main__':
new_main()
diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py
index 6751a8e5..1896bc52 100644
--- a/wqflask/maintenance/quantile_normalize.py
+++ b/wqflask/maintenance/quantile_normalize.py
@@ -14,6 +14,7 @@ from wqflask import app
from utility.elasticsearch_tools import get_elasticsearch_connection
from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT, SQL_URI
+
def parse_db_uri():
"""Converts a database URI to the db name, host name, user name, and password"""
@@ -28,6 +29,7 @@ def parse_db_uri():
print(db_conn_info)
return db_conn_info
+
def create_dataframe(input_file):
with open(input_file) as f:
ncols = len(f.readline().split("\t"))
@@ -36,6 +38,8 @@ def create_dataframe(input_file):
return pd.DataFrame(input_array)
# This function taken from https://github.com/ShawnLYU/Quantile_Normalize
+
+
def quantileNormalize(df_input):
df = df_input.copy()
# compute rank
@@ -50,6 +54,7 @@ def quantileNormalize(df_input):
df[col] = [rank[i] for i in t]
return df
+
def set_data(dataset_name):
orig_file = "/home/zas1024/cfw_data/" + dataset_name + ".txt"
@@ -95,6 +100,7 @@ def set_data(dataset_name):
}
}
+
if __name__ == '__main__':
Conn = MySQLdb.Connect(**parse_db_uri())
Cursor = Conn.cursor()
diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py
index 286094dd..c6c4f44c 100644
--- a/wqflask/maintenance/set_resource_defaults.py
+++ b/wqflask/maintenance/set_resource_defaults.py
@@ -37,6 +37,7 @@ import urllib.parse
from utility.logger import getLogger
logger = getLogger(__name__)
+
def parse_db_uri():
"""Converts a database URI to the db name, host name, user name, and password"""
@@ -51,6 +52,7 @@ def parse_db_uri():
print(db_conn_info)
return db_conn_info
+
def insert_probeset_resources(default_owner_id):
current_resources = Redis.hgetall("resources")
Cursor.execute(""" SELECT
@@ -77,6 +79,7 @@ def insert_probeset_resources(default_owner_id):
add_resource(resource_ob, update=False)
+
def insert_publish_resources(default_owner_id):
current_resources = Redis.hgetall("resources")
Cursor.execute(""" SELECT
@@ -110,6 +113,7 @@ def insert_publish_resources(default_owner_id):
else:
continue
+
def insert_geno_resources(default_owner_id):
current_resources = Redis.hgetall("resources")
Cursor.execute(""" SELECT
@@ -139,6 +143,7 @@ def insert_geno_resources(default_owner_id):
add_resource(resource_ob, update=False)
+
def insert_resources(default_owner_id):
current_resources = get_resources()
print("START")
@@ -149,6 +154,7 @@ def insert_resources(default_owner_id):
insert_probeset_resources(default_owner_id)
print("AFTER PROBESET")
+
def main():
"""Generates and outputs (as json file) the data for the main dropdown menus on the home page"""
@@ -158,6 +164,7 @@ def main():
insert_resources(owner_id)
+
if __name__ == '__main__':
Conn = MySQLdb.Connect(**parse_db_uri())
Cursor = Conn.cursor()
diff --git a/wqflask/run_gunicorn.py b/wqflask/run_gunicorn.py
index 58108e03..03f310eb 100644
--- a/wqflask/run_gunicorn.py
+++ b/wqflask/run_gunicorn.py
@@ -14,9 +14,11 @@ from utility.startup_config import app_config
app_config()
+
@app.route("/gunicorn")
def hello():
return "<h1 style='color:blue'>Hello There!</h1>"
+
if __name__ == "__main__":
app.run(host='0.0.0.0')
diff --git a/wqflask/tests/unit/base/test_webqtl_case_data.py b/wqflask/tests/unit/base/test_webqtl_case_data.py
index 8e8ba482..cebd41ce 100644
--- a/wqflask/tests/unit/base/test_webqtl_case_data.py
+++ b/wqflask/tests/unit/base/test_webqtl_case_data.py
@@ -4,6 +4,7 @@ import unittest
from wqflask import app # Required because of utility.tools in webqtlCaseData.py
from base.webqtlCaseData import webqtlCaseData
+
class TestWebqtlCaseData(unittest.TestCase):
"""Tests for WebqtlCaseData class"""
diff --git a/wqflask/tests/unit/utility/test_authentication_tools.py b/wqflask/tests/unit/utility/test_authentication_tools.py
index 42dcae88..024ab43f 100644
--- a/wqflask/tests/unit/utility/test_authentication_tools.py
+++ b/wqflask/tests/unit/utility/test_authentication_tools.py
@@ -5,6 +5,7 @@ from unittest import mock
from utility.authentication_tools import check_resource_availability
from utility.authentication_tools import add_new_resource
+
class TestResponse:
"""Mock Test Response after a request"""
@property
diff --git a/wqflask/tests/unit/utility/test_chunks.py b/wqflask/tests/unit/utility/test_chunks.py
index 8d90a1ec..1d349193 100644
--- a/wqflask/tests/unit/utility/test_chunks.py
+++ b/wqflask/tests/unit/utility/test_chunks.py
@@ -7,6 +7,7 @@ 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),
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py b/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py
index 8ae0f09f..219a6a29 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py
@@ -9,6 +9,7 @@ from wqflask.marker_regression.display_mapping_results import (
class TestDisplayMappingResults(unittest.TestCase):
"""Basic Methods to test Mapping Results"""
+
def test_pil_colors(self):
"""Test that colors use PILLOW color format"""
self.assertEqual(DisplayMappingResults.CLICKABLE_WEBQTL_REGION_COLOR,
@@ -17,6 +18,7 @@ class TestDisplayMappingResults(unittest.TestCase):
class TestHtmlGenWrapper(unittest.TestCase):
"""Test Wrapper around HTMLGen"""
+
def test_create_image(self):
"""Test HT.Image method"""
self.assertEqual(
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py
index 5eec93f1..fd21a825 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py
@@ -12,9 +12,10 @@ class AttributeSetter:
def __init__(self, obj):
for key, val in obj.items():
setattr(self, key, val)
-class TestPlinkMapping(unittest.TestCase):
+class TestPlinkMapping(unittest.TestCase):
+
def test_build_line_list(self):
"""test for building line list"""
line_1 = "this is line one test"
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
index bbb79f98..5cc8fd0f 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
@@ -4,6 +4,8 @@ from wqflask.marker_regression.qtlreaper_mapping import gen_pheno_txt_file
# issues some methods in genofile object are not defined
# modify samples should equal to vals
+
+
class TestQtlReaperMapping(unittest.TestCase):
@mock.patch("wqflask.marker_regression.qtlreaper_mapping.TEMPDIR", "/home/user/data")
def test_gen_pheno_txt_file(self):
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
index 0e617e93..6267ce9a 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
@@ -5,6 +5,7 @@ from wqflask.marker_regression.rqtl_mapping import get_trait_data_type
from wqflask.marker_regression.rqtl_mapping import sanitize_rqtl_phenotype
from wqflask.marker_regression.rqtl_mapping import sanitize_rqtl_names
+
class TestRqtlMapping(unittest.TestCase):
def setUp(self):
@@ -14,7 +15,6 @@ class TestRqtlMapping(unittest.TestCase):
def tearDown(self):
self.app_context.pop()
-
@mock.patch("wqflask.marker_regression.rqtl_mapping.g")
@mock.patch("wqflask.marker_regression.rqtl_mapping.logger")
def test_get_trait_data(self, mock_logger, mock_db):
diff --git a/wqflask/tests/unit/wqflask/test_collect.py b/wqflask/tests/unit/wqflask/test_collect.py
index 9a36132d..2a914fb2 100644
--- a/wqflask/tests/unit/wqflask/test_collect.py
+++ b/wqflask/tests/unit/wqflask/test_collect.py
@@ -11,6 +11,7 @@ app = Flask(__name__)
class MockSession:
"""Helper class for mocking wqflask.collect.g.user_session.logged_in"""
+
def __init__(self, is_logged_in=False):
self.is_logged_in = is_logged_in
@@ -21,6 +22,7 @@ class MockSession:
class MockFlaskG:
"""Helper class for mocking wqflask.collect.g.user_session"""
+
def __init__(self, is_logged_in=False):
self.is_logged_in = is_logged_in
diff --git a/wqflask/tests/wqflask/show_trait/test_show_trait.py b/wqflask/tests/wqflask/show_trait/test_show_trait.py
index 8c866874..24c3923e 100644
--- a/wqflask/tests/wqflask/show_trait/test_show_trait.py
+++ b/wqflask/tests/wqflask/show_trait/test_show_trait.py
@@ -242,7 +242,6 @@ class TestTraits(unittest.TestCase):
self.assertEqual(get_genotype_scales(file_location), expected_results)
mock_get_scales.assert_called_once_with(file_location)
-
@mock.patch("wqflask.show_trait.show_trait.locate_ignore_error")
def test_get_scales_from_genofile_found(self, mock_ignore_location):
""""add test for get scales from genofile where file is found"""
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index 68c2cb72..d35b2089 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -47,6 +47,7 @@ COUR_FILE = "./wqflask/static/fonts/courbd.ttf"
TAHOMA_FILE = "./wqflask/static/fonts/tahoma.ttf"
# ---- END: FONT FILES ---- #
+
def cformat(d, rank=0):
'custom string format'
strD = "%2.6f" % d
@@ -68,6 +69,7 @@ def cformat(d, rank=0):
strD = '0.0'
return strD
+
def frange(start, end=None, inc=1.0):
"A faster range-like function that does accept float increments..."
if end == None:
@@ -84,6 +86,7 @@ def frange(start, end=None, inc=1.0):
L[i] = start + i * inc
return L
+
def find_outliers(vals):
"""Calculates the upper and lower bounds of a set of sample/case values
@@ -119,6 +122,8 @@ def find_outliers(vals):
# parameter: data is either object returned by reaper permutation function (called by MarkerRegressionPage.py)
# or the first object returned by direct (pair-scan) permu function (called by DirectPlotPage.py)
+
+
def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLabel=None, YLabel=None, title=None, offset=(60, 20, 40, 40), zoom=1):
im_drawer = ImageDraw.Draw(canvas)
xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
@@ -230,6 +235,8 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
font=labelFont, fill=labelColor)
# This function determines the scale of the plot
+
+
def detScaleOld(min, max):
if min >= max:
return None
@@ -246,6 +253,7 @@ def detScaleOld(min, max):
high = c * ceil(max / c)
return [low, high, round((high - low) / c)]
+
def detScale(min=0, max=0):
if min >= max:
@@ -283,15 +291,19 @@ def detScale(min=0, max=0):
return [low, high, n]
+
def bluefunc(x):
return 1.0 / (1.0 + exp(-10 * (x - 0.6)))
+
def redfunc(x):
return 1.0 / (1.0 + exp(10 * (x - 0.5)))
+
def greenfunc(x):
return 1 - pow(redfunc(x + 0.2), 2) - bluefunc(x - 0.3)
+
def colorSpectrum(n=100):
multiple = 10
if n == 1:
@@ -319,6 +331,7 @@ def colorSpectrum(n=100):
out2.append(out[-1])
return out2
+
def _test():
import doctest
doctest.testmod()
diff --git a/wqflask/utility/__init__.py b/wqflask/utility/__init__.py
index ec7e72d0..d540c96e 100644
--- a/wqflask/utility/__init__.py
+++ b/wqflask/utility/__init__.py
@@ -2,8 +2,10 @@ from pprint import pformat as pf
# Todo: Move these out of __init__
+
class Bunch:
"""Like a dictionary but using object notation"""
+
def __init__(self, **kw):
self.__dict__ = kw
diff --git a/wqflask/utility/after.py b/wqflask/utility/after.py
index 06091ecb..2b560e48 100644
--- a/wqflask/utility/after.py
+++ b/wqflask/utility/after.py
@@ -7,6 +7,7 @@ from flask import g
from wqflask import app
+
def after_this_request(f):
if not hasattr(g, 'after_request_callbacks'):
g.after_request_callbacks = []
diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index 672b36d5..57dbf8ba 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -11,6 +11,7 @@ from utility.redis_tools import (get_redis_conn,
add_resource)
Redis = get_redis_conn()
+
def check_resource_availability(dataset, trait_id=None):
# At least for now assume temporary entered traits are accessible
if type(dataset) == str or dataset.type == "Temp":
diff --git a/wqflask/utility/benchmark.py b/wqflask/utility/benchmark.py
index 3d40a3b8..48ab1dc0 100644
--- a/wqflask/utility/benchmark.py
+++ b/wqflask/utility/benchmark.py
@@ -6,6 +6,7 @@ from utility.tools import LOG_BENCH
from utility.logger import getLogger
logger = getLogger(__name__)
+
class Bench:
entries = collections.OrderedDict()
diff --git a/wqflask/utility/corestats.py b/wqflask/utility/corestats.py
index 15d1cb8d..523280a1 100644
--- a/wqflask/utility/corestats.py
+++ b/wqflask/utility/corestats.py
@@ -16,6 +16,8 @@
import sys
# ZS: Should switch to using some third party library for this; maybe scipy has an equivalent
+
+
class Stats:
def __init__(self, sequence):
diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py
index ae1181e4..9415cef0 100644
--- a/wqflask/utility/elasticsearch_tools.py
+++ b/wqflask/utility/elasticsearch_tools.py
@@ -47,11 +47,13 @@ logger = getLogger(__name__)
from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT
+
def test_elasticsearch_connection():
es = Elasticsearch(['http://' + ELASTICSEARCH_HOST + ":" + str(ELASTICSEARCH_PORT) + '/'], verify_certs=True)
if not es.ping():
logger.warning("Elasticsearch is DOWN")
+
def get_elasticsearch_connection(for_user=True):
"""Return a connection to ES. Returns None on failure"""
logger.info("get_elasticsearch_connection")
@@ -77,6 +79,7 @@ def get_elasticsearch_connection(for_user=True):
return es
+
def setup_users_index(es_connection):
if es_connection:
index_settings = {
@@ -87,12 +90,15 @@ def setup_users_index(es_connection):
es_connection.indices.create(index='users', ignore=400)
es_connection.indices.put_mapping(body=index_settings, index="users", doc_type="local")
+
def get_user_by_unique_column(es, column_name, column_value, index="users", doc_type="local"):
return get_item_by_unique_column(es, column_name, column_value, index=index, doc_type=doc_type)
+
def save_user(es, user, user_id):
es_save_data(es, "users", "local", user, user_id)
+
def get_item_by_unique_column(es, column_name, column_value, index, doc_type):
item_details = None
try:
@@ -106,6 +112,7 @@ def get_item_by_unique_column(es, column_name, column_value, index, doc_type):
pass
return item_details
+
def es_save_data(es, index, doc_type, data_item, data_id,):
from time import sleep
es.create(index, doc_type, body=data_item, id=data_id)
diff --git a/wqflask/utility/external.py b/wqflask/utility/external.py
index c1bf4043..805d2ffe 100644
--- a/wqflask/utility/external.py
+++ b/wqflask/utility/external.py
@@ -4,6 +4,7 @@ import os
import sys
import subprocess
+
def shell(command):
if subprocess.call(command, shell=True) != 0:
raise Exception("ERROR: failed on " + command)
diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py
index 9cfa39f9..24604e58 100644
--- a/wqflask/utility/gen_geno_ob.py
+++ b/wqflask/utility/gen_geno_ob.py
@@ -1,6 +1,7 @@
import utility.logger
logger = utility.logger.getLogger(__name__)
+
class genotype:
"""
Replacement for reaper.Dataset so we can remove qtlreaper use while still generating mapping output figure
@@ -119,6 +120,7 @@ class genotype:
self.chromosomes.append(chr_ob)
+
class Chr:
def __init__(self, name, geno_ob):
self.name = name
@@ -140,6 +142,7 @@ class Chr:
def add_marker(self, marker_row):
self.loci.append(Locus(self.geno_ob, marker_row))
+
class Locus:
def __init__(self, geno_ob, marker_row=None):
self.chr = None
diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py
index f8e96d19..94a08c17 100644
--- a/wqflask/utility/genofile_parser.py
+++ b/wqflask/utility/genofile_parser.py
@@ -12,6 +12,7 @@ import simplejson as json
from pprint import pformat as pf
+
class Marker:
def __init__(self):
self.name = None
diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py
index 16912e58..47079818 100644
--- a/wqflask/utility/logger.py
+++ b/wqflask/utility/logger.py
@@ -35,6 +35,7 @@ import datetime
from utility.tools import LOG_LEVEL, LOG_LEVEL_DEBUG, LOG_SQL
+
class GNLogger:
"""A logger class with some additional functionality, such as
multiple parameter logging, SQL logging, timing, colors, and lazy
@@ -139,6 +140,8 @@ LOG_LEVEL_DEBUG (NYI).
# Get the module logger. You can override log levels at the
# module level
+
+
def getLogger(name, level=None):
gnlogger = GNLogger(name)
logger = gnlogger.logger
diff --git a/wqflask/utility/pillow_utils.py b/wqflask/utility/pillow_utils.py
index 6e95beb0..5713e155 100644
--- a/wqflask/utility/pillow_utils.py
+++ b/wqflask/utility/pillow_utils.py
@@ -9,6 +9,8 @@ BLACK = ImageColor.getrgb("black")
WHITE = ImageColor.getrgb("white")
# def draw_rotated_text(canvas: Image, text: str, font: ImageFont, xy: tuple, fill: ImageColor=BLACK, angle: int=-90):
+
+
def draw_rotated_text(canvas, text, font, xy, fill=BLACK, angle=-90):
# type: (Image, str, ImageFont, tuple, ImageColor, int)
"""Utility function draw rotated text"""
@@ -20,6 +22,8 @@ def draw_rotated_text(canvas, text, font, xy, fill=BLACK, angle=-90):
canvas.paste(im=tmp_img2, box=tuple([int(i) for i in xy]))
# def draw_open_polygon(canvas: Image, xy: tuple, fill: ImageColor=WHITE, outline: ImageColor=BLACK):
+
+
def draw_open_polygon(canvas, xy, fill=None, outline=BLACK, width=0):
# type: (Image, tuple, ImageColor, ImageColor)
draw_ctx = ImageDraw.Draw(canvas)
diff --git a/wqflask/utility/startup_config.py b/wqflask/utility/startup_config.py
index f22f4b14..92f944bc 100644
--- a/wqflask/utility/startup_config.py
+++ b/wqflask/utility/startup_config.py
@@ -10,6 +10,7 @@ GREEN = '\033[92m'
BOLD = '\033[1m'
ENDC = '\033[0m'
+
def app_config():
app.config['SESSION_TYPE'] = 'filesystem'
if not app.config.get('SECRET_KEY'):
diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py
index 4c478c36..f5ef81e1 100644
--- a/wqflask/utility/svg.py
+++ b/wqflask/utility/svg.py
@@ -459,11 +459,13 @@ class rect(SVGelement):
if stroke_width != None:
self.attributes['stroke-width'] = stroke_width
+
class ellipse(SVGelement):
"""e=ellipse(rx,ry,x,y,fill,stroke,stroke_width,**args)
an ellipse is defined as a center and a x and y radius.
"""
+
def __init__(self, cx=None, cy=None, rx=None, ry=None,fill=None,stroke=None,stroke_width=None,**args):
if rx == None or ry == None:
raise ValueError('both rx and ry are required')
@@ -486,6 +488,7 @@ class circle(SVGelement):
The circle creates an element using a x, y and radius values eg
"""
+
def __init__(self, cx=None, cy=None, r=None, fill=None,stroke=None,stroke_width=None,**args):
if r == None:
raise ValueError('r is required')
@@ -501,20 +504,24 @@ class circle(SVGelement):
if stroke_width != None:
self.attributes['stroke-width'] = stroke_width
+
class point(circle):
"""p=point(x,y,color)
A point is defined as a circle with a size 1 radius. It may be more efficient to use a
very small rectangle if you use many points because a circle is difficult to render.
"""
+
def __init__(self, x, y, fill='black', **args):
circle.__init__(self, x, y, 1, fill, **args)
+
class line(SVGelement):
"""l=line(x1,y1,x2,y2,stroke,stroke_width,**args)
A line is defined by a begin x,y pair and an end x,y pair
"""
+
def __init__(self, x1=None, y1=None, x2=None, y2=None,stroke=None,stroke_width=None,**args):
SVGelement.__init__(self, 'line', **args)
if x1 != None:
@@ -530,11 +537,13 @@ class line(SVGelement):
if stroke != None:
self.attributes['stroke'] = stroke
+
class polyline(SVGelement):
"""pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args)
a polyline is defined by a list of xy pairs
"""
+
def __init__(self, points, fill=None, stroke=None, stroke_width=None,**args):
SVGelement.__init__(self, 'polyline', {'points': _xypointlist(points)}, **args)
if fill != None:
@@ -544,11 +553,13 @@ class polyline(SVGelement):
if stroke != None:
self.attributes['stroke'] = stroke
+
class polygon(SVGelement):
"""pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args)
a polygon is defined by a list of xy pairs
"""
+
def __init__(self, points, fill=None, stroke=None, stroke_width=None,**args):
SVGelement.__init__(self, 'polygon', {'points': _xypointlist(points)}, **args)
if fill != None:
@@ -558,11 +569,13 @@ class polygon(SVGelement):
if stroke != None:
self.attributes['stroke'] = stroke
+
class path(SVGelement):
"""p=path(path,fill,stroke,stroke_width,**args)
a path is defined by a path object and optional width, stroke and fillcolor
"""
+
def __init__(self, pathdata, fill=None, stroke=None, stroke_width=None,id=None,**args):
SVGelement.__init__(self, 'path', {'d': str(pathdata)}, **args)
if stroke != None:
@@ -580,6 +593,7 @@ class text(SVGelement):
a text element can bge used for displaying text on the screen
"""
+
def __init__(self, x=None, y=None, text=None, font_size=None,font_family=None,text_anchor=None,**args):
SVGelement.__init__(self, 'text', **args)
if x != None:
@@ -601,11 +615,13 @@ class textpath(SVGelement):
a textpath places a text on a path which is referenced by a link.
"""
+
def __init__(self, link, text=None, **args):
SVGelement.__init__(self, 'textPath', {'xlink:href': link}, **args)
if text != None:
self.text = text
+
class pattern(SVGelement):
"""p=pattern(x,y,width,height,patternUnits,**args)
@@ -613,6 +629,7 @@ class pattern(SVGelement):
graphic object which can be replicated ("tiled") at fixed intervals
in x and y to cover the areas to be painted.
"""
+
def __init__(self, x=None, y=None, width=None, height=None,patternUnits=None,**args):
SVGelement.__init__(self, 'pattern', **args)
if x != None:
@@ -626,34 +643,40 @@ class pattern(SVGelement):
if patternUnits != None:
self.attributes['patternUnits'] = patternUnits
+
class title(SVGelement):
"""t=title(text,**args)
a title is a text element. The text is displayed in the title bar
add at least one to the root svg element
"""
+
def __init__(self, text=None, **args):
SVGelement.__init__(self, 'title', **args)
if text != None:
self.text = text
+
class description(SVGelement):
"""d=description(text,**args)
a description can be added to any element and is used for a tooltip
Add this element before adding other elements.
"""
+
def __init__(self, text=None, **args):
SVGelement.__init__(self, 'desc', **args)
if text != None:
self.text = text
+
class lineargradient(SVGelement):
"""lg=lineargradient(x1,y1,x2,y2,id,**args)
defines a lineargradient using two xy pairs.
stop elements van be added to define the gradient colors.
"""
+
def __init__(self, x1=None, y1=None, x2=None, y2=None,id=None,**args):
SVGelement.__init__(self, 'linearGradient', **args)
if x1 != None:
@@ -667,12 +690,14 @@ class lineargradient(SVGelement):
if id != None:
self.attributes['id'] = id
+
class radialgradient(SVGelement):
"""rg=radialgradient(cx,cy,r,fx,fy,id,**args)
defines a radial gradient using a outer circle which are defined by a cx,cy and r and by using a focalpoint.
stop elements van be added to define the gradient colors.
"""
+
def __init__(self, cx=None, cy=None, r=None, fx=None,fy=None,id=None,**args):
SVGelement.__init__(self, 'radialGradient', **args)
if cx != None:
@@ -688,21 +713,25 @@ class radialgradient(SVGelement):
if id != None:
self.attributes['id'] = id
+
class stop(SVGelement):
"""st=stop(offset,stop_color,**args)
Puts a stop color at the specified radius
"""
+
def __init__(self, offset, stop_color=None, **args):
SVGelement.__init__(self, 'stop', {'offset': offset}, **args)
if stop_color != None:
self.attributes['stop-color'] = stop_color
+
class style(SVGelement):
"""st=style(type,cdata=None,**args)
Add a CDATA element to this element for defing in line stylesheets etc..
"""
+
def __init__(self, type, cdata=None, **args):
SVGelement.__init__(self, 'style', {'type': type}, cdata=cdata, **args)
@@ -712,6 +741,7 @@ class image(SVGelement):
adds an image to the drawing. Supported formats are .png, .jpg and .svg.
"""
+
def __init__(self, url, x=None, y=None, width=None,height=None,**args):
if width == None or height == None:
raise ValueError('both height and width are required')
@@ -721,11 +751,13 @@ class image(SVGelement):
if y != None:
self.attributes['y'] = y
+
class cursor(SVGelement):
"""c=cursor(url,**args)
defines a custom cursor for a element or a drawing
"""
+
def __init__(self, url, **args):
SVGelement.__init__(self, 'cursor', {'xlink:href': url}, **args)
@@ -736,6 +768,7 @@ class marker(SVGelement):
defines a marker which can be used as an endpoint for a line or other pathtypes
add an element to it which should be used as a marker.
"""
+
def __init__(self, id=None, viewBox=None, refx=None, refy=None,markerWidth=None,markerHeight=None,**args):
SVGelement.__init__(self, 'marker', **args)
if id != None:
@@ -751,17 +784,20 @@ class marker(SVGelement):
if markerHeight != None:
self.attributes['markerHeight'] = markerHeight
+
class group(SVGelement):
"""g=group(id,**args)
a group is defined by an id and is used to contain elements
g.addElement(SVGelement)
"""
+
def __init__(self, id=None, **args):
SVGelement.__init__(self, 'g', **args)
if id != None:
self.attributes['id'] = id
+
class symbol(SVGelement):
"""sy=symbol(id,viewbox,**args)
@@ -778,14 +814,17 @@ class symbol(SVGelement):
if viewBox != None:
self.attributes['viewBox'] = _viewboxlist(viewBox)
+
class defs(SVGelement):
"""d=defs(**args)
container for defining elements
"""
+
def __init__(self, **args):
SVGelement.__init__(self, 'defs', **args)
+
class switch(SVGelement):
"""sw=switch(**args)
@@ -793,6 +832,7 @@ class switch(SVGelement):
requiredFeatures, requiredExtensions and systemLanguage.
Refer to the SVG specification for details.
"""
+
def __init__(self, **args):
SVGelement.__init__(self, 'switch', **args)
@@ -802,6 +842,7 @@ class use(SVGelement):
references a symbol by linking to its id and its position, height and width
"""
+
def __init__(self, link, x=None, y=None, width=None,height=None,**args):
SVGelement.__init__(self, 'use', {'xlink:href': link}, **args)
if x != None:
@@ -821,32 +862,39 @@ class link(SVGelement):
a link is defined by a hyperlink. add elements which have to be linked
a.addElement(SVGelement)
"""
+
def __init__(self, link='', **args):
SVGelement.__init__(self, 'a', {'xlink:href': link}, **args)
+
class view(SVGelement):
"""v=view(id,**args)
a view can be used to create a view with different attributes"""
+
def __init__(self, id=None, **args):
SVGelement.__init__(self, 'view', **args)
if id != None:
self.attributes['id'] = id
+
class script(SVGelement):
"""sc=script(type,type,cdata,**args)
adds a script element which contains CDATA to the SVG drawing
"""
+
def __init__(self, type, cdata=None, **args):
SVGelement.__init__(self, 'script', {'type': type}, cdata=cdata, **args)
+
class animate(SVGelement):
"""an=animate(attribute,from,to,during,**args)
animates an attribute.
"""
+
def __init__(self, attribute, fr=None, to=None, dur=None,**args):
SVGelement.__init__(self, 'animate', {'attributeName': attribute}, **args)
if fr != None:
@@ -856,11 +904,13 @@ class animate(SVGelement):
if dur != None:
self.attributes['dur'] = dur
+
class animateMotion(SVGelement):
"""an=animateMotion(pathdata,dur,**args)
animates a SVGelement over the given path in dur seconds
"""
+
def __init__(self, pathdata, dur, **args):
SVGelement.__init__(self, 'animateMotion', **args)
if pathdata != None:
@@ -868,11 +918,13 @@ class animateMotion(SVGelement):
if dur != None:
self.attributes['dur'] = dur
+
class animateTransform(SVGelement):
"""antr=animateTransform(type,from,to,dur,**args)
transform an element from and to a value.
"""
+
def __init__(self, type=None, fr=None, to=None, dur=None,**args):
SVGelement.__init__(self, 'animateTransform', {'attributeName': 'transform'}, **args)
# As far as I know the attributeName is always transform
@@ -884,11 +936,14 @@ class animateTransform(SVGelement):
self.attributes['to'] = to
if dur != None:
self.attributes['dur'] = dur
+
+
class animateColor(SVGelement):
"""ac=animateColor(attribute,type,from,to,dur,**args)
Animates the color of a element
"""
+
def __init__(self, attribute, type=None, fr=None, to=None,dur=None,**args):
SVGelement.__init__(self, 'animateColor', {'attributeName': attribute}, **args)
if type != None:
@@ -899,11 +954,14 @@ class animateColor(SVGelement):
self.attributes['to'] = to
if dur != None:
self.attributes['dur'] = dur
+
+
class set(SVGelement):
"""st=set(attribute,to,during,**args)
sets an attribute to a value for a
"""
+
def __init__(self, attribute, to=None, dur=None, **args):
SVGelement.__init__(self, 'set', {'attributeName': attribute}, **args)
if to != None:
@@ -912,7 +970,6 @@ class set(SVGelement):
self.attributes['dur'] = dur
-
class svg(SVGelement):
"""s=svg(viewbox,width,height,**args)
@@ -928,6 +985,7 @@ class svg(SVGelement):
d.setSVG(s)
d.toXml()
"""
+
def __init__(self, viewBox=None, width=None, height=None, **args):
SVGelement.__init__(self, 'svg', **args)
if viewBox != None:
@@ -938,6 +996,7 @@ class svg(SVGelement):
self.attributes['height'] = height
self.namespace = "http://www.w3.org/2000/svg"
+
class drawing:
"""d=drawing()
@@ -952,6 +1011,7 @@ class drawing:
def __init__(self, entity={}):
self.svg = None
self.entity = entity
+
def setSVG(self, svg):
self.svg = svg
# Voeg een element toe aan de grafiek toe.
@@ -1005,6 +1065,7 @@ class drawing:
root = implementation.createDocument(None, None, doctype)
# Create the xml document.
global appender
+
def appender(element, elementroot):
"""This recursive function appends elements to an element and sets the attributes
and type. It stops when alle elements have been appended"""
@@ -1053,6 +1114,7 @@ class drawing:
f.close()
except:
print(("Cannot write SVG file: " + filename))
+
def validate(self):
try:
import xml.parsers.xmlproc.xmlval
@@ -1066,9 +1128,10 @@ class drawing:
raise Exception("SVG is not well formed, see messages above")
else:
print("SVG well formed")
-if __name__ == '__main__':
+if __name__ == '__main__':
+
d = drawing()
s = svg((0, 0, 100, 100))
r = rect(-100, -100, 300, 300, 'cyan')
diff --git a/wqflask/utility/temp_data.py b/wqflask/utility/temp_data.py
index 2088ba9a..07c5a318 100644
--- a/wqflask/utility/temp_data.py
+++ b/wqflask/utility/temp_data.py
@@ -2,6 +2,7 @@ from redis import Redis
import simplejson as json
+
class TempData:
def __init__(self, temp_uuid):
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 9b751344..4fe4db08 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -13,11 +13,13 @@ logger = logging.getLogger(__name__)
OVERRIDES = {}
+
def app_set(command_id, value):
"""Set application wide value"""
app.config.setdefault(command_id, value)
return value
+
def get_setting(command_id, guess=None):
"""Resolve a setting from the environment or the global settings in
app.config, with valid_path is a function checking whether the
@@ -66,12 +68,14 @@ def get_setting(command_id, guess=None):
# print("Set "+command_id+"="+str(command))
return command
+
def get_setting_bool(id):
v = get_setting(id)
if v not in [0, False, 'False', 'FALSE', None]:
return True
return False
+
def get_setting_int(id):
v = get_setting(id)
if isinstance(v, str):
@@ -80,21 +84,25 @@ def get_setting_int(id):
return 0
return v
+
def valid_bin(bin):
if os.path.islink(bin) or valid_file(bin):
return bin
return None
+
def valid_file(fn):
if os.path.isfile(fn):
return fn
return None
+
def valid_path(dir):
if os.path.isdir(dir):
return dir
return None
+
def js_path(module=None):
"""
Find the JS module in the two paths
@@ -107,38 +115,47 @@ def js_path(module=None):
return try_guix
raise "No JS path found for " + module + " (if not in Guix check JS_GN_PATH)"
+
def reaper_command(guess=None):
return get_setting("REAPER_COMMAND", guess)
+
def gemma_command(guess=None):
return assert_bin(get_setting("GEMMA_COMMAND", guess))
+
def gemma_wrapper_command(guess=None):
return assert_bin(get_setting("GEMMA_WRAPPER_COMMAND", guess))
+
def plink_command(guess=None):
return assert_bin(get_setting("PLINK_COMMAND", guess))
+
def flat_file_exists(subdir):
base = get_setting("GENENETWORK_FILES")
return valid_path(base + "/" + subdir)
+
def flat_files(subdir=None):
base = get_setting("GENENETWORK_FILES")
if subdir:
return assert_dir(base + "/" + subdir)
return assert_dir(base)
+
def assert_bin(fn):
if not valid_bin(fn):
raise Exception("ERROR: can not find binary " + fn)
return fn
+
def assert_dir(dir):
if not valid_path(dir):
raise Exception("ERROR: can not find directory " + dir)
return dir
+
def assert_writable_dir(dir):
try:
fn = dir + "/test.txt"
@@ -150,16 +167,19 @@ def assert_writable_dir(dir):
raise Exception('Unable to write test.txt to directory ' + dir)
return dir
+
def assert_file(fn):
if not valid_file(fn):
raise Exception('Unable to find file ' + fn)
return fn
+
def mk_dir(dir):
if not valid_path(dir):
os.makedirs(dir)
return assert_dir(dir)
+
def locate(name, subdir=None):
"""
Locate a static flat file in the GENENETWORK_FILES environment.
@@ -179,9 +199,11 @@ def locate(name, subdir=None):
if subdir: sys.stderr.write(subdir)
raise Exception("Can not locate " + name + " in " + base)
+
def locate_phewas(name, subdir=None):
return locate(name, '/phewas/' + subdir)
+
def locate_ignore_error(name, subdir=None):
"""
Locate a static flat file in the GENENETWORK_FILES environment.
@@ -200,17 +222,20 @@ def locate_ignore_error(name, subdir=None):
logger.info("WARNING: file " + name + " not found\n")
return None
+
def tempdir():
"""
Get UNIX TMPDIR by default
"""
return valid_path(get_setting("TMPDIR", "/tmp"))
+
BLUE = '\033[94m'
GREEN = '\033[92m'
BOLD = '\033[1m'
ENDC = '\033[0m'
+
def show_settings():
from utility.tools import LOG_LEVEL
diff --git a/wqflask/utility/type_checking.py b/wqflask/utility/type_checking.py
index 662bf794..00f14ba9 100644
--- a/wqflask/utility/type_checking.py
+++ b/wqflask/utility/type_checking.py
@@ -7,6 +7,7 @@ def is_float(value):
except:
return False
+
def is_int(value):
try:
int(value)
@@ -14,6 +15,7 @@ def is_int(value):
except:
return False
+
def is_str(value):
if value is None:
return False
@@ -23,18 +25,21 @@ def is_str(value):
except:
return False
+
def get_float(vars_obj, name, default=None):
if name in vars_obj:
if is_float(vars_obj[name]):
return float(vars_obj[name])
return default
+
def get_int(vars_obj, name, default=None):
if name in vars_obj:
if is_int(vars_obj[name]):
return float(vars_obj[name])
return default
+
def get_string(vars_obj, name, default=None):
if name in vars_obj:
if not vars_obj[name] is None:
diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py
index ed59b0eb..f355a865 100644
--- a/wqflask/utility/webqtlUtil.py
+++ b/wqflask/utility/webqtlUtil.py
@@ -64,6 +64,7 @@ ParInfo = {
# Accessory Functions
#########################################
+
def genRandStr(prefix="", length=8, chars=string.ascii_letters + string.digits):
from random import choice
_str = prefix[:]
@@ -71,6 +72,7 @@ def genRandStr(prefix="", length=8, chars=string.ascii_letters + string.digits):
_str += choice(chars)
return _str
+
def ListNotNull(lst):
'''Obsolete - Use built in function any (or all or whatever)
@@ -83,6 +85,7 @@ def ListNotNull(lst):
return 1
return None
+
def readLineCSV(line): # dcrowell July 2008
"""Parses a CSV string of text and returns a list containing each element as a string.
Used by correlationPage"""
@@ -91,6 +94,7 @@ def readLineCSV(line): # dcrowell July 2008
returnList[0] = returnList[0][1:]
return returnList
+
def cmpEigenValue(A, B):
try:
if A[0] > B[0]:
@@ -102,6 +106,7 @@ def cmpEigenValue(A, B):
except:
return 0
+
def hasAccessToConfidentialPhenotypeTrait(privilege, userName, authorized_users):
access_to_confidential_phenotype_trait = 0
if webqtlConfig.USERDICT[privilege] > webqtlConfig.USERDICT['user']:
diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py
index bab87115..712517a3 100644
--- a/wqflask/wqflask/__init__.py
+++ b/wqflask/wqflask/__init__.py
@@ -30,6 +30,7 @@ app.register_blueprint(policies_blueprint, url_prefix="/policies")
app.register_blueprint(environments_blueprint, url_prefix="/environments")
app.register_blueprint(facilities_blueprint, url_prefix="/facilities")
+
@app.before_request
def before_request():
g.request_start_time = time.time()
diff --git a/wqflask/wqflask/api/correlation.py b/wqflask/wqflask/api/correlation.py
index e0b7fea0..f1dd148f 100644
--- a/wqflask/wqflask/api/correlation.py
+++ b/wqflask/wqflask/api/correlation.py
@@ -18,6 +18,7 @@ from utility.benchmark import Bench
import utility.logger
logger = utility.logger.getLogger(__name__)
+
def do_correlation(start_vars):
assert('db' in start_vars)
assert('target_db' in start_vars)
@@ -66,6 +67,7 @@ def do_correlation(start_vars):
return final_results
+
def calculate_results(this_trait, this_dataset, target_dataset, corr_params):
corr_results = {}
@@ -91,6 +93,7 @@ def calculate_results(this_trait, this_dataset, target_dataset, corr_params):
return sorted_results
+
def do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_params, tissue_dataset_id=1):
# Gets tissue expression values for the primary trait
primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(symbol_list=[this_trait.symbol])
@@ -113,6 +116,7 @@ def do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_par
return tissue_corr_data
+
def do_literature_correlation_for_all_traits(this_trait, target_dataset, trait_geneid_dict, corr_params):
input_trait_mouse_gene_id = convert_to_mouse_gene_id(target_dataset.group.species.lower(), this_trait.geneid)
@@ -145,6 +149,7 @@ def do_literature_correlation_for_all_traits(this_trait, target_dataset, trait_g
return lit_corr_data
+
def get_sample_r_and_p_values(this_trait, this_dataset, target_vals, target_dataset, type):
"""
Calculates the sample r (or rho) and p-value
@@ -176,6 +181,7 @@ def get_sample_r_and_p_values(this_trait, this_dataset, target_vals, target_data
else:
return [sample_r, sample_p, num_overlap]
+
def convert_to_mouse_gene_id(species=None, gene_id=None):
"""If the species is rat or human, translate the gene_id to the mouse geneid
@@ -212,6 +218,7 @@ def convert_to_mouse_gene_id(species=None, gene_id=None):
return mouse_gene_id
+
def init_corr_params(start_vars):
method = "pearson"
if 'method' in start_vars:
diff --git a/wqflask/wqflask/api/mapping.py b/wqflask/wqflask/api/mapping.py
index fbfbc879..662090d5 100644
--- a/wqflask/wqflask/api/mapping.py
+++ b/wqflask/wqflask/api/mapping.py
@@ -10,6 +10,7 @@ from wqflask.marker_regression import gemma_mapping, rqtl_mapping, qtlreaper_map
import utility.logger
logger = utility.logger.getLogger(__name__)
+
def do_mapping_for_api(start_vars):
assert('db' in start_vars)
assert('trait_id' in start_vars)
@@ -74,7 +75,6 @@ def do_mapping_for_api(start_vars):
return result_markers, None
-
def initialize_parameters(start_vars, dataset, this_trait):
mapping_params = {}
diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py
index b0559a07..4f9cc6e5 100644
--- a/wqflask/wqflask/api/router.py
+++ b/wqflask/wqflask/api/router.py
@@ -27,10 +27,12 @@ logger = utility.logger.getLogger(__name__)
version = "pre1"
+
@app.route("/api/v_{}/".format(version))
def hello_world():
return flask.jsonify({"hello": "world"})
+
@app.route("/api/v_{}/species".format(version))
def get_species_list():
results = g.db.execute("SELECT SpeciesId, Name, FullName, TaxonomyId FROM Species;")
@@ -47,6 +49,7 @@ def get_species_list():
return flask.jsonify(species_list)
+
@app.route("/api/v_{}/species/<path:species_name>".format(version))
@app.route("/api/v_{}/species/<path:species_name>.<path:file_format>".format(version))
def get_species_info(species_name, file_format="json"):
@@ -64,6 +67,7 @@ def get_species_info(species_name, file_format="json"):
return flask.jsonify(species_dict)
+
@app.route("/api/v_{}/groups".format(version))
@app.route("/api/v_{}/groups/<path:species_name>".format(version))
def get_groups_list(species_name=None):
@@ -102,6 +106,7 @@ def get_groups_list(species_name=None):
else:
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+
@app.route("/api/v_{}/group/<path:group_name>".format(version))
@app.route("/api/v_{}/group/<path:group_name>.<path:file_format>".format(version))
@app.route("/api/v_{}/group/<path:species_name>/<path:group_name>".format(version))
@@ -145,6 +150,7 @@ def get_group_info(group_name, species_name=None, file_format="json"):
else:
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+
@app.route("/api/v_{}/datasets/<path:group_name>".format(version))
@app.route("/api/v_{}/datasets/<path:species_name>/<path:group_name>".format(version))
def get_datasets_for_group(group_name, species_name=None):
@@ -197,6 +203,7 @@ def get_datasets_for_group(group_name, species_name=None):
else:
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+
@app.route("/api/v_{}/dataset/<path:dataset_name>".format(version))
@app.route("/api/v_{}/dataset/<path:dataset_name>.<path:file_format>".format(version))
@app.route("/api/v_{}/dataset/<path:group_name>/<path:dataset_name>".format(version))
@@ -302,6 +309,7 @@ def get_dataset_info(dataset_name, group_name=None, file_format="json"):
else:
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+
@app.route("/api/v_{}/traits/<path:dataset_name>".format(version), methods=("GET",))
@app.route("/api/v_{}/traits/<path:dataset_name>.<path:file_format>".format(version), methods=("GET",))
def fetch_traits(dataset_name, file_format="json"):
@@ -430,6 +438,7 @@ def fetch_traits(dataset_name, file_format="json"):
else:
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+
@app.route("/api/v_{}/sample_data/<path:dataset_name>".format(version))
@app.route("/api/v_{}/sample_data/<path:dataset_name>.<path:file_format>".format(version))
def all_sample_data(dataset_name, file_format="csv"):
@@ -536,6 +545,7 @@ def all_sample_data(dataset_name, file_format="csv"):
else:
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+
@app.route("/api/v_{}/sample_data/<path:dataset_name>/<path:trait_name>".format(version))
@app.route("/api/v_{}/sample_data/<path:dataset_name>/<path:trait_name>.<path:file_format>".format(version))
def trait_sample_data(dataset_name, trait_name, file_format="json"):
@@ -625,6 +635,7 @@ def trait_sample_data(dataset_name, trait_name, file_format="json"):
else:
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+
@app.route("/api/v_{}/trait/<path:dataset_name>/<path:trait_name>".format(version))
@app.route("/api/v_{}/trait/<path:dataset_name>/<path:trait_name>.<path:file_format>".format(version))
@app.route("/api/v_{}/trait_info/<path:dataset_name>/<path:trait_name>".format(version))
@@ -694,6 +705,7 @@ def get_trait_info(dataset_name, trait_name, file_format="json"):
else:
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+
@app.route("/api/v_{}/correlation".format(version), methods=("GET",))
def get_corr_results():
results = correlation.do_correlation(request.args)
@@ -703,6 +715,7 @@ def get_corr_results():
else:
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+
@app.route("/api/v_{}/mapping".format(version), methods=("GET",))
def get_mapping_results():
results, format = mapping.do_mapping_for_api(request.args)
@@ -726,6 +739,7 @@ def get_mapping_results():
else:
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+
@app.route("/api/v_{}/genotypes/<string:file_format>/<string:group_name>/<string:dataset_name>.zip".format(version))
@app.route("/api/v_{}/genotypes/<string:file_format>/<string:group_name>/<string:dataset_name>".format(version))
@app.route("/api/v_{}/genotypes/<string:file_format>/<string:group_name>.zip".format(version))
@@ -813,6 +827,7 @@ def get_genotypes(group_name, file_format="csv", dataset_name=None):
return output
+
@app.route("/api/v_{}/gen_dropdown".format(version), methods=("GET",))
def gen_dropdown_menu():
results = gen_menu.gen_dropdown_json()
@@ -822,6 +837,7 @@ def gen_dropdown_menu():
else:
return return_error(code=500, source=request.url_rule.rule, title="Some error occurred", details="")
+
def return_error(code, source, title, details):
json_ob = {"errors": [
{
@@ -834,6 +850,7 @@ def return_error(code, source, title, details):
return flask.jsonify(json_ob)
+
def get_dataset_trait_ids(dataset_name, start_vars):
if 'limit_to' in start_vars:
@@ -906,6 +923,7 @@ def get_dataset_trait_ids(dataset_name, start_vars):
dataset_id = results[0][2]
return trait_ids, trait_names, data_type, dataset_id
+
def get_samplelist(dataset_name):
group_id = get_group_id_from_dataset(dataset_name)
@@ -922,6 +940,7 @@ def get_samplelist(dataset_name):
return samplelist
+
def get_group_id_from_dataset(dataset_name):
if "Publish" in dataset_name:
query = """
@@ -962,6 +981,7 @@ def get_group_id_from_dataset(dataset_name):
else:
return None
+
def get_group_id(group_name):
query = """
SELECT InbredSet.Id
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index 6a1b88ca..61f73106 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -40,6 +40,7 @@ def process_traits(unprocessed_traits):
return traits
+
def report_change(len_before, len_now):
new_length = len_now - len_before
if new_length:
@@ -48,6 +49,7 @@ def report_change(len_before, len_now):
else:
logger.debug("No new traits were added.")
+
@app.route("/collections/store_trait_list", methods=('POST',))
def store_traits_list():
params = request.form
@@ -59,6 +61,7 @@ def store_traits_list():
return hash
+
@app.route("/collections/add")
def collections_add():
@@ -82,6 +85,7 @@ def collections_add():
collections=collections,
)
+
@app.route("/collections/new")
def collections_new():
params = request.args
@@ -118,6 +122,7 @@ def collections_new():
# CauseAnError
pass
+
def create_new(collection_name):
params = request.args
@@ -133,6 +138,7 @@ def create_new(collection_name):
return redirect(url_for('view_collection', uc_id=uc_id))
+
@app.route("/collections/list")
def list_collections():
params = request.args
@@ -143,6 +149,7 @@ def list_collections():
collections=user_collections,
)
+
@app.route("/collections/remove", methods=('POST',))
def remove_traits():
params = request.form
@@ -216,6 +223,7 @@ def view_collection():
**collection_info
)
+
@app.route("/collections/change_name", methods=('POST',))
def change_collection_name():
params = request.form
diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py
index 22941ad5..6afea715 100644
--- a/wqflask/wqflask/correlation/corr_scatter_plot.py
+++ b/wqflask/wqflask/correlation/corr_scatter_plot.py
@@ -11,6 +11,7 @@ import numpy as np
import utility.logger
logger = utility.logger.getLogger(__name__)
+
class CorrScatterPlot:
"""Page that displays a correlation scatterplot with a line fitted to it"""
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 051ac1cb..e2fe1ff4 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -172,7 +172,6 @@ class CorrelationResults:
self.correlation_data = collections.OrderedDict(sorted(list(self.correlation_data.items()),
key=lambda t: -abs(t[1][0])))
-
# ZS: Convert min/max chromosome to an int for the location range option
range_chr_as_int = None
for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()):
@@ -348,7 +347,6 @@ class CorrelationResults:
else:
trait.lit_corr = 0
-
def do_lit_correlation_for_all_traits(self):
input_trait_mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), self.this_trait.geneid)
@@ -484,6 +482,7 @@ def do_bicor(this_trait_vals, target_trait_vals):
return the_r, the_p
+
def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_api=False):
results_list = []
for i, trait in enumerate(corr_results):
@@ -574,6 +573,7 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap
return json.dumps(results_list)
+
def get_header_fields(data_type, corr_method):
if data_type == "ProbeSet":
if corr_method == "spearman":
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index 94c8931f..331cb1dc 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -233,6 +233,7 @@ class CorrelationMatrix:
loadings_array.append(loadings_row)
return loadings_array
+
def export_corr_matrix(corr_results):
corr_matrix_filename = "corr_matrix_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
matrix_export_path = "{}{}.csv".format(GENERATED_TEXT_DIR, corr_matrix_filename)
@@ -263,6 +264,7 @@ def export_corr_matrix(corr_results):
return corr_matrix_filename, matrix_export_path
+
def zScore(trait_data_array):
NN = len(trait_data_array[0])
if NN < 10:
@@ -283,6 +285,7 @@ def zScore(trait_data_array):
i += 1
return trait_data_array
+
def sortEigenVectors(vector):
try:
eigenValues = vector[0].tolist()
diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py
index 2fa90a93..ec66e59f 100644
--- a/wqflask/wqflask/ctl/ctl_analysis.py
+++ b/wqflask/wqflask/ctl/ctl_analysis.py
@@ -39,6 +39,7 @@ r_write_table = ro.r["write.table"] # Map the write.table function
r_data_frame = ro.r["data.frame"] # Map the write.table function
r_as_numeric = ro.r["as.numeric"] # Map the write.table function
+
class CTL:
def __init__(self):
logger.info("Initialization of CTL")
diff --git a/wqflask/wqflask/database.py b/wqflask/wqflask/database.py
index b6e85494..e743c4b3 100644
--- a/wqflask/wqflask/database.py
+++ b/wqflask/wqflask/database.py
@@ -17,6 +17,7 @@ db_session = scoped_session(sessionmaker(autocommit=False,
Base = declarative_base()
Base.query = db_session.query_property()
+
def init_db():
# import all modules here that might define models so that
# they will be registered properly on the metadata. Otherwise
@@ -27,4 +28,5 @@ def init_db():
Base.metadata.create_all(bind=engine)
logger.info("Done creating all model metadata")
+
init_db()
diff --git a/wqflask/wqflask/db_info.py b/wqflask/wqflask/db_info.py
index 25e624ef..c7558ed8 100644
--- a/wqflask/wqflask/db_info.py
+++ b/wqflask/wqflask/db_info.py
@@ -90,6 +90,7 @@ class InfoPage:
except Exception as e:
pass
+
def process_query_results(results):
info_ob = {
'info_page_name': results[0],
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 115182e4..7442dc72 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -73,6 +73,7 @@ class DoSearch:
else:
return None
+
class MrnaAssaySearch(DoSearch):
"""A search within an expression dataset, including mRNA, protein, SNP, but not phenotype or metabolites"""
@@ -296,6 +297,7 @@ class PhenotypeSearch(DoSearch):
return self.execute(query)
+
class GenotypeSearch(DoSearch):
"""A search within a genotype dataset"""
@@ -339,7 +341,6 @@ class GenotypeSearch(DoSearch):
from_clause = self.normalize_spaces(from_clause)
-
if self.search_term[0] == "*":
query = (self.base_query +
"""WHERE Geno.Id = GenoXRef.GenoId
@@ -367,6 +368,7 @@ class GenotypeSearch(DoSearch):
return self.execute(self.query)
+
class RifSearch(MrnaAssaySearch):
"""Searches for traits with a Gene RIF entry including the search term."""
@@ -390,6 +392,7 @@ class RifSearch(MrnaAssaySearch):
return self.execute(query)
+
class WikiSearch(MrnaAssaySearch):
"""Searches GeneWiki for traits other people have annotated"""
@@ -415,6 +418,7 @@ class WikiSearch(MrnaAssaySearch):
return self.execute(query)
+
class GoSearch(MrnaAssaySearch):
"""Searches for synapse-associated genes listed in the Gene Ontology."""
@@ -449,6 +453,8 @@ class GoSearch(MrnaAssaySearch):
return self.execute(query)
# ZS: Not sure what the best way to deal with LRS searches is
+
+
class LrsSearch(DoSearch):
"""Searches for genes with a QTL within the given LRS values
@@ -526,7 +532,6 @@ class LrsSearch(DoSearch):
return where_clause
-
def run(self):
self.from_clause = self.get_from_clause()
@@ -550,6 +555,7 @@ class MrnaLrsSearch(LrsSearch, MrnaAssaySearch):
return self.execute(self.query)
+
class PhenotypeLrsSearch(LrsSearch, PhenotypeSearch):
for search_key in ('LRS', 'LOD'):
@@ -649,6 +655,7 @@ class CisTransLrsSearch(DoSearch):
return where_clause
+
class CisLrsSearch(CisTransLrsSearch, MrnaAssaySearch):
"""
Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values
@@ -680,6 +687,7 @@ class CisLrsSearch(CisTransLrsSearch, MrnaAssaySearch):
return self.execute(self.query)
+
class TransLrsSearch(CisTransLrsSearch, MrnaAssaySearch):
"""Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values
@@ -744,6 +752,7 @@ class MeanSearch(MrnaAssaySearch):
return self.execute(self.query)
+
class RangeSearch(MrnaAssaySearch):
"""Searches for genes with a range of expression varying between two values"""
@@ -779,6 +788,7 @@ class RangeSearch(MrnaAssaySearch):
return self.execute(self.query)
+
class PositionSearch(DoSearch):
"""Searches for genes/markers located within a specified range on a specified chromosome"""
@@ -800,7 +810,6 @@ class PositionSearch(DoSearch):
self.dataset.type,
max(self.mb_min, self.mb_max))
-
return where_clause
def get_chr(self):
@@ -819,6 +828,7 @@ class PositionSearch(DoSearch):
return self.execute(self.query)
+
class MrnaPositionSearch(PositionSearch, MrnaAssaySearch):
"""Searches for genes located within a specified range on a specified chromosome"""
@@ -832,6 +842,7 @@ class MrnaPositionSearch(PositionSearch, MrnaAssaySearch):
return self.execute(self.query)
+
class GenotypePositionSearch(PositionSearch, GenotypeSearch):
"""Searches for genes located within a specified range on a specified chromosome"""
@@ -845,6 +856,7 @@ class GenotypePositionSearch(PositionSearch, GenotypeSearch):
return self.execute(self.query)
+
class PvalueSearch(MrnaAssaySearch):
"""Searches for traits with a permutationed p-value between low and high"""
@@ -878,6 +890,7 @@ class PvalueSearch(MrnaAssaySearch):
logger.sql(self.query)
return self.execute(self.query)
+
class AuthorSearch(PhenotypeSearch):
"""Searches for phenotype traits with specified author(s)"""
@@ -900,6 +913,7 @@ def is_number(s):
except ValueError:
return False
+
def get_aliases(symbol, species):
if species == "mouse":
symbol_string = symbol.capitalize()
@@ -923,6 +937,7 @@ def get_aliases(symbol, species):
return filtered_aliases
+
if __name__ == "__main__":
# Usually this will be used as a library, but call it from the command line for testing
# And it runs the code below
diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py
index 207767c4..81424b9c 100644
--- a/wqflask/wqflask/docs.py
+++ b/wqflask/wqflask/docs.py
@@ -5,6 +5,7 @@ from flask import g
from utility.logger import getLogger
logger = getLogger(__name__)
+
class Docs:
def __init__(self, entry, start_vars={}):
@@ -23,7 +24,6 @@ class Docs:
self.title = result[0]
self.content = result[1].decode("utf-8")
-
self.editable = "false"
# ZS: Removing option to edit to see if text still gets vandalized
try:
diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py
index 95c20673..d0745ef7 100644
--- a/wqflask/wqflask/export_traits.py
+++ b/wqflask/wqflask/export_traits.py
@@ -15,6 +15,7 @@ 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'])
@@ -132,6 +133,7 @@ def export_search_results_csv(targs):
return file_list
+
def sort_traits_by_group(trait_list=[]):
traits_by_group = {}
for trait in trait_list:
diff --git a/wqflask/wqflask/external_tools/send_to_bnw.py b/wqflask/wqflask/external_tools/send_to_bnw.py
index 9836eb9c..1556c6a0 100644
--- a/wqflask/wqflask/external_tools/send_to_bnw.py
+++ b/wqflask/wqflask/external_tools/send_to_bnw.py
@@ -24,6 +24,7 @@ from utility import helper_functions, corr_result_helpers
import utility.logger
logger = utility.logger.getLogger(__name__)
+
class SendToBNW:
def __init__(self, start_vars):
trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')]
diff --git a/wqflask/wqflask/external_tools/send_to_geneweaver.py b/wqflask/wqflask/external_tools/send_to_geneweaver.py
index 36f1b8e5..c55c43e6 100644
--- a/wqflask/wqflask/external_tools/send_to_geneweaver.py
+++ b/wqflask/wqflask/external_tools/send_to_geneweaver.py
@@ -29,6 +29,7 @@ from utility import helper_functions, corr_result_helpers
import utility.logger
logger = utility.logger.getLogger(__name__)
+
class SendToGeneWeaver:
def __init__(self, start_vars):
trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')]
@@ -58,6 +59,7 @@ class SendToGeneWeaver:
'list': ",".join(trait_name_list),
}
+
def get_trait_name_list(trait_list):
name_list = []
for trait_db in trait_list:
@@ -65,6 +67,7 @@ def get_trait_name_list(trait_list):
return name_list
+
def test_chip(trait_list):
final_chip_name = ""
diff --git a/wqflask/wqflask/external_tools/send_to_webgestalt.py b/wqflask/wqflask/external_tools/send_to_webgestalt.py
index f50eeb8b..6b78725c 100644
--- a/wqflask/wqflask/external_tools/send_to_webgestalt.py
+++ b/wqflask/wqflask/external_tools/send_to_webgestalt.py
@@ -29,6 +29,7 @@ from utility import helper_functions, corr_result_helpers
import utility.logger
logger = utility.logger.getLogger(__name__)
+
class SendToWebGestalt:
def __init__(self, start_vars):
trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')]
@@ -69,6 +70,7 @@ class SendToWebGestalt:
else:
self.hidden_vars['organism'] = "others"
+
def test_chip(trait_list):
final_chip_name = ""
@@ -113,6 +115,7 @@ def test_chip(trait_list):
return chip_name
+
def gen_gene_id_list(trait_list):
trait_name_list = []
gene_id_list = []
diff --git a/wqflask/wqflask/group_manager.py b/wqflask/wqflask/group_manager.py
index f29c0e4d..92a65112 100644
--- a/wqflask/wqflask/group_manager.py
+++ b/wqflask/wqflask/group_manager.py
@@ -12,6 +12,7 @@ from utility.redis_tools import get_user_groups, get_group_info, save_user, crea
from utility.logger import getLogger
logger = getLogger(__name__)
+
@app.route("/groups/manage", methods=('GET', 'POST'))
def manage_groups():
params = request.form if request.form else request.args
@@ -21,6 +22,7 @@ def manage_groups():
admin_groups, member_groups = get_user_groups(g.user_session.user_id)
return render_template("admin/group_manager.html", admin_groups=admin_groups, member_groups=member_groups)
+
@app.route("/groups/view", methods=('GET', 'POST'))
def view_group():
params = request.form if request.form else request.args
@@ -58,6 +60,7 @@ def view_group():
return render_template("admin/view_group.html", group_info=group_info, admins=admins_info, members=members_info, user_is_admin=user_is_admin, resources=resources_info)
+
@app.route("/groups/remove", methods=('POST',))
def remove_groups():
group_ids_to_remove = request.form['selected_group_ids']
@@ -66,6 +69,7 @@ def remove_groups():
return redirect(url_for('manage_groups'))
+
@app.route("/groups/remove_users", methods=('POST',))
def remove_users():
group_id = request.form['group_id']
@@ -77,6 +81,7 @@ def remove_users():
return redirect(url_for('view_group', id=group_id))
+
@app.route("/groups/add_<path:user_type>", methods=('POST',))
def add_users(user_type='members'):
group_id = request.form['group_id']
@@ -89,6 +94,7 @@ def add_users(user_type='members'):
return redirect(url_for('view_group', id=group_id))
+
@app.route("/groups/change_name", methods=('POST',))
def change_name():
group_id = request.form['group_id']
@@ -97,6 +103,7 @@ def change_name():
return new_name
+
@app.route("/groups/create", methods=('GET', 'POST'))
def add_or_edit_group():
params = request.form if request.form else request.args
@@ -125,6 +132,8 @@ def add_or_edit_group():
return render_template("admin/create_group.html")
# ZS: Will integrate this later, for now just letting users be added directly
+
+
def send_group_invites(group_id, user_email_list=[], user_type="members"):
for user_email in user_email_list:
user_details = get_user_by_unique_column("email_address", user_email)
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index 8cb81dcc..a21dae84 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -18,6 +18,7 @@ from utility.type_checking import is_float, is_int, is_str, get_float, get_int,
from utility.logger import getLogger
logger = getLogger(__name__)
+
class GSearch:
def __init__(self, kw):
diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py
index f8ef7028..0b477446 100644
--- a/wqflask/wqflask/heatmap/heatmap.py
+++ b/wqflask/wqflask/heatmap/heatmap.py
@@ -14,6 +14,7 @@ Redis = Redis()
logger = getLogger(__name__)
+
class Heatmap:
def __init__(self, start_vars, temp_uuid):
@@ -132,6 +133,7 @@ class Heatmap:
else:
self.trait_results[this_trait.name].append(float(qtl['lrs_value']))
+
def gen_pheno_txt_file(samples, vals, filename):
"""Generates phenotype file for GEMMA"""
@@ -151,6 +153,7 @@ def gen_pheno_txt_file(samples, vals, filename):
values_string = "\t".join(filtered_vals_list)
outfile.write(values_string)
+
def parse_reaper_output(gwa_filename):
included_markers = []
p_values = []
diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py
index 9779878e..8dd1c7c0 100644
--- a/wqflask/wqflask/interval_analyst/GeneUtil.py
+++ b/wqflask/wqflask/interval_analyst/GeneUtil.py
@@ -4,6 +4,8 @@ from flask import Flask, g
# Just return a list of dictionaries
# each dictionary contains sub-dictionary
+
+
def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
fetchFields = ['SpeciesId', 'Id', 'GeneSymbol', 'GeneDescription', 'Chromosome', 'TxStart', 'TxEnd',
'Strand', 'GeneID', 'NM_ID', 'kgID', 'GenBankID', 'UnigenID', 'ProteinID', 'AlignID',
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 3753d1ce..5c7b81dd 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -509,9 +509,6 @@ class DisplayMappingResults:
self.graphHeight = self.graphHeight + 2 * (self.NR_INDIVIDUALS + 10) * self.EACH_GENE_HEIGHT
# END HaplotypeAnalyst
-
-
-
#########################
# Get the sorting column
#########################
@@ -1640,7 +1637,6 @@ class DisplayMappingResults:
geneYLocation + 2 *ind*self.EACH_GENE_HEIGHT + 2*self.EACH_GENE_HEIGHT*zoom)),
outline=outlineColor, fill=fillColor)
-
COORDS = "%d, %d, %d, %d" % (geneStartPix, geneYLocation + ind * self.EACH_GENE_HEIGHT, geneEndPix + 1, (geneYLocation + ind * self.EACH_GENE_HEIGHT))
TITLE = "Strain: %s, marker (%s) \n Position %2.3f Mb." % (samplelist[k], _chr[j].name, float(txStart))
HREF = ''
@@ -1663,7 +1659,6 @@ class DisplayMappingResults:
geneYLocation + 7 + 2*ind*self.EACH_GENE_HEIGHT*zoom)),
fill= mylineColor, width=zoom * (self.EACH_GENE_HEIGHT + 2))
-
if lastGene == 0:
draw_rotated_text(
canvas, text="%s" % (_chr[j].name),
@@ -2085,7 +2080,6 @@ class DisplayMappingResults:
im_drawer.line(xy=((xLeftOffset, yZero), (xLeftOffset + plotWidth, yZero)),
fill=BLACK, width=X_AXIS_THICKNESS) # Draw the X axis itself
-
def drawQTL(self, canvas, drawAreaHeight, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None):
im_drawer = ImageDraw.Draw(canvas)
xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
@@ -2427,7 +2421,6 @@ class DisplayMappingResults:
yLRS = yZero - (item / LRS_LOD_Max) * LRSHeightThresh
-
if 'lrs_value' in qtlresult:
if self.LRS_LOD == "LOD" or self.LRS_LOD == "-logP":
if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value'] == 'inf':
@@ -2621,7 +2614,6 @@ class DisplayMappingResults:
# , clipX=(xLeftOffset, xLeftOffset + plotWidth)
)
-
# draw additive scale
if not self.multipleInterval and self.additiveChecked:
additiveScaleFont = ImageFont.truetype(font=VERDANA_FILE, size=16 * zoom)
@@ -2653,7 +2645,6 @@ class DisplayMappingResults:
xy=((xLeftOffset, yZero), (xLeftOffset, yTopOffset + 30 * (zoom - 1))),
fill=self.LRS_COLOR, width=1 * zoom) # the blue line running up the y axis
-
def drawGraphBackground(self, canvas, gifmap, offset=(80, 120, 80, 50), zoom=1, startMb= None, endMb = None):
# conditions
# multiple Chromosome view
diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py
index e6c78536..22a50bb8 100644
--- a/wqflask/wqflask/marker_regression/plink_mapping.py
+++ b/wqflask/wqflask/marker_regression/plink_mapping.py
@@ -8,11 +8,11 @@ from utility.tools import flat_files, PLINK_COMMAND
import utility.logger
logger = utility.logger.getLogger(__name__)
+
def run_plink(this_trait, dataset, species, vals, maf):
plink_output_filename = webqtlUtil.genRandStr(f"{dataset.group.name}_{this_trait.name}_")
gen_pheno_txt_file(dataset, vals)
-
plink_command = f"{PLINK_COMMAND} --noweb --bfile {flat_files('mapping')}/{dataset.group.name} --no-pheno --no-fid --no-parents --no-sex --maf {maf} --out { TMPDIR}{plink_output_filename} --assoc "
logger.debug("plink_command:", plink_command)
@@ -25,6 +25,7 @@ def run_plink(this_trait, dataset, species, vals, maf):
return dataset.group.markers.markers
+
def gen_pheno_txt_file(this_dataset, vals):
"""Generates phenotype file for GEMMA/PLINK"""
@@ -42,6 +43,7 @@ def gen_pheno_txt_file(this_dataset, vals):
this_val = vals[i]
outfile.write("0 " + line[1] + " " + line[2] + " " + line[3] + " " + line[4] + " " + str(this_val) + "\n")
+
def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename=''):
ped_sample_list = get_samples_from_ped_file(dataset)
output_file = open(f"{TMPDIR}{pheno_filename}.txt", "wb")
@@ -77,6 +79,8 @@ def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename=''):
output_file.close()
# get strain name from ped file in order
+
+
def get_samples_from_ped_file(dataset):
ped_file = open(f"{flat_files('mapping')}{dataset.group.name}.ped", "r")
line = ped_file.readline()
@@ -93,6 +97,7 @@ def get_samples_from_ped_file(dataset):
return sample_list
+
def parse_plink_output(output_filename, species):
plink_results = {}
@@ -154,6 +159,8 @@ def parse_plink_output(output_filename, species):
# function: convert line from str to list;
# output: lineList list
#######################################################
+
+
def build_line_list(line=""):
line_list = line.strip().split(' ') # irregular number of whitespaces between columns
line_list = [item for item in line_list if item != '']
diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
index dd044cb0..313c40ca 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -8,6 +8,7 @@ from utility.tools import flat_files, REAPER_COMMAND, TEMPDIR
import utility.logger
logger = utility.logger.getLogger(__name__)
+
def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boot_check, num_bootstrap, do_control, control_marker, manhattan_plot, first_run=True, output_files=None):
"""Generates p-values for each marker using qtlreaper"""
@@ -73,6 +74,7 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
return (marker_obs, permu_vals, suggestive, significant, bootstrap_vals,
[output_filename, permu_filename, bootstrap_filename])
+
def gen_pheno_txt_file(samples, vals, trait_filename):
"""Generates phenotype file for GEMMA"""
@@ -92,6 +94,7 @@ def gen_pheno_txt_file(samples, vals, trait_filename):
values_string = "\t".join(filtered_vals_list)
outfile.write(values_string)
+
def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename):
included_markers = []
p_values = []
@@ -163,6 +166,7 @@ def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename):
return marker_obs, permu_vals, bootstrap_vals
+
def run_original_reaper(this_trait, dataset, samples_before, trait_vals, json_data, num_perm, bootCheck, num_bootstrap, do_control, control_marker, manhattan_plot):
genotype = dataset.group.read_genotype_file(use_reaper=True)
@@ -255,6 +259,7 @@ def run_original_reaper(this_trait, dataset, samples_before, trait_vals, json_da
qtl_results.append(qtl)
return qtl_results, json_data, perm_output, suggestive, significant, bootstrap_results
+
def natural_sort(marker_list):
"""
Function to naturally sort numbers + strings, adopted from user Mark Byers here: https://stackoverflow.com/questions/4836710/does-python-have-a-built-in-function-for-string-natural-sort
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index 2bd94512..588600f5 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -16,6 +16,8 @@ import utility.logger
logger = utility.logger.getLogger(__name__)
# Get a trait's type (numeric, categorical, etc) from the DB
+
+
def get_trait_data_type(trait_db_string):
logger.info("get_trait_data_type");
the_query = "SELECT value FROM TraitMetadata WHERE type='trait_data_type'"
@@ -133,6 +135,7 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec
else:
return process_rqtl_results(result_data_frame, dataset.group.species)
+
def generate_cross_from_rdata(dataset):
rdata_location = locate(dataset.group.name + ".RData", "genotype/rdata")
ro.r("""
@@ -143,6 +146,7 @@ def generate_cross_from_rdata(dataset):
}
""" % (rdata_location))
+
def generate_cross_from_geno(dataset, scale_units): # TODO: Need to figure out why some genofiles have the wrong format and don't convert properly
ro.r("""
@@ -187,6 +191,7 @@ def generate_cross_from_geno(dataset, scale_units): # TODO: Need to figur
}
""" % (dataset.group.genofile, scale_units))
+
def add_perm_strata(cross, perm_strata):
col_string = 'c("the_strata")'
perm_strata_string = "c("
@@ -201,6 +206,7 @@ def add_perm_strata(cross, perm_strata):
return cross, strata_ob
+
def sanitize_rqtl_phenotype(vals):
pheno_as_string = "c("
for i, val in enumerate(vals):
@@ -218,6 +224,7 @@ def sanitize_rqtl_phenotype(vals):
return pheno_as_string
+
def sanitize_rqtl_names(vals):
pheno_as_string = "c("
for i, val in enumerate(vals):
@@ -235,12 +242,14 @@ def sanitize_rqtl_names(vals):
return pheno_as_string
+
def add_phenotype(cross, pheno_as_string, col_name):
ro.globalenv["the_cross"] = cross
ro.r('pheno <- data.frame(pull.pheno(the_cross))')
ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = as.numeric(' + pheno_as_string + '))')
return ro.r["the_cross"]
+
def add_categorical_covar(cross, covar_as_string, i):
ro.globalenv["the_cross"] = cross
logger.info("cross set");
@@ -275,12 +284,14 @@ def add_names(cross, names_as_string, col_name):
ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = ' + names_as_string + ')')
return ro.r["the_cross"]
+
def pull_var(var_name, cross, var_string):
ro.globalenv["the_cross"] = cross
ro.r(var_name + ' <- pull.pheno(the_cross, ' + var_string + ')')
return ro.r[var_name]
+
def add_cofactors(cross, this_dataset, covariates, samples):
ro.numpy2ri.activate()
@@ -341,6 +352,7 @@ def add_cofactors(cross, this_dataset, covariates, samples):
covars_ob = pull_var("trait_covars", cross, covar_name_string)
return cross, covars_ob
+
def create_marker_covariates(control_marker, cross):
ro.globalenv["the_cross"] = cross
ro.r('genotypes <- pull.geno(the_cross)') # Get the genotype matrix
@@ -358,6 +370,7 @@ def create_marker_covariates(control_marker, cross):
# TODO: Create a design matrix from the marker covars for the markers in case of an F2, 4way, etc
return ro.r["marker_covars"]
+
def process_pair_scan_results(result):
pair_scan_results = []
@@ -374,6 +387,7 @@ def process_pair_scan_results(result):
return pair_scan_results
+
def process_rqtl_perm_results(num_perm, results):
perm_vals = []
for line in str(results).split("\n")[1:(num_perm + 1)]:
@@ -386,6 +400,7 @@ def process_rqtl_perm_results(num_perm, results):
return perm_output, suggestive, significant
+
def process_rqtl_results(result, species_name): # TODO: how to make this a one liner and not copy the stuff in a loop
qtl_results = []
output = [tuple([result[j][i] for j in range(result.ncol)]) for i in range(result.nrow)]
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index f1665570..31c58083 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -45,6 +45,7 @@ from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR
import utility.logger
logger = utility.logger.getLogger(__name__)
+
class RunMapping:
def __init__(self, start_vars, temp_uuid):
@@ -504,6 +505,7 @@ class RunMapping:
trimmed_genotype_data.append(new_genotypes)
return trimmed_genotype_data
+
def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, score_type, transform, covariates, n_samples):
with open(results_path, "w+") as output_file:
output_file.write("Time/Date: " + datetime.datetime.now().strftime("%x / %X") + "\n")
@@ -564,6 +566,7 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale,
if i < (len(markers) - 1):
output_file.write("\n")
+
def trim_markers_for_figure(markers):
if 'p_wald' in list(markers[0].keys()):
score_type = 'p_wald'
@@ -624,6 +627,7 @@ def trim_markers_for_figure(markers):
filtered_markers.append(marker)
return filtered_markers
+
def trim_markers_for_table(markers):
if 'lod_score' in list(markers[0].keys()):
sorted_markers = sorted(markers, key=lambda k: k['lod_score'], reverse=True)
@@ -637,6 +641,7 @@ def trim_markers_for_table(markers):
else:
return sorted_markers
+
def write_input_for_browser(this_dataset, gwas_results, annotations):
file_base = this_dataset.group.name + "_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
gwas_filename = file_base + "_GWAS"
@@ -650,6 +655,7 @@ def write_input_for_browser(this_dataset, gwas_results, annotations):
return [gwas_filename, annot_filename]
+
def geno_db_exists(this_dataset):
geno_db_name = this_dataset.group.name + "Geno"
try:
@@ -658,6 +664,7 @@ def geno_db_exists(this_dataset):
except:
return "False"
+
def get_chr_lengths(mapping_scale, mapping_method, dataset, qtl_results):
chr_lengths = []
if mapping_scale == "physic":
@@ -696,6 +703,7 @@ def get_chr_lengths(mapping_scale, mapping_method, dataset, qtl_results):
return chr_lengths
+
def get_genofile_samplelist(dataset):
genofile_samplelist = []
@@ -706,6 +714,7 @@ def get_genofile_samplelist(dataset):
return genofile_samplelist
+
def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples):
perm_strata_strings = []
for sample in used_samples:
diff --git a/wqflask/wqflask/model.py b/wqflask/wqflask/model.py
index 8abd6516..d7c9ef95 100644
--- a/wqflask/wqflask/model.py
+++ b/wqflask/wqflask/model.py
@@ -14,6 +14,7 @@ from sqlalchemy.orm import relationship
from wqflask.database import Base, init_db
+
class User(Base):
__tablename__ = "user"
id = Column(Unicode(36), primary_key=True, default=lambda: str(uuid.uuid4()))
@@ -63,7 +64,6 @@ class User(Base):
print("Couldn't display_num_collections:", why)
return ""
-
def get_collection_by_name(self, collection_name):
try:
collect = self.user_collections.filter_by(name=collection_name).first()
@@ -83,7 +83,6 @@ class User(Base):
def login_count(self):
return self.logins.filter_by(successful=True).count()
-
@property
def confirmed_at(self):
if self.confirmed:
@@ -116,6 +115,7 @@ class User(Base):
except IndexError:
return None
+
class Login(Base):
__tablename__ = "login"
id = Column(Unicode(36), primary_key=True, default=lambda: str(uuid.uuid4()))
@@ -134,6 +134,7 @@ class Login(Base):
##################################################################################################
+
class UserCollection(Base):
__tablename__ = "user_collection"
id = Column(Unicode(36), primary_key=True, default=lambda: str(uuid.uuid4()))
@@ -158,12 +159,14 @@ class UserCollection(Base):
def members_as_set(self):
return set(json.loads(self.members))
+
def display_collapsible(number):
if number:
return number
else:
return ""
+
def user_uuid():
"""Unique cookie for a user"""
user_uuid = request.cookies.get('user_uuid')
diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py
index 93785a3a..e089643e 100644
--- a/wqflask/wqflask/network_graph/network_graph.py
+++ b/wqflask/wqflask/network_graph/network_graph.py
@@ -27,6 +27,7 @@ from utility import helper_functions
from utility import corr_result_helpers
from utility.tools import GN2_BRANCH_URL
+
class NetworkGraph:
def __init__(self, start_vars):
diff --git a/wqflask/wqflask/news.py b/wqflask/wqflask/news.py
index 861a93f2..e262dd51 100644
--- a/wqflask/wqflask/news.py
+++ b/wqflask/wqflask/news.py
@@ -1,5 +1,6 @@
from flask import g
+
class News:
def __init__(self):
diff --git a/wqflask/wqflask/parser.py b/wqflask/wqflask/parser.py
index dfd374e2..6b836e20 100644
--- a/wqflask/wqflask/parser.py
+++ b/wqflask/wqflask/parser.py
@@ -24,6 +24,7 @@ from pprint import pformat as pf
from utility.logger import getLogger
logger = getLogger(__name__)
+
def parse(pstring):
"""
diff --git a/wqflask/wqflask/pbkdf2.py b/wqflask/wqflask/pbkdf2.py
index 6346df03..1a965fc5 100644
--- a/wqflask/wqflask/pbkdf2.py
+++ b/wqflask/wqflask/pbkdf2.py
@@ -4,6 +4,8 @@ from werkzeug.security import safe_str_cmp as ssc
# Replace this because it just wraps around Python3's internal
# functions. Added this during migration.
+
+
def pbkdf2_hex(data, salt, iterations=1000, keylen=24, hashfunc="sha1"):
"""Wrapper function of python's hashlib.pbkdf2_hmac.
"""
diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py
index a1fe0f8f..4591710c 100644
--- a/wqflask/wqflask/resource_manager.py
+++ b/wqflask/wqflask/resource_manager.py
@@ -11,6 +11,7 @@ from utility.redis_tools import get_resource_info, get_group_info, get_groups_li
from utility.logger import getLogger
logger = getLogger(__name__)
+
@app.route("/resources/manage", methods=('GET', 'POST'))
def manage_resource():
params = request.form if request.form else request.args
@@ -40,6 +41,7 @@ def manage_resource():
return render_template("admin/manage_resource.html", owner_name=owner_display_name, resource_id=resource_id, resource_info=resource_info, default_mask=default_mask, group_masks=group_masks_with_names, admin_status=admin_status)
+
@app.route("/search_for_users", methods=('POST',))
def search_for_user():
params = request.form
@@ -49,6 +51,7 @@ def search_for_user():
return json.dumps(user_list)
+
@app.route("/search_for_groups", methods=('POST',))
def search_for_groups():
params = request.form
@@ -65,6 +68,7 @@ def search_for_groups():
return json.dumps(group_list)
+
@app.route("/resources/change_owner", methods=('POST',))
def change_owner():
resource_id = request.form['resource_id']
@@ -81,6 +85,7 @@ def change_owner():
else:
return render_template("admin/change_resource_owner.html", resource_id=resource_id)
+
@app.route("/resources/change_default_privileges", methods=('POST',))
def change_default_privileges():
resource_id = request.form['resource_id']
@@ -99,6 +104,7 @@ def change_default_privileges():
else:
return redirect(url_for("no_access_page"))
+
@app.route("/resources/add_group", methods=('POST',))
def add_group_to_resource():
resource_id = request.form['resource_id']
@@ -125,6 +131,7 @@ def add_group_to_resource():
else:
return redirect(url_for("no_access_page"))
+
def get_group_names(group_masks):
group_masks_with_names = {}
for group_id, group_mask in list(group_masks.items()):
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 16eb1864..ed5f9bad 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -24,6 +24,7 @@ from utility.type_checking import is_str
from utility.logger import getLogger
logger = getLogger(__name__)
+
class SearchResultPage:
#maxReturn = 3000
@@ -270,6 +271,7 @@ class SearchResultPage:
else:
return None
+
def get_GO_symbols(a_search):
query = """SELECT genes
FROM GORef
@@ -287,6 +289,7 @@ def get_GO_symbols(a_search):
return new_terms
+
def insert_newlines(string, every=64):
""" This is because it is seemingly impossible to change the width of the description column, so I'm just manually adding line breaks """
lines = []
@@ -294,6 +297,7 @@ def insert_newlines(string, every=64):
lines.append(string[i:i + every])
return '\n'.join(lines)
+
def get_aliases(symbol_list, species):
updated_symbols = []
diff --git a/wqflask/wqflask/send_mail.py b/wqflask/wqflask/send_mail.py
index 86e8a558..299c866a 100644
--- a/wqflask/wqflask/send_mail.py
+++ b/wqflask/wqflask/send_mail.py
@@ -8,10 +8,12 @@ Redis = StrictRedis()
import mailer
+
def timestamp():
ts = datetime.datetime.utcnow()
return ts.isoformat()
+
def main():
while True:
print("I'm alive!")
@@ -31,7 +33,6 @@ def main():
process_message(msg)
-
def process_message(msg):
msg = json.loads(msg)
diff --git a/wqflask/wqflask/server_side.py b/wqflask/wqflask/server_side.py
index 48761fa0..8b3a4faa 100644
--- a/wqflask/wqflask/server_side.py
+++ b/wqflask/wqflask/server_side.py
@@ -1,7 +1,6 @@
# handles server side table processing
-
class ServerSideTable:
"""
This class is used to do server-side processing
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 388f831f..496dee57 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -8,6 +8,7 @@ from pprint import pformat as pf
from utility import Plot
from utility import Bunch
+
class SampleList:
def __init__(self,
dataset,
diff --git a/wqflask/wqflask/show_trait/export_trait_data.py b/wqflask/wqflask/show_trait/export_trait_data.py
index 379b746c..f0fcd27d 100644
--- a/wqflask/wqflask/show_trait/export_trait_data.py
+++ b/wqflask/wqflask/show_trait/export_trait_data.py
@@ -5,6 +5,7 @@ from functools import cmp_to_key
from base.trait import create_trait
from base import data_set
+
def export_sample_table(targs):
sample_data = json.loads(targs['export_data'])
@@ -28,6 +29,7 @@ def export_sample_table(targs):
return trait_name, final_sample_data
+
def get_export_metadata(trait_id, dataset_name):
dataset = data_set.create_dataset(dataset_name)
this_trait = create_trait(dataset=dataset,
@@ -64,6 +66,7 @@ def dict_to_sorted_list(dictionary):
sorted_values = [item[1] for item in sorted_list]
return sorted_values
+
def cmp_samples(a, b):
if b[0] == 'name':
return 1
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index 7a0df94b..e5c67165 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -9,6 +9,7 @@ logger = getLogger(__name__)
from base import species
from base import webqtlConfig
+
class SnpBrowser:
def __init__(self, start_vars):
@@ -472,7 +473,6 @@ class SnpBrowser:
base_color_dict = {"A": "#C33232", "C": "#1569C7", "T": "#CFCF32", "G": "#32C332",
"t": "#FF6", "c": "#5CB3FF", "a": "#F66", "g": "#CF9", ":": "#FFFFFF", "-": "#FFFFFF", "?": "#FFFFFF"}
-
the_bases = []
for j, item in enumerate(allele_value_list):
if item and isinstance(item, str):
@@ -641,6 +641,7 @@ class SnpBrowser:
# for i in range(n_click):
# href = url_for('snp_browser', first_run="false", chosen_strains_mouse=self.chosen_strains_mouse, chosen_strains_rat=self.chosen_strains_rat, variant=self.variant_type, species=self.species_name, gene_name=self.gene_name, chr=self.chr, start_mb=self.start_mb, end_mb=self.end_mb, limit_strains=self.limit_strains, domain=self.domain, function=self.function, criteria=self.criteria, score=self.score, diff_alleles=self.diff_alleles)
+
def get_browser_sample_lists(species_id=1):
strain_lists = {}
mouse_strain_list = []
@@ -660,6 +661,7 @@ def get_browser_sample_lists(species_id=1):
return strain_lists
+
def get_header_list(variant_type, strains, species=None, empty_columns=None):
if species == "Mouse":
strain_list = strains['mouse']
@@ -715,6 +717,7 @@ def get_header_list(variant_type, strains, species=None, empty_columns=None):
return header_fields, empty_field_count, header_data_names
+
def get_effect_details_by_category(effect_name=None, effect_value=None):
gene_list = []
transcript_list = []
@@ -764,6 +767,7 @@ def get_effect_details_by_category(effect_name=None, effect_value=None):
return [gene_list, transcript_list, exon_list, function_list, function_detail_list]
+
def get_effect_info(effect_list):
domain = ""
effect_detail_list = []
@@ -836,6 +840,7 @@ def get_effect_info(effect_list):
return effect_info_dict
+
def get_gene_id(species_id, gene_name):
query = """
SELECT
@@ -853,6 +858,7 @@ def get_gene_id(species_id, gene_name):
else:
return ""
+
def get_gene_id_name_dict(species_id, gene_name_list):
gene_id_name_dict = {}
if len(gene_name_list) == 0:
@@ -877,6 +883,7 @@ def get_gene_id_name_dict(species_id, gene_name_list):
return gene_id_name_dict
+
def check_if_in_gene(species_id, chr, mb):
if species_id != 0: # ZS: Check if this is necessary
query = """SELECT geneId, geneSymbol
diff --git a/wqflask/wqflask/submit_bnw.py b/wqflask/wqflask/submit_bnw.py
index 4ad6f9e3..b21a88cc 100644
--- a/wqflask/wqflask/submit_bnw.py
+++ b/wqflask/wqflask/submit_bnw.py
@@ -5,5 +5,6 @@ from utility import helper_functions
import utility.logger
logger = utility.logger.getLogger(__name__)
+
def get_bnw_input(start_vars):
logger.debug("BNW VARS:", start_vars)
diff --git a/wqflask/wqflask/update_search_results.py b/wqflask/wqflask/update_search_results.py
index 08b4f9f5..07073d6a 100644
--- a/wqflask/wqflask/update_search_results.py
+++ b/wqflask/wqflask/update_search_results.py
@@ -10,6 +10,7 @@ from utility.benchmark import Bench
from utility.logger import getLogger
logger = getLogger(__name__)
+
class GSearch:
def __init__(self, kw):
diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py
index 3f5b43ee..2a2f8484 100644
--- a/wqflask/wqflask/user_login.py
+++ b/wqflask/wqflask/user_login.py
@@ -29,9 +29,11 @@ from utility.tools import SMTP_CONNECT, SMTP_USERNAME, SMTP_PASSWORD, LOG_SQL_AL
THREE_DAYS = 60 * 60 * 24 * 3
+
def timestamp():
return datetime.datetime.utcnow().isoformat()
+
def basic_info():
return dict(timestamp=timestamp(),
ip_address=request.remote_addr,
@@ -54,6 +56,7 @@ def encode_password(pass_gen_fields, unencrypted_password):
return pass_gen_fields
+
def set_password(password):
pass_gen_fields = {
"unencrypted_password": password,
@@ -71,6 +74,7 @@ def set_password(password):
return encoded_password
+
def get_signed_session_id(user):
session_id = str(uuid.uuid4())
@@ -109,6 +113,7 @@ def get_signed_session_id(user):
return session_id_signed
+
def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"):
"""Send an E-mail through SMTP_CONNECT host. If SMTP_USERNAME is not
'UNKNOWN' TLS is used
@@ -125,6 +130,7 @@ def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"):
server.quit()
logger.info("Successfully sent email to " + toaddr)
+
def send_verification_email(user_details, template_name="email/user_verification.txt", key_prefix="verification_code", subject = "GeneNetwork e-mail verification"):
verification_code = str(uuid.uuid4())
key = key_prefix + ":" + verification_code
@@ -139,12 +145,14 @@ def send_verification_email(user_details, template_name="email/user_verification
send_email(recipient, subject, body)
return {"recipient": recipient, "subject": subject, "body": body}
+
def send_invitation_email(user_email, temp_password, template_name="email/user_invitation.txt", subject= "You've been added to a GeneNetwork user group"):
recipient = user_email
body = render_template(template_name, temp_password)
send_email(recipient, subject, body)
return {"recipient": recipient, "subject": subject, "body": body}
+
@app.route("/manage/verify_email")
def verify_email():
if 'code' in request.args:
@@ -160,6 +168,7 @@ def verify_email():
else:
flash("Invalid code: Password reset code does not exist or might have expired!", "error")
+
@app.route("/n/login", methods=('GET', 'POST'))
def login():
params = request.form if request.form else request.args
@@ -232,6 +241,7 @@ def login():
return response
+
@app.route("/n/login/github_oauth2", methods=('GET', 'POST'))
def github_oauth2():
from utility.tools import GITHUB_CLIENT_ID, GITHUB_CLIENT_SECRET, GITHUB_AUTH_URL
@@ -264,12 +274,14 @@ def github_oauth2():
url = "/n/login?type=github&uid=" + user_details["user_id"]
return redirect(url)
+
def get_github_user_details(access_token):
from utility.tools import GITHUB_API_URL
result = requests.get(GITHUB_API_URL, headers={'Authorization': 'token ' + access_token}).content
return json.loads(result)
+
@app.route("/n/login/orcid_oauth2", methods=('GET', 'POST'))
def orcid_oauth2():
from uuid import uuid4
@@ -308,6 +320,7 @@ def orcid_oauth2():
flash("There was an error getting code from ORCID")
return redirect(url)
+
def get_github_user_details(access_token):
from utility.tools import GITHUB_API_URL
result = requests.get(GITHUB_API_URL, headers={'Authorization': 'token ' + access_token}).content
@@ -325,6 +338,7 @@ def logout():
response.set_cookie(UserSession.user_cookie_name, '', expires=0)
return response
+
@app.route("/n/forgot_password", methods=['GET'])
def forgot_password():
"""Entry point for forgotten password"""
@@ -333,6 +347,7 @@ def forgot_password():
print("ERRORS: ", errors)
return render_template("new_security/forgot_password.html", errors=errors)
+
def send_forgot_password_email(verification_email):
from email.mime.multipart import MIMEMultipart
from email.mime.text import MIMEText
@@ -365,6 +380,7 @@ def send_forgot_password_email(verification_email):
return subject
+
@app.route("/n/forgot_password_submit", methods=('POST',))
def forgot_password_submit():
"""When a forgotten password form is submitted we get here"""
@@ -386,6 +402,7 @@ def forgot_password_submit():
flash("You MUST provide an email", "alert-danger")
return redirect(url_for("forgot_password"))
+
@app.route("/n/password_reset", methods=['GET'])
def password_reset():
"""Entry point after user clicks link in E-mail"""
@@ -405,6 +422,7 @@ def password_reset():
else:
return redirect(url_for("login"))
+
@app.route("/n/password_reset_step2", methods=('POST',))
def password_reset_step2():
"""Handle confirmation E-mail for password reset"""
@@ -422,6 +440,7 @@ def password_reset_step2():
flash("Password changed successfully. You can now sign in.", "alert-info")
return redirect(url_for('login'))
+
def register_user(params):
thank_you_mode = False
errors = []
@@ -461,6 +480,7 @@ def register_user(params):
return errors
+
@app.route("/n/register", methods=('GET', 'POST'))
def register():
errors = []
@@ -478,6 +498,7 @@ def register():
return render_template("new_security/register_user.html", values=params, errors=errors)
+
@app.errorhandler(401)
def unauthorized(error):
return redirect(url_for('login'))
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index 013920f9..a9bd65e6 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -151,6 +151,7 @@ def verify_cookie(cookie):
assert the_signature == actual_hmac_creation(the_uuid), "Uh-oh, someone tampering with the cookie?"
return the_uuid
+
def create_signed_cookie():
the_uuid = str(uuid.uuid4())
signature = actual_hmac_creation(the_uuid)
@@ -158,6 +159,7 @@ def create_signed_cookie():
logger.debug("uuid_signed:", uuid_signed)
return the_uuid, uuid_signed
+
class UserSession:
"""Logged in user handling"""
@@ -341,6 +343,7 @@ class UserSession:
Redis.delete(self.cookie_name)
logger.debug("At end of delete_session")
+
@app.before_request
def get_cookie():
logger.info("@app.before_request get cookie")
@@ -348,16 +351,20 @@ def get_cookie():
g.cookie_session = AnonUser()
# @app.after_request
+
+
def set_cookie(response):
if not request.cookies.get(g.cookie_session.cookie_name):
response.set_cookie(g.cookie_session.cookie_name, g.cookie_session.cookie)
return response
+
class UsersManager:
def __init__(self):
self.users = model.User.query.all()
logger.debug("Users are:", self.users)
+
class UserManager:
def __init__(self, kw):
self.user_id = kw['user_id']
@@ -419,6 +426,7 @@ class RegisterUser:
self.user.registration_info = json.dumps(basic_info(), sort_keys=True)
save_user(self.user.__dict__, self.user.user_id)
+
def set_password(password, user):
pwfields = Bunch()
@@ -476,6 +484,7 @@ class VerificationEmail:
verification_code=verification_code)
send_email(to, subject, body)
+
class ForgotPasswordEmail(VerificationEmail):
template_name = "email/forgot_password.txt"
key_prefix = "forgot_password_code"
@@ -496,7 +505,6 @@ class ForgotPasswordEmail(VerificationEmail):
save_verification_code(toaddr, verification_code)
-
subject = self.subject
body = render_template(
self.template_name,
@@ -530,6 +538,8 @@ def basic_info():
user_agent=request.headers.get('User-Agent'))
# @app.route("/manage/verify_email")
+
+
def verify_email():
user = DecodeUser(VerificationEmail.key_prefix).user
user.confirmed = json.dumps(basic_info(), sort_keys=True)
@@ -544,6 +554,8 @@ def verify_email():
return response
# @app.route("/n/password_reset", methods=['GET'])
+
+
def password_reset():
"""Entry point after user clicks link in E-mail"""
logger.debug("in password_reset request.url is:", request.url)
@@ -568,6 +580,8 @@ def password_reset():
return redirect(url_for("login"))
# @app.route("/n/password_reset_step2", methods=('POST',))
+
+
def password_reset_step2():
"""Handle confirmation E-mail for password reset"""
logger.debug("in password_reset request.url is:", request.url)
@@ -577,7 +591,6 @@ def password_reset_step2():
logger.debug("locals are:", locals())
-
user = Bunch()
password = request.form['password']
set_password(password, user)
@@ -589,6 +602,7 @@ def password_reset_step2():
return response
+
class DecodeUser:
def __init__(self, code_prefix):
@@ -612,6 +626,8 @@ class DecodeUser:
return model.User.query.get(data['id'])
# @app.route("/n/login", methods=('GET', 'POST'))
+
+
def login():
lu = LoginUser()
login_type = request.args.get("type")
@@ -622,6 +638,8 @@ def login():
return lu.standard_login()
# @app.route("/n/login/github_oauth2", methods=('GET', 'POST'))
+
+
def github_oauth2():
from utility.tools import GITHUB_CLIENT_ID, GITHUB_CLIENT_SECRET
code = request.args.get("code")
@@ -646,6 +664,8 @@ def github_oauth2():
return redirect(url)
# @app.route("/n/login/orcid_oauth2", methods=('GET', 'POST'))
+
+
def orcid_oauth2():
from uuid import uuid4
from utility.tools import ORCID_CLIENT_ID, ORCID_CLIENT_SECRET, ORCID_TOKEN_URL, ORCID_AUTH_URL
@@ -673,11 +693,13 @@ def orcid_oauth2():
flash("There was an error getting code from ORCID")
return redirect(url)
+
def get_github_user_details(access_token):
from utility.tools import GITHUB_API_URL
result = requests.get(GITHUB_API_URL, params={"access_token": access_token})
return result.json()
+
class LoginUser:
remember_time = 60 * 60 * 24 * 30 # One month in seconds
@@ -814,6 +836,8 @@ class LoginUser:
db_session.commit()
# @app.route("/n/logout")
+
+
def logout():
logger.debug("Logging out...")
UserSession().delete_session()
@@ -833,6 +857,8 @@ def forgot_password():
return render_template("new_security/forgot_password.html", errors=errors)
# @app.route("/n/forgot_password_submit", methods=('POST',))
+
+
def forgot_password_submit():
"""When a forgotten password form is submitted we get here"""
params = request.form
@@ -853,10 +879,12 @@ def forgot_password_submit():
flash("You MUST provide an email", "alert-danger")
return redirect(url_for("forgot_password"))
+
@app.errorhandler(401)
def unauthorized(error):
return redirect(url_for('login'))
+
def is_redis_available():
try:
Redis.ping()
@@ -922,7 +950,6 @@ def register():
params = None
errors = None
-
params = request.form if request.form else request.args
params = params.to_dict(flat=True)
@@ -952,6 +979,7 @@ def url_for_hmac(endpoint, **values):
combiner = "?"
return url + combiner + "hm=" + hm
+
def data_hmac(stringy):
"""Takes arbitray data string and appends :hmac so we know data hasn't been tampered with"""
return stringy + ":" + actual_hmac_creation(stringy)
@@ -974,6 +1002,7 @@ def verify_url_hmac(url):
assert hm == hmac, "Unexpected url (stage 3)"
+
def actual_hmac_creation(stringy):
"""Helper function to create the actual hmac"""
@@ -986,6 +1015,7 @@ def actual_hmac_creation(stringy):
hm = hm[:20]
return hm
+
app.jinja_env.globals.update(url_for_hmac=url_for_hmac,
data_hmac=data_hmac)
@@ -998,6 +1028,7 @@ app.jinja_env.globals.update(url_for_hmac=url_for_hmac,
# Body=body))
# Redis.rpush("mail_queue", msg)
+
def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"):
"""Send an E-mail through SMTP_CONNECT host. If SMTP_USERNAME is not
'UNKNOWN' TLS is used
@@ -1020,6 +1051,7 @@ def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"):
server.quit()
logger.info("Successfully sent email to " + toaddr)
+
class GroupsManager:
def __init__(self, kw):
self.datasets = create_datasets_list()
diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py
index 78db7bd2..f0f0d60c 100644
--- a/wqflask/wqflask/user_session.py
+++ b/wqflask/wqflask/user_session.py
@@ -20,6 +20,7 @@ logger = getLogger(__name__)
THREE_DAYS = 60 * 60 * 24 * 3
THIRTY_DAYS = 60 * 60 * 24 * 30
+
@app.before_request
def get_user_session():
logger.info("@app.before_request get_session")
@@ -30,6 +31,7 @@ def get_user_session():
response.set_cookie('session_id_v2', '', expires=0)
return response
+
@app.after_request
def set_user_session(response):
if hasattr(g, 'user_session'):
@@ -37,6 +39,7 @@ def set_user_session(response):
response.set_cookie(g.user_session.cookie_name, g.user_session.cookie)
return response
+
def verify_cookie(cookie):
the_uuid, separator, the_signature = cookie.partition(':')
assert len(the_uuid) == 36, "Is session_id a uuid?"
@@ -44,6 +47,7 @@ def verify_cookie(cookie):
assert the_signature == hmac.hmac_creation(the_uuid), "Uh-oh, someone tampering with the cookie?"
return the_uuid
+
def create_signed_cookie():
the_uuid = str(uuid.uuid4())
signature = hmac.hmac_creation(the_uuid)
@@ -51,6 +55,7 @@ def create_signed_cookie():
logger.debug("uuid_signed:", uuid_signed)
return the_uuid, uuid_signed
+
@app.route("/user/manage", methods=('GET', 'POST'))
def manage_user():
params = request.form if request.form else request.args
@@ -63,6 +68,7 @@ def manage_user():
return render_template("admin/manage_user.html", user_details=user_details)
+
class UserSession:
"""Logged in user handling"""