autopep8: Fix E301,E302,E303,E304,E305,E306

43 files changed, 226 insertions, 25 deletions

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"""