Removed file tracer.py that wasn't being used

Removed some unused code from the other files listed

10 files changed, 29 insertions, 196 deletions

diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py
index 4de88f00..2f327faf 100644
--- a/wqflask/wqflask/marker_regression/plink_mapping.py
+++ b/wqflask/wqflask/marker_regression/plink_mapping.py
@@ -10,9 +10,7 @@ logger = utility.logger.getLogger(__name__ )
 
 def run_plink(this_trait, dataset, species, vals, maf):
     plink_output_filename = webqtlUtil.genRandStr("%s_%s_"%(dataset.group.name, this_trait.name))
-
     gen_pheno_txt_file(dataset, vals)
-    #gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = plink_output_filename)
 
     plink_command = PLINK_COMMAND + ' --noweb --bfile %s/%s --no-pheno --no-fid --no-parents --no-sex --maf %s --out %s%s --assoc ' % (
         flat_files('mapping'), dataset.group.name, maf, TMPDIR, plink_output_filename)
@@ -22,12 +20,6 @@ def run_plink(this_trait, dataset, species, vals, maf):
 
     count, p_values = parse_plink_output(plink_output_filename, species)
 
-    #for marker in self.dataset.group.markers.markers:
-    #    if marker['name'] not in included_markers:
-    #        logger.debug("marker:", marker)
-    #        self.dataset.group.markers.markers.remove(marker)
-    #        #del self.dataset.group.markers.markers[marker]
-
     logger.debug("p_values:", p_values)
     dataset.group.markers.add_pvalues(p_values)
 
@@ -108,7 +100,6 @@ def parse_plink_output(output_filename, species):
 
     result_fp = open("%s%s.qassoc"% (TMPDIR, output_filename), "rb")
 
-    header_line = result_fp.readline()# read header line
     line = result_fp.readline()
 
     value_list = [] # initialize value list, this list will include snp, bp and pvalue info
@@ -156,11 +147,6 @@ def parse_plink_output(output_filename, species):
         else:
             line = result_fp.readline()
 
-    #if p_value_list:
-    #    min_p_value = min(p_value_list)
-    #else:
-    #    min_p_value = 0
-
     return count, p_value_dict
 
 ######################################################
@@ -173,4 +159,4 @@ def build_line_list(line=None):
     line_list = [item for item in line_list if item <>'']
     line_list = map(string.strip, line_list)
 
-    return line_list
+    return line_list
\ No newline at end of file
diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
index 6b58190f..ffbfb5c5 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -26,7 +26,7 @@ def gen_reaper_results(this_trait, dataset, samples_before, trait_vals, json_dat
         perm_output = genotype.permutation(strains = trimmed_samples, trait = trimmed_values, nperm=num_perm)
         suggestive = perm_output[int(num_perm*0.37-1)]
         significant = perm_output[int(num_perm*0.95-1)]
-        highly_significant = perm_output[int(num_perm*0.99-1)]
+        #highly_significant = perm_output[int(num_perm*0.99-1)] #ZS: Currently not used, but leaving it here just in case
 
     json_data['suggestive'] = suggestive
     json_data['significant'] = significant
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index f3694f0b..41d67012 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -5,15 +5,16 @@ from base.webqtlConfig import TMPDIR
 from utility import webqtlUtil
 from utility.tools import locate, TEMPDIR
 
+import utility.logger
+logger = utility.logger.getLogger(__name__ )
+
 def run_rqtl_geno(vals, dataset, method, model, permCheck, num_perm, do_control, control_marker, manhattan_plot, pair_scan):
     geno_to_rqtl_function(dataset)
 
     ## Get pointers to some common R functions
     r_library     = ro.r["library"]                 # Map the library function
     r_c           = ro.r["c"]                       # Map the c function
-    r_sum         = ro.r["sum"]                     # Map the sum function
     plot          = ro.r["plot"]                    # Map the plot function
-    postscript    = ro.r["postscript"]              # Map the postscript function
     png           = ro.r["png"]                     # Map the png function
     dev_off       = ro.r["dev.off"]                 # Map the device off function
 
@@ -23,17 +24,13 @@ def run_rqtl_geno(vals, dataset, method, model, permCheck, num_perm, do_control,
     scanone         = ro.r["scanone"]               # Map the scanone function
     scantwo         = ro.r["scantwo"]               # Map the scantwo function
     calc_genoprob   = ro.r["calc.genoprob"]         # Map the calc.genoprob function
-    read_cross      = ro.r["read.cross"]            # Map the read.cross function
-    write_cross     = ro.r["write.cross"]           # Map the write.cross function
     GENOtoCSVR      = ro.r["GENOtoCSVR"]            # Map the local GENOtoCSVR function
 
     crossname = dataset.group.name
     genofilelocation  = locate(crossname + ".geno", "genotype")
     crossfilelocation = TMPDIR + crossname + ".cross"
 
-    #print("Conversion of geno to cross at location:", genofilelocation, " to ", crossfilelocation)
-
-    cross_object = GENOtoCSVR(genofilelocation, crossfilelocation)                                  # TODO: Add the SEX if that is available
+    cross_object = GENOtoCSVR(genofilelocation, crossfilelocation)                            # TODO: Add the SEX if that is available
 
     if manhattan_plot:
         cross_object = calc_genoprob(cross_object)
@@ -42,18 +39,14 @@ def run_rqtl_geno(vals, dataset, method, model, permCheck, num_perm, do_control,
 
     cross_object = add_phenotype(cross_object, sanitize_rqtl_phenotype(vals))                 # Add the phenotype
 
-    # for debug: write_cross(cross_object, "csvr", "test.csvr")
-
     # Scan for QTLs
-    covar = create_covariates(control_marker, cross_object)                                                    # Create the additive covariate matrix
+    covar = create_covariates(control_marker, cross_object)                                   # Create the additive covariate matrix
 
     if pair_scan:
-        if do_control == "true":                                                # If sum(covar) > 0 we have a covariate matrix
-            print("Using covariate"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", addcovar = covar, model=model, method=method, n_cluster = 16)
+        if do_control == "true":
+            logger.info("Using covariate"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", addcovar = covar, model=model, method=method, n_cluster = 16)
         else:
-            print("No covariates"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", model=model, method=method, n_cluster = 16)
-
-        #print("Pair scan results:", result_data_frame)
+            logger.info("No covariates"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", model=model, method=method, n_cluster = 16)
 
         pair_scan_filename = webqtlUtil.genRandStr("scantwo_") + ".png"
         png(file=TEMPDIR+pair_scan_filename)
@@ -63,9 +56,9 @@ def run_rqtl_geno(vals, dataset, method, model, permCheck, num_perm, do_control,
         return process_pair_scan_results(result_data_frame)
     else:
         if do_control == "true":
-            print("Using covariate"); result_data_frame = scanone(cross_object, pheno = "the_pheno", addcovar = covar, model=model, method=method)
+            logger.info("Using covariate"); result_data_frame = scanone(cross_object, pheno = "the_pheno", addcovar = covar, model=model, method=method)
         else:
-            print("No covariates"); result_data_frame = scanone(cross_object, pheno = "the_pheno", model=model, method=method)
+            logger.info("No covariates"); result_data_frame = scanone(cross_object, pheno = "the_pheno", model=model, method=method)
 
         if num_perm > 0 and permCheck == "ON":                                                                   # Do permutation (if requested by user)
             if do_control == "true":
@@ -79,7 +72,6 @@ def run_rqtl_geno(vals, dataset, method, model, permCheck, num_perm, do_control,
             return process_rqtl_results(result_data_frame)
 
 def geno_to_rqtl_function(dataset):        # TODO: Need to figure out why some genofiles have the wrong format and don't convert properly
-
     ro.r("""
        trim <- function( x ) { gsub("(^[[:space:]]+|[[:space:]]+$)", "", x) }
 
@@ -117,15 +109,13 @@ def add_phenotype(cross, pheno_as_string):
 def create_covariates(control_marker, cross):
     ro.globalenv["the_cross"] = cross
     ro.r('genotypes <- pull.geno(the_cross)')                             # Get the genotype matrix
-    userinputS = control_marker.replace(" ", "").split(",")                 # TODO: sanitize user input, Never Ever trust a user
+    userinputS = control_marker.replace(" ", "").split(",")               # TODO: sanitize user input, Never Ever trust a user
     covariate_names = ', '.join('"{0}"'.format(w) for w in userinputS)
-    #print("Marker names of selected covariates:", covariate_names)
     ro.r('covnames <- c(' + covariate_names + ')')
     ro.r('covInGeno <- which(covnames %in% colnames(genotypes))')
     ro.r('covnames <- covnames[covInGeno]')
     ro.r("cat('covnames (purged): ', covnames,'\n')")
     ro.r('covariates <- genotypes[,covnames]')                            # Get the covariate matrix by using the marker name as index to the genotype file
-    #print("R/qtl matrix of covariates:", ro.r["covariates"])
     return ro.r["covariates"]
 
 def sanitize_rqtl_phenotype(vals):
@@ -149,7 +139,6 @@ def process_pair_scan_results(result):
 
     result = result[1]
     output = [tuple([result[j][i] for j in range(result.ncol)]) for i in range(result.nrow)]
-    #print("R/qtl scantwo output:", output)
 
     for i, line in enumerate(result.iter_row()):
         marker = {}
@@ -175,9 +164,7 @@ def process_rqtl_perm_results(num_perm, results):
 
 def process_rqtl_results(result):        # 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)]
-    #print("R/qtl scanone output:", output)
 
     for i, line in enumerate(result.iter_row()):
         marker = {}
@@ -187,5 +174,4 @@ def process_rqtl_results(result):        # TODO: how to make this a one liner an
         marker['lod_score'] = output[i][2]
         qtl_results.append(marker)
 
-    return qtl_results
-
+    return qtl_results
\ No newline at end of file
diff --git a/wqflask/wqflask/model.py b/wqflask/wqflask/model.py
index 5321e420..38117a8e 100644
--- a/wqflask/wqflask/model.py
+++ b/wqflask/wqflask/model.py
@@ -6,31 +6,16 @@ import datetime
 import simplejson as json
 
 from flask import request
-from flask.ext.sqlalchemy import SQLAlchemy
 
 from wqflask import app
 
 import sqlalchemy
-
-from sqlalchemy import (Column, Integer, String, Table, ForeignKey, Unicode, Boolean, DateTime,
+from sqlalchemy import (Column, ForeignKey, Unicode, Boolean, DateTime,
                         Text, Index)
-from sqlalchemy.orm import relationship, backref
+from sqlalchemy.orm import relationship
 
 from wqflask.database import Base, init_db
 
-
-
-# Define models
-#roles_users = Table('roles_users',
-#        Column('user_id', Integer(), ForeignKey('user.the_id')),
-#        Column('role_id', Integer(), ForeignKey('role.the_id')))
-
-#class Role(Base):
-#    __tablename__ = "role"
-#    id = Column(Unicode(36), primary_key=True, default=lambda: unicode(uuid.uuid4()))
-#    name = Column(Unicode(80), unique=True, nullable=False)
-#    description = Column(Unicode(255))
-
 class User(Base):
     __tablename__ = "user"
     id = Column(Unicode(36), primary_key=True, default=lambda: unicode(uuid.uuid4()))
@@ -133,11 +118,6 @@ class User(Base):
         except IndexError:
             return None
 
-
-    #roles = relationship('Role', secondary=roles_users,
-    #                        backref=backref('users', lazy='dynamic'))
-
-
 class Login(Base):
     __tablename__ = "login"
     id = Column(Unicode(36), primary_key=True, default=lambda: unicode(uuid.uuid4()))
@@ -177,22 +157,15 @@ class UserCollection(Base):
         except:
             return 0
 
-    #@property
-    #def display_num_members(self):
-    #    return display_collapsible(self.num_members)
-
     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')
-
+    user_uuid = request.cookies.get('user_uuid')
\ No newline at end of file
diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py
index b42904a4..63273a29 100644
--- a/wqflask/wqflask/network_graph/network_graph.py
+++ b/wqflask/wqflask/network_graph/network_graph.py
@@ -21,9 +21,7 @@
 from __future__ import absolute_import, print_function, division
 
 import sys
-# sys.path.append(".")   Never do this in a webserver!
 
-import gc
 import string
 import cPickle
 import os
@@ -95,7 +93,6 @@ class NetworkGraph(object):
 
         self.lowest_overlap = 8 #ZS: Variable set to the lowest overlapping samples in order to notify user, or 8, whichever is lower (since 8 is when we want to display warning)
 
-        self.network_data = {}
         self.nodes_list = []
         self.edges_list = []
         for trait_db in self.trait_list:
@@ -107,9 +104,9 @@ class NetworkGraph(object):
 
             corr_result_row = []
             is_spearman = False #ZS: To determine if it's above or below the diagonal
-            
+
             max_corr = 0 #ZS: Used to determine whether node should be hidden when correlation coefficient slider is used
-            
+
             for target in self.trait_list:
                 target_trait = target[0]
                 target_db = target[1]
@@ -141,7 +138,7 @@ class NetworkGraph(object):
                             continue
                     else:
                         sample_r, sample_p = scipy.stats.spearmanr(this_trait_vals, target_vals)
- 
+
                     if -1 <= sample_r < -0.7:
                         color = "#0000ff"
                         width = 3
@@ -163,10 +160,10 @@ class NetworkGraph(object):
                     else:
                         color = "#000000"
                         width = 0                      
- 
+
                     if abs(sample_r) > max_corr:
                         max_corr = abs(sample_r)
- 
+
                     edge_data = {'id' : str(this_trait.name) + '_to_' + str(target_trait.name),
                                  'source' : str(this_trait.name) + ":" + str(this_trait.dataset.name),
                                  'target' : str(target_trait.name) + ":" + str(target_trait.dataset.name),
@@ -176,11 +173,11 @@ class NetworkGraph(object):
                                  'overlap' : num_overlap,
                                  'color' : color,
                                  'width' : width }
-                                 
+
                     edge_dict = { 'data' : edge_data }
-                                 
+
                     self.edges_list.append(edge_dict)
-      
+
             if trait_db[1].type == "ProbeSet":
                 node_dict = { 'data' : {'id' : str(this_trait.name) + ":" + str(this_trait.dataset.name), 
                                         'label' : this_trait.symbol,
@@ -197,19 +194,13 @@ class NetworkGraph(object):
                                         'label' : this_trait.name,
                                         'max_corr' : max_corr } }
             self.nodes_list.append(node_dict)
-      
-        #self.network_data['dataSchema'] = {'nodes' : [{'name' : "label" , 'type' : "string"}],
-        #                                   'edges' : [{'name' : "label" , 'type' : "string"}] }
-        
-        #self.network_data['data'] = {'nodes' : self.nodes_list,
-        #                             'edges' : self.edges_list }
 
         self.elements = json.dumps(self.nodes_list + self.edges_list)
-        
+
         groups = []
         for sample in self.all_sample_list:
             groups.append(1)
-            
+
         self.js_data = dict(traits = [trait.name for trait in self.traits],
                             groups = groups,
                             cols = range(len(self.traits)),
@@ -217,7 +208,6 @@ class NetworkGraph(object):
                             samples = self.all_sample_list,
                             sample_data = self.sample_data,
                             elements = self.elements,)
-        #                    corr_results = [result[1] for result in result_row for result_row in self.corr_results])
 
     def get_trait_db_obs(self, trait_db_list):
         self.trait_list = []
@@ -229,4 +219,4 @@ class NetworkGraph(object):
             trait_ob = GeneralTrait(dataset=dataset_ob,
                                    name=trait_name,
                                    cellid=None)
-            self.trait_list.append((trait_ob, dataset_ob))
+            self.trait_list.append((trait_ob, dataset_ob))
\ No newline at end of file
diff --git a/wqflask/wqflask/show_trait/export_trait_data.py b/wqflask/wqflask/show_trait/export_trait_data.py
index ac3cd366..558372bb 100644
--- a/wqflask/wqflask/show_trait/export_trait_data.py
+++ b/wqflask/wqflask/show_trait/export_trait_data.py
@@ -1,7 +1,5 @@
 from __future__ import print_function, division
 
-import operator
-
 import simplejson as json
 
 from pprint import pformat as pf
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 1f000564..8b801396 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -6,7 +6,6 @@ import datetime
 import cPickle
 import uuid
 import json as json
-#import pyXLWriter as xl
 
 from collections import OrderedDict
 
@@ -73,14 +72,6 @@ class ShowTrait(object):
                                            cellid=None)
             self.trait_vals = Redis.get(self.trait_id).split()
 
-        #self.dataset.group.read_genotype_file()
-
-        #if this_trait:
-        #    if this_trait.dataset and this_trait.dataset.type and this_trait.dataset.type == 'ProbeSet':
-        #            self.cursor.execute("SELECT h2 from ProbeSetXRef WHERE DataId = %d" %
-        #                                this_trait.mysqlid)
-        #            heritability = self.cursor.fetchone()
-
         #ZS: Get verify/rna-seq link URLs
         try:
             blatsequence = self.this_trait.blatseq
@@ -192,7 +183,7 @@ class ShowTrait(object):
             self.sample_group_types['samples_primary'] = self.dataset.group.name
         sample_lists = [group.sample_list for group in self.sample_groups]
 
-        self.get_mapping_methods()
+        self.genofiles = get_genofiles(self.dataset)
 
         self.stats_table_width, self.trait_table_width = get_table_widths(self.sample_groups)
 
@@ -211,28 +202,6 @@ class ShowTrait(object):
                        temp_uuid = self.temp_uuid)
         self.js_data = js_data
 
-    def get_mapping_methods(self):
-        '''Only display mapping methods when the dataset group's genotype file exists'''
-        def check_plink_gemma():
-            if flat_file_exists("mapping"):
-                MAPPING_PATH = flat_files("mapping")+"/"
-                if (os.path.isfile(MAPPING_PATH+self.dataset.group.name+".bed") and
-                    (os.path.isfile(MAPPING_PATH+self.dataset.group.name+".map") or
-                     os.path.isfile(MAPPING_PATH+self.dataset.group.name+".bim"))):
-                    return True
-            return False
-
-        def check_pylmm_rqtl():
-            if os.path.isfile(webqtlConfig.GENODIR+self.dataset.group.name+".geno") and (os.path.getsize(webqtlConfig.JSON_GENODIR+self.dataset.group.name+".json") > 0):
-                return True
-            else:
-                return False
-
-        self.genofiles = get_genofiles(self.dataset)
-        self.use_plink_gemma = check_plink_gemma()
-        self.use_pylmm_rqtl = check_pylmm_rqtl()
-
-
     def build_correlation_tools(self):
         if self.temp_trait == True:
             this_group = self.temp_group
@@ -245,7 +214,6 @@ class ShowTrait(object):
             this_group = 'BXD'
 
         if this_group:
-            #dataset_menu = self.dataset.group.datasets()
             if self.temp_trait == True:
                 dataset_menu = data_set.datasets(this_group)
             else:
@@ -263,7 +231,6 @@ class ShowTrait(object):
                                           return_results_menu = return_results_menu,
                                           return_results_menu_selected = return_results_menu_selected,)
 
-
     def make_sample_lists(self):
         all_samples_ordered = self.dataset.group.all_samples_ordered()
         
@@ -315,10 +282,6 @@ class ShowTrait(object):
                                             sample_group_type='primary',
                                             header="%s Only" % (self.dataset.group.name))
             self.sample_groups = (primary_samples,)
-        #TODO: Figure out why this if statement is written this way - Zach
-        #if (other_sample_names or (fd.f1list and this_trait.data.has_key(fd.f1list[0]))
-        #        or (fd.f1list and this_trait.data.has_key(fd.f1list[1]))):
-        #    logger.debug("hjs")
         self.dataset.group.allsamples = all_samples_ordered
 
 def get_nearest_marker(this_trait, this_db):
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 03590c2c..0ecf1eb9 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -35,7 +35,6 @@
             </ul>
 
             <div class="tab-content">
-                {# if use_pylmm_rqtl and not use_plink_gemma and dataset.group.species != "human" #}
                 {% if dataset.group.mapping_id == "1" %}
                 <div class="tab-pane active" id="gemma">
                     <div style="padding-top: 20px;" class="form-horizontal">
@@ -70,10 +69,6 @@
                                </label>
                             </div>
                         </div>
-                    <!--
-                    </div>
-                    <div style="padding-top: 5px; padding-bottom: 5px; padding-left: 20px;" class="form-horizontal">
-                    -->
                         <div class="mapping_method_fields form-group">
                             <label style="text-align: right;" class="col-xs-3 control-label">Covariates</label>
                             <div style="margin-left:20px;" class="col-xs-7">
@@ -99,18 +94,6 @@
                           </div>
                         </div>
                     </div>
-<!--
-                    <div class="form-group">
-                        <div class="col-xs-4 controls">
-                            <label class="col-xs-2 control-label"></label>
-                            <div class="col-xs-4">
-                            <button id="gemma_bimbam_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
-                                Compute
-                            </button>
-                            </div>
-                        </div>
-                    </div>
--->
                 </div>
                 <div class="tab-pane" id="interval_mapping">
                     <div style="margin-top: 20px" class="form-horizontal">
diff --git a/wqflask/wqflask/tracer.py b/wqflask/wqflask/tracer.py
deleted file mode 100644
index a1043d28..00000000
--- a/wqflask/wqflask/tracer.py
+++ /dev/null
@@ -1,41 +0,0 @@
-from __future__ import absolute_import, division, print_function
-
-print("At top of tracer")
-
-import sys
-
-####################################################################################
-
-# Originally based on http://stackoverflow.com/a/8315566
-def tracefunc(frame, event, arg, indent=[0]):
-
-    func = dict(funcname = frame.f_code.co_name,
-                     filename = frame.f_code.co_filename,
-                     lineno = frame.f_lineno)
-
-    #These are too common to bother printing...
-    too_common = (
-        '/home/sam/ve27/local/lib/python2.7/site-packages/werkzeug/',
-        '/home/sam/ve27/local/lib/python2.7/site-packages/jinja2/',
-    )
-
-
-    if func['filename'].startswith(too_common):
-        return tracefunc
-
-    info = "{funcname} [{filename}: {lineno}]".format(**func)
-
-    if event == "call":
-        indent[0] += 2
-        #print("-" * indent[0] + "> call function", frame.f_code.co_name)
-        print("-" * indent[0] + "> call function:", info)
-    elif event == "return":
-        print("<" + "-" * indent[0], "exit function:", info)
-        indent[0] -= 2
-    return tracefunc
-
-def turn_on():
-    sys.settrace(tracefunc)
-    print("Tracing turned on!!!!")
-####################################################################################
-
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 8ff359a7..49b47123 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -89,11 +89,6 @@ def shutdown_session(exception=None):
         db_session.remove()
         g.db = None
 
-#@app.before_request
-#def trace_it():
-#    from wqflask import tracer
-#    tracer.turn_on()
-
 @app.errorhandler(Exception)
 def handle_bad_request(e):
     err_msg = str(e)