From 2602be69f2869de376d1b9ced6131d880e9476c2 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Tue, 13 Feb 2018 08:54:46 +0000
Subject: @zsloan: we should introduce full parameter checking and sensible
defaults for every page we work on. It will help bug tracking.
Probably fixes #279
---
wqflask/wqflask/correlation/show_corr_results.py | 100 ++++++++++++++++-------
1 file changed, 70 insertions(+), 30 deletions(-)
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 24432ad0..3d1c0d17 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -75,6 +75,46 @@ def print_mem(stage=""):
mem = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss
#print("{}: {}".format(stage, mem/1024))
+def is_float(value):
+ try:
+ float(value)
+ return True
+ except:
+ return False
+
+def is_int(value):
+ try:
+ int(value)
+ return True
+ except:
+ return False
+
+def is_str(value):
+ if value is None:
+ return False
+ try:
+ str(value)
+ return True
+ except:
+ return False
+
+def get_float(vars,name,default=None):
+ if name in vars:
+ if is_float(vars[name]):
+ return float(vars[name])
+ return None
+
+def get_int(vars,name,default=None):
+ if name in vars:
+ if is_int(vars[name]):
+ return float(vars[name])
+ return default
+
+def get_string(vars,name,default=None):
+ if name in vars:
+ if not vars[name] is None:
+ return str(vars[name])
+ return default
class AuthException(Exception):
pass
@@ -96,7 +136,19 @@ class CorrelationResults(object):
# get trait list from db (database name)
# calculate correlation with Base vector and targets
- print("TESTING...")
+ # Check parameters
+ assert('corr_type' in start_vars)
+ assert(is_str(start_vars['corr_type']))
+ assert('dataset' in start_vars)
+ # assert('group' in start_vars) permitted to be empty?
+ assert('corr_sample_method' in start_vars)
+ assert('corr_samples_group' in start_vars)
+ assert('corr_dataset' in start_vars)
+ assert('min_expr' in start_vars)
+ assert('corr_return_results' in start_vars)
+ if 'loc_chr' in start_vars:
+ assert('min_loc_mb' in start_vars)
+ assert('max_loc_mb' in start_vars)
with Bench("Doing correlations"):
if start_vars['dataset'] == "Temp":
@@ -115,27 +167,17 @@ class CorrelationResults(object):
self.sample_data = {}
self.corr_type = start_vars['corr_type']
self.corr_method = start_vars['corr_sample_method']
- if 'min_expr' in start_vars:
- if start_vars['min_expr'] != "":
- self.min_expr = float(start_vars['min_expr'])
- else:
- self.min_expr = None
- self.p_range_lower = float(start_vars['p_range_lower'])
- self.p_range_upper = float(start_vars['p_range_upper'])
+ self.min_expr = get_float(start_vars,'min_expr')
+ self.p_range_lower = get_float(start_vars,'p_range_lower',-1.0)
+ self.p_range_upper = get_float(start_vars,'p_range_upper',1.0)
if ('loc_chr' in start_vars and
'min_loc_mb' in start_vars and
'max_loc_mb' in start_vars):
- self.location_chr = start_vars['loc_chr']
- if start_vars['min_loc_mb'].isdigit():
- self.min_location_mb = start_vars['min_loc_mb']
- else:
- self.min_location_mb = None
- if start_vars['max_loc_mb'].isdigit():
- self.max_location_mb = start_vars['max_loc_mb']
- else:
- self.max_location_mb = None
+ self.location_chr = get_string(start_vars,'loc_chr')
+ self.min_location_mb = get_int(start_vars,'min_loc_mb')
+ self.max_location_mb = get_int(start_vars,'max_loc_mb')
self.get_formatted_corr_type()
self.return_number = int(start_vars['corr_return_results'])
@@ -183,7 +225,7 @@ class CorrelationResults(object):
else:
for trait, values in self.target_dataset.trait_data.iteritems():
self.get_sample_r_and_p_values(trait, values)
-
+
elif self.corr_type == "lit":
self.trait_geneid_dict = self.dataset.retrieve_genes("GeneId")
lit_corr_data = self.do_lit_correlation_for_all_traits()
@@ -564,7 +606,7 @@ class CorrelationResults(object):
self.this_trait_vals.append(sample_value)
target_vals.append(target_sample_value)
- self.this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(self.this_trait_vals, target_vals)
+ self.this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(self.this_trait_vals, target_vals)
#ZS: 2015 could add biweight correlation, see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465711/
if self.corr_method == 'pearson':
@@ -574,8 +616,8 @@ class CorrelationResults(object):
if num_overlap > 5:
self.correlation_data[trait] = [sample_r, sample_p, num_overlap]
-
-
+
+
"""
correlations = []
@@ -673,8 +715,8 @@ class CorrelationResults(object):
method=self.method)
return trait_list
- """
-
+ """
+
def do_tissue_corr_for_all_traits_2(self):
"""Comments Possibly Out of Date!!!!!
@@ -1089,7 +1131,7 @@ class CorrelationResults(object):
totalTraits = len(traits) #XZ, 09/18/2008: total trait number
return traits
-
+
def calculate_corr_for_all_tissues(self, tissue_dataset_id=None):
symbol_corr_dict = {}
@@ -1129,7 +1171,7 @@ class CorrelationResults(object):
values_2.append(target_value)
correlation = calCorrelation(values_1, values_2)
self.correlation_data[trait] = correlation
-
+
def getFileName(self, target_db_name): ### dcrowell August 2008
"""Returns the name of the reference database file with which correlations are calculated.
Takes argument cursor which is a cursor object of any instance of a subclass of templatePage
@@ -1144,7 +1186,7 @@ class CorrelationResults(object):
return FileName
def do_parallel_correlation(self, db_filename, num_overlap):
-
+
#XZ, 01/14/2009: This method is for parallel computing only.
#XZ: It is supposed to be called when "Genetic Correlation, Pearson's r" (method 1)
#XZ: or "Genetic Correlation, Spearman's rho" (method 2) is selected
@@ -1313,7 +1355,7 @@ class CorrelationResults(object):
z_value = z_value*math.sqrt(nOverlap-3)
sample_p = 2.0*(1.0 - reaper.normp(abs(z_value)))
- correlation_data[traitdataName] = [sample_r, sample_p, nOverlap]
+ correlation_data[traitdataName] = [sample_r, sample_p, nOverlap]
# traitinfo = [traitdataName, sample_r, nOverlap]
# allcorrelations.append(traitinfo)
@@ -1321,7 +1363,7 @@ class CorrelationResults(object):
return correlation_data
# return allcorrelations
-
+
datasetFile = open(webqtlConfig.GENERATED_TEXT_DIR+db_filename,'r')
print("Invoking parallel computing")
@@ -1378,5 +1420,3 @@ class CorrelationResults(object):
# for one_result in results:
# for one_traitinfo in one_result:
# allcorrelations.append( one_traitinfo )
-
-
--
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