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-rw-r--r--wqflask/run_gunicorn.py2
-rw-r--r--wqflask/utility/startup_config.py4
-rw-r--r--wqflask/utility/svg.py10
-rw-r--r--wqflask/utility/tools.py8
-rw-r--r--wqflask/wqflask/marker_regression/rqtl_mapping.py2
-rw-r--r--wqflask/wqflask/pbkdf2.py16
-rw-r--r--wqflask/wqflask/views.py4
-rw-r--r--wqflask/wqflask/wgcna/wgcna_analysis.py12
8 files changed, 29 insertions, 29 deletions
diff --git a/wqflask/run_gunicorn.py b/wqflask/run_gunicorn.py
index adffdca3..58108e03 100644
--- a/wqflask/run_gunicorn.py
+++ b/wqflask/run_gunicorn.py
@@ -7,7 +7,7 @@
# from flask import Flask
# application = Flask(__name__)
-print "===> Starting up Gunicorn process"
+print("===> Starting up Gunicorn process")
from wqflask import app
from utility.startup_config import app_config
diff --git a/wqflask/utility/startup_config.py b/wqflask/utility/startup_config.py
index 817284dd..42ead709 100644
--- a/wqflask/utility/startup_config.py
+++ b/wqflask/utility/startup_config.py
@@ -27,7 +27,7 @@ def app_config():
port = get_setting_int("SERVER_PORT")
if get_setting_bool("USE_GN_SERVER"):
- print("GN2 API server URL is ["+BLUE+get_setting("GN_SERVER_URL")+ENDC+"]")
+ print(("GN2 API server URL is ["+BLUE+get_setting("GN_SERVER_URL")+ENDC+"]"))
import requests
page = requests.get(get_setting("GN_SERVER_URL"))
if page.status_code != 200:
@@ -36,4 +36,4 @@ def app_config():
# import utility.elasticsearch_tools as es
# es.test_elasticsearch_connection()
- print("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" % (BLUE,str(port),ENDC,get_setting("WEBSERVER_URL")))
+ print(("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" % (BLUE,str(port),ENDC,get_setting("WEBSERVER_URL"))))
diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py
index db13b9d1..6285ea63 100644
--- a/wqflask/utility/svg.py
+++ b/wqflask/utility/svg.py
@@ -102,7 +102,7 @@ if use_dom_implementation<>0:
from xml.dom import implementation
from xml.dom.ext import PrettyPrint
except:
- raise exceptions.ImportError, "PyXML is required for using the dom implementation"
+ raise exceptions.ImportError("PyXML is required for using the dom implementation")
#The implementation is used for the creating the XML document.
#The prettyprint module is used for converting the xml document object to a xml file
@@ -1018,12 +1018,12 @@ class drawing:
PrettyPrint(root,f)
f.close()
except:
- print "Cannot write SVG file: " + filename
+ print(("Cannot write SVG file: " + filename))
def validate(self):
try:
import xml.parsers.xmlproc.xmlval
except:
- raise exceptions.ImportError,'PyXml is required for validating SVG'
+ raise exceptions.ImportError('PyXml is required for validating SVG')
svg=self.toXml()
xv=xml.parsers.xmlproc.xmlval.XMLValidator()
try:
@@ -1031,7 +1031,7 @@ class drawing:
except:
raise Exception("SVG is not well formed, see messages above")
else:
- print "SVG well formed"
+ print("SVG well formed")
if __name__=='__main__':
@@ -1065,4 +1065,4 @@ if __name__=='__main__':
s.addElement(c)
d.setSVG(s)
- print d.toXml()
+ print((d.toXml()))
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 77db5d53..f790d424 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -214,20 +214,20 @@ ENDC = '\033[0m'
def show_settings():
from utility.tools import LOG_LEVEL
- print("Set global log level to "+BLUE+LOG_LEVEL+ENDC)
+ print(("Set global log level to "+BLUE+LOG_LEVEL+ENDC))
log_level = getattr(logging, LOG_LEVEL.upper())
logging.basicConfig(level=log_level)
logger.info(OVERRIDES)
logger.info(BLUE+"Mr. Mojo Risin 2"+ENDC)
- print "runserver.py: ****** Webserver configuration - k,v pairs from app.config ******"
keylist = app.config.keys()
+ print("runserver.py: ****** Webserver configuration - k,v pairs from app.config ******")
keylist.sort()
for k in keylist:
try:
- print("%s: %s%s%s%s" % (k,BLUE,BOLD,get_setting(k),ENDC))
+ print(("%s: %s%s%s%s" % (k,BLUE,BOLD,get_setting(k),ENDC)))
except:
- print("%s: %s%s%s%s" % (k,GREEN,BOLD,app.config[k],ENDC))
+ print(("%s: %s%s%s%s" % (k,GREEN,BOLD,app.config[k],ENDC)))
# Cached values
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index c5590a85..0a5758af 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -42,7 +42,7 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec
png = ro.r["png"] # Map the png function
dev_off = ro.r["dev.off"] # Map the device off function
- print(r_library("qtl")) # Load R/qtl
+ print((r_library("qtl"))) # Load R/qtl
logger.info("QTL library loaded");
diff --git a/wqflask/wqflask/pbkdf2.py b/wqflask/wqflask/pbkdf2.py
index f7f61a09..811c83b0 100644
--- a/wqflask/wqflask/pbkdf2.py
+++ b/wqflask/wqflask/pbkdf2.py
@@ -92,14 +92,14 @@ def test():
def check(data, salt, iterations, keylen, expected):
rv = pbkdf2_hex(data, salt, iterations, keylen)
if rv != expected:
- print 'Test failed:'
- print ' Expected: %s' % expected
- print ' Got: %s' % rv
- print ' Parameters:'
- print ' data=%s' % data
- print ' salt=%s' % salt
- print ' iterations=%d' % iterations
- print
+ print('Test failed:')
+ print((' Expected: %s' % expected))
+ print((' Got: %s' % rv))
+ print(' Parameters:')
+ print((' data=%s' % data))
+ print((' salt=%s' % salt))
+ print((' iterations=%d' % iterations))
+ print()
failed.append(1)
# From RFC 6070
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index dde22bf7..d67f1a2e 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -943,5 +943,5 @@ def json_default_handler(obj):
# logger.info("Not going to serialize Dataset")
# return None
else:
- raise TypeError, 'Object of type %s with value of %s is not JSON serializable' % (
- type(obj), repr(obj))
+ raise TypeError('Object of type %s with value of %s is not JSON serializable' % (
+ type(obj), repr(obj)))
diff --git a/wqflask/wqflask/wgcna/wgcna_analysis.py b/wqflask/wqflask/wgcna/wgcna_analysis.py
index 880a1cb2..d79ad6df 100644
--- a/wqflask/wqflask/wgcna/wgcna_analysis.py
+++ b/wqflask/wqflask/wgcna/wgcna_analysis.py
@@ -60,7 +60,7 @@ class WGCNA(object):
print("Starting WGCNA analysis on dataset")
self.r_enableWGCNAThreads() # Enable multi threading
self.trait_db_list = [trait.strip() for trait in requestform['trait_list'].split(',')]
- print("Retrieved phenotype data from database", requestform['trait_list'])
+ print(("Retrieved phenotype data from database", requestform['trait_list']))
helper_functions.get_trait_db_obs(self, self.trait_db_list)
self.input = {} # self.input contains the phenotype values we need to send to R
@@ -101,13 +101,13 @@ class WGCNA(object):
if requestform.get('SoftThresholds') is not None:
powers = [int(threshold.strip()) for threshold in requestform['SoftThresholds'].rstrip().split(",")]
rpow = r_unlist(r_c(powers))
- print "SoftThresholds: {} == {}".format(powers, rpow)
+ print(("SoftThresholds: {} == {}".format(powers, rpow)))
self.sft = self.r_pickSoftThreshold(rM, powerVector = rpow, verbose = 5)
- print "PowerEstimate: {}".format(self.sft[0])
+ print(("PowerEstimate: {}".format(self.sft[0])))
self.results['PowerEstimate'] = self.sft[0]
if self.sft[0][0] is ri.NA_Integer:
- print "No power is suitable for the analysis, just use 1"
+ print("No power is suitable for the analysis, just use 1")
self.results['Power'] = 1 # No power could be estimated
else:
self.results['Power'] = self.sft[0][0] # Use the estimated power
@@ -122,7 +122,7 @@ class WGCNA(object):
self.results['network'] = network
# How many modules and how many gene per module ?
- print "WGCNA found {} modules".format(r_table(network[1]))
+ print(("WGCNA found {} modules".format(r_table(network[1]))))
self.results['nmod'] = r_length(r_table(network[1]))[0]
# The iconic WCGNA plot of the modules in the hanging tree
@@ -135,7 +135,7 @@ class WGCNA(object):
sys.stdout.flush()
def render_image(self, results):
- print("pre-loading imgage results:", self.results['imgloc'])
+ print(("pre-loading imgage results:", self.results['imgloc']))
imgfile = open(self.results['imgloc'], 'rb')
imgdata = imgfile.read()
imgB64 = imgdata.encode("base64")
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 21:13:34 +0000