Wrap print statements in parentheses

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")