diff options
author | BonfaceKilz | 2020-08-17 17:41:58 +0300 |
---|---|---|
committer | BonfaceKilz | 2020-08-18 16:59:52 +0300 |
commit | af330a2aa7b36fd0cf8505eb20fa06d2ed58b86b (patch) | |
tree | ebc6ee429df52b7ae82d1f2017a356898348c0f9 | |
parent | e49ef0954e111ace2044cced0a83b4d9dc00bc72 (diff) | |
download | genenetwork2-af330a2aa7b36fd0cf8505eb20fa06d2ed58b86b.tar.gz |
Wrap print statements in parentheses
-rwxr-xr-x | scripts/maintenance/QTL_Reaper_v6.py | 6 | ||||
-rw-r--r-- | scripts/maintenance/Update_Case_Attributes_MySQL_tab.py | 2 | ||||
-rwxr-xr-x | scripts/maintenance/delete_genotypes.py | 14 | ||||
-rwxr-xr-x | scripts/maintenance/delete_phenotypes.py | 14 | ||||
-rwxr-xr-x | scripts/maintenance/load_genotypes.py | 16 | ||||
-rwxr-xr-x | scripts/maintenance/load_phenotypes.py | 30 | ||||
-rwxr-xr-x | scripts/maintenance/readProbeSetMean_v7.py | 40 | ||||
-rwxr-xr-x | scripts/maintenance/readProbeSetSE_v7.py | 22 | ||||
-rw-r--r-- | wqflask/run_gunicorn.py | 2 | ||||
-rw-r--r-- | wqflask/utility/startup_config.py | 4 | ||||
-rw-r--r-- | wqflask/utility/svg.py | 10 | ||||
-rw-r--r-- | wqflask/utility/tools.py | 8 | ||||
-rw-r--r-- | wqflask/wqflask/marker_regression/rqtl_mapping.py | 2 | ||||
-rw-r--r-- | wqflask/wqflask/pbkdf2.py | 16 | ||||
-rw-r--r-- | wqflask/wqflask/views.py | 4 | ||||
-rw-r--r-- | wqflask/wqflask/wgcna/wgcna_analysis.py | 12 |
16 files changed, 101 insertions, 101 deletions
diff --git a/scripts/maintenance/QTL_Reaper_v6.py b/scripts/maintenance/QTL_Reaper_v6.py index e50dbd40..7fb56eca 100755 --- a/scripts/maintenance/QTL_Reaper_v6.py +++ b/scripts/maintenance/QTL_Reaper_v6.py @@ -53,7 +53,7 @@ for ProbeSetFreezeId in ProbeSetFreezeIds: #if InbredSetId==12: # InbredSetId=2 - print ProbeSetFreezeId, InbredSets[InbredSetId] + print((ProbeSetFreezeId, InbredSets[InbredSetId])) genotype_1.read(InbredSets[InbredSetId]) locuses = [] @@ -102,7 +102,7 @@ for ProbeSetFreezeId in ProbeSetFreezeIds: kj += 1 if kj%1000==0: - print ProbeSetFreezeId, InbredSets[InbredSetId],kj + print((ProbeSetFreezeId, InbredSets[InbredSetId],kj)) - print ProbeSetFreezeIds + print(ProbeSetFreezeIds) diff --git a/scripts/maintenance/Update_Case_Attributes_MySQL_tab.py b/scripts/maintenance/Update_Case_Attributes_MySQL_tab.py index 0f8602c9..bf796df4 100644 --- a/scripts/maintenance/Update_Case_Attributes_MySQL_tab.py +++ b/scripts/maintenance/Update_Case_Attributes_MySQL_tab.py @@ -24,4 +24,4 @@ for row in csv_data: #close the connection to the database. mydb.commit() cursor.close() -print "Done"
\ No newline at end of file +print("Done")
\ No newline at end of file diff --git a/scripts/maintenance/delete_genotypes.py b/scripts/maintenance/delete_genotypes.py index fa693f0f..060640e1 100755 --- a/scripts/maintenance/delete_genotypes.py +++ b/scripts/maintenance/delete_genotypes.py @@ -8,13 +8,13 @@ import genotypes def main(argv): # config config = utilities.get_config(argv[1]) - print "config:" + print("config:") for item in config.items('config'): - print "\t%s" % (str(item)) + print(("\t%s" % (str(item)))) # var - print "variable:" + print("variable:") inbredsetid = config.get('config', 'inbredsetid') - print "\tinbredsetid: %s" % inbredsetid + print(("\tinbredsetid: %s" % inbredsetid)) # datafile datafile = open(config.get('config', 'datafile'), 'r') datafile = csv.reader(datafile, delimiter='\t', quotechar='"') @@ -25,9 +25,9 @@ def main(argv): continue genoname = row[0] delrowcount += genotypes.delete(genoname, inbredsetid) - print "deleted %d genotypes" % (delrowcount) + print(("deleted %d genotypes" % (delrowcount))) if __name__ == "__main__": - print "command line arguments:\n\t%s" % sys.argv + print(("command line arguments:\n\t%s" % sys.argv)) main(sys.argv) - print "exit successfully" + print("exit successfully") diff --git a/scripts/maintenance/delete_phenotypes.py b/scripts/maintenance/delete_phenotypes.py index 326c466e..60dbec61 100755 --- a/scripts/maintenance/delete_phenotypes.py +++ b/scripts/maintenance/delete_phenotypes.py @@ -8,13 +8,13 @@ import phenotypes def main(argv): # config config = utilities.get_config(argv[1]) - print "config:" + print("config:") for item in config.items('config'): - print "\t%s" % (str(item)) + print(("\t%s" % (str(item)))) # var - print "variable:" + print("variable:") inbredsetid = config.get('config', 'inbredsetid') - print "\tinbredsetid: %s" % inbredsetid + print(("\tinbredsetid: %s" % inbredsetid)) # datafile datafile = open(config.get('config', 'datafile'), 'r') datafile = csv.reader(datafile, delimiter='\t', quotechar='"') @@ -27,9 +27,9 @@ def main(argv): except: continue delrowcount += phenotypes.delete(publishxrefid=publishxrefid, inbredsetid=inbredsetid) - print "deleted %d phenotypes" % (delrowcount) + print(("deleted %d phenotypes" % (delrowcount))) if __name__ == "__main__": - print "command line arguments:\n\t%s" % sys.argv + print(("command line arguments:\n\t%s" % sys.argv)) main(sys.argv) - print "exit successfully" + print("exit successfully") diff --git a/scripts/maintenance/load_genotypes.py b/scripts/maintenance/load_genotypes.py index 338483f4..c235a31f 100755 --- a/scripts/maintenance/load_genotypes.py +++ b/scripts/maintenance/load_genotypes.py @@ -8,7 +8,7 @@ def main(argv): config = utilities.get_config(argv[1]) print("config file:") for item in config.items('config'): - print("\t%s" % str(item)) + print(("\t%s" % str(item))) parse_genofile(config, fetch_parameters(config)) def fetch_parameters(config): @@ -20,7 +20,7 @@ def fetch_parameters(config): config_dic['genofile'] = config.get('config', 'genofile') print("config dictionary:") for k, v in config_dic.items(): - print("\t%s: %s" % (k, v)) + print(("\t%s: %s" % (k, v))) return config_dic def parse_genofile(config, config_dic): @@ -43,9 +43,9 @@ def parse_genofile(config, config_dic): # print("geno file meta dictionary:") for k, v in meta_dic.items(): - print("\t%s: %s" % (k, v)) + print(("\t%s: %s" % (k, v))) # - print("geno file head:\n\t%s" % line) + print(("geno file head:\n\t%s" % line)) strainnames = line.split()[4:] config_dic['strains'] = datastructure.get_strains_bynames(inbredsetid=config_dic['inbredsetid'], strainnames=strainnames, updatestrainxref="yes") continue @@ -81,7 +81,7 @@ def check_or_insert_geno(config_dic, marker_dic): result = cursor.fetchone() if result: genoid = result[0] - print("get geno record: %d" % genoid) + print(("get geno record: %d" % genoid)) else: sql = """ INSERT INTO Geno @@ -95,7 +95,7 @@ def check_or_insert_geno(config_dic, marker_dic): cursor.execute(sql, (config_dic['speciesid'], marker_dic['locus'], marker_dic['locus'], marker_dic['chromosome'], marker_dic['mb'])) rowcount = cursor.rowcount genoid = con.insert_id() - print("INSERT INTO Geno: %d record: %d" % (rowcount, genoid)) + print(("INSERT INTO Geno: %d record: %d" % (rowcount, genoid))) return genoid def check_genoxref(config_dic, marker_dic): @@ -146,9 +146,9 @@ def insert_genoxref(config_dic, marker_dic): """ cursor.execute(sql, (config_dic['genofreezeid'], marker_dic['genoid'], config_dic['dataid'], marker_dic['cm'], 'N')) rowcount = cursor.rowcount - print("INSERT INTO GenoXRef: %d record" % (rowcount)) + print(("INSERT INTO GenoXRef: %d record" % (rowcount))) if __name__ == "__main__": - print("command line arguments:\n\t%s" % sys.argv) + print(("command line arguments:\n\t%s" % sys.argv)) main(sys.argv) print("exit successfully") diff --git a/scripts/maintenance/load_phenotypes.py b/scripts/maintenance/load_phenotypes.py index c3c6570b..61d527d4 100755 --- a/scripts/maintenance/load_phenotypes.py +++ b/scripts/maintenance/load_phenotypes.py @@ -7,31 +7,31 @@ import datastructure def main(argv): # config config = utilities.get_config(argv[1]) - print "config:" + print("config:") for item in config.items('config'): - print "\t%s" % (str(item)) + print(("\t%s" % (str(item)))) # var inbredsetid = config.get('config', 'inbredsetid') - print "inbredsetid: %s" % inbredsetid + print(("inbredsetid: %s" % inbredsetid)) species = datastructure.get_species(inbredsetid) speciesid = species[0] - print "speciesid: %s" % speciesid + print(("speciesid: %s" % speciesid)) dataid = datastructure.get_nextdataid_phenotype() - print "next data id: %s" % dataid + print(("next data id: %s" % dataid)) cursor, con = utilities.get_cursor() # datafile datafile = open(config.get('config', 'datafile'), 'r') phenotypedata = csv.reader(datafile, delimiter='\t', quotechar='"') phenotypedata_head = phenotypedata.next() - print "phenotypedata head:\n\t%s" % phenotypedata_head + print(("phenotypedata head:\n\t%s" % phenotypedata_head)) strainnames = phenotypedata_head[1:] strains = datastructure.get_strains_bynames(inbredsetid=inbredsetid, strainnames=strainnames, updatestrainxref="yes") # metafile metafile = open(config.get('config', 'metafile'), 'r') phenotypemeta = csv.reader(metafile, delimiter='\t', quotechar='"') phenotypemeta_head = phenotypemeta.next() - print "phenotypemeta head:\n\t%s" % phenotypemeta_head - print + print(("phenotypemeta head:\n\t%s" % phenotypemeta_head)) + print() # load for metarow in phenotypemeta: # @@ -67,7 +67,7 @@ def main(argv): )) rowcount = cursor.rowcount phenotypeid = con.insert_id() - print "INSERT INTO Phenotype: %d record: %d" % (rowcount, phenotypeid) + print(("INSERT INTO Phenotype: %d record: %d" % (rowcount, phenotypeid))) # Publication publicationid = None # reset pubmed_id = utilities.to_db_string(metarow[0], None) @@ -81,7 +81,7 @@ def main(argv): re = cursor.fetchone() if re: publicationid = re[0] - print "get Publication record: %d" % publicationid + print(("get Publication record: %d" % publicationid)) if not publicationid: sql = """ INSERT INTO Publication @@ -109,7 +109,7 @@ def main(argv): )) rowcount = cursor.rowcount publicationid = con.insert_id() - print "INSERT INTO Publication: %d record: %d" % (rowcount, publicationid) + print(("INSERT INTO Publication: %d record: %d" % (rowcount, publicationid))) # data for index, strain in enumerate(strains): # @@ -158,14 +158,14 @@ def main(argv): cursor.execute(sql, (inbredsetid, phenotypeid, publicationid, dataid, "")) rowcount = cursor.rowcount publishxrefid = con.insert_id() - print "INSERT INTO PublishXRef: %d record: %d" % (rowcount, publishxrefid) + print(("INSERT INTO PublishXRef: %d record: %d" % (rowcount, publishxrefid))) # for loop next dataid += 1 - print + print() # release con.close() if __name__ == "__main__": - print "command line arguments:\n\t%s" % sys.argv + print(("command line arguments:\n\t%s" % sys.argv)) main(sys.argv) - print "exit successfully" + print("exit successfully") diff --git a/scripts/maintenance/readProbeSetMean_v7.py b/scripts/maintenance/readProbeSetMean_v7.py index e9c8f25c..e7a4c826 100755 --- a/scripts/maintenance/readProbeSetMean_v7.py +++ b/scripts/maintenance/readProbeSetMean_v7.py @@ -42,9 +42,9 @@ try: con = MySQLdb.Connect(db='db_webqtl',host='localhost', user='username',passwd=passwd) db = con.cursor() - print "You have successfully connected to mysql.\n" + print("You have successfully connected to mysql.\n") except: - print "You entered incorrect password.\n" + print("You entered incorrect password.\n") sys.exit(0) time0 = time.time() @@ -55,7 +55,7 @@ time0 = time.time() # generate the gene list of expression data here # ######################################################################### -print 'Checking if each line have same number of members' +print('Checking if each line have same number of members') GeneList = [] isCont = 1 @@ -70,7 +70,7 @@ while line: line2 = string.split(string.strip(line),'\t') line2 = map(string.strip, line2) if len(line2) != nfield: - print "Error : " + line + print(("Error : " + line)) isCont = 0 GeneList.append(line2[0]) @@ -78,7 +78,7 @@ while line: kj+=1 if kj%100000 == 0: - print 'checked ',kj,' lines' + print(('checked ',kj,' lines')) GeneList = map(string.lower, GeneList) GeneList.sort() @@ -87,14 +87,14 @@ if isCont==0: sys.exit(0) -print 'used ',time.time()-time0,' seconds' +print(('used ',time.time()-time0,' seconds')) ######################################################################### # # Check if each strain exist in database # generate the string id list of expression data here # ######################################################################### -print 'Checking if each strain exist in database' +print('Checking if each strain exist in database') isCont = 1 fp.seek(0) @@ -109,20 +109,20 @@ for item in header: db.execute('select Id from Strain where Name = "%s"' % item) Ids.append(db.fetchall()[0][0]) except: - print item,'does not exist, check the if the strain name is correct' + print((item,'does not exist, check the if the strain name is correct')) isCont=0 if isCont==0: sys.exit(0) -print 'used ',time.time()-time0,' seconds' +print(('used ',time.time()-time0,' seconds')) ######################################################################## # # Check if each ProbeSet exist in database # ######################################################################## -print 'Check if each ProbeSet exist in database' +print('Check if each ProbeSet exist in database') ##---- find PID is name or target ----## line = fp.readline() @@ -146,7 +146,7 @@ Names = [] for item in results: Names.append(item[0]) -print Names +print(Names) Names = map(string.lower, Names) @@ -170,7 +170,7 @@ while x<len(GeneList) and y<len(Names): y += 1 if x%100000==0: - print 'check Name, checked %d lines'%x + print(('check Name, checked %d lines'%x)) while x<len(GeneList): GeneList2.append(GeneList[x]) @@ -180,20 +180,20 @@ isCont=1 ferror = open("ProbeSetError.txt", "wb") for item in GeneList2: ferror.write(item + " doesn't exist \n") - print item, " doesn't exist, check if the ProbeSet name is correct" + print((item, " doesn't exist, check if the ProbeSet name is correct")) isCont = 0 if isCont==0: sys.exit(0) -print 'used ',time.time()-time0,' seconds' +print(('used ',time.time()-time0,' seconds')) ######################################################################### # # Insert data into database # ######################################################################### -print 'getting ProbeSet/Id' +print('getting ProbeSet/Id') #---- get Name/Id map ----# @@ -202,16 +202,16 @@ results = db.fetchall() NameIds = {} for item in results: NameIds[item[0]] = item[1] -print 'used ',time.time()-time0,' seconds' +print(('used ',time.time()-time0,' seconds')) -print 'inserting data' +print('inserting data') ##---- get old max dataId ----## db.execute('select max(Id) from ProbeSetData') maxDataId = int(db.fetchall()[0][0]) bmax = maxDataId -print "old_max = %d\n" % bmax +print(("old_max = %d\n" % bmax)) ##---- insert data ----## fp.seek(0) @@ -255,8 +255,8 @@ while line: values1=[] values2=[] - print 'Inserted ', kj,' lines' - print 'used ',time.time()-time0,' seconds' + print(('Inserted ', kj,' lines')) + print(('used ',time.time()-time0,' seconds')) line = fp.readline() diff --git a/scripts/maintenance/readProbeSetSE_v7.py b/scripts/maintenance/readProbeSetSE_v7.py index 0b15ce09..79ed455f 100755 --- a/scripts/maintenance/readProbeSetSE_v7.py +++ b/scripts/maintenance/readProbeSetSE_v7.py @@ -82,14 +82,14 @@ while line: line2 = map(string.strip, line2) if len(line2) != nfield: isCont = 0 - print("Error : " + line) + print(("Error : " + line)) GeneList.append(line2[0]) line = fp.readline() kj += 1 if kj % 100000 == 0: - print('checked ', kj, ' lines') + print(('checked ', kj, ' lines')) GeneList = map(string.lower, GeneList) GeneList.sort() @@ -98,7 +98,7 @@ if isCont == 0: sys.exit(0) -print('used ', time.time()-time0, ' seconds') +print(('used ', time.time()-time0, ' seconds')) ######################################################################### # # Check if each strain exist in database @@ -121,13 +121,13 @@ for item in header: Ids.append(db.fetchall()[0][0]) except: isCont = 0 - print(item, 'does not exist, check the if the strain name is correct') + print((item, 'does not exist, check the if the strain name is correct')) if isCont == 0: sys.exit(0) -print('used ', time.time()-time0, ' seconds') +print(('used ', time.time()-time0, ' seconds')) ######################################################################## # # Check if each ProbeSet exist in database @@ -178,7 +178,7 @@ while x < len(GeneList) and y < len(Names): y += 1 if x % 100000 == 0: - print('check Name, checked %d lines' % x) + print(('check Name, checked %d lines' % x)) while x < len(GeneList): GeneList2.append(GeneList[x]) @@ -190,12 +190,12 @@ for item in GeneList2: ferror.write(item + " doesn't exist \n") isCont = 0 - print(item, " doesn't exist") + print((item, " doesn't exist")) if isCont == 0: sys.exit(0) -print('used ', time.time()-time0, ' seconds') +print(('used ', time.time()-time0, ' seconds')) ############################# # Insert new Data into SE ############################ @@ -244,9 +244,9 @@ while line: DataValues = [] line = fp.readline() - print(CellId, " doesn't exist") - print('inserted ', kj, ' lines') - print('used ', time.time()-time0, ' seconds') + print((CellId, " doesn't exist")) + print(('inserted ', kj, ' lines')) + print(('used ', time.time()-time0, ' seconds')) if len(DataValues) > 0: DataValues = ','.join(DataValues) 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") |