From e49ef0954e111ace2044cced0a83b4d9dc00bc72 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Mon, 17 Aug 2020 20:45:08 +0300 Subject: Fix malformed docstring * wqflask/utility/Plot.py: Update docstring. --- wqflask/utility/Plot.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py index d4373412..82bf6070 100644 --- a/wqflask/utility/Plot.py +++ b/wqflask/utility/Plot.py @@ -97,7 +97,7 @@ def find_outliers(vals): >>> find_outliers([3.504, 5.234, 6.123, 7.234, 3.542, 5.341, 7.852, 4.555, 12.537]) (11.252500000000001, 0.5364999999999993) - >>> >>> find_outliers([9,12,15,17,31,50,7,5,6,8]) + >>> find_outliers([9,12,15,17,31,50,7,5,6,8]) (32.0, -8.0) If there are no vals, returns None for the upper and lower bounds, -- cgit v1.2.3 From af330a2aa7b36fd0cf8505eb20fa06d2ed58b86b Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Mon, 17 Aug 2020 17:41:58 +0300 Subject: Wrap print statements in parentheses --- scripts/maintenance/QTL_Reaper_v6.py | 6 ++-- .../Update_Case_Attributes_MySQL_tab.py | 2 +- scripts/maintenance/delete_genotypes.py | 14 ++++---- scripts/maintenance/delete_phenotypes.py | 14 ++++---- scripts/maintenance/load_genotypes.py | 16 ++++----- scripts/maintenance/load_phenotypes.py | 30 ++++++++-------- scripts/maintenance/readProbeSetMean_v7.py | 40 +++++++++++----------- scripts/maintenance/readProbeSetSE_v7.py | 22 ++++++------ wqflask/run_gunicorn.py | 2 +- wqflask/utility/startup_config.py | 4 +-- wqflask/utility/svg.py | 10 +++--- wqflask/utility/tools.py | 8 ++--- wqflask/wqflask/marker_regression/rqtl_mapping.py | 2 +- wqflask/wqflask/pbkdf2.py | 16 ++++----- wqflask/wqflask/views.py | 4 +-- wqflask/wqflask/wgcna/wgcna_analysis.py | 12 +++---- 16 files changed, 101 insertions(+), 101 deletions(-) (limited to 'wqflask') 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 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") -- cgit v1.2.3 From acdc611247c8eaccbba3dec00ad640e10a4c99b1 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Mon, 17 Aug 2020 21:45:04 +0300 Subject: Replace "<>" with "!=" * wqflask/utility/svg.py: Use "!=". The operator, "<>" is removed in Python3 --- wqflask/utility/svg.py | 196 ++++++++++++++++++++++++------------------------- 1 file changed, 98 insertions(+), 98 deletions(-) (limited to 'wqflask') diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py index 6285ea63..f737d2f2 100644 --- a/wqflask/utility/svg.py +++ b/wqflask/utility/svg.py @@ -97,7 +97,7 @@ use_dom_implementation=0 import exceptions -if use_dom_implementation<>0: +if use_dom_implementation!=0: try: from xml.dom import implementation from xml.dom.ext import PrettyPrint @@ -398,22 +398,22 @@ class rect(SVGelement): """ def __init__(self,x=None,y=None,width=None,height=None,fill=None,stroke=None,stroke_width=None,**args): if width==None or height==None: - if width<>None: raise ValueError, 'height is required' - if height<>None: raise ValueError, 'width is required' + if width!=None: + if height!=None: else: raise ValueError, 'both height and width are required' SVGelement.__init__(self,'rect',{'width':width,'height':height},**args) - if x<>None: + if x!=None: self.attributes['x']=x - if y<>None: + if y!=None: self.attributes['y']=y - if fill<>None: + if fill!=None: self.attributes['fill']=fill - if stroke<>None: + if stroke!=None: self.attributes['stroke']=stroke - if stroke_width<>None: + if stroke_width!=None: self.attributes['stroke-width']=stroke_width class ellipse(SVGelement): @@ -423,22 +423,22 @@ class ellipse(SVGelement): """ def __init__(self,cx=None,cy=None,rx=None,ry=None,fill=None,stroke=None,stroke_width=None,**args): if rx==None or ry== None: - if rx<>None: raise ValueError, 'rx is required' - if ry<>None: raise ValueError, 'ry is required' + if rx!=None: + if ry!=None: else: raise ValueError, 'both rx and ry are required' SVGelement.__init__(self,'ellipse',{'rx':rx,'ry':ry},**args) - if cx<>None: + if cx!=None: self.attributes['cx']=cx - if cy<>None: + if cy!=None: self.attributes['cy']=cy - if fill<>None: + if fill!=None: self.attributes['fill']=fill - if stroke<>None: + if stroke!=None: self.attributes['stroke']=stroke - if stroke_width<>None: + if stroke_width!=None: self.attributes['stroke-width']=stroke_width @@ -451,15 +451,15 @@ class circle(SVGelement): if r==None: raise ValueError, 'r is required' SVGelement.__init__(self,'circle',{'r':r},**args) - if cx<>None: + if cx!=None: self.attributes['cx']=cx - if cy<>None: + if cy!=None: self.attributes['cy']=cy - if fill<>None: + if fill!=None: self.attributes['fill']=fill - if stroke<>None: + if stroke!=None: self.attributes['stroke']=stroke - if stroke_width<>None: + if stroke_width!=None: self.attributes['stroke-width']=stroke_width class point(circle): @@ -478,17 +478,17 @@ class line(SVGelement): """ def __init__(self,x1=None,y1=None,x2=None,y2=None,stroke=None,stroke_width=None,**args): SVGelement.__init__(self,'line',**args) - if x1<>None: + if x1!=None: self.attributes['x1']=x1 - if y1<>None: + if y1!=None: self.attributes['y1']=y1 - if x2<>None: + if x2!=None: self.attributes['x2']=x2 - if y2<>None: + if y2!=None: self.attributes['y2']=y2 - if stroke_width<>None: + if stroke_width!=None: self.attributes['stroke-width']=stroke_width - if stroke<>None: + if stroke!=None: self.attributes['stroke']=stroke class polyline(SVGelement): @@ -498,11 +498,11 @@ class polyline(SVGelement): """ def __init__(self,points,fill=None,stroke=None,stroke_width=None,**args): SVGelement.__init__(self,'polyline',{'points':_xypointlist(points)},**args) - if fill<>None: + if fill!=None: self.attributes['fill']=fill - if stroke_width<>None: + if stroke_width!=None: self.attributes['stroke-width']=stroke_width - if stroke<>None: + if stroke!=None: self.attributes['stroke']=stroke class polygon(SVGelement): @@ -512,11 +512,11 @@ class polygon(SVGelement): """ def __init__(self,points,fill=None,stroke=None,stroke_width=None,**args): SVGelement.__init__(self,'polygon',{'points':_xypointlist(points)},**args) - if fill<>None: + if fill!=None: self.attributes['fill']=fill - if stroke_width<>None: + if stroke_width!=None: self.attributes['stroke-width']=stroke_width - if stroke<>None: + if stroke!=None: self.attributes['stroke']=stroke class path(SVGelement): @@ -526,13 +526,13 @@ class path(SVGelement): """ def __init__(self,pathdata,fill=None,stroke=None,stroke_width=None,id=None,**args): SVGelement.__init__(self,'path',{'d':str(pathdata)},**args) - if stroke<>None: + if stroke!=None: self.attributes['stroke']=stroke - if fill<>None: + if fill!=None: self.attributes['fill']=fill - if stroke_width<>None: + if stroke_width!=None: self.attributes['stroke-width']=stroke_width - if id<>None: + if id!=None: self.attributes['id']=id @@ -543,17 +543,17 @@ class text(SVGelement): """ def __init__(self,x=None,y=None,text=None,font_size=None,font_family=None,text_anchor=None,**args): SVGelement.__init__(self,'text',**args) - if x<>None: + if x!=None: self.attributes['x']=x - if y<>None: + if y!=None: self.attributes['y']=y - if font_size<>None: + if font_size!=None: self.attributes['font-size']=font_size - if font_family<>None: + if font_family!=None: self.attributes['font-family']=font_family - if text<>None: + if text!=None: self.text=text - if text_anchor<>None: + if text_anchor!=None: self.attributes['text-anchor']=text_anchor @@ -564,7 +564,7 @@ class textpath(SVGelement): """ def __init__(self,link,text=None,**args): SVGelement.__init__(self,'textPath',{'xlink:href':link},**args) - if text<>None: + if text!=None: self.text=text class pattern(SVGelement): @@ -576,15 +576,15 @@ class pattern(SVGelement): """ def __init__(self,x=None,y=None,width=None,height=None,patternUnits=None,**args): SVGelement.__init__(self,'pattern',**args) - if x<>None: + if x!=None: self.attributes['x']=x - if y<>None: + if y!=None: self.attributes['y']=y - if width<>None: + if width!=None: self.attributes['width']=width - if height<>None: + if height!=None: self.attributes['height']=height - if patternUnits<>None: + if patternUnits!=None: self.attributes['patternUnits']=patternUnits class title(SVGelement): @@ -595,7 +595,7 @@ class title(SVGelement): """ def __init__(self,text=None,**args): SVGelement.__init__(self,'title',**args) - if text<>None: + if text!=None: self.text=text class description(SVGelement): @@ -606,7 +606,7 @@ class description(SVGelement): """ def __init__(self,text=None,**args): SVGelement.__init__(self,'desc',**args) - if text<>None: + if text!=None: self.text=text class lineargradient(SVGelement): @@ -617,15 +617,15 @@ class lineargradient(SVGelement): """ def __init__(self,x1=None,y1=None,x2=None,y2=None,id=None,**args): SVGelement.__init__(self,'linearGradient',**args) - if x1<>None: + if x1!=None: self.attributes['x1']=x1 - if y1<>None: + if y1!=None: self.attributes['y1']=y1 - if x2<>None: + if x2!=None: self.attributes['x2']=x2 - if y2<>None: + if y2!=None: self.attributes['y2']=y2 - if id<>None: + if id!=None: self.attributes['id']=id class radialgradient(SVGelement): @@ -636,17 +636,17 @@ class radialgradient(SVGelement): """ def __init__(self,cx=None,cy=None,r=None,fx=None,fy=None,id=None,**args): SVGelement.__init__(self,'radialGradient',**args) - if cx<>None: + if cx!=None: self.attributes['cx']=cx - if cy<>None: + if cy!=None: self.attributes['cy']=cy - if r<>None: + if r!=None: self.attributes['r']=r - if fx<>None: + if fx!=None: self.attributes['fx']=fx - if fy<>None: + if fy!=None: self.attributes['fy']=fy - if id<>None: + if id!=None: self.attributes['id']=id class stop(SVGelement): @@ -656,7 +656,7 @@ class stop(SVGelement): """ def __init__(self,offset,stop_color=None,**args): SVGelement.__init__(self,'stop',{'offset':offset},**args) - if stop_color<>None: + if stop_color!=None: self.attributes['stop-color']=stop_color class style(SVGelement): @@ -675,16 +675,16 @@ class image(SVGelement): """ def __init__(self,url,x=None,y=None,width=None,height=None,**args): if width==None or height==None: - if width<>None: raise ValueError, 'height is required' - if height<>None: raise ValueError, 'width is required' + if width!=None: + if height!=None: else: raise ValueError, 'both height and width are required' SVGelement.__init__(self,'image',{'xlink:href':url,'width':width,'height':height},**args) - if x<>None: + if x!=None: self.attributes['x']=x - if y<>None: + if y!=None: self.attributes['y']=y class cursor(SVGelement): @@ -704,17 +704,17 @@ class marker(SVGelement): """ def __init__(self,id=None,viewBox=None,refx=None,refy=None,markerWidth=None,markerHeight=None,**args): SVGelement.__init__(self,'marker',**args) - if id<>None: + if id!=None: self.attributes['id']=id - if viewBox<>None: + if viewBox!=None: self.attributes['viewBox']=_viewboxlist(viewBox) - if refx<>None: + if refx!=None: self.attributes['refX']=refx - if refy<>None: + if refy!=None: self.attributes['refY']=refy - if markerWidth<>None: + if markerWidth!=None: self.attributes['markerWidth']=markerWidth - if markerHeight<>None: + if markerHeight!=None: self.attributes['markerHeight']=markerHeight class group(SVGelement): @@ -725,7 +725,7 @@ class group(SVGelement): """ def __init__(self,id=None,**args): SVGelement.__init__(self,'g',**args) - if id<>None: + if id!=None: self.attributes['id']=id class symbol(SVGelement): @@ -739,9 +739,9 @@ class symbol(SVGelement): def __init__(self,id=None,viewBox=None,**args): SVGelement.__init__(self,'symbol',**args) - if id<>None: + if id!=None: self.attributes['id']=id - if viewBox<>None: + if viewBox!=None: self.attributes['viewBox']=_viewboxlist(viewBox) class defs(SVGelement): @@ -770,14 +770,14 @@ class use(SVGelement): """ def __init__(self,link,x=None,y=None,width=None,height=None,**args): SVGelement.__init__(self,'use',{'xlink:href':link},**args) - if x<>None: + if x!=None: self.attributes['x']=x - if y<>None: + if y!=None: self.attributes['y']=y - if width<>None: + if width!=None: self.attributes['width']=width - if height<>None: + if height!=None: self.attributes['height']=height @@ -796,7 +796,7 @@ class view(SVGelement): a view can be used to create a view with different attributes""" def __init__(self,id=None,**args): SVGelement.__init__(self,'view',**args) - if id<>None: + if id!=None: self.attributes['id']=id class script(SVGelement): @@ -815,11 +815,11 @@ class animate(SVGelement): """ def __init__(self,attribute,fr=None,to=None,dur=None,**args): SVGelement.__init__(self,'animate',{'attributeName':attribute},**args) - if fr<>None: + if fr!=None: self.attributes['from']=fr - if to<>None: + if to!=None: self.attributes['to']=to - if dur<>None: + if dur!=None: self.attributes['dur']=dur class animateMotion(SVGelement): @@ -829,9 +829,9 @@ class animateMotion(SVGelement): """ def __init__(self,pathdata,dur,**args): SVGelement.__init__(self,'animateMotion',**args) - if pathdata<>None: + if pathdata!=None: self.attributes['path']=str(pathdata) - if dur<>None: + if dur!=None: self.attributes['dur']=dur class animateTransform(SVGelement): @@ -842,13 +842,13 @@ class animateTransform(SVGelement): def __init__(self,type=None,fr=None,to=None,dur=None,**args): SVGelement.__init__(self,'animateTransform',{'attributeName':'transform'},**args) #As far as I know the attributeName is always transform - if type<>None: + if type!=None: self.attributes['type']=type - if fr<>None: + if fr!=None: self.attributes['from']=fr - if to<>None: + if to!=None: self.attributes['to']=to - if dur<>None: + if dur!=None: self.attributes['dur']=dur class animateColor(SVGelement): """ac=animateColor(attribute,type,from,to,dur,**args) @@ -857,13 +857,13 @@ class animateColor(SVGelement): """ def __init__(self,attribute,type=None,fr=None,to=None,dur=None,**args): SVGelement.__init__(self,'animateColor',{'attributeName':attribute},**args) - if type<>None: + if type!=None: self.attributes['type']=type - if fr<>None: + if fr!=None: self.attributes['from']=fr - if to<>None: + if to!=None: self.attributes['to']=to - if dur<>None: + if dur!=None: self.attributes['dur']=dur class set(SVGelement): """st=set(attribute,to,during,**args) @@ -872,9 +872,9 @@ class set(SVGelement): """ def __init__(self,attribute,to=None,dur=None,**args): SVGelement.__init__(self,'set',{'attributeName':attribute},**args) - if to<>None: + if to!=None: self.attributes['to']=to - if dur<>None: + if dur!=None: self.attributes['dur']=dur @@ -896,11 +896,11 @@ class svg(SVGelement): """ def __init__(self,viewBox=None, width=None, height=None,**args): SVGelement.__init__(self,'svg',**args) - if viewBox<>None: + if viewBox!=None: self.attributes['viewBox']=_viewboxlist(viewBox) - if width<>None: + if width!=None: self.attributes['width']=width - if height<>None: + if height!=None: self.attributes['height']=height self.namespace="http://www.w3.org/2000/svg" -- cgit v1.2.3 From 4e10f4bd8fb902810ee033abb8d509ab641308e1 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 18 Aug 2020 17:09:51 +0300 Subject: Apply pep8 * wqflask/utility/svg.py: Apply pep8 to fix indentation error when running `2to3-3.8 -w .`: ```` RefactoringTool: Can't parse ./wqflask/utility/svg.py: IndentationError: unindent does not match any outer indentation level (, line 403) ```` --- wqflask/utility/svg.py | 321 ++++++++++++++++++++++++++++--------------------- 1 file changed, 184 insertions(+), 137 deletions(-) (limited to 'wqflask') diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py index f737d2f2..c850feb8 100644 --- a/wqflask/utility/svg.py +++ b/wqflask/utility/svg.py @@ -25,54 +25,56 @@ # Last updated by GeneNetwork Core Team 2010/10/20 #!/usr/bin/env python -##Copyright (c) 2002, Fedor Baart & Hans de Wit (Stichting Farmaceutische Kengetallen) -##All rights reserved. +# Copyright (c) 2002, Fedor Baart & Hans de Wit (Stichting Farmaceutische Kengetallen) +# All rights reserved. ## -##Redistribution and use in source and binary forms, with or without modification, -##are permitted provided that the following conditions are met: +# Redistribution and use in source and binary forms, with or without modification, +# are permitted provided that the following conditions are met: ## -##Redistributions of source code must retain the above copyright notice, this -##list of conditions and the following disclaimer. +# Redistributions of source code must retain the above copyright notice, this +# list of conditions and the following disclaimer. ## -##Redistributions in binary form must reproduce the above copyright notice, -##this list of conditions and the following disclaimer in the documentation and/or -##other materials provided with the distribution. +# Redistributions in binary form must reproduce the above copyright notice, +# this list of conditions and the following disclaimer in the documentation and/or +# other materials provided with the distribution. ## -##Neither the name of the Stichting Farmaceutische Kengetallen nor the names of -##its contributors may be used to endorse or promote products derived from this -##software without specific prior written permission. +# Neither the name of the Stichting Farmaceutische Kengetallen nor the names of +# its contributors may be used to endorse or promote products derived from this +# software without specific prior written permission. ## -##THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" -##AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -##IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -##DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE -##FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL -##DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR -##SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER -##CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, -##OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE -##OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE +# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +# Thanks to Gerald Rosennfellner for his help and useful comments. -##Thanks to Gerald Rosennfellner for his help and useful comments. - -__doc__="""Use SVGdraw to generate your SVGdrawings. +import sys +import exceptions +__doc__ = """Use SVGdraw to generate your SVGdrawings. SVGdraw uses an object model drawing and a method toXML to create SVG graphics by using easy to use classes and methods usualy you start by creating a drawing eg d=drawing() - #then you create a SVG root element + # then you create a SVG root element s=svg() - #then you add some elements eg a circle and add it to the svg root element + # then you add some elements eg a circle and add it to the svg root element c=circle() - #you can supply attributes by using named arguments. + # you can supply attributes by using named arguments. c=circle(fill='red',stroke='blue') - #or by updating the attributes attribute: + # or by updating the attributes attribute: c.attributes['stroke-width']=1 s.addElement(c) - #then you add the svg root element to the drawing + # then you add the svg root element to the drawing d.setSVG(s) - #and finaly you xmlify the drawing + # and finaly you xmlify the drawing d.toXml() @@ -82,7 +84,7 @@ This module was created using the SVG specification of www.w3c.org and the O'Reilly (www.oreilly.com) python books as information sources. A svg viewer is available from www.adobe.com""" -__version__="1.0" +__version__ = "1.0" # there are two possibilities to generate svg: # via a dom implementation and directly using text strings @@ -93,33 +95,34 @@ __version__="1.0" # Note that PyXML is required for using the dom implementation. # It is also possible to use the standard minidom. But I didn't try that one. # Anyway the text based approach is about 60 times faster than using the full dom implementation. -use_dom_implementation=0 +use_dom_implementation = 0 -import exceptions -if use_dom_implementation!=0: +if use_dom_implementation != 0: try: from xml.dom import implementation from xml.dom.ext import PrettyPrint except: - 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 + 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 + +assert sys.version_info[0] >= 2 +if sys.version_info[1] < 2: + True = 1 + False = 0 + file = open + +sys.setrecursionlimit = 50 +# The recursion limit is set conservative so mistakes like s=svg() s.addElement(s) +# won't eat up too much processor time. + +# the following code is pasted form xml.sax.saxutils +# it makes it possible to run the code without the xml sax package installed +# To make it possible to have in your text elements, it is necessary to escape the texts + -import sys -assert sys.version_info[0]>=2 -if sys.version_info[1]<2: - True=1 - False=0 - file=open - -sys.setrecursionlimit=50 -#The recursion limit is set conservative so mistakes like s=svg() s.addElement(s) -#won't eat up too much processor time. - -#the following code is pasted form xml.sax.saxutils -#it makes it possible to run the code without the xml sax package installed -#To make it possible to have in your text elements, it is necessary to escape the texts def _escape(data, entities={}): """Escape &, <, and > in a string of data. @@ -127,13 +130,14 @@ def _escape(data, entities={}): the optional entities parameter. The keys and values must all be strings; each key will be replaced with its corresponding value. """ - #data = data.replace("&", "&") + # data = data.replace("&", "&") data = data.replace("<", "<") data = data.replace(">", ">") for chars, entity in entities.items(): data = data.replace(chars, entity) return data + def _quoteattr(data, entities={}): """Escape and quote an attribute value. @@ -156,96 +160,121 @@ def _quoteattr(data, entities={}): return data - def _xypointlist(a): """formats a list of xy pairs""" - s='' - for e in a: #this could be done more elegant - s+=str(e)[1:-1] +' ' + s = '' + for e in a: # this could be done more elegant + s += str(e)[1:-1] + ' ' return s + def _viewboxlist(a): """formats a tuple""" - s='' + s = '' for e in a: - s+=str(e)+' ' + s += str(e)+' ' return s + def _pointlist(a): """formats a list of numbers""" return str(a)[1:-1] + class pathdata: """class used to create a pathdata object which can be used for a path. although most methods are pretty straightforward it might be useful to look at the SVG specification.""" - #I didn't test the methods below. - def __init__(self,x=None,y=None): - self.path=[] + # I didn't test the methods below. + + def __init__(self, x=None, y=None): + self.path = [] if x is not None and y is not None: self.path.append('M '+str(x)+' '+str(y)) + def closepath(self): """ends the path""" self.path.append('z') - def move(self,x,y): + + def move(self, x, y): """move to absolute""" self.path.append('M '+str(x)+' '+str(y)) - def relmove(self,x,y): + + def relmove(self, x, y): """move to relative""" self.path.append('m '+str(x)+' '+str(y)) - def line(self,x,y): + + def line(self, x, y): """line to absolute""" self.path.append('L '+str(x)+' '+str(y)) - def relline(self,x,y): + + def relline(self, x, y): """line to relative""" self.path.append('l '+str(x)+' '+str(y)) - def hline(self,x): + + def hline(self, x): """horizontal line to absolute""" self.path.append('H'+str(x)) - def relhline(self,x): + + def relhline(self, x): """horizontal line to relative""" self.path.append('h'+str(x)) - def vline(self,y): + + def vline(self, y): """verical line to absolute""" self.path.append('V'+str(y)) - def relvline(self,y): + + def relvline(self, y): """vertical line to relative""" self.path.append('v'+str(y)) - def bezier(self,x1,y1,x2,y2,x,y): + + def bezier(self, x1, y1, x2, y2, x, y): """bezier with xy1 and xy2 to xy absolut""" - self.path.append('C'+str(x1)+','+str(y1)+' '+str(x2)+','+str(y2)+' '+str(x)+','+str(y)) - def relbezier(self,x1,y1,x2,y2,x,y): + self.path.append('C'+str(x1)+','+str(y1)+' '+str(x2) + + ','+str(y2)+' '+str(x)+','+str(y)) + + def relbezier(self, x1, y1, x2, y2, x, y): """bezier with xy1 and xy2 to xy relative""" - self.path.append('c'+str(x1)+','+str(y1)+' '+str(x2)+','+str(y2)+' '+str(x)+','+str(y)) - def smbezier(self,x2,y2,x,y): + self.path.append('c'+str(x1)+','+str(y1)+' '+str(x2) + + ','+str(y2)+' '+str(x)+','+str(y)) + + def smbezier(self, x2, y2, x, y): """smooth bezier with xy2 to xy absolut""" self.path.append('S'+str(x2)+','+str(y2)+' '+str(x)+','+str(y)) - def relsmbezier(self,x2,y2,x,y): + + def relsmbezier(self, x2, y2, x, y): """smooth bezier with xy2 to xy relative""" self.path.append('s'+str(x2)+','+str(y2)+' '+str(x)+','+str(y)) - def qbezier(self,x1,y1,x,y): + + def qbezier(self, x1, y1, x, y): """quadratic bezier with xy1 to xy absolut""" self.path.append('Q'+str(x1)+','+str(y1)+' '+str(x)+','+str(y)) - def relqbezier(self,x1,y1,x,y): + + def relqbezier(self, x1, y1, x, y): """quadratic bezier with xy1 to xy relative""" self.path.append('q'+str(x1)+','+str(y1)+' '+str(x)+','+str(y)) - def smqbezier(self,x,y): + + def smqbezier(self, x, y): """smooth quadratic bezier to xy absolut""" self.path.append('T'+str(x)+','+str(y)) - def relsmqbezier(self,x,y): + + def relsmqbezier(self, x, y): """smooth quadratic bezier to xy relative""" self.path.append('t'+str(x)+','+str(y)) - def ellarc(self,rx,ry,xrot,laf,sf,x,y): + + def ellarc(self, rx, ry, xrot, laf, sf, x, y): """elliptival arc with rx and ry rotating with xrot using large-arc-flag and sweep-flag to xy absolut""" - self.path.append('A'+str(rx)+','+str(ry)+' '+str(xrot)+' '+str(laf)+' '+str(sf)+' '+str(x)+' '+str(y)) - def relellarc(self,rx,ry,xrot,laf,sf,x,y): + self.path.append('A'+str(rx)+','+str(ry)+' '+str(xrot) + + ' '+str(laf)+' '+str(sf)+' '+str(x)+' '+str(y)) + + def relellarc(self, rx, ry, xrot, laf, sf, x, y): """elliptival arc with rx and ry rotating with xrot using large-arc-flag and sweep-flag to xy relative""" - self.path.append('a'+str(rx)+','+str(ry)+' '+str(xrot)+' '+str(laf)+' '+str(sf)+' '+str(x)+' '+str(y)) + self.path.append('a'+str(rx)+','+str(ry)+' '+str(xrot) + + ' '+str(laf)+' '+str(sf)+' '+str(x)+' '+str(y)) + def __repr__(self): return ' '.join(self.path) - - class SVGelement: """SVGelement(type,attributes,elements,text,namespace,**args) Creates a arbitrary svg element and is intended to be subclassed not used on its own. @@ -256,52 +285,56 @@ class SVGelement: namespace. Note the elements==None, if elements = None:self.elements=[] construction. This is done because if you default to elements=[] every object has a reference to the same empty list.""" - def __init__(self,type='',attributes=None,elements=None,text='',namespace='',cdata=None, **args): - self.type=type - if attributes==None: - self.attributes={} + + def __init__(self, type='', attributes=None, elements=None, text='', namespace='', cdata=None, **args): + self.type = type + if attributes == None: + self.attributes = {} else: - self.attributes=attributes - if elements==None: - self.elements=[] + self.attributes = attributes + if elements == None: + self.elements = [] else: - self.elements=elements - self.text=text - self.namespace=namespace - self.cdata=cdata + self.elements = elements + self.text = text + self.namespace = namespace + self.cdata = cdata for arg in args.keys(): arg2 = arg.replace("__", ":") arg2 = arg2.replace("_", "-") - self.attributes[arg2]=args[arg] - def addElement(self,SVGelement): + self.attributes[arg2] = args[arg] + + def addElement(self, SVGelement): """adds an element to a SVGelement SVGelement.addElement(SVGelement) """ self.elements.append(SVGelement) - def toXml(self,level,f): + def toXml(self, level, f): f.write('\t'*level) f.write('<'+self.type) for attkey in self.attributes.keys(): - f.write(' '+_escape(str(attkey))+'='+_quoteattr(str(self.attributes[attkey]))) + f.write(' '+_escape(str(attkey))+'=' + + _quoteattr(str(self.attributes[attkey]))) if self.namespace: - f.write(' xmlns="'+ _escape(str(self.namespace))+'" xmlns:xlink="http://www.w3.org/1999/xlink"') + f.write(' xmlns="' + _escape(str(self.namespace)) + + '" xmlns:xlink="http://www.w3.org/1999/xlink"') if self.elements or self.text or self.cdata: f.write('>') if self.elements: f.write('\n') for element in self.elements: - element.toXml(level+1,f) + element.toXml(level+1, f) if self.cdata: f.write('\n'+'\t'*(level+1)+'\n') if self.text: - if type(self.text)==type(''): #If the text is only text + if type(self.text) == type(''): # If the text is only text f.write(_escape(str(self.text))) - else: #If the text is a spannedtext class + else: # If the text is a spannedtext class f.write(str(self.text)) if self.elements: f.write('\t'*level+'\n') @@ -312,6 +345,7 @@ class SVGelement: else: f.write('/>\n') + class tspan(SVGelement): """ts=tspan(text='',**args) @@ -323,19 +357,22 @@ class tspan(SVGelement): st.addtspan(ts) t=text(3,5,st) """ - def __init__(self,text=None,**args): - SVGelement.__init__(self,'tspan',**args) - if self.text<>None: - self.text=text + + def __init__(self, text=None, **args): + SVGelement.__init__(self, 'tspan', **args) + if self.text <> None: + self.text = text + def __repr__(self): - s=" --- scripts/maintenance/QTL_Reaper_v6.py | 2 +- scripts/maintenance/readProbeSetMean_v7.py | 16 ++++++++-------- scripts/maintenance/readProbeSetSE_v7.py | 16 ++++++++-------- test/requests/link_checker.py | 3 +-- wqflask/utility/webqtlUtil.py | 2 +- wqflask/wqflask/api/router.py | 2 +- wqflask/wqflask/correlation_matrix/show_corr_matrix.py | 4 ++-- wqflask/wqflask/export_traits.py | 2 +- wqflask/wqflask/interval_analyst/GeneUtil.py | 2 +- .../wqflask/marker_regression/display_mapping_results.py | 10 +++++----- wqflask/wqflask/marker_regression/plink_mapping.py | 4 ++-- wqflask/wqflask/pbkdf2.py | 2 +- wqflask/wqflask/snp_browser/snp_browser.py | 6 +++--- 13 files changed, 35 insertions(+), 36 deletions(-) (limited to 'wqflask') diff --git a/scripts/maintenance/QTL_Reaper_v6.py b/scripts/maintenance/QTL_Reaper_v6.py index 7fb56eca..2fbeb53b 100755 --- a/scripts/maintenance/QTL_Reaper_v6.py +++ b/scripts/maintenance/QTL_Reaper_v6.py @@ -23,7 +23,7 @@ for item in results: ProbeSetFreezeIds=sys.argv[1:] if ProbeSetFreezeIds: #####convert the Ids to integer - ProbeSetFreezeIds=map(int, ProbeSetFreezeIds) + ProbeSetFreezeIds=list(map(int, ProbeSetFreezeIds)) else: #####get all of the dataset that need be updated diff --git a/scripts/maintenance/readProbeSetMean_v7.py b/scripts/maintenance/readProbeSetMean_v7.py index fea26731..97767715 100755 --- a/scripts/maintenance/readProbeSetMean_v7.py +++ b/scripts/maintenance/readProbeSetMean_v7.py @@ -61,14 +61,14 @@ GeneList = [] isCont = 1 header = fp.readline() header = string.split(string.strip(header),'\t') -header = map(string.strip, header) +header = list(map(string.strip, header)) nfield = len(header) line = fp.readline() kj=0 while line: line2 = string.split(string.strip(line),'\t') - line2 = map(string.strip, line2) + line2 = list(map(string.strip, line2)) if len(line2) != nfield: print(("Error : " + line)) isCont = 0 @@ -80,7 +80,7 @@ while line: if kj%100000 == 0: print(('checked ',kj,' lines')) -GeneList = map(string.lower, GeneList) +GeneList = list(map(string.lower, GeneList)) GeneList.sort() if isCont==0: @@ -100,8 +100,8 @@ isCont = 1 fp.seek(0) header = fp.readline() header = string.split(string.strip(header),'\t') -header = map(string.strip, header) -header = map(translateAlias, header) +header = list(map(string.strip, header)) +header = list(map(translateAlias, header)) header = header[dataStart:] Ids = [] for item in header: @@ -128,7 +128,7 @@ print('Check if each ProbeSet exist in database') line = fp.readline() line = fp.readline() line2 = string.split(string.strip(line),'\t') -line2 = map(string.strip, line2) +line2 = list(map(string.strip, line2)) PId = line2[0] db.execute('select Id from ProbeSet where Name="%s" and ChipId=%d' % (PId, GeneChipId) ) @@ -148,7 +148,7 @@ for item in results: print(Names) -Names = map(string.lower, Names) +Names = list(map(string.lower, Names)) Names.sort() # -- Fixed the lower case problem of ProbeSets affx-mur_b2_at doesn't exist --# @@ -223,7 +223,7 @@ values1 = [] values2 = [] while line: line2 = string.split(string.strip(line),'\t') - line2 = map(string.strip, line2) + line2 = list(map(string.strip, line2)) PId = line2[0] recordId = NameIds[PId] diff --git a/scripts/maintenance/readProbeSetSE_v7.py b/scripts/maintenance/readProbeSetSE_v7.py index 79ed455f..7b2fee87 100755 --- a/scripts/maintenance/readProbeSetSE_v7.py +++ b/scripts/maintenance/readProbeSetSE_v7.py @@ -72,14 +72,14 @@ GeneList = [] isCont = 1 header = fp.readline() header = string.split(string.strip(header), '\t') -header = map(string.strip, header) +header = list(map(string.strip, header)) nfield = len(header) line = fp.readline() kj = 0 while line: line2 = string.split(string.strip(line), '\t') - line2 = map(string.strip, line2) + line2 = list(map(string.strip, line2)) if len(line2) != nfield: isCont = 0 print(("Error : " + line)) @@ -91,7 +91,7 @@ while line: if kj % 100000 == 0: print(('checked ', kj, ' lines')) -GeneList = map(string.lower, GeneList) +GeneList = list(map(string.lower, GeneList)) GeneList.sort() if isCont == 0: @@ -111,8 +111,8 @@ isCont = 1 fp.seek(0) header = fp.readline() header = string.split(string.strip(header), '\t') -header = map(string.strip, header) -header = map(translateAlias, header) +header = list(map(string.strip, header)) +header = list(map(translateAlias, header)) header = header[dataStart:] Ids = [] for item in header: @@ -139,7 +139,7 @@ print('Check if each ProbeSet exist in database') line = fp.readline() line = fp.readline() line2 = string.split(string.strip(line), '\t') -line2 = map(string.strip, line2) +line2 = list(map(string.strip, line2)) PId = line2[0] db.execute('select Id from ProbeSet where Name="%s" and ChipId=%d' % @@ -158,7 +158,7 @@ results = db.fetchall() Names = [] for item in results: Names.append(item[0]) - Names = map(string.lower, Names) + Names = list(map(string.lower, Names)) Names.sort() # -- Fixed the lower case problem of ProbeSets affx-mur_b2_at doesn't exist --# ##---- compare genelist with names ----## @@ -220,7 +220,7 @@ line = fp.readline() kj = 0 while line: line2 = string.split(string.strip(line), '\t') - line2 = map(string.strip, line2) + line2 = list(map(string.strip, line2)) CellId = line2[0] if not ProbeNameId.has_key(CellId): diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py index 715f330c..df4d32d8 100644 --- a/test/requests/link_checker.py +++ b/test/requests/link_checker.py @@ -27,8 +27,7 @@ def get_links(doc): lambda x: not ( is_root_link(x) or is_mailto_link(x)) - , map(lambda y: y.get("href") - , doc.cssselect("a"))) + , [y.get("href") for y in doc.cssselect("a")]) def verify_link(link): if link[0] == "#": diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py index 53661ae4..79991149 100644 --- a/wqflask/utility/webqtlUtil.py +++ b/wqflask/utility/webqtlUtil.py @@ -107,7 +107,7 @@ def hasAccessToConfidentialPhenotypeTrait(privilege, userName, authorized_users) if webqtlConfig.USERDICT[privilege] > webqtlConfig.USERDICT['user']: access_to_confidential_phenotype_trait = 1 else: - AuthorizedUsersList=map(string.strip, string.split(authorized_users, ',')) + AuthorizedUsersList=list(map(string.strip, string.split(authorized_users, ','))) if AuthorizedUsersList.__contains__(userName): access_to_confidential_phenotype_trait = 1 return access_to_confidential_phenotype_trait \ No newline at end of file diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py index 6324cabe..3fa1d5ba 100644 --- a/wqflask/wqflask/api/router.py +++ b/wqflask/wqflask/api/router.py @@ -517,7 +517,7 @@ def all_sample_data(dataset_name, file_format = "csv"): line_list.append("x") results_list.append(line_list) - results_list = map(list, zip(*results_list)) + results_list = list(map(list, zip(*results_list))) si = StringIO.StringIO() csv_writer = csv.writer(si) diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index 0ac94139..a912344f 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -278,7 +278,7 @@ def zScore(trait_data_array): stdev = math.sqrt(var/(N-1)) if stdev == 0: stdev = 1e-100 - data2 = map(lambda x:(x-mean)/stdev,data) + data2 = [(x-mean)/stdev for x in data] trait_data_array[i] = data2 i += 1 return trait_data_array @@ -299,7 +299,7 @@ def sortEigenVectors(vector): A.append(item[0]) B.append(item[1]) sum = reduce(lambda x,y: x+y, A, 0.0) - A = map(lambda x:x*100.0/sum, A) + A = [x*100.0/sum for x in A] return [A, B] except: return [] \ No newline at end of file diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py index 3272c03d..6646cc36 100644 --- a/wqflask/wqflask/export_traits.py +++ b/wqflask/wqflask/export_traits.py @@ -122,7 +122,7 @@ def export_search_results_csv(targs): csv_rows.append(row_contents) - csv_rows = map(list, itertools.izip_longest(*[row for row in csv_rows])) + csv_rows = list(map(list, itertools.izip_longest(*[row for row in csv_rows]))) writer.writerows(csv_rows) csv_data = buff.getvalue() buff.close() diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py index 2c60dd70..273168a8 100644 --- a/wqflask/wqflask/interval_analyst/GeneUtil.py +++ b/wqflask/wqflask/interval_analyst/GeneUtil.py @@ -24,7 +24,7 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'): ##List current Species and other Species speciesId = speciesDict[species] - otherSpecies = map(lambda X: [X, speciesDict[X]], speciesDict.keys()) + otherSpecies = [[X, speciesDict[X]] for X in speciesDict.keys()] otherSpecies.remove([species, speciesId]) results = g.db.execute(""" diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index bda899fb..7b6e70d2 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -389,9 +389,9 @@ class DisplayMappingResults(object): Chr_Length.Name in (%s) Order by Chr_Length.OrderId - """ % (self.dataset.group.name, string.join(map(lambda X: "'%s'" % X[0], self.ChrList[1:]), ", "))) + """ % (self.dataset.group.name, string.join(["'%s'" % X[0] for X in self.ChrList[1:]], ", "))) - self.ChrLengthMbList = map(lambda x: x[0]/1000000.0, self.ChrLengthMbList) + self.ChrLengthMbList = [x[0]/1000000.0 for x in self.ChrLengthMbList] self.ChrLengthMbSum = reduce(lambda x, y:x+y, self.ChrLengthMbList, 0.0) if self.ChrLengthMbList: self.MbGraphInterval = self.ChrLengthMbSum/(len(self.ChrLengthMbList)*12) #Empirical Mb interval @@ -1147,8 +1147,8 @@ class DisplayMappingResults(object): tenPercentLength = geneLength*0.0001 SNPdensity = theGO["snpCount"]/geneLength - exonStarts = map(float, theGO['exonStarts'].split(",")[:-1]) - exonEnds = map(float, theGO['exonEnds'].split(",")[:-1]) + exonStarts = list(map(float, theGO['exonStarts'].split(",")[:-1])) + exonEnds = list(map(float, theGO['exonEnds'].split(",")[:-1])) cdsStart = theGO['cdsStart'] cdsEnd = theGO['cdsEnd'] accession = theGO['NM_ID'] @@ -2145,7 +2145,7 @@ class DisplayMappingResults(object): lrsEdgeWidth = 1 else: if self.additiveChecked: - additiveMax = max(map(lambda X : abs(X['additive']), self.qtlresults)) + additiveMax = max([abs(X['additive']) for X in self.qtlresults]) lrsEdgeWidth = 3 if zoom == 2: diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py index 2f327faf..9571015e 100644 --- a/wqflask/wqflask/marker_regression/plink_mapping.py +++ b/wqflask/wqflask/marker_regression/plink_mapping.py @@ -84,7 +84,7 @@ def get_samples_from_ped_file(dataset): while line: lineList = string.split(string.strip(line), '\t') - lineList = map(string.strip, lineList) + lineList = list(map(string.strip, lineList)) sample_name = lineList[0] sample_list.append(sample_name) @@ -157,6 +157,6 @@ def parse_plink_output(output_filename, species): def build_line_list(line=None): line_list = string.split(string.strip(line),' ')# irregular number of whitespaces between columns line_list = [item for item in line_list if item <>''] - line_list = map(string.strip, line_list) + line_list = list(map(string.strip, line_list)) return line_list \ No newline at end of file diff --git a/wqflask/wqflask/pbkdf2.py b/wqflask/wqflask/pbkdf2.py index 811c83b0..731c8843 100644 --- a/wqflask/wqflask/pbkdf2.py +++ b/wqflask/wqflask/pbkdf2.py @@ -66,7 +66,7 @@ def pbkdf2_bin(data, salt, iterations=1000, keylen=24, hashfunc=None): def _pseudorandom(x, mac=mac): h = mac.copy() h.update(x) - return map(ord, h.digest()) + return list(map(ord, h.digest())) buf = [] for block in xrange(1, -(-keylen // mac.digest_size) + 1): rv = u = _pseudorandom(salt + _pack_int(block)) diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py index 1d28d76a..b18bfc62 100644 --- a/wqflask/wqflask/snp_browser/snp_browser.py +++ b/wqflask/wqflask/snp_browser/snp_browser.py @@ -459,7 +459,7 @@ class SnpBrowser(object): function_list = [] if function_details: function_list = string.split(string.strip(function_details), ",") - function_list = map(string.strip, function_list) + function_list = list(map(string.strip, function_list)) function_list[0] = function_list[0].title() function_details = ", ".join(item for item in function_list) function_details = function_details.replace("_", " ") @@ -725,11 +725,11 @@ def get_effect_details_by_category(effect_name = None, effect_value = None): codon_effect_group_list = ['Start Lost', 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous'] effect_detail_list = string.split(string.strip(effect_value), '|') - effect_detail_list = map(string.strip, effect_detail_list) + effect_detail_list = list(map(string.strip, effect_detail_list)) for index, item in enumerate(effect_detail_list): item_list = string.split(string.strip(item), ',') - item_list = map(string.strip, item_list) + item_list = list(map(string.strip, item_list)) gene_id = item_list[0] gene_name = item_list[1] -- cgit v1.2.3 From bafbb5b7a4b7db2ca230f292eb45be7e67985259 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 19 Aug 2020 02:05:05 +0300 Subject: Remove erroneous `if .. else` branch * wqflask/utility/svg.py [roct, ellipse, SVGelement]: Raise only a single value error if either height or width is not defined. Fixes parsing error when running `2to3-3.8 -f apply -w .` --- wqflask/utility/svg.py | 23 +++++------------------ 1 file changed, 5 insertions(+), 18 deletions(-) (limited to 'wqflask') diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py index c850feb8..d66c954e 100644 --- a/wqflask/utility/svg.py +++ b/wqflask/utility/svg.py @@ -445,12 +445,8 @@ class rect(SVGelement): def __init__(self, x=None, y=None, width=None, height=None, fill=None, stroke=None, stroke_width=None, **args): if width == None or height == None: - raise ValueError, 'height is required' - raise ValueError, 'width is required' - if width!=None: - if height!=None: - else: - raise ValueError, 'both height and width are required' + raise ValueError, 'both height and width are required' + SVGelement.__init__(self,'rect',{'width':width,'height':height},**args) if x!=None: self.attributes['x']=x @@ -470,12 +466,8 @@ class ellipse(SVGelement): """ def __init__(self,cx=None,cy=None,rx=None,ry=None,fill=None,stroke=None,stroke_width=None,**args): if rx==None or ry== None: - raise ValueError, 'rx is required' - raise ValueError, 'ry is required' - if rx!=None: - if ry!=None: - else: - raise ValueError, 'both rx and ry are required' + raise ValueError, 'both rx and ry are required' + SVGelement.__init__(self,'ellipse',{'rx':rx,'ry':ry},**args) if cx!=None: self.attributes['cx']=cx @@ -722,12 +714,7 @@ class image(SVGelement): """ def __init__(self,url,x=None,y=None,width=None,height=None,**args): if width==None or height==None: - raise ValueError, 'height is required' - raise ValueError, 'width is required' - if width!=None: - if height!=None: - else: - raise ValueError, 'both height and width are required' + raise ValueError, 'both height and width are required' SVGelement.__init__(self,'image',{'xlink:href':url,'width':width,'height':height},**args) if x!=None: self.attributes['x']=x -- cgit v1.2.3 From ba123e1e0fe693f9778993c3f8e5a70a28658a4c Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 19 Aug 2020 02:31:31 +0300 Subject: Fix dictionary iteration methods Run `2to3-3.8 -f dict -w .` See: and --- scripts/maintenance/load_genotypes.py | 4 +-- wqflask/base/GeneralObject.py | 8 ++--- wqflask/base/trait.py | 4 +-- wqflask/maintenance/gen_select_dataset.py | 6 ++-- .../maintenance/generate_probesetfreeze_file.py | 2 +- wqflask/utility/__init__.py | 4 +-- wqflask/utility/benchmark.py | 4 +-- wqflask/utility/gen_geno_ob.py | 2 +- wqflask/utility/helper_functions.py | 2 +- wqflask/utility/svg.py | 14 ++++---- wqflask/utility/temp_data.py | 2 +- wqflask/utility/tools.py | 2 +- wqflask/wqflask/api/correlation.py | 16 ++++----- wqflask/wqflask/api/gen_menu.py | 6 ++-- wqflask/wqflask/correlation/corr_scatter_plot.py | 6 ++-- wqflask/wqflask/correlation/show_corr_results.py | 30 ++++++++--------- wqflask/wqflask/ctl/ctl_analysis.py | 2 +- wqflask/wqflask/export_traits.py | 4 +-- wqflask/wqflask/heatmap/heatmap.py | 4 +-- wqflask/wqflask/interval_analyst/GeneUtil.py | 2 +- .../marker_regression/display_mapping_results.py | 38 +++++++++++----------- wqflask/wqflask/marker_regression/run_mapping.py | 24 +++++++------- wqflask/wqflask/resource_manager.py | 2 +- wqflask/wqflask/show_trait/export_trait_data.py | 2 +- wqflask/wqflask/show_trait/show_trait.py | 8 ++--- wqflask/wqflask/views.py | 6 ++-- 26 files changed, 102 insertions(+), 102 deletions(-) (limited to 'wqflask') diff --git a/scripts/maintenance/load_genotypes.py b/scripts/maintenance/load_genotypes.py index c235a31f..51278d48 100755 --- a/scripts/maintenance/load_genotypes.py +++ b/scripts/maintenance/load_genotypes.py @@ -19,7 +19,7 @@ def fetch_parameters(config): config_dic['dataid'] = datastructure.get_nextdataid_genotype() config_dic['genofile'] = config.get('config', 'genofile') print("config dictionary:") - for k, v in config_dic.items(): + for k, v in list(config_dic.items()): print(("\t%s: %s" % (k, v))) return config_dic @@ -42,7 +42,7 @@ def parse_genofile(config, config_dic): if line.lower().startswith("chr"): # print("geno file meta dictionary:") - for k, v in meta_dic.items(): + for k, v in list(meta_dic.items()): print(("\t%s: %s" % (k, v))) # print(("geno file head:\n\t%s" % line)) diff --git a/wqflask/base/GeneralObject.py b/wqflask/base/GeneralObject.py index 0fccaab3..707569db 100644 --- a/wqflask/base/GeneralObject.py +++ b/wqflask/base/GeneralObject.py @@ -33,7 +33,7 @@ class GeneralObject: def __init__(self, *args, **kw): self.contents = list(args) - for name, value in kw.items(): + for name, value in list(kw.items()): setattr(self, name, value) def __setitem__(self, key, value): @@ -50,16 +50,16 @@ class GeneralObject: def __str__(self): s = '' - for key in self.__dict__.keys(): + for key in list(self.__dict__.keys()): if key != 'contents': s += '%s = %s\n' % (key, self.__dict__[key]) return s def __repr__(self): s = '' - for key in self.__dict__.keys(): + for key in list(self.__dict__.keys()): s += '%s = %s\n' % (key, self.__dict__[key]) return s def __cmp__(self, other): - return len(self.__dict__.keys()).__cmp__(len(other.__dict__.keys())) + return len(list(self.__dict__.keys())).__cmp__(len(list(other.__dict__.keys()))) diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 7666348e..e82df226 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -118,7 +118,7 @@ class GeneralTrait(object): vals = [] the_vars = [] sample_aliases = [] - for sample_name, sample_data in self.data.items(): + for sample_name, sample_data in list(self.data.items()): if sample_data.value != None: if not include_variance or sample_data.variance != None: samples.append(sample_name) @@ -260,7 +260,7 @@ def get_sample_data(): trait_dict['pubmed_link'] = trait_ob.pubmed_link trait_dict['pubmed_text'] = trait_ob.pubmed_text - return json.dumps([trait_dict, {key: value.value for key, value in trait_ob.data.iteritems() }]) + return json.dumps([trait_dict, {key: value.value for key, value in list(trait_ob.data.items()) }]) else: return None diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index 647e58a2..78217587 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -108,7 +108,7 @@ def get_types(groups): """Build types list""" types = {} #print("Groups: ", pf(groups)) - for species, group_dict in groups.iteritems(): + for species, group_dict in list(groups.items()): types[species] = {} for group_name, _group_full_name in group_dict: # make group an alias to shorten the code @@ -195,9 +195,9 @@ def build_types(species, group): def get_datasets(types): """Build datasets list""" datasets = {} - for species, group_dict in types.iteritems(): + for species, group_dict in list(types.items()): datasets[species] = {} - for group, type_list in group_dict.iteritems(): + for group, type_list in list(group_dict.items()): datasets[species][group] = {} for type_name in type_list: these_datasets = build_datasets(species, group, type_name[0]) diff --git a/wqflask/maintenance/generate_probesetfreeze_file.py b/wqflask/maintenance/generate_probesetfreeze_file.py index b7b2dc8e..4231cc7c 100644 --- a/wqflask/maintenance/generate_probesetfreeze_file.py +++ b/wqflask/maintenance/generate_probesetfreeze_file.py @@ -82,7 +82,7 @@ def get_probeset_vals(cursor, dataset_name): def trim_strains(strains, probeset_vals): trimmed_strains = [] #print("probeset_vals is:", pf(probeset_vals)) - first_probeset = list(probeset_vals.itervalues())[0] + first_probeset = list(probeset_vals.values())[0] print("\n**** first_probeset is:", pf(first_probeset)) for strain in strains: print("\n**** strain is:", pf(strain)) diff --git a/wqflask/utility/__init__.py b/wqflask/utility/__init__.py index d9856eed..204ff59a 100644 --- a/wqflask/utility/__init__.py +++ b/wqflask/utility/__init__.py @@ -19,7 +19,7 @@ class Struct(object): ''' def __init__(self, obj): - for k, v in obj.iteritems(): + for k, v in list(obj.items()): if isinstance(v, dict): setattr(self, k, Struct(v)) else: @@ -30,6 +30,6 @@ class Struct(object): def __repr__(self): return '{%s}' % str(', '.join('%s : %s' % (k, repr(v)) for - (k, v) in self.__dict__.iteritems())) + (k, v) in list(self.__dict__.items()))) diff --git a/wqflask/utility/benchmark.py b/wqflask/utility/benchmark.py index 8f1c916b..221e5151 100644 --- a/wqflask/utility/benchmark.py +++ b/wqflask/utility/benchmark.py @@ -38,9 +38,9 @@ class Bench(object): @classmethod def report(cls): - total_time = sum((time_taken for time_taken in cls.entries.itervalues())) + total_time = sum((time_taken for time_taken in list(cls.entries.values()))) print("\nTiming report\n") - for name, time_taken in cls.entries.iteritems(): + for name, time_taken in list(cls.entries.items()): percent = int(round((time_taken/total_time) * 100)) print("[{}%] {}: {}".format(percent, name, time_taken)) print() diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py index 23b0b650..ae42f834 100644 --- a/wqflask/utility/gen_geno_ob.py +++ b/wqflask/utility/gen_geno_ob.py @@ -175,7 +175,7 @@ class Locus(object): start_pos = 3 for allele in marker_row[start_pos:]: - if allele in geno_table.keys(): + if allele in list(geno_table.keys()): self.genotype.append(geno_table[allele]) else: #ZS: Some genotype appears that isn't specified in the metadata, make it unknown self.genotype.append("U") \ No newline at end of file diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py index 9ce809b6..9a4a235a 100644 --- a/wqflask/utility/helper_functions.py +++ b/wqflask/utility/helper_functions.py @@ -13,7 +13,7 @@ logger = logging.getLogger(__name__ ) def get_species_dataset_trait(self, start_vars): #assert type(read_genotype) == type(bool()), "Expecting boolean value for read_genotype" - if "temp_trait" in start_vars.keys(): + if "temp_trait" in list(start_vars.keys()): if start_vars['temp_trait'] == "True": self.dataset = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = start_vars['group']) else: diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py index d66c954e..c6a5c260 100644 --- a/wqflask/utility/svg.py +++ b/wqflask/utility/svg.py @@ -133,7 +133,7 @@ def _escape(data, entities={}): # data = data.replace("&", "&") data = data.replace("<", "<") data = data.replace(">", ">") - for chars, entity in entities.items(): + for chars, entity in list(entities.items()): data = data.replace(chars, entity) return data @@ -299,7 +299,7 @@ class SVGelement: self.text = text self.namespace = namespace self.cdata = cdata - for arg in args.keys(): + for arg in list(args.keys()): arg2 = arg.replace("__", ":") arg2 = arg2.replace("_", "-") self.attributes[arg2] = args[arg] @@ -314,7 +314,7 @@ class SVGelement: def toXml(self, level, f): f.write('\t'*level) f.write('<'+self.type) - for attkey in self.attributes.keys(): + for attkey in list(self.attributes.keys()): f.write(' '+_escape(str(attkey))+'=' + _quoteattr(str(self.attributes[attkey]))) if self.namespace: @@ -365,7 +365,7 @@ class tspan(SVGelement): def __repr__(self): s = "\n" % (item, self.entity[item])) xml.write("]") xml.write(">\n") @@ -1015,7 +1015,7 @@ class drawing: if element.text: textnode=root.createTextNode(element.text) e.appendChild(textnode) - for attribute in element.attributes.keys(): #in element.attributes is supported from python 2.2 + for attribute in list(element.attributes.keys()): #in element.attributes is supported from python 2.2 e.setAttribute(attribute,str(element.attributes[attribute])) if element.elements: for el in element.elements: diff --git a/wqflask/utility/temp_data.py b/wqflask/utility/temp_data.py index 5bf700c9..2f2726c6 100644 --- a/wqflask/utility/temp_data.py +++ b/wqflask/utility/temp_data.py @@ -20,6 +20,6 @@ class TempData(object): if __name__ == "__main__": redis = Redis() - for key in redis.keys(): + for key in list(redis.keys()): for field in redis.hkeys(key): print("{}.{}={}".format(key, field, redis.hget(key, field))) diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index f790d424..51a87fe1 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -220,7 +220,7 @@ def show_settings(): logger.info(OVERRIDES) logger.info(BLUE+"Mr. Mojo Risin 2"+ENDC) - keylist = app.config.keys() + keylist = list(app.config.keys()) print("runserver.py: ****** Webserver configuration - k,v pairs from app.config ******") keylist.sort() for k in keylist: diff --git a/wqflask/wqflask/api/correlation.py b/wqflask/wqflask/api/correlation.py index 7f5312c1..eb05645e 100644 --- a/wqflask/wqflask/api/correlation.py +++ b/wqflask/wqflask/api/correlation.py @@ -36,7 +36,7 @@ def do_correlation(start_vars): #corr_results = collections.OrderedDict(sorted(corr_results.items(), key=lambda t: -abs(t[1][0]))) final_results = [] - for _trait_counter, trait in enumerate(corr_results.keys()[:corr_params['return_count']]): + for _trait_counter, trait in enumerate(list(corr_results.keys())[:corr_params['return_count']]): if corr_params['type'] == "tissue": [sample_r, num_overlap, sample_p, symbol] = corr_results[trait] result_dict = { @@ -76,20 +76,20 @@ def calculate_results(this_trait, this_dataset, target_dataset, corr_params): if corr_params['type'] == "tissue": trait_symbol_dict = this_dataset.retrieve_genes("Symbol") corr_results = do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_params) - sorted_results = collections.OrderedDict(sorted(corr_results.items(), + sorted_results = collections.OrderedDict(sorted(list(corr_results.items()), key=lambda t: -abs(t[1][1]))) elif corr_params['type'] == "literature" or corr_params['type'] == "lit": #ZS: Just so a user can use either "lit" or "literature" trait_geneid_dict = this_dataset.retrieve_genes("GeneId") corr_results = do_literature_correlation_for_all_traits(this_trait, this_dataset, trait_geneid_dict, corr_params) - sorted_results = collections.OrderedDict(sorted(corr_results.items(), + sorted_results = collections.OrderedDict(sorted(list(corr_results.items()), key=lambda t: -abs(t[1][1]))) else: - for target_trait, target_vals in target_dataset.trait_data.iteritems(): + for target_trait, target_vals in list(target_dataset.trait_data.items()): result = get_sample_r_and_p_values(this_trait, this_dataset, target_vals, target_dataset, corr_params['type']) if result is not None: corr_results[target_trait] = result - sorted_results = collections.OrderedDict(sorted(corr_results.items(), key=lambda t: -abs(t[1][0]))) + sorted_results = collections.OrderedDict(sorted(list(corr_results.items()), key=lambda t: -abs(t[1][0]))) return sorted_results @@ -100,10 +100,10 @@ def do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_par if this_trait.symbol.lower() in primary_trait_tissue_vals_dict: primary_trait_tissue_values = primary_trait_tissue_vals_dict[this_trait.symbol.lower()] - corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(symbol_list=trait_symbol_dict.values()) + corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(symbol_list=list(trait_symbol_dict.values())) tissue_corr_data = {} - for trait, symbol in trait_symbol_dict.iteritems(): + for trait, symbol in list(trait_symbol_dict.items()): if symbol and symbol.lower() in corr_result_tissue_vals_dict: this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower()] @@ -119,7 +119,7 @@ def do_literature_correlation_for_all_traits(this_trait, target_dataset, trait_g input_trait_mouse_gene_id = convert_to_mouse_gene_id(target_dataset.group.species.lower(), this_trait.geneid) lit_corr_data = {} - for trait, gene_id in trait_geneid_dict.iteritems(): + for trait, gene_id in list(trait_geneid_dict.items()): mouse_gene_id = convert_to_mouse_gene_id(target_dataset.group.species.lower(), gene_id) if mouse_gene_id and str(mouse_gene_id).find(";") == -1: diff --git a/wqflask/wqflask/api/gen_menu.py b/wqflask/wqflask/api/gen_menu.py index cc11e14b..71d9ee03 100644 --- a/wqflask/wqflask/api/gen_menu.py +++ b/wqflask/wqflask/api/gen_menu.py @@ -61,7 +61,7 @@ def get_types(groups): """Build types list""" types = {} - for species, group_dict in groups.iteritems(): + for species, group_dict in list(groups.items()): types[species] = {} for group_name, _group_full_name, _family_name in group_dict: if phenotypes_exist(group_name): @@ -136,9 +136,9 @@ def build_types(species, group): def get_datasets(types): """Build datasets list""" datasets = {} - for species, group_dict in types.iteritems(): + for species, group_dict in list(types.items()): datasets[species] = {} - for group, type_list in group_dict.iteritems(): + for group, type_list in list(group_dict.items()): datasets[species][group] = {} for type_name in type_list: these_datasets = build_datasets(species, group, type_name[0]) diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py index 819836b1..57a8d85f 100644 --- a/wqflask/wqflask/correlation/corr_scatter_plot.py +++ b/wqflask/wqflask/correlation/corr_scatter_plot.py @@ -36,13 +36,13 @@ class CorrScatterPlot(object): samples_1, samples_2, num_overlap = corr_result_helpers.normalize_values_with_samples(self.trait_1.data, self.trait_2.data) self.data = [] - self.indIDs = samples_1.keys() + self.indIDs = list(samples_1.keys()) vals_1 = [] - for sample in samples_1.keys(): + for sample in list(samples_1.keys()): vals_1.append(samples_1[sample].value) self.data.append(vals_1) vals_2 = [] - for sample in samples_2.keys(): + for sample in list(samples_2.keys()): vals_2.append(samples_2[sample].value) self.data.append(vals_2) diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index de7a1c0c..15a21ee6 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -145,10 +145,10 @@ class CorrelationResults(object): if corr_samples_group == 'samples_other': primary_samples = [x for x in primary_samples if x not in ( self.dataset.group.parlist + self.dataset.group.f1list)] - self.process_samples(start_vars, self.this_trait.data.keys(), primary_samples) + self.process_samples(start_vars, list(self.this_trait.data.keys()), primary_samples) self.target_dataset = data_set.create_dataset(start_vars['corr_dataset']) - self.target_dataset.get_trait_data(self.sample_data.keys()) + self.target_dataset.get_trait_data(list(self.sample_data.keys())) self.header_fields = get_header_fields(self.target_dataset.type, self.corr_method) @@ -168,41 +168,41 @@ class CorrelationResults(object): tissue_corr_data = self.do_tissue_correlation_for_all_traits() if tissue_corr_data != None: - for trait in tissue_corr_data.keys()[:self.return_number]: + for trait in list(tissue_corr_data.keys())[:self.return_number]: self.get_sample_r_and_p_values(trait, self.target_dataset.trait_data[trait]) else: - for trait, values in self.target_dataset.trait_data.iteritems(): + for trait, values in list(self.target_dataset.trait_data.items()): 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() - for trait in lit_corr_data.keys()[:self.return_number]: + for trait in list(lit_corr_data.keys())[:self.return_number]: self.get_sample_r_and_p_values(trait, self.target_dataset.trait_data[trait]) elif self.corr_type == "sample": - for trait, values in self.target_dataset.trait_data.iteritems(): + for trait, values in list(self.target_dataset.trait_data.items()): self.get_sample_r_and_p_values(trait, values) - self.correlation_data = collections.OrderedDict(sorted(self.correlation_data.items(), + self.correlation_data = collections.OrderedDict(sorted(list(self.correlation_data.items()), key=lambda t: -abs(t[1][0]))) if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno": #ZS: Convert min/max chromosome to an int for the location range option range_chr_as_int = None - for order_id, chr_info in self.dataset.species.chromosomes.chromosomes.iteritems(): + for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()): if 'loc_chr' in start_vars: if chr_info.name == self.location_chr: range_chr_as_int = order_id - for _trait_counter, trait in enumerate(self.correlation_data.keys()[:self.return_number]): + for _trait_counter, trait in enumerate(list(self.correlation_data.keys())[:self.return_number]): trait_object = create_trait(dataset=self.target_dataset, name=trait, get_qtl_info=True, get_sample_info=False) if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno": #ZS: Convert trait chromosome to an int for the location range option chr_as_int = 0 - for order_id, chr_info in self.dataset.species.chromosomes.chromosomes.iteritems(): + for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()): if chr_info.name == trait_object.chr: chr_as_int = order_id @@ -297,14 +297,14 @@ class CorrelationResults(object): #print("trait_gene_symbols: ", pf(trait_gene_symbols.values())) corr_result_tissue_vals_dict= correlation_functions.get_trait_symbol_and_tissue_values( - symbol_list=self.trait_symbol_dict.values()) + symbol_list=list(self.trait_symbol_dict.values())) #print("corr_result_tissue_vals: ", pf(corr_result_tissue_vals_dict)) #print("trait_gene_symbols: ", pf(trait_gene_symbols)) tissue_corr_data = {} - for trait, symbol in self.trait_symbol_dict.iteritems(): + for trait, symbol in list(self.trait_symbol_dict.items()): if symbol and symbol.lower() in corr_result_tissue_vals_dict: this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower()] @@ -314,7 +314,7 @@ class CorrelationResults(object): tissue_corr_data[trait] = [symbol, result[0], result[2]] - tissue_corr_data = collections.OrderedDict(sorted(tissue_corr_data.items(), + tissue_corr_data = collections.OrderedDict(sorted(list(tissue_corr_data.items()), key=lambda t: -abs(t[1][1]))) return tissue_corr_data @@ -359,7 +359,7 @@ class CorrelationResults(object): input_trait_mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), self.this_trait.geneid) lit_corr_data = {} - for trait, gene_id in self.trait_geneid_dict.iteritems(): + for trait, gene_id in list(self.trait_geneid_dict.items()): mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), gene_id) if mouse_gene_id and str(mouse_gene_id).find(";") == -1: @@ -387,7 +387,7 @@ class CorrelationResults(object): else: lit_corr_data[trait] = [gene_id, 0] - lit_corr_data = collections.OrderedDict(sorted(lit_corr_data.items(), + lit_corr_data = collections.OrderedDict(sorted(list(lit_corr_data.items()), key=lambda t: -abs(t[1][1]))) return lit_corr_data diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py index 35067036..f0be7a98 100644 --- a/wqflask/wqflask/ctl/ctl_analysis.py +++ b/wqflask/wqflask/ctl/ctl_analysis.py @@ -125,7 +125,7 @@ class CTL(object): gt = create_trait(name = ts[0], dataset_name = ts[1]) gt = retrieve_sample_data(gt, dataset, individuals) for ind in individuals: - if ind in gt.data.keys(): + if ind in list(gt.data.keys()): traits.append(gt.data[ind].value) else: traits.append("-999") diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py index 6646cc36..28c6593d 100644 --- a/wqflask/wqflask/export_traits.py +++ b/wqflask/wqflask/export_traits.py @@ -61,7 +61,7 @@ def export_search_results_csv(targs): traits_by_group = sort_traits_by_group(trait_list) file_list = [] - for group in traits_by_group.keys(): + for group in list(traits_by_group.keys()): group_traits = traits_by_group[group] buff = StringIO.StringIO() writer = csv.writer(buff) @@ -135,7 +135,7 @@ def export_search_results_csv(targs): def sort_traits_by_group(trait_list=[]): traits_by_group = {} for trait in trait_list: - if trait.dataset.group.name not in traits_by_group.keys(): + if trait.dataset.group.name not in list(traits_by_group.keys()): traits_by_group[trait.dataset.group.name] = [] traits_by_group[trait.dataset.group.name].append(trait) diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py index 5098a184..577426b0 100644 --- a/wqflask/wqflask/heatmap/heatmap.py +++ b/wqflask/wqflask/heatmap/heatmap.py @@ -60,7 +60,7 @@ class Heatmap(object): chrnames = [] self.species = species.TheSpecies(dataset=self.trait_list[0][1]) - for key in self.species.chromosomes.chromosomes.keys(): + for key in list(self.species.chromosomes.chromosomes.keys()): chrnames.append([self.species.chromosomes.chromosomes[key].name, self.species.chromosomes.chromosomes[key].mb_length]) for trait_db in self.trait_list: @@ -93,7 +93,7 @@ class Heatmap(object): pos = [] markernames = [] - for trait in self.trait_results.keys(): + for trait in list(self.trait_results.keys()): lodnames.append(trait) self.dataset.group.get_markers() diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py index 273168a8..a39e5d0f 100644 --- a/wqflask/wqflask/interval_analyst/GeneUtil.py +++ b/wqflask/wqflask/interval_analyst/GeneUtil.py @@ -24,7 +24,7 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'): ##List current Species and other Species speciesId = speciesDict[species] - otherSpecies = [[X, speciesDict[X]] for X in speciesDict.keys()] + otherSpecies = [[X, speciesDict[X]] for X in list(speciesDict.keys())] otherSpecies.remove([species, speciesId]) results = g.db.execute(""" diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 7b6e70d2..0328ce85 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -229,7 +229,7 @@ class DisplayMappingResults(object): self.manhattan_plot = start_vars['manhattan_plot'] - if 'permCheck' in start_vars.keys(): + if 'permCheck' in list(start_vars.keys()): self.permChecked = start_vars['permCheck'] else: self.permChecked = False @@ -242,46 +242,46 @@ class DisplayMappingResults(object): else: self.nperm = 0 - if 'bootCheck' in start_vars.keys(): + if 'bootCheck' in list(start_vars.keys()): self.bootChecked = start_vars['bootCheck'] else: self.bootChecked = False - if 'num_bootstrap' in start_vars.keys(): + if 'num_bootstrap' in list(start_vars.keys()): self.nboot = int(start_vars['num_bootstrap']) else: self.nboot = 0 - if 'bootstrap_results' in start_vars.keys(): + if 'bootstrap_results' in list(start_vars.keys()): self.bootResult = start_vars['bootstrap_results'] else: self.bootResult = [] - if 'do_control' in start_vars.keys(): + if 'do_control' in list(start_vars.keys()): self.doControl = start_vars['do_control'] else: self.doControl = "false" - if 'control_marker' in start_vars.keys(): + if 'control_marker' in list(start_vars.keys()): self.controlLocus = start_vars['control_marker'] else: self.controlLocus = "" - if 'covariates' in start_vars.keys(): + if 'covariates' in list(start_vars.keys()): self.covariates = start_vars['covariates'] - if 'maf' in start_vars.keys(): + if 'maf' in list(start_vars.keys()): self.maf = start_vars['maf'] else: self.maf = "" - if 'output_files' in start_vars.keys(): + if 'output_files' in list(start_vars.keys()): self.output_files = start_vars['output_files'] - if 'use_loco' in start_vars.keys() and self.mapping_method == "gemma": + if 'use_loco' in list(start_vars.keys()) and self.mapping_method == "gemma": self.use_loco = start_vars['use_loco'] - if 'reaper_version' in start_vars.keys() and self.mapping_method == "reaper": + if 'reaper_version' in list(start_vars.keys()) and self.mapping_method == "reaper": self.reaper_version = start_vars['reaper_version'] if 'output_files' in start_vars: self.output_files = ",".join(start_vars['output_files']) self.categorical_vars = "" self.perm_strata = "" - if 'perm_strata' in start_vars.keys() and 'categorical_vars' in start_vars.keys(): + if 'perm_strata' in list(start_vars.keys()) and 'categorical_vars' in list(start_vars.keys()): self.categorical_vars = start_vars['categorical_vars'] self.perm_strata = start_vars['perm_strata'] @@ -323,7 +323,7 @@ class DisplayMappingResults(object): self.graphWidth = self.MULT_GRAPH_DEFAULT_WIDTH ## BEGIN HaplotypeAnalyst - if 'haplotypeAnalystCheck' in start_vars.keys(): + if 'haplotypeAnalystCheck' in list(start_vars.keys()): self.haplotypeAnalystChecked = start_vars['haplotypeAnalystCheck'] else: self.haplotypeAnalystChecked = False @@ -331,25 +331,25 @@ class DisplayMappingResults(object): self.graphHeight = self.GRAPH_DEFAULT_HEIGHT self.dominanceChecked = False - if 'LRSCheck' in start_vars.keys(): + if 'LRSCheck' in list(start_vars.keys()): self.LRS_LOD = start_vars['LRSCheck'] else: self.LRS_LOD = start_vars['score_type'] self.intervalAnalystChecked = True self.draw2X = False - if 'additiveCheck' in start_vars.keys(): + if 'additiveCheck' in list(start_vars.keys()): self.additiveChecked = start_vars['additiveCheck'] else: self.additiveChecked = False - if 'viewLegend' in start_vars.keys(): + if 'viewLegend' in list(start_vars.keys()): self.legendChecked = start_vars['viewLegend'] else: self.legendChecked = False - if 'showSNP' in start_vars.keys(): + if 'showSNP' in list(start_vars.keys()): self.SNPChecked = start_vars['showSNP'] else: self.SNPChecked = False - if 'showGenes' in start_vars.keys(): + if 'showGenes' in list(start_vars.keys()): self.geneChecked = start_vars['showGenes'] else: self.geneChecked = False @@ -530,7 +530,7 @@ class DisplayMappingResults(object): showLocusForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name=showLocusForm, submit=HT.Input(type='hidden')) hddn = {'FormID':'showDatabase', 'ProbeSetID':'_','database':fd.RISet+"Geno",'CellID':'_', 'RISet':fd.RISet, 'incparentsf1':'ON'} - for key in hddn.keys(): + for key in list(hddn.keys()): showLocusForm.append(HT.Input(name=key, value=hddn[key], type='hidden')) showLocusForm.append(intImg) else: diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index c9d10f7c..145dbc77 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -347,7 +347,7 @@ class RunMapping(object): if marker['chr1'] > 0 or marker['chr1'] == "X" or marker['chr1'] == "X/Y": if marker['chr1'] > highest_chr or marker['chr1'] == "X" or marker['chr1'] == "X/Y": highest_chr = marker['chr1'] - if 'lod_score' in marker.keys(): + if 'lod_score' in list(marker.keys()): self.qtl_results.append(marker) self.trimmed_markers = results @@ -411,7 +411,7 @@ class RunMapping(object): if marker['chr'] > 0 or marker['chr'] == "X" or marker['chr'] == "X/Y": if marker['chr'] > highest_chr or marker['chr'] == "X" or marker['chr'] == "X/Y": highest_chr = marker['chr'] - if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()): + if ('lod_score' in list(marker.keys())) or ('lrs_value' in list(marker.keys())): self.qtl_results.append(marker) with Bench("Exporting Results"): @@ -538,28 +538,28 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, output_file.write("Mb," + score_type) else: output_file.write("Cm," + score_type) - if "additive" in markers[0].keys(): + if "additive" in list(markers[0].keys()): output_file.write(",Additive") - if "dominance" in markers[0].keys(): + if "dominance" in list(markers[0].keys()): output_file.write(",Dominance") output_file.write("\n") for i, marker in enumerate(markers): output_file.write(marker['name'] + "," + str(marker['chr']) + "," + str(marker['Mb']) + ",") - if "lod_score" in marker.keys(): + if "lod_score" in list(marker.keys()): output_file.write(str(marker['lod_score'])) else: output_file.write(str(marker['lrs_value'])) - if "additive" in marker.keys(): + if "additive" in list(marker.keys()): output_file.write("," + str(marker['additive'])) - if "dominance" in marker.keys(): + if "dominance" in list(marker.keys()): output_file.write("," + str(marker['dominance'])) if i < (len(markers) - 1): output_file.write("\n") def trim_markers_for_figure(markers): - if 'p_wald' in markers[0].keys(): + if 'p_wald' in list(markers[0].keys()): score_type = 'p_wald' - elif 'lod_score' in markers[0].keys(): + elif 'lod_score' in list(markers[0].keys()): score_type = 'lod_score' else: score_type = 'lrs_value' @@ -617,7 +617,7 @@ def trim_markers_for_figure(markers): return filtered_markers def trim_markers_for_table(markers): - if 'lod_score' in markers[0].keys(): + if 'lod_score' in list(markers[0].keys()): sorted_markers = sorted(markers, key=lambda k: k['lod_score'], reverse=True) else: sorted_markers = sorted(markers, key=lambda k: k['lrs_value'], reverse=True) @@ -695,10 +695,10 @@ def get_genofile_samplelist(dataset): def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples): perm_strata_strings = [] for sample in used_samples: - if sample in sample_list.sample_attribute_values.keys(): + if sample in list(sample_list.sample_attribute_values.keys()): combined_string = "" for var in categorical_vars: - if var in sample_list.sample_attribute_values[sample].keys(): + if var in list(sample_list.sample_attribute_values[sample].keys()): combined_string += str(sample_list.sample_attribute_values[sample][var]) else: combined_string += "NA" diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py index 39a07310..6b3e00fb 100644 --- a/wqflask/wqflask/resource_manager.py +++ b/wqflask/wqflask/resource_manager.py @@ -125,7 +125,7 @@ def add_group_to_resource(): def get_group_names(group_masks): group_masks_with_names = {} - for group_id, group_mask in group_masks.iteritems(): + for group_id, group_mask in list(group_masks.items()): this_mask = group_mask group_name = get_group_info(group_id)['name'] this_mask['name'] = group_name diff --git a/wqflask/wqflask/show_trait/export_trait_data.py b/wqflask/wqflask/show_trait/export_trait_data.py index 253c887b..68c3ad7d 100644 --- a/wqflask/wqflask/show_trait/export_trait_data.py +++ b/wqflask/wqflask/show_trait/export_trait_data.py @@ -47,7 +47,7 @@ def get_export_metadata(trait_id, dataset_name): def dict_to_sorted_list(dictionary): - sorted_list = [item for item in dictionary.iteritems()] + sorted_list = [item for item in list(dictionary.items())] sorted_list = sorted(sorted_list, cmp=cmp_samples) sorted_values = [item[1] for item in sorted_list] return sorted_values diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index f188fd9d..c156e61b 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -261,7 +261,7 @@ class ShowTrait(object): hddn['export_data'] = "" hddn['export_format'] = "excel" if len(self.scales_in_geno) < 2: - hddn['mapping_scale'] = self.scales_in_geno[self.scales_in_geno.keys()[0]][0][0] + hddn['mapping_scale'] = self.scales_in_geno[list(self.scales_in_geno.keys())[0]][0][0] # We'll need access to this_trait and hddn in the Jinja2 Template, so we put it inside self self.hddn = hddn @@ -405,7 +405,7 @@ class ShowTrait(object): if not self.temp_trait: other_sample_names = [] - for sample in self.this_trait.data.keys(): + for sample in list(self.this_trait.data.keys()): if (self.this_trait.data[sample].name2 in primary_sample_names) and (self.this_trait.data[sample].name not in primary_sample_names): primary_sample_names.append(self.this_trait.data[sample].name) primary_sample_names.remove(self.this_trait.data[sample].name2) @@ -558,7 +558,7 @@ def get_table_widths(sample_groups, has_num_cases=False): def has_num_cases(this_trait): has_n = False if this_trait.dataset.type != "ProbeSet" and this_trait.dataset.type != "Geno": - for name, sample in this_trait.data.iteritems(): + for name, sample in list(this_trait.data.items()): if sample.num_cases: has_n = True break @@ -611,7 +611,7 @@ def get_categorical_variables(this_trait, sample_list): if len(sample_list.attributes) > 0: for attribute in sample_list.attributes: attribute_vals = [] - for sample_name in this_trait.data.keys(): + for sample_name in list(this_trait.data.keys()): if sample_list.attributes[attribute].name in this_trait.data[sample_name].extra_attributes: attribute_vals.append(this_trait.data[sample_name].extra_attributes[sample_list.attributes[attribute].name]) else: diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index d67f1a2e..394a9e28 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -533,7 +533,7 @@ def heatmap_page(): result = template_vars.__dict__ - for item in template_vars.__dict__.keys(): + for item in list(template_vars.__dict__.keys()): logger.info(" ---**--- {}: {}".format(type(template_vars.__dict__[item]), item)) pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL) @@ -637,7 +637,7 @@ def loading_page(): if 'wanted_inputs' in initial_start_vars: wanted = initial_start_vars['wanted_inputs'].split(",") start_vars = {} - for key, value in initial_start_vars.iteritems(): + for key, value in list(initial_start_vars.items()): if key in wanted or key.startswith(('value:')): start_vars[key] = value @@ -737,7 +737,7 @@ def mapping_results_page(): 'transform' ) start_vars = {} - for key, value in initial_start_vars.iteritems(): + for key, value in list(initial_start_vars.items()): if key in wanted or key.startswith(('value:')): start_vars[key] = value #logger.debug("Mapping called with start_vars:", start_vars) -- cgit v1.2.3 From e55b1502340cc99cd8a5d705261a5ff3c87f3718 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 19 Aug 2020 02:41:46 +0300 Subject: Change `dict.has_key(key)` to `key in dict` Run `2to3-3.8 -f has_key -w .` See: --- scripts/maintenance/readProbeSetSE_v7.py | 2 +- wqflask/wqflask/marker_regression/plink_mapping.py | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) (limited to 'wqflask') diff --git a/scripts/maintenance/readProbeSetSE_v7.py b/scripts/maintenance/readProbeSetSE_v7.py index 7b2fee87..2700a8ef 100755 --- a/scripts/maintenance/readProbeSetSE_v7.py +++ b/scripts/maintenance/readProbeSetSE_v7.py @@ -223,7 +223,7 @@ while line: line2 = list(map(string.strip, line2)) CellId = line2[0] - if not ProbeNameId.has_key(CellId): + if CellId not in ProbeNameId: ferror.write(CellId + " doesn't exist\n") else: DataId = ProbeNameId[CellId] diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py index 9571015e..38ef7190 100644 --- a/wqflask/wqflask/marker_regression/plink_mapping.py +++ b/wqflask/wqflask/marker_regression/plink_mapping.py @@ -111,7 +111,7 @@ def parse_plink_output(output_filename, species): line_list = build_line_list(line=line) # only keep the records whose chromosome name is in db - if species.chromosomes.chromosomes.has_key(int(line_list[0])) and line_list[-1] and line_list[-1].strip()!='NA': + if int(line_list[0]) in species.chromosomes.chromosomes and line_list[-1] and line_list[-1].strip()!='NA': chr_name = species.chromosomes.chromosomes[int(line_list[0])] snp = line_list[1] @@ -121,7 +121,7 @@ def parse_plink_output(output_filename, species): if p_value < threshold_p_value: p_value_dict[snp] = float(p_value) - if plink_results.has_key(chr_name): + if chr_name in plink_results: value_list = plink_results[chr_name] # pvalue range is [0,1] -- cgit v1.2.3 From e63331da5ed0a11f2a558d799dd570bf44ad584e Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 19 Aug 2020 03:01:33 +0300 Subject: Replace `izip` with python's built-in equivalent Run `2to3-3.8 -f itertools -w . && 2to3-3.8 -f itertools_imports -w .` See: and --- wqflask/base/data_set.py | 2 +- wqflask/maintenance/quantile_normalize.py | 4 ++-- wqflask/wqflask/export_traits.py | 2 +- wqflask/wqflask/pbkdf2.py | 6 +++--- 4 files changed, 7 insertions(+), 7 deletions(-) (limited to 'wqflask') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index cfba9104..b0119b58 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -259,7 +259,7 @@ class Markers(object): # if len(self.markers) > len(p_values): # self.markers = self.markers[:len(p_values)] - for marker, p_value in itertools.izip(self.markers, p_values): + for marker, p_value in zip(self.markers, p_values): if not p_value: continue marker['p_value'] = float(p_value) diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py index 41a3aad8..34886f44 100644 --- a/wqflask/maintenance/quantile_normalize.py +++ b/wqflask/maintenance/quantile_normalize.py @@ -3,7 +3,7 @@ from __future__ import absolute_import, print_function, division import sys sys.path.insert(0,'./') -from itertools import izip + import MySQLdb import urlparse @@ -60,7 +60,7 @@ def set_data(dataset_name): sample_list = [] with open(orig_file, 'r') as orig_fh, open('/home/zas1024/cfw_data/quant_norm.csv', 'r') as quant_fh: - for i, (line1, line2) in enumerate(izip(orig_fh, quant_fh)): + for i, (line1, line2) in enumerate(zip(orig_fh, quant_fh)): trait_dict = {} sample_list = [] if i == 0: diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py index 28c6593d..a8b49829 100644 --- a/wqflask/wqflask/export_traits.py +++ b/wqflask/wqflask/export_traits.py @@ -122,7 +122,7 @@ def export_search_results_csv(targs): csv_rows.append(row_contents) - csv_rows = list(map(list, itertools.izip_longest(*[row for row in csv_rows]))) + csv_rows = list(map(list, itertools.zip_longest(*[row for row in csv_rows]))) writer.writerows(csv_rows) csv_data = buff.getvalue() buff.close() diff --git a/wqflask/wqflask/pbkdf2.py b/wqflask/wqflask/pbkdf2.py index 731c8843..0ed50790 100644 --- a/wqflask/wqflask/pbkdf2.py +++ b/wqflask/wqflask/pbkdf2.py @@ -44,7 +44,7 @@ import hmac import hashlib from struct import Struct from operator import xor -from itertools import izip, starmap +from itertools import starmap _pack_int = Struct('>I').pack @@ -72,7 +72,7 @@ def pbkdf2_bin(data, salt, iterations=1000, keylen=24, hashfunc=None): rv = u = _pseudorandom(salt + _pack_int(block)) for i in xrange(iterations - 1): u = _pseudorandom(''.join(map(chr, u))) - rv = list(starmap(xor, izip(rv, u))) + rv = list(starmap(xor, zip(rv, u))) buf.extend(rv) return ''.join(map(chr, buf))[:keylen] @@ -81,7 +81,7 @@ def safe_str_cmp(a, b): if len(a) != len(b): return False rv = 0 - for x, y in izip(a, b): + for x, y in zip(a, b): rv |= ord(x) ^ ord(y) return rv == 0 -- cgit v1.2.3 From caec08fa1e738fa9bc1b0b6bf626d8325f798712 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 19 Aug 2020 03:08:08 +0300 Subject: Convert the old not-equal syntax, <>, to != Run `2to3-3.8 -f ne -w .` See: --- wqflask/utility/svg.py | 2 +- wqflask/wqflask/marker_regression/plink_mapping.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) (limited to 'wqflask') diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py index c6a5c260..c7356e57 100644 --- a/wqflask/utility/svg.py +++ b/wqflask/utility/svg.py @@ -360,7 +360,7 @@ class tspan(SVGelement): def __init__(self, text=None, **args): SVGelement.__init__(self, 'tspan', **args) - if self.text <> None: + if self.text != None: self.text = text def __repr__(self): diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py index 38ef7190..d4ee6fe6 100644 --- a/wqflask/wqflask/marker_regression/plink_mapping.py +++ b/wqflask/wqflask/marker_regression/plink_mapping.py @@ -156,7 +156,7 @@ def parse_plink_output(output_filename, species): ####################################################### def build_line_list(line=None): line_list = string.split(string.strip(line),' ')# irregular number of whitespaces between columns - line_list = [item for item in line_list if item <>''] + line_list = [item for item in line_list if item !=''] line_list = list(map(string.strip, line_list)) return line_list \ No newline at end of file -- cgit v1.2.3 From 8be6ecf3d6b70b40be97d4abebb59eabcce8c8f8 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 19 Aug 2020 03:10:33 +0300 Subject: Convert the use of iterator’s next() methods to the next() function Run `2to3-3.8 -f next -w .` See: --- scripts/maintenance/delete_genotypes.py | 2 +- scripts/maintenance/load_phenotypes.py | 10 +++++----- wqflask/wqflask/collect.py | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-) (limited to 'wqflask') diff --git a/scripts/maintenance/delete_genotypes.py b/scripts/maintenance/delete_genotypes.py index 060640e1..b7f83758 100755 --- a/scripts/maintenance/delete_genotypes.py +++ b/scripts/maintenance/delete_genotypes.py @@ -18,7 +18,7 @@ def main(argv): # datafile datafile = open(config.get('config', 'datafile'), 'r') datafile = csv.reader(datafile, delimiter='\t', quotechar='"') - datafile.next() + next(datafile) delrowcount = 0 for row in datafile: if len(row) == 0: diff --git a/scripts/maintenance/load_phenotypes.py b/scripts/maintenance/load_phenotypes.py index 61d527d4..759d2eec 100755 --- a/scripts/maintenance/load_phenotypes.py +++ b/scripts/maintenance/load_phenotypes.py @@ -22,22 +22,22 @@ def main(argv): # datafile datafile = open(config.get('config', 'datafile'), 'r') phenotypedata = csv.reader(datafile, delimiter='\t', quotechar='"') - phenotypedata_head = phenotypedata.next() + phenotypedata_head = next(phenotypedata) 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() + phenotypemeta_head = next(phenotypemeta) print(("phenotypemeta head:\n\t%s" % phenotypemeta_head)) print() # load for metarow in phenotypemeta: # - datarow_value = phenotypedata.next() - datarow_se = phenotypedata.next() - datarow_n = phenotypedata.next() + datarow_value = next(phenotypedata) + datarow_se = next(phenotypedata) + datarow_n = next(phenotypedata) # Phenotype sql = """ INSERT INTO Phenotype diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py index 42a09fed..4c6e38e6 100644 --- a/wqflask/wqflask/collect.py +++ b/wqflask/wqflask/collect.py @@ -193,7 +193,7 @@ def view_collection(): params = request.args uc_id = params['uc_id'] - uc = (collection for collection in g.user_session.user_collections if collection["id"] == uc_id).next() + uc = next((collection for collection in g.user_session.user_collections if collection["id"] == uc_id)) traits = uc["members"] trait_obs = [] -- cgit v1.2.3 From 7e60647223017220747d248ed1c986cc8374435e Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 19 Aug 2020 03:13:53 +0300 Subject: Wrap `raise` statements in parenthesis Run `2to3-3.8 -f raise -w .` See: --- wqflask/base/trait.py | 2 +- wqflask/utility/svg.py | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) (limited to 'wqflask') diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index e82df226..c2d260e3 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -605,6 +605,6 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): if trait.lrs != "": trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs else: - raise KeyError, `trait.name`+' information is not found in the database.' + raise KeyError(`trait.name`+' information is not found in the database.') return trait \ No newline at end of file diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py index c7356e57..872f22fe 100644 --- a/wqflask/utility/svg.py +++ b/wqflask/utility/svg.py @@ -445,7 +445,7 @@ class rect(SVGelement): def __init__(self, x=None, y=None, width=None, height=None, fill=None, stroke=None, stroke_width=None, **args): if width == None or height == None: - raise ValueError, 'both height and width are required' + raise ValueError('both height and width are required') SVGelement.__init__(self,'rect',{'width':width,'height':height},**args) if x!=None: @@ -466,7 +466,7 @@ class ellipse(SVGelement): """ def __init__(self,cx=None,cy=None,rx=None,ry=None,fill=None,stroke=None,stroke_width=None,**args): if rx==None or ry== None: - raise ValueError, 'both rx and ry are required' + raise ValueError('both rx and ry are required') SVGelement.__init__(self,'ellipse',{'rx':rx,'ry':ry},**args) if cx!=None: @@ -488,7 +488,7 @@ class circle(SVGelement): """ def __init__(self,cx=None,cy=None,r=None,fill=None,stroke=None,stroke_width=None,**args): if r==None: - raise ValueError, 'r is required' + raise ValueError('r is required') SVGelement.__init__(self,'circle',{'r':r},**args) if cx!=None: self.attributes['cx']=cx @@ -714,7 +714,7 @@ class image(SVGelement): """ def __init__(self,url,x=None,y=None,width=None,height=None,**args): if width==None or height==None: - raise ValueError, 'both height and width are required' + raise ValueError('both height and width are required') SVGelement.__init__(self,'image',{'xlink:href':url,'width':width,'height':height},**args) if x!=None: self.attributes['x']=x -- cgit v1.2.3 From 17a72093f829666cc6e8df722771d31066dd71d0 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 19 Aug 2020 03:24:27 +0300 Subject: Handle the move of reduce() to functools.reduce() Run `2to3-3.8 -f reduce -w .` See: --- wqflask/wqflask/correlation_matrix/show_corr_matrix.py | 6 +++++- wqflask/wqflask/marker_regression/display_mapping_results.py | 4 ++++ 2 files changed, 9 insertions(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index a912344f..e6c817e7 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -42,6 +42,10 @@ import rpy2.robjects as robjects from pprint import pformat as pf from utility.redis_tools import get_redis_conn +try: # Only import this for Python3 + from functools import reduce +except: + pass Redis = get_redis_conn() THIRTY_DAYS = 60 * 60 * 24 * 30 @@ -302,4 +306,4 @@ def sortEigenVectors(vector): A = [x*100.0/sum for x in A] return [A, B] except: - return [] \ No newline at end of file + return [] diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 0328ce85..c8b9c405 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -48,6 +48,10 @@ from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR, GENERATED_IMAGE_DIR from utility.pillow_utils import draw_rotated_text, draw_open_polygon import utility.logger +try: # Only import this for Python3 + from functools import reduce +except: + pass logger = utility.logger.getLogger(__name__ ) RED = ImageColor.getrgb("red") -- cgit v1.2.3 From 1c3ade2f739608563cc1659dd93e5b2abc446046 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 19 Aug 2020 03:27:21 +0300 Subject: Replace backtick repr with the repr() function * wqflask/base/trait.py: See --- wqflask/base/trait.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index c2d260e3..a513b589 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -605,6 +605,6 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): if trait.lrs != "": trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs else: - raise KeyError(`trait.name`+' information is not found in the database.') + raise KeyError(repr(trait.name)+' information is not found in the database.') return trait \ No newline at end of file -- cgit v1.2.3 From 606ec8b9b3bbb8b2269ab546ebafa454f1753176 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 19 Aug 2020 03:31:53 +0300 Subject: Handle the rename of urllib and urllib2 to the urllib package See: --- wqflask/base/trait.py | 2 +- wqflask/db/call.py | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) (limited to 'wqflask') diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index a513b589..2b8f2e72 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -6,7 +6,7 @@ import resource import codecs import requests import random -import urllib +import urllib.request, urllib.parse, urllib.error from base import webqtlConfig from base.webqtlCaseData import webqtlCaseData diff --git a/wqflask/db/call.py b/wqflask/db/call.py index 1a1b3adc..82cfebb4 100644 --- a/wqflask/db/call.py +++ b/wqflask/db/call.py @@ -3,7 +3,7 @@ from flask import g import string -import urllib2 +import urllib.request, urllib.error, urllib.parse import json from utility.tools import USE_GN_SERVER, LOG_SQL, GN_SERVER_URL from utility.benchmark import Bench @@ -59,7 +59,7 @@ def gn_server(path): """ with Bench("GN_SERVER",LOG_SQL): - res = urllib2.urlopen(GN_SERVER_URL+path) + res = urllib.request.urlopen(GN_SERVER_URL+path) rest = res.read() res2 = json.loads(rest) logger.debug(res2) -- cgit v1.2.3 From 9d5dff44fb4d07f926659dde0c6205bf12a1ca5b Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 19 Aug 2020 03:36:24 +0300 Subject: Rename xrange() to range() and wrap existing range() calls with list See: --- wqflask/maintenance/quantile_normalize.py | 2 +- wqflask/utility/Plot.py | 2 +- wqflask/wqflask/correlation/correlation_functions.py | 4 ++-- wqflask/wqflask/correlation_matrix/show_corr_matrix.py | 6 +++--- wqflask/wqflask/marker_regression/qtlreaper_mapping.py | 2 +- wqflask/wqflask/network_graph/network_graph.py | 4 ++-- wqflask/wqflask/pbkdf2.py | 4 ++-- wqflask/wqflask/search_results.py | 2 +- 8 files changed, 13 insertions(+), 13 deletions(-) (limited to 'wqflask') diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py index 34886f44..82b695f4 100644 --- a/wqflask/maintenance/quantile_normalize.py +++ b/wqflask/maintenance/quantile_normalize.py @@ -37,7 +37,7 @@ def create_dataframe(input_file): with open(input_file) as f: ncols = len(f.readline().split("\t")) - input_array = np.loadtxt(open(input_file, "rb"), delimiter="\t", skiprows=1, usecols=range(1, ncols)) + input_array = np.loadtxt(open(input_file, "rb"), delimiter="\t", skiprows=1, usecols=list(range(1, ncols))) return pd.DataFrame(input_array) #This function taken from https://github.com/ShawnLYU/Quantile_Normalize diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py index 82bf6070..c9053dde 100644 --- a/wqflask/utility/Plot.py +++ b/wqflask/utility/Plot.py @@ -86,7 +86,7 @@ def frange(start, end=None, inc=1.0): # Need to adjust the count. AFAICT, it always comes up one short. count += 1 L = [start] * count - for i in xrange(1, count): + for i in range(1, count): L[i] = start + i * inc return L diff --git a/wqflask/wqflask/correlation/correlation_functions.py b/wqflask/wqflask/correlation/correlation_functions.py index 06dec795..abaa212f 100644 --- a/wqflask/wqflask/correlation/correlation_functions.py +++ b/wqflask/wqflask/correlation/correlation_functions.py @@ -50,12 +50,12 @@ from flask import Flask, g def cal_zero_order_corr_for_tiss (primaryValue=[], targetValue=[], method='pearson'): - R_primary = rpy2.robjects.FloatVector(range(len(primaryValue))) + R_primary = rpy2.robjects.FloatVector(list(range(len(primaryValue)))) N = len(primaryValue) for i in range(len(primaryValue)): R_primary[i] = primaryValue[i] - R_target = rpy2.robjects.FloatVector(range(len(targetValue))) + R_target = rpy2.robjects.FloatVector(list(range(len(targetValue)))) for i in range(len(targetValue)): R_target[i]=targetValue[i] diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index e6c817e7..832746bb 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -194,7 +194,7 @@ class CorrelationMatrix(object): if self.do_PCA == True: self.pca_works = "True" self.pca_trait_ids = [] - pca = self.calculate_pca(range(len(self.traits)), corr_eigen_value, corr_eigen_vectors) + pca = self.calculate_pca(list(range(len(self.traits))), corr_eigen_value, corr_eigen_vectors) self.loadings_array = self.process_loadings() else: self.pca_works = "False" @@ -203,8 +203,8 @@ class CorrelationMatrix(object): self.js_data = dict(traits = [trait.name for trait in self.traits], groups = groups, - cols = range(len(self.traits)), - rows = range(len(self.traits)), + cols = list(range(len(self.traits))), + rows = list(range(len(self.traits))), samples = self.all_sample_list, sample_data = self.sample_data,) # corr_results = [result[1] for result in result_row for result_row in self.corr_results]) diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py index 0c560582..189c1985 100644 --- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py +++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py @@ -228,4 +228,4 @@ def natural_sort(marker_list): """ convert = lambda text: int(text) if text.isdigit() else text.lower() alphanum_key = lambda key: [ convert(c) for c in re.split('([0-9]+)', str(marker_list[key]['chr'])) ] - return sorted(range(len(marker_list)), key = alphanum_key) \ No newline at end of file + return sorted(list(range(len(marker_list))), key = alphanum_key) \ 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 f61c40b4..ac2ff017 100644 --- a/wqflask/wqflask/network_graph/network_graph.py +++ b/wqflask/wqflask/network_graph/network_graph.py @@ -202,8 +202,8 @@ class NetworkGraph(object): self.js_data = dict(traits = [trait.name for trait in self.traits], groups = groups, - cols = range(len(self.traits)), - rows = range(len(self.traits)), + cols = list(range(len(self.traits))), + rows = list(range(len(self.traits))), samples = self.all_sample_list, sample_data = self.sample_data, elements = self.elements,) diff --git a/wqflask/wqflask/pbkdf2.py b/wqflask/wqflask/pbkdf2.py index 0ed50790..917b9d31 100644 --- a/wqflask/wqflask/pbkdf2.py +++ b/wqflask/wqflask/pbkdf2.py @@ -68,9 +68,9 @@ def pbkdf2_bin(data, salt, iterations=1000, keylen=24, hashfunc=None): h.update(x) return list(map(ord, h.digest())) buf = [] - for block in xrange(1, -(-keylen // mac.digest_size) + 1): + for block in range(1, -(-keylen // mac.digest_size) + 1): rv = u = _pseudorandom(salt + _pack_int(block)) - for i in xrange(iterations - 1): + for i in range(iterations - 1): u = _pseudorandom(''.join(map(chr, u))) rv = list(starmap(xor, zip(rv, u))) buf.extend(rv) diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index de4b01eb..5b3946e3 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -266,7 +266,7 @@ def get_GO_symbols(a_search): def insert_newlines(string, every=64): """ This is because it is seemingly impossible to change the width of the description column, so I'm just manually adding line breaks """ lines = [] - for i in xrange(0, len(string), every): + for i in range(0, len(string), every): lines.append(string[i:i+every]) return '\n'.join(lines) -- cgit v1.2.3 From 3aaa28ea762c496eeb84e09e45194e3fd2a51673 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 19 Aug 2020 03:45:49 +0300 Subject: Make Python more idiomatic Run `2to3-3.8 -f idioms -w .` See: --- scripts/maintenance/readProbeSetMean_v7.py | 6 ++---- scripts/maintenance/readProbeSetSE_v7.py | 6 ++---- wqflask/base/data_set.py | 4 ++-- wqflask/utility/authentication_tools.py | 2 +- wqflask/utility/svg.py | 2 +- wqflask/wqflask/ctl/ctl_analysis.py | 2 +- wqflask/wqflask/show_trait/SampleList.py | 2 +- wqflask/wqflask/show_trait/show_trait.py | 2 +- wqflask/wqflask/user_login.py | 2 +- 9 files changed, 12 insertions(+), 16 deletions(-) (limited to 'wqflask') diff --git a/scripts/maintenance/readProbeSetMean_v7.py b/scripts/maintenance/readProbeSetMean_v7.py index 97767715..864b4e08 100755 --- a/scripts/maintenance/readProbeSetMean_v7.py +++ b/scripts/maintenance/readProbeSetMean_v7.py @@ -80,8 +80,7 @@ while line: if kj%100000 == 0: print(('checked ',kj,' lines')) -GeneList = list(map(string.lower, GeneList)) -GeneList.sort() +GeneList = sorted(map(string.lower, GeneList)) if isCont==0: sys.exit(0) @@ -148,9 +147,8 @@ for item in results: print(Names) -Names = list(map(string.lower, Names)) +Names = sorted(map(string.lower, Names)) -Names.sort() # -- Fixed the lower case problem of ProbeSets affx-mur_b2_at doesn't exist --# ##---- compare genelist with names ----## diff --git a/scripts/maintenance/readProbeSetSE_v7.py b/scripts/maintenance/readProbeSetSE_v7.py index 833c3f5f..20a846a4 100755 --- a/scripts/maintenance/readProbeSetSE_v7.py +++ b/scripts/maintenance/readProbeSetSE_v7.py @@ -91,8 +91,7 @@ while line: if kj % 100000 == 0: print(('checked ', kj, ' lines')) -GeneList = list(map(string.lower, GeneList)) -GeneList.sort() +GeneList = sorted(map(string.lower, GeneList)) if isCont == 0: sys.exit(0) @@ -158,8 +157,7 @@ results = db.fetchall() Names = [] for item in results: Names.append(item[0]) - Names = list(map(string.lower, Names)) - Names.sort() # -- Fixed the lower case problem of ProbeSets affx-mur_b2_at doesn't exist --# + Names = sorted(map(string.lower, Names)) ##---- compare genelist with names ----## x = y = 0 diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index b0119b58..06e1c551 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -254,7 +254,7 @@ class Markers(object): logger.debug("length of self.markers:", len(self.markers)) logger.debug("length of p_values:", len(p_values)) - if type(p_values) is list: + if isinstance(p_values, list): # THIS IS only needed for the case when we are limiting the number of p-values calculated # if len(self.markers) > len(p_values): # self.markers = self.markers[:len(p_values)] @@ -270,7 +270,7 @@ class Markers(object): marker['lod_score'] = -math.log10(marker['p_value']) # Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61 - elif type(p_values) is dict: + elif isinstance(p_values, dict): filtered_markers = [] for marker in self.markers: #logger.debug("marker[name]", marker['name']) diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py index ece7022c..bc03eb55 100644 --- a/wqflask/utility/authentication_tools.py +++ b/wqflask/utility/authentication_tools.py @@ -17,7 +17,7 @@ logger = logging.getLogger(__name__ ) def check_resource_availability(dataset, trait_id=None): #At least for now assume temporary entered traits are accessible - if type(dataset) == str: + if isinstance(dataset, str): return webqtlConfig.DEFAULT_PRIVILEGES if dataset.type == "Temp": return webqtlConfig.DEFAULT_PRIVILEGES diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py index 872f22fe..874ada9d 100644 --- a/wqflask/utility/svg.py +++ b/wqflask/utility/svg.py @@ -332,7 +332,7 @@ class SVGelement: f.write('\n'+'\t'*(level+2)+line) f.write('\n'+'\t'*(level+1)+']]>\n') if self.text: - if type(self.text) == type(''): # If the text is only text + if isinstance(self.text, type('')): # If the text is only text f.write(_escape(str(self.text))) else: # If the text is a spannedtext class f.write(str(self.text)) diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py index f0be7a98..e58a7b87 100644 --- a/wqflask/wqflask/ctl/ctl_analysis.py +++ b/wqflask/wqflask/ctl/ctl_analysis.py @@ -175,7 +175,7 @@ class CTL(object): sys.stdout.flush() # Create the interactive graph for cytoscape visualization (Nodes and Edges) - if not type(significant) == ri.RNULLType: + if not isinstance(significant, ri.RNULLType): for x in range(len(significant[0])): logger.debug(significant[0][x], significant[1][x], significant[2][x]) # Debug to console tsS = significant[0][x].split(':') # Source diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py index ad78ebcc..21ba7f63 100644 --- a/wqflask/wqflask/show_trait/SampleList.py +++ b/wqflask/wqflask/show_trait/SampleList.py @@ -43,7 +43,7 @@ class SampleList(object): for counter, sample_name in enumerate(sample_names, 1): sample_name = sample_name.replace("_2nd_", "") - if type(self.this_trait) is list: #ZS: self.this_trait will be a list if it is a Temp trait + if isinstance(self.this_trait, list): #ZS: self.this_trait will be a list if it is a Temp trait if counter <= len(self.this_trait) and str(self.this_trait[counter-1]).upper() != 'X': sample = webqtlCaseData.webqtlCaseData(name=sample_name, value=float(self.this_trait[counter-1])) else: diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index c156e61b..65899ab2 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -625,7 +625,7 @@ def get_categorical_variables(this_trait, sample_list): def get_genotype_scales(genofiles): geno_scales = {} - if type(genofiles) is list: + if isinstance(genofiles, list): for the_file in genofiles: file_location = the_file['location'] geno_scales[file_location] = get_scales_from_genofile(file_location) diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py index cfee0079..04672b45 100644 --- a/wqflask/wqflask/user_login.py +++ b/wqflask/wqflask/user_login.py @@ -193,7 +193,7 @@ def login(): if user_details: submitted_password = params['password'] pwfields = user_details['password'] - if type(pwfields) is str: + if isinstance(pwfields, str): pwfields = json.loads(pwfields) encrypted_pass_fields = encode_password(pwfields, submitted_password) password_match = pbkdf2.safe_str_cmp(encrypted_pass_fields['password'], pwfields['password']) -- cgit v1.2.3 From db41cd49b6d8ccd2c3318209118ffe098bc9293e Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 19 Aug 2020 03:57:05 +0300 Subject: Remove extra whitespace(or add it) from comma separated items See: --- etc/default_settings.py | 2 +- scripts/maintenance/QTL_Reaper_v6.py | 4 +- scripts/maintenance/readProbeSetMean_v7.py | 28 ++-- setup.py | 2 +- wqflask/base/trait.py | 6 +- wqflask/db/call.py | 10 +- wqflask/db/webqtlDatabaseFunction.py | 8 +- wqflask/maintenance/gen_select_dataset.py | 2 +- wqflask/maintenance/quantile_normalize.py | 2 +- wqflask/maintenance/set_resource_defaults.py | 2 +- wqflask/utility/Plot.py | 48 +++--- wqflask/utility/elasticsearch_tools.py | 2 +- wqflask/utility/logger.py | 26 +-- wqflask/utility/pillow_utils.py | 4 +- wqflask/utility/startup_config.py | 2 +- wqflask/utility/svg.py | 130 +++++++------- wqflask/utility/tools.py | 32 ++-- wqflask/utility/webqtlUtil.py | 16 +- wqflask/wqflask/api/router.py | 8 +- wqflask/wqflask/correlation/show_corr_results.py | 12 +- .../wqflask/correlation_matrix/show_corr_matrix.py | 8 +- wqflask/wqflask/do_search.py | 4 +- .../wqflask/external_tools/send_to_geneweaver.py | 8 +- .../marker_regression/display_mapping_results.py | 186 ++++++++++----------- wqflask/wqflask/marker_regression/plink_mapping.py | 6 +- wqflask/wqflask/marker_regression/run_mapping.py | 2 +- wqflask/wqflask/search_results.py | 2 +- wqflask/wqflask/show_trait/SampleList.py | 2 +- wqflask/wqflask/user_manager.py | 2 +- wqflask/wqflask/views.py | 8 +- 30 files changed, 287 insertions(+), 287 deletions(-) (limited to 'wqflask') diff --git a/etc/default_settings.py b/etc/default_settings.py index f368237b..82c605da 100644 --- a/etc/default_settings.py +++ b/etc/default_settings.py @@ -24,7 +24,7 @@ import os import sys -GN_VERSION = open("../etc/VERSION","r").read() +GN_VERSION = open("../etc/VERSION", "r").read() GN_SERVER_URL = "http://localhost:8880/" # REST API server # ---- MySQL diff --git a/scripts/maintenance/QTL_Reaper_v6.py b/scripts/maintenance/QTL_Reaper_v6.py index 2fbeb53b..35f2d1a1 100755 --- a/scripts/maintenance/QTL_Reaper_v6.py +++ b/scripts/maintenance/QTL_Reaper_v6.py @@ -7,7 +7,7 @@ import reaper import MySQLdb import time -con = MySQLdb.Connect(db='db_webqtl',user='username',passwd='', host="localhost") +con = MySQLdb.Connect(db='db_webqtl', user='username', passwd='', host="localhost") cursor = con.cursor() genotypeDir = '/gnshare/gn/web/genotypes/' @@ -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) diff --git a/scripts/maintenance/readProbeSetMean_v7.py b/scripts/maintenance/readProbeSetMean_v7.py index 864b4e08..59a51cf9 100755 --- a/scripts/maintenance/readProbeSetMean_v7.py +++ b/scripts/maintenance/readProbeSetMean_v7.py @@ -39,7 +39,7 @@ fp = open("%s" % input_file_name, 'rb') try: passwd = getpass.getpass('Please enter mysql password here : ') - con = MySQLdb.Connect(db='db_webqtl',host='localhost', user='username',passwd=passwd) + con = MySQLdb.Connect(db='db_webqtl', host='localhost', user='username', passwd=passwd) db = con.cursor() print("You have successfully connected to mysql.\n") @@ -60,14 +60,14 @@ print('Checking if each line have same number of members') GeneList = [] isCont = 1 header = fp.readline() -header = string.split(string.strip(header),'\t') +header = string.split(string.strip(header), '\t') header = list(map(string.strip, header)) nfield = len(header) line = fp.readline() kj=0 while line: - line2 = string.split(string.strip(line),'\t') + line2 = string.split(string.strip(line), '\t') line2 = list(map(string.strip, line2)) if len(line2) != nfield: print(("Error : " + line)) @@ -78,7 +78,7 @@ while line: kj+=1 if kj%100000 == 0: - print(('checked ',kj,' lines')) + print(('checked ', kj, ' lines')) GeneList = sorted(map(string.lower, GeneList)) @@ -86,7 +86,7 @@ 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 @@ -98,7 +98,7 @@ print('Checking if each strain exist in database') isCont = 1 fp.seek(0) header = fp.readline() -header = string.split(string.strip(header),'\t') +header = string.split(string.strip(header), '\t') header = list(map(string.strip, header)) header = list(map(translateAlias, header)) header = header[dataStart:] @@ -108,14 +108,14 @@ 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 @@ -126,7 +126,7 @@ print('Check if each ProbeSet exist in database') ##---- find PID is name or target ----## line = fp.readline() line = fp.readline() -line2 = string.split(string.strip(line),'\t') +line2 = string.split(string.strip(line), '\t') line2 = list(map(string.strip, line2)) PId = line2[0] @@ -185,7 +185,7 @@ if isCont==0: sys.exit(0) -print(('used ',time.time()-time0,' seconds')) +print(('used ', time.time()-time0, ' seconds')) ######################################################################### # # Insert data into database @@ -200,7 +200,7 @@ 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') @@ -220,7 +220,7 @@ kj = 0 values1 = [] values2 = [] while line: - line2 = string.split(string.strip(line),'\t') + line2 = string.split(string.strip(line), '\t') line2 = list(map(string.strip, line2)) PId = line2[0] recordId = NameIds[PId] @@ -253,8 +253,8 @@ 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/setup.py b/setup.py index a9b71fab..8436dcd3 100644 --- a/setup.py +++ b/setup.py @@ -9,7 +9,7 @@ setup(name='genenetwork2', url = "https://github.com/genenetwork/genenetwork2/blob/master/README.md", description = 'Website and tools for genetics.', include_package_data=True, - packages=['wqflask','etc'], + packages=['wqflask', 'etc'], scripts=['bin/genenetwork2'], # package_data = { # 'etc': ['*.py'] diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 2b8f2e72..05b272c3 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -193,7 +193,7 @@ class GeneralTrait(object): ''' if self.chr and self.mb: - self.location = 'Chr %s @ %s Mb' % (self.chr,self.mb) + self.location = 'Chr %s @ %s Mb' % (self.chr, self.mb) elif self.chr: self.location = 'Chr %s @ Unknown position' % (self.chr) else: @@ -440,7 +440,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): #XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name # to avoid the problem of same marker name from different species. elif dataset.type == 'Geno': - display_fields_string = string.join(dataset.display_fields,',Geno.') + display_fields_string = string.join(dataset.display_fields, ',Geno.') display_fields_string = 'Geno.' + display_fields_string query = """ SELECT %s @@ -459,7 +459,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): query = """SELECT %s FROM %s WHERE Name = %s""" logger.sql(query) trait_info = g.db.execute(query, - (string.join(dataset.display_fields,','), + (string.join(dataset.display_fields, ','), dataset.type, trait.name)).fetchone() if trait_info: diff --git a/wqflask/db/call.py b/wqflask/db/call.py index 82cfebb4..3b8f782e 100644 --- a/wqflask/db/call.py +++ b/wqflask/db/call.py @@ -26,8 +26,8 @@ GN_SERVER result when set (which should return a Tuple) else: res2 = result, if LOG_SQL: - logger.debug("Replaced SQL call",query) - logger.debug(path,res2) + logger.debug("Replaced SQL call", query) + logger.debug(path, res2) return res2 else: return fetchone(query) @@ -37,7 +37,7 @@ def fetchone(query): original fetchone, but with logging) """ - with Bench("SQL",LOG_SQL): + with Bench("SQL", LOG_SQL): def helper(query): res = g.db.execute(query) return res.fetchone() @@ -48,7 +48,7 @@ def fetchall(query): original fetchall, but with logging) """ - with Bench("SQL",LOG_SQL): + with Bench("SQL", LOG_SQL): def helper(query): res = g.db.execute(query) return res.fetchall() @@ -58,7 +58,7 @@ def gn_server(path): """Return JSON record by calling GN_SERVER """ - with Bench("GN_SERVER",LOG_SQL): + with Bench("GN_SERVER", LOG_SQL): res = urllib.request.urlopen(GN_SERVER_URL+path) rest = res.read() res2 = json.loads(rest) diff --git a/wqflask/db/webqtlDatabaseFunction.py b/wqflask/db/webqtlDatabaseFunction.py index 8a9dc79d..2805febd 100644 --- a/wqflask/db/webqtlDatabaseFunction.py +++ b/wqflask/db/webqtlDatabaseFunction.py @@ -35,13 +35,13 @@ def retrieve_species(group): """Get the species of a group (e.g. returns string "mouse" on "BXD" """ - result = fetch1("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (group),"/cross/"+group+".json",lambda r: (r["species"],))[0] - logger.debug("retrieve_species result:",result) + result = fetch1("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (group), "/cross/"+group+".json", lambda r: (r["species"],))[0] + logger.debug("retrieve_species result:", result) return result def retrieve_species_id(group): - result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % (group),"/cross/"+group+".json",lambda r: (r["species_id"],))[0] - logger.debug("retrieve_species_id result:",result) + result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % (group), "/cross/"+group+".json", lambda r: (r["species_id"],))[0] + logger.debug("retrieve_species_id result:", result) return result diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index 78217587..d12b328f 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -41,7 +41,7 @@ from __future__ import print_function, division import sys # NEW: Note we prepend the current path - otherwise a guix instance of GN2 may be used instead -sys.path.insert(0,'./') +sys.path.insert(0, './') # NEW: import app to avoid a circular dependency on utility.tools from wqflask import app diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py index 82b695f4..43edfd13 100644 --- a/wqflask/maintenance/quantile_normalize.py +++ b/wqflask/maintenance/quantile_normalize.py @@ -1,7 +1,7 @@ from __future__ import absolute_import, print_function, division import sys -sys.path.insert(0,'./') +sys.path.insert(0, './') diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py index 54fd8e7e..d53a255b 100644 --- a/wqflask/maintenance/set_resource_defaults.py +++ b/wqflask/maintenance/set_resource_defaults.py @@ -22,7 +22,7 @@ import sys import json # NEW: Note we prepend the current path - otherwise a guix instance of GN2 may be used instead -sys.path.insert(0,'./') +sys.path.insert(0, './') # NEW: import app to avoid a circular dependency on utility.tools from wqflask import app diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py index c9053dde..4f6e694e 100644 --- a/wqflask/utility/Plot.py +++ b/wqflask/utility/Plot.py @@ -58,7 +58,7 @@ def cformat(d, rank=0): strD = "%2.6f" % d if rank == 0: - while strD[-1] in ('0','.'): + while strD[-1] in ('0', '.'): if strD[-1] == '0' and strD[-2] == '.' and len(strD) <= 4: break elif strD[-1] == '.': @@ -162,7 +162,7 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab j = int((item-xLow)/step) Count[j] += 1 - yLow, yTop, stepY=detScale(0,max(Count)) + yLow, yTop, stepY=detScale(0, max(Count)) #draw data xScale = plotWidth/(xTop-xLow) @@ -174,7 +174,7 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab xc = (dataXY[i]-xLow)*xScale+xLeftOffset yc =-(count-yLow)*yScale+yTopOffset+plotHeight im_drawer.rectangle( - xy=((xc+2,yc),(xc+barWidth-2,yTopOffset+plotHeight)), + xy=((xc+2, yc), (xc+barWidth-2, yTopOffset+plotHeight)), outline=barColor, fill=barColor) #draw drawing region @@ -183,81 +183,81 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab ) #draw scale - scaleFont=ImageFont.truetype(font=COUR_FILE,size=11) + scaleFont=ImageFont.truetype(font=COUR_FILE, size=11) x=xLow for i in range(int(stepX)+1): xc=xLeftOffset+(x-xLow)*xScale im_drawer.line( - xy=((xc,yTopOffset+plotHeight),(xc,yTopOffset+plotHeight+5)), + xy=((xc, yTopOffset+plotHeight), (xc, yTopOffset+plotHeight+5)), fill=axesColor) strX = cformat(d=x, rank=0) im_drawer.text( text=strX, - xy=(xc-im_drawer.textsize(strX,font=scaleFont)[0]/2, - yTopOffset+plotHeight+14),font=scaleFont) + xy=(xc-im_drawer.textsize(strX, font=scaleFont)[0]/2, + yTopOffset+plotHeight+14), font=scaleFont) x+= (xTop - xLow)/stepX y=yLow for i in range(int(stepY)+1): yc=yTopOffset+plotHeight-(y-yLow)*yScale - im_drawer.line(xy=((xLeftOffset,yc),(xLeftOffset-5,yc)), fill=axesColor) + im_drawer.line(xy=((xLeftOffset, yc), (xLeftOffset-5, yc)), fill=axesColor) strY = "%d" %y im_drawer.text( text=strY, - xy=(xLeftOffset-im_drawer.textsize(strY,font=scaleFont)[0]-6,yc+5), + xy=(xLeftOffset-im_drawer.textsize(strY, font=scaleFont)[0]-6, yc+5), font=scaleFont) y+= (yTop - yLow)/stepY #draw label - labelFont=ImageFont.truetype(font=TAHOMA_FILE,size=17) + labelFont=ImageFont.truetype(font=TAHOMA_FILE, size=17) if XLabel: im_drawer.text( text=XLabel, xy=(xLeftOffset+( - plotWidth-im_drawer.textsize(XLabel,font=labelFont)[0])/2.0, + plotWidth-im_drawer.textsize(XLabel, font=labelFont)[0])/2.0, yTopOffset+plotHeight+yBottomOffset-10), - font=labelFont,fill=labelColor) + font=labelFont, fill=labelColor) if YLabel: draw_rotated_text(canvas, text=YLabel, xy=(19, yTopOffset+plotHeight-( plotHeight-im_drawer.textsize( - YLabel,font=labelFont)[0])/2.0), + YLabel, font=labelFont)[0])/2.0), font=labelFont, fill=labelColor, angle=90) - labelFont=ImageFont.truetype(font=VERDANA_FILE,size=16) + labelFont=ImageFont.truetype(font=VERDANA_FILE, size=16) if title: im_drawer.text( text=title, xy=(xLeftOffset+(plotWidth-im_drawer.textsize( - title,font=labelFont)[0])/2.0, + title, font=labelFont)[0])/2.0, 20), - font=labelFont,fill=labelColor) + font=labelFont, fill=labelColor) # This function determines the scale of the plot -def detScaleOld(min,max): +def detScaleOld(min, max): if min>=max: return None elif min == -1.0 and max == 1.0: - return [-1.2,1.2,12] + return [-1.2, 1.2, 12] else: a=max-min b=floor(log10(a)) - c=pow(10.0,b) + c=pow(10.0, b) if a < c*5.0: c/=2.0 #print a,b,c low=c*floor(min/c) high=c*ceil(max/c) - return [low,high,round((high-low)/c)] + return [low, high, round((high-low)/c)] def detScale(min=0,max=0): if min>=max: return None elif min == -1.0 and max == 1.0: - return [-1.2,1.2,12] + return [-1.2, 1.2, 12] else: a=max-min if max != 0: @@ -269,7 +269,7 @@ def detScale(min=0,max=0): min -= 0.1*a a=max-min b=floor(log10(a)) - c=pow(10.0,b) + c=pow(10.0, b) low=c*floor(min/c) high=c*ceil(max/c) n = round((high-low)/c) @@ -287,7 +287,7 @@ def detScale(min=0,max=0): high=c*ceil(max/c) n = round((high-low)/c) - return [low,high,n] + return [low, high, n] def bluefunc(x): return 1.0 / (1.0 + exp(-10*(x-0.6))) @@ -296,7 +296,7 @@ def redfunc(x): return 1.0 / (1.0 + exp(10*(x-0.5))) def greenfunc(x): - return 1 - pow(redfunc(x+0.2),2) - bluefunc(x-0.3) + return 1 - pow(redfunc(x+0.2), 2) - bluefunc(x-0.3) def colorSpectrum(n=100): multiple = 10 diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py index 15cdd0bc..a5580811 100644 --- a/wqflask/utility/elasticsearch_tools.py +++ b/wqflask/utility/elasticsearch_tools.py @@ -59,7 +59,7 @@ def get_elasticsearch_connection(for_user=True): try: assert(ELASTICSEARCH_HOST) assert(ELASTICSEARCH_PORT) - logger.info("ES HOST",ELASTICSEARCH_HOST) + logger.info("ES HOST", ELASTICSEARCH_HOST) es = Elasticsearch([{ "host": ELASTICSEARCH_HOST, "port": ELASTICSEARCH_PORT diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py index 510b1041..e904eb94 100644 --- a/wqflask/utility/logger.py +++ b/wqflask/utility/logger.py @@ -42,10 +42,10 @@ class GNLogger: """ - def __init__(self,name): + def __init__(self, name): self.logger = logging.getLogger(name) - def setLevel(self,value): + def setLevel(self, value): """Set the undelying log level""" self.logger.setLevel(value) @@ -54,7 +54,7 @@ class GNLogger: level=num to filter on LOG_LEVEL_DEBUG. """ - self.collect(self.logger.debug,*args) + self.collect(self.logger.debug, *args) def debug20(self,*args): """Call logging.debug for multiple args. Use level=num to filter on @@ -63,15 +63,15 @@ LOG_LEVEL_DEBUG (NYI). """ if level <= LOG_LEVEL_DEBUG: if self.logger.getEffectiveLevel() < 20: - self.collect(self.logger.debug,*args) + self.collect(self.logger.debug, *args) def info(self,*args): """Call logging.info for multiple args""" - self.collect(self.logger.info,*args) + self.collect(self.logger.info, *args) def warning(self,*args): """Call logging.warning for multiple args""" - self.collect(self.logger.warning,*args) + self.collect(self.logger.warning, *args) # self.logger.warning(self.collect(*args)) def error(self,*args): @@ -79,13 +79,13 @@ LOG_LEVEL_DEBUG (NYI). now = datetime.datetime.utcnow() time_str = now.strftime('%H:%M:%S UTC %Y%m%d') l = [time_str]+list(args) - self.collect(self.logger.error,*l) + self.collect(self.logger.error, *l) def infof(self,*args): """Call logging.info for multiple args lazily""" # only evaluate function when logging if self.logger.getEffectiveLevel() < 30: - self.collectf(self.logger.debug,*args) + self.collectf(self.logger.debug, *args) def debugf(self,level=0,*args): """Call logging.debug for multiple args lazily and handle @@ -95,15 +95,15 @@ LOG_LEVEL_DEBUG (NYI). # only evaluate function when logging if level <= LOG_LEVEL_DEBUG: if self.logger.getEffectiveLevel() < 20: - self.collectf(self.logger.debug,*args) + self.collectf(self.logger.debug, *args) def sql(self, sqlcommand, fun = None): """Log SQL command, optionally invoking a timed fun""" if LOG_SQL: caller = stack()[1][3] - if caller in ['fetchone','fetch1','fetchall']: + if caller in ['fetchone', 'fetch1', 'fetchall']: caller = stack()[2][3] - self.info(caller,sqlcommand) + self.info(caller, sqlcommand) if fun: result = fun(sqlcommand) if LOG_SQL: @@ -119,7 +119,7 @@ LOG_LEVEL_DEBUG (NYI). if isinstance(a, str): out = out + a else: - out = out + pf(a,width=160) + out = out + pf(a, width=160) fun(out) def collectf(self,fun,*args): @@ -134,7 +134,7 @@ LOG_LEVEL_DEBUG (NYI). if isinstance(a, str): out = out + a else: - out = out + pf(a,width=160) + out = out + pf(a, width=160) fun(out) # Get the module logger. You can override log levels at the diff --git a/wqflask/utility/pillow_utils.py b/wqflask/utility/pillow_utils.py index dfbf3e19..1e2ed075 100644 --- a/wqflask/utility/pillow_utils.py +++ b/wqflask/utility/pillow_utils.py @@ -10,9 +10,9 @@ WHITE = ImageColor.getrgb("white") def draw_rotated_text(canvas, text, font, xy, fill=BLACK, angle=-90): # type: (Image, str, ImageFont, tuple, ImageColor, int) """Utility function draw rotated text""" - tmp_img = Image.new("RGBA", font.getsize(text), color=(0,0,0,0)) + tmp_img = Image.new("RGBA", font.getsize(text), color=(0, 0, 0, 0)) draw_text = ImageDraw.Draw(tmp_img) - draw_text.text(text=text, xy=(0,0), font=font, fill=fill) + draw_text.text(text=text, xy=(0, 0), font=font, fill=fill) tmp_img2 = tmp_img.rotate(angle, expand=1) tmp_img2.save("/tmp/{}.png".format(text), format="png") canvas.paste(im=tmp_img2, box=tuple([int(i) for i in xy])) diff --git a/wqflask/utility/startup_config.py b/wqflask/utility/startup_config.py index 42ead709..f1aaebb6 100644 --- a/wqflask/utility/startup_config.py +++ b/wqflask/utility/startup_config.py @@ -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 874ada9d..19eda0ce 100644 --- a/wqflask/utility/svg.py +++ b/wqflask/utility/svg.py @@ -447,7 +447,7 @@ class rect(SVGelement): if width == None or height == None: raise ValueError('both height and width are required') - SVGelement.__init__(self,'rect',{'width':width,'height':height},**args) + SVGelement.__init__(self, 'rect', {'width':width,'height':height}, **args) if x!=None: self.attributes['x']=x if y!=None: @@ -468,7 +468,7 @@ class ellipse(SVGelement): if rx==None or ry== None: raise ValueError('both rx and ry are required') - SVGelement.__init__(self,'ellipse',{'rx':rx,'ry':ry},**args) + SVGelement.__init__(self, 'ellipse', {'rx':rx,'ry':ry}, **args) if cx!=None: self.attributes['cx']=cx if cy!=None: @@ -489,7 +489,7 @@ class circle(SVGelement): def __init__(self,cx=None,cy=None,r=None,fill=None,stroke=None,stroke_width=None,**args): if r==None: raise ValueError('r is required') - SVGelement.__init__(self,'circle',{'r':r},**args) + SVGelement.__init__(self, 'circle', {'r':r}, **args) if cx!=None: self.attributes['cx']=cx if cy!=None: @@ -508,7 +508,7 @@ class point(circle): very small rectangle if you use many points because a circle is difficult to render. """ def __init__(self,x,y,fill='black',**args): - circle.__init__(self,x,y,1,fill,**args) + circle.__init__(self, x, y, 1, fill, **args) class line(SVGelement): """l=line(x1,y1,x2,y2,stroke,stroke_width,**args) @@ -516,7 +516,7 @@ class line(SVGelement): A line is defined by a begin x,y pair and an end x,y pair """ def __init__(self,x1=None,y1=None,x2=None,y2=None,stroke=None,stroke_width=None,**args): - SVGelement.__init__(self,'line',**args) + SVGelement.__init__(self, 'line', **args) if x1!=None: self.attributes['x1']=x1 if y1!=None: @@ -536,7 +536,7 @@ class polyline(SVGelement): a polyline is defined by a list of xy pairs """ def __init__(self,points,fill=None,stroke=None,stroke_width=None,**args): - SVGelement.__init__(self,'polyline',{'points':_xypointlist(points)},**args) + SVGelement.__init__(self, 'polyline', {'points':_xypointlist(points)}, **args) if fill!=None: self.attributes['fill']=fill if stroke_width!=None: @@ -550,7 +550,7 @@ class polygon(SVGelement): a polygon is defined by a list of xy pairs """ def __init__(self,points,fill=None,stroke=None,stroke_width=None,**args): - SVGelement.__init__(self,'polygon',{'points':_xypointlist(points)},**args) + SVGelement.__init__(self, 'polygon', {'points':_xypointlist(points)}, **args) if fill!=None: self.attributes['fill']=fill if stroke_width!=None: @@ -564,7 +564,7 @@ class path(SVGelement): a path is defined by a path object and optional width, stroke and fillcolor """ def __init__(self,pathdata,fill=None,stroke=None,stroke_width=None,id=None,**args): - SVGelement.__init__(self,'path',{'d':str(pathdata)},**args) + SVGelement.__init__(self, 'path', {'d':str(pathdata)}, **args) if stroke!=None: self.attributes['stroke']=stroke if fill!=None: @@ -581,7 +581,7 @@ class text(SVGelement): a text element can bge used for displaying text on the screen """ def __init__(self,x=None,y=None,text=None,font_size=None,font_family=None,text_anchor=None,**args): - SVGelement.__init__(self,'text',**args) + SVGelement.__init__(self, 'text', **args) if x!=None: self.attributes['x']=x if y!=None: @@ -602,7 +602,7 @@ class textpath(SVGelement): a textpath places a text on a path which is referenced by a link. """ def __init__(self,link,text=None,**args): - SVGelement.__init__(self,'textPath',{'xlink:href':link},**args) + SVGelement.__init__(self, 'textPath', {'xlink:href':link}, **args) if text!=None: self.text=text @@ -614,7 +614,7 @@ class pattern(SVGelement): in x and y to cover the areas to be painted. """ def __init__(self,x=None,y=None,width=None,height=None,patternUnits=None,**args): - SVGelement.__init__(self,'pattern',**args) + SVGelement.__init__(self, 'pattern', **args) if x!=None: self.attributes['x']=x if y!=None: @@ -633,7 +633,7 @@ class title(SVGelement): add at least one to the root svg element """ def __init__(self,text=None,**args): - SVGelement.__init__(self,'title',**args) + SVGelement.__init__(self, 'title', **args) if text!=None: self.text=text @@ -644,7 +644,7 @@ class description(SVGelement): Add this element before adding other elements. """ def __init__(self,text=None,**args): - SVGelement.__init__(self,'desc',**args) + SVGelement.__init__(self, 'desc', **args) if text!=None: self.text=text @@ -655,7 +655,7 @@ class lineargradient(SVGelement): stop elements van be added to define the gradient colors. """ def __init__(self,x1=None,y1=None,x2=None,y2=None,id=None,**args): - SVGelement.__init__(self,'linearGradient',**args) + SVGelement.__init__(self, 'linearGradient', **args) if x1!=None: self.attributes['x1']=x1 if y1!=None: @@ -674,7 +674,7 @@ class radialgradient(SVGelement): stop elements van be added to define the gradient colors. """ def __init__(self,cx=None,cy=None,r=None,fx=None,fy=None,id=None,**args): - SVGelement.__init__(self,'radialGradient',**args) + SVGelement.__init__(self, 'radialGradient', **args) if cx!=None: self.attributes['cx']=cx if cy!=None: @@ -694,7 +694,7 @@ class stop(SVGelement): Puts a stop color at the specified radius """ def __init__(self,offset,stop_color=None,**args): - SVGelement.__init__(self,'stop',{'offset':offset},**args) + SVGelement.__init__(self, 'stop', {'offset':offset}, **args) if stop_color!=None: self.attributes['stop-color']=stop_color @@ -704,7 +704,7 @@ class style(SVGelement): Add a CDATA element to this element for defing in line stylesheets etc.. """ def __init__(self,type,cdata=None,**args): - SVGelement.__init__(self,'style',{'type':type},cdata=cdata, **args) + SVGelement.__init__(self, 'style', {'type':type}, cdata=cdata, **args) class image(SVGelement): @@ -715,7 +715,7 @@ class image(SVGelement): def __init__(self,url,x=None,y=None,width=None,height=None,**args): if width==None or height==None: raise ValueError('both height and width are required') - SVGelement.__init__(self,'image',{'xlink:href':url,'width':width,'height':height},**args) + SVGelement.__init__(self, 'image', {'xlink:href':url,'width':width,'height':height}, **args) if x!=None: self.attributes['x']=x if y!=None: @@ -727,7 +727,7 @@ class cursor(SVGelement): defines a custom cursor for a element or a drawing """ def __init__(self,url,**args): - SVGelement.__init__(self,'cursor',{'xlink:href':url},**args) + SVGelement.__init__(self, 'cursor', {'xlink:href':url}, **args) class marker(SVGelement): @@ -737,7 +737,7 @@ class marker(SVGelement): add an element to it which should be used as a marker. """ def __init__(self,id=None,viewBox=None,refx=None,refy=None,markerWidth=None,markerHeight=None,**args): - SVGelement.__init__(self,'marker',**args) + SVGelement.__init__(self, 'marker', **args) if id!=None: self.attributes['id']=id if viewBox!=None: @@ -758,7 +758,7 @@ class group(SVGelement): g.addElement(SVGelement) """ def __init__(self,id=None,**args): - SVGelement.__init__(self,'g',**args) + SVGelement.__init__(self, 'g', **args) if id!=None: self.attributes['id']=id @@ -772,7 +772,7 @@ class symbol(SVGelement): """ def __init__(self,id=None,viewBox=None,**args): - SVGelement.__init__(self,'symbol',**args) + SVGelement.__init__(self, 'symbol', **args) if id!=None: self.attributes['id']=id if viewBox!=None: @@ -784,7 +784,7 @@ class defs(SVGelement): container for defining elements """ def __init__(self,**args): - SVGelement.__init__(self,'defs',**args) + SVGelement.__init__(self, 'defs', **args) class switch(SVGelement): """sw=switch(**args) @@ -794,7 +794,7 @@ class switch(SVGelement): Refer to the SVG specification for details. """ def __init__(self,**args): - SVGelement.__init__(self,'switch',**args) + SVGelement.__init__(self, 'switch', **args) class use(SVGelement): @@ -803,7 +803,7 @@ class use(SVGelement): references a symbol by linking to its id and its position, height and width """ def __init__(self,link,x=None,y=None,width=None,height=None,**args): - SVGelement.__init__(self,'use',{'xlink:href':link},**args) + SVGelement.__init__(self, 'use', {'xlink:href':link}, **args) if x!=None: self.attributes['x']=x if y!=None: @@ -822,14 +822,14 @@ class link(SVGelement): a.addElement(SVGelement) """ def __init__(self,link='',**args): - SVGelement.__init__(self,'a',{'xlink:href':link},**args) + SVGelement.__init__(self, 'a', {'xlink:href':link}, **args) class view(SVGelement): """v=view(id,**args) a view can be used to create a view with different attributes""" def __init__(self,id=None,**args): - SVGelement.__init__(self,'view',**args) + SVGelement.__init__(self, 'view', **args) if id!=None: self.attributes['id']=id @@ -840,7 +840,7 @@ class script(SVGelement): """ def __init__(self,type,cdata=None,**args): - SVGelement.__init__(self,'script',{'type':type},cdata=cdata,**args) + SVGelement.__init__(self, 'script', {'type':type}, cdata=cdata, **args) class animate(SVGelement): """an=animate(attribute,from,to,during,**args) @@ -848,7 +848,7 @@ class animate(SVGelement): animates an attribute. """ def __init__(self,attribute,fr=None,to=None,dur=None,**args): - SVGelement.__init__(self,'animate',{'attributeName':attribute},**args) + SVGelement.__init__(self, 'animate', {'attributeName':attribute}, **args) if fr!=None: self.attributes['from']=fr if to!=None: @@ -862,7 +862,7 @@ class animateMotion(SVGelement): animates a SVGelement over the given path in dur seconds """ def __init__(self,pathdata,dur,**args): - SVGelement.__init__(self,'animateMotion',**args) + SVGelement.__init__(self, 'animateMotion', **args) if pathdata!=None: self.attributes['path']=str(pathdata) if dur!=None: @@ -874,7 +874,7 @@ class animateTransform(SVGelement): transform an element from and to a value. """ def __init__(self,type=None,fr=None,to=None,dur=None,**args): - SVGelement.__init__(self,'animateTransform',{'attributeName':'transform'},**args) + SVGelement.__init__(self, 'animateTransform', {'attributeName':'transform'}, **args) # As far as I know the attributeName is always transform if type!=None: self.attributes['type']=type @@ -890,7 +890,7 @@ class animateColor(SVGelement): Animates the color of a element """ def __init__(self,attribute,type=None,fr=None,to=None,dur=None,**args): - SVGelement.__init__(self,'animateColor',{'attributeName':attribute},**args) + SVGelement.__init__(self, 'animateColor', {'attributeName':attribute}, **args) if type!=None: self.attributes['type']=type if fr!=None: @@ -905,7 +905,7 @@ class set(SVGelement): sets an attribute to a value for a """ def __init__(self,attribute,to=None,dur=None,**args): - SVGelement.__init__(self,'set',{'attributeName':attribute},**args) + SVGelement.__init__(self, 'set', {'attributeName':attribute}, **args) if to!=None: self.attributes['to']=to if dur!=None: @@ -929,7 +929,7 @@ class svg(SVGelement): d.toXml() """ def __init__(self,viewBox=None, width=None, height=None,**args): - SVGelement.__init__(self,'svg',**args) + SVGelement.__init__(self, 'svg', **args) if viewBox!=None: self.attributes['viewBox']=_viewboxlist(viewBox) if width!=None: @@ -952,7 +952,7 @@ class drawing: def __init__(self, entity={}): self.svg=None self.entity = entity - def setSVG(self,svg): + def setSVG(self, svg): self.svg=svg # Voeg een element toe aan de grafiek toe. if use_dom_implementation==0: @@ -967,12 +967,12 @@ class drawing: xml.write("\n" % (item, self.entity[item])) xml.write("]") xml.write(">\n") - self.svg.toXml(0,xml) + self.svg.toXml(0, xml) if not filename: if compress: import gzip f=cStringIO.StringIO() - zf=gzip.GzipFile(fileobj=f,mode='wb') + zf=gzip.GzipFile(fileobj=f, mode='wb') zf.write(xml.getvalue()) zf.close() f.seek(0) @@ -982,11 +982,11 @@ class drawing: else: if filename[-4:]=='svgz': import gzip - f=gzip.GzipFile(filename=filename,mode="wb", compresslevel=9) + f=gzip.GzipFile(filename=filename, mode="wb", compresslevel=9) f.write(xml.getvalue()) f.close() else: - f=file(filename,'w') + f=file(filename, 'w') f.write(xml.getvalue()) f.close() @@ -997,40 +997,40 @@ class drawing: writes a svg drawing to the screen or to a file compresses if filename ends with svgz or if compress is true """ - doctype = implementation.createDocumentType('svg',"-//W3C//DTD SVG 1.0//EN""",'http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd ') + doctype = implementation.createDocumentType('svg', "-//W3C//DTD SVG 1.0//EN""", 'http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd ') global root # root is defined global so it can be used by the appender. Its also possible to use it as an arugument but # that is a bit messy. - root=implementation.createDocument(None,None,doctype) + root=implementation.createDocument(None, None, doctype) # Create the xml document. global appender - def appender(element,elementroot): + def appender(element, elementroot): """This recursive function appends elements to an element and sets the attributes and type. It stops when alle elements have been appended""" if element.namespace: - e=root.createElementNS(element.namespace,element.type) + e=root.createElementNS(element.namespace, element.type) else: e=root.createElement(element.type) if element.text: textnode=root.createTextNode(element.text) e.appendChild(textnode) for attribute in list(element.attributes.keys()): #in element.attributes is supported from python 2.2 - e.setAttribute(attribute,str(element.attributes[attribute])) + e.setAttribute(attribute, str(element.attributes[attribute])) if element.elements: for el in element.elements: - e=appender(el,e) + e=appender(el, e) elementroot.appendChild(e) return elementroot - root=appender(self.svg,root) + root=appender(self.svg, root) if not filename: import cStringIO xml=cStringIO.StringIO() - PrettyPrint(root,xml) + PrettyPrint(root, xml) if compress: import gzip f=cStringIO.StringIO() - zf=gzip.GzipFile(fileobj=f,mode='wb') + zf=gzip.GzipFile(fileobj=f, mode='wb') zf.write(xml.getvalue()) zf.close() f.seek(0) @@ -1043,13 +1043,13 @@ class drawing: import gzip import cStringIO xml=cStringIO.StringIO() - PrettyPrint(root,xml) - f=gzip.GzipFile(filename=filename,mode='wb',compresslevel=9) + PrettyPrint(root, xml) + f=gzip.GzipFile(filename=filename, mode='wb', compresslevel=9) f.write(xml.getvalue()) f.close() else: - f=open(filename,'w') - PrettyPrint(root,f) + f=open(filename, 'w') + PrettyPrint(root, f) f.close() except: print(("Cannot write SVG file: " + filename)) @@ -1070,32 +1070,32 @@ if __name__=='__main__': d=drawing() - s=svg((0,0,100,100)) - r=rect(-100,-100,300,300,'cyan') + s=svg((0, 0, 100, 100)) + r=rect(-100, -100, 300, 300, 'cyan') s.addElement(r) t=title('SVGdraw Demo') s.addElement(t) g=group('animations') - e=ellipse(0,0,5,2) + e=ellipse(0, 0, 5, 2) g.addElement(e) - c=circle(0,0,1,'red') + c=circle(0, 0, 1, 'red') g.addElement(c) - pd=pathdata(0,-10) + pd=pathdata(0, -10) for i in range(6): - pd.relsmbezier(10,5,0,10) - pd.relsmbezier(-10,5,0,10) - an=animateMotion(pd,10) + pd.relsmbezier(10, 5, 0, 10) + pd.relsmbezier(-10, 5, 0, 10) + an=animateMotion(pd, 10) an.attributes['rotate']='auto-reverse' an.attributes['repeatCount']="indefinite" g.addElement(an) s.addElement(g) - for i in range(20,120,20): - u=use('#animations',i,0) + for i in range(20, 120, 20): + u=use('#animations', i, 0) s.addElement(u) - for i in range(0,120,20): - for j in range(5,105,10): - c=circle(i,j,1,'red','black',.5) + for i in range(0, 120, 20): + for j in range(5, 105, 10): + c=circle(i, j, 1, 'red', 'black', .5) s.addElement(c) d.setSVG(s) diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 51a87fe1..68ef0f04 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -15,7 +15,7 @@ OVERRIDES = {} def app_set(command_id, value): """Set application wide value""" - app.config.setdefault(command_id,value) + app.config.setdefault(command_id, value) return value def get_setting(command_id,guess=None): @@ -45,7 +45,7 @@ def get_setting(command_id,guess=None): def value(command): if command: # sys.stderr.write("Found "+command+"\n") - app_set(command_id,command) + app_set(command_id, command) return command else: return None @@ -68,7 +68,7 @@ def get_setting(command_id,guess=None): def get_setting_bool(id): v = get_setting(id) - if v not in [0,False,'False','FALSE',None]: + if v not in [0, False, 'False', 'FALSE', None]: return True return False @@ -108,16 +108,16 @@ def js_path(module=None): raise "No JS path found for "+module+" (if not in Guix check JS_GN_PATH)" def reaper_command(guess=None): - return get_setting("REAPER_COMMAND",guess) + return get_setting("REAPER_COMMAND", guess) def gemma_command(guess=None): - return assert_bin(get_setting("GEMMA_COMMAND",guess)) + return assert_bin(get_setting("GEMMA_COMMAND", guess)) def gemma_wrapper_command(guess=None): - return assert_bin(get_setting("GEMMA_WRAPPER_COMMAND",guess)) + return assert_bin(get_setting("GEMMA_WRAPPER_COMMAND", guess)) def plink_command(guess=None): - return assert_bin(get_setting("PLINK_COMMAND",guess)) + return assert_bin(get_setting("PLINK_COMMAND", guess)) def flat_file_exists(subdir): base = get_setting("GENENETWORK_FILES") @@ -180,7 +180,7 @@ def locate(name, subdir=None): raise Exception("Can not locate "+name+" in "+base) def locate_phewas(name, subdir=None): - return locate(name,'/phewas/'+subdir) + return locate(name, '/phewas/'+subdir) def locate_ignore_error(name, subdir=None): """ @@ -204,7 +204,7 @@ def tempdir(): """ Get UNIX TMPDIR by default """ - return valid_path(get_setting("TMPDIR","/tmp")) + return valid_path(get_setting("TMPDIR", "/tmp")) BLUE = '\033[94m' GREEN = '\033[92m' @@ -225,9 +225,9 @@ def show_settings(): 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 @@ -279,10 +279,10 @@ SMTP_CONNECT = get_setting('SMTP_CONNECT') SMTP_USERNAME = get_setting('SMTP_USERNAME') SMTP_PASSWORD = get_setting('SMTP_PASSWORD') -REAPER_COMMAND = app_set("REAPER_COMMAND",reaper_command()) -GEMMA_COMMAND = app_set("GEMMA_COMMAND",gemma_command()) +REAPER_COMMAND = app_set("REAPER_COMMAND", reaper_command()) +GEMMA_COMMAND = app_set("GEMMA_COMMAND", gemma_command()) assert(GEMMA_COMMAND is not None) -PLINK_COMMAND = app_set("PLINK_COMMAND",plink_command()) +PLINK_COMMAND = app_set("PLINK_COMMAND", plink_command()) GEMMA_WRAPPER_COMMAND = gemma_wrapper_command() TEMPDIR = tempdir() # defaults to UNIX TMPDIR assert_dir(TEMPDIR) @@ -295,11 +295,11 @@ assert_dir(JS_GUIX_PATH+'/cytoscape-panzoom') CSS_PATH = JS_GUIX_PATH # The CSS is bundled together with the JS # assert_dir(JS_PATH) -JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH",js_path("javascript-twitter-post-fetcher")) +JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH", js_path("javascript-twitter-post-fetcher")) assert_dir(JS_TWITTER_POST_FETCHER_PATH) assert_file(JS_TWITTER_POST_FETCHER_PATH+"/js/twitterFetcher_min.js") -JS_CYTOSCAPE_PATH = get_setting("JS_CYTOSCAPE_PATH",js_path("cytoscape")) +JS_CYTOSCAPE_PATH = get_setting("JS_CYTOSCAPE_PATH", js_path("cytoscape")) assert_dir(JS_CYTOSCAPE_PATH) assert_file(JS_CYTOSCAPE_PATH+'/cytoscape.min.js') diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py index 79991149..77cc3416 100644 --- a/wqflask/utility/webqtlUtil.py +++ b/wqflask/utility/webqtlUtil.py @@ -41,22 +41,22 @@ ParInfo ={ 'C57BL-6JxC57BL-6NJF2':['', '', 'C57BL/6J', 'C57BL/6NJ'], 'BXD300':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'], 'B6BTBRF2':['B6BTBRF1', 'BTBRB6F1', 'C57BL/6J', 'BTBRT<+>tf/J'], -'BHHBF2':['B6HF2','HB6F2','C57BL/6J','C3H/HeJ'], -'BHF2':['B6HF2','HB6F2','C57BL/6J','C3H/HeJ'], +'BHHBF2':['B6HF2', 'HB6F2', 'C57BL/6J', 'C3H/HeJ'], +'BHF2':['B6HF2', 'HB6F2', 'C57BL/6J', 'C3H/HeJ'], 'B6D2F2':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'], 'BDF2-1999':['B6D2F2', 'D2B6F2', 'C57BL/6J', 'DBA/2J'], 'BDF2-2005':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'], -'CTB6F2':['CTB6F2','B6CTF2','C57BL/6J','Castaneous'], +'CTB6F2':['CTB6F2', 'B6CTF2', 'C57BL/6J', 'Castaneous'], 'CXB':['CBF1', 'BCF1', 'C57BL/6ByJ', 'BALB/cByJ'], 'AXBXA':['ABF1', 'BAF1', 'C57BL/6J', 'A/J'], 'AXB':['ABF1', 'BAF1', 'C57BL/6J', 'A/J'], 'BXA':['BAF1', 'ABF1', 'C57BL/6J', 'A/J'], 'LXS':['LSF1', 'SLF1', 'ISS', 'ILS'], 'HXBBXH':['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv'], -'BayXSha':['BayXShaF1', 'ShaXBayF1', 'Bay-0','Shahdara'], -'ColXBur':['ColXBurF1', 'BurXColF1', 'Col-0','Bur-0'], -'ColXCvi':['ColXCviF1', 'CviXColF1', 'Col-0','Cvi'], -'SXM':['SMF1', 'MSF1', 'Steptoe','Morex'], +'BayXSha':['BayXShaF1', 'ShaXBayF1', 'Bay-0', 'Shahdara'], +'ColXBur':['ColXBurF1', 'BurXColF1', 'Col-0', 'Bur-0'], +'ColXCvi':['ColXCviF1', 'CviXColF1', 'Col-0', 'Cvi'], +'SXM':['SMF1', 'MSF1', 'Steptoe', 'Morex'], 'HRDP':['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv'] } @@ -91,7 +91,7 @@ def readLineCSV(line): ### dcrowell July 2008 returnList[0]=returnList[0][1:] return returnList -def cmpEigenValue(A,B): +def cmpEigenValue(A, B): try: if A[0] > B[0]: return -1 diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py index 3fa1d5ba..b81da0dc 100644 --- a/wqflask/wqflask/api/router.py +++ b/wqflask/wqflask/api/router.py @@ -558,10 +558,10 @@ def trait_sample_data(dataset_name, trait_name, file_format = "json"): sample_list = [] for sample in sample_data: sample_dict = { - "sample_name" : sample[0], - "sample_name_2" : sample[1], - "value" : sample[2], - "data_id" : sample[3], + "sample_name": sample[0], + "sample_name_2": sample[1], + "value": sample[2], + "data_id": sample[3], } if sample[4]: sample_dict["se"] = sample[4] diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 15a21ee6..4116e2df 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -108,17 +108,17 @@ class CorrelationResults(object): self.sample_data = {} self.corr_type = start_vars['corr_type'] self.corr_method = start_vars['corr_sample_method'] - 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) + 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 = 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.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') else: self.location_chr = self.min_location_mb = self.max_location_mb = None diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index 832746bb..b582cd23 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -275,8 +275,8 @@ def zScore(trait_data_array): i = 0 for data in trait_data_array: N = len(data) - S = reduce(lambda x,y: x+y, data, 0.) - SS = reduce(lambda x,y: x+y*y, data, 0.) + S = reduce(lambda x, y: x+y, data, 0.) + SS = reduce(lambda x, y: x+y*y, data, 0.) mean = S/N var = SS - S*S/N stdev = math.sqrt(var/(N-1)) @@ -294,7 +294,7 @@ def sortEigenVectors(vector): combines = [] i = 0 for item in eigenValues: - combines.append([eigenValues[i],eigenVectors[i]]) + combines.append([eigenValues[i], eigenVectors[i]]) i += 1 combines.sort(webqtlUtil.cmpEigenValue) A = [] @@ -302,7 +302,7 @@ def sortEigenVectors(vector): for item in combines: A.append(item[0]) B.append(item[1]) - sum = reduce(lambda x,y: x+y, A, 0.0) + sum = reduce(lambda x, y: x+y, A, 0.0) A = [x*100.0/sum for x in A] return [A, B] except: diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 1e15d28f..cc9c1860 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -46,8 +46,8 @@ class DoSearch(object): def handle_wildcard(self, str): keyword = str.strip() - keyword = keyword.replace("*",".*") - keyword = keyword.replace("?",".") + keyword = keyword.replace("*", ".*") + keyword = keyword.replace("?", ".") return keyword diff --git a/wqflask/wqflask/external_tools/send_to_geneweaver.py b/wqflask/wqflask/external_tools/send_to_geneweaver.py index 7a5dba73..9844bab4 100644 --- a/wqflask/wqflask/external_tools/send_to_geneweaver.py +++ b/wqflask/wqflask/external_tools/send_to_geneweaver.py @@ -54,10 +54,10 @@ class SendToGeneWeaver(object): trait_name_list = get_trait_name_list(self.trait_list) self.hidden_vars = { - 'client' : "genenetwork", - 'species' : species_name, - 'idtype' : self.chip_name, - 'list' : string.join(trait_name_list, ","), + 'client': "genenetwork", + 'species': species_name, + 'idtype': self.chip_name, + 'list': string.join(trait_name_list, ","), } def get_trait_name_list(trait_list): diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index c8b9c405..f282b010 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -27,8 +27,8 @@ import datetime import string from math import * -from PIL import (Image,ImageDraw,ImageFont,ImageColor) -import sys,os +from PIL import (Image, ImageDraw, ImageFont, ImageColor) +import sys, os import cPickle import httplib import json @@ -426,7 +426,7 @@ class DisplayMappingResults(object): else: continue samplelist = list(self.genotype.prgy) - for j,_geno in enumerate (self.genotype[0][1].genotype): + for j, _geno in enumerate (self.genotype[0][1].genotype): for item in smd: if item.name == samplelist[j]: self.NR_INDIVIDUALS = self.NR_INDIVIDUALS + 1 @@ -518,7 +518,7 @@ class DisplayMappingResults(object): #Scales plot differently for high resolution if self.draw2X: - intCanvasX2 = Image.new("RGBA", size=(self.graphWidth*2,self.graphHeight*2)) + intCanvasX2 = Image.new("RGBA", size=(self.graphWidth*2, self.graphHeight*2)) gifmapX2 = self.plotIntMapping(intCanvasX2, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm, zoom=2) intCanvasX2.save( "{}.png".format( @@ -745,17 +745,17 @@ class DisplayMappingResults(object): bootScale = bootScale[:-1] + [highestPercent] bootOffset = 50*fontZoom - bootScaleFont=ImageFont.truetype(font=VERDANA_FILE,size=13*fontZoom) + bootScaleFont=ImageFont.truetype(font=VERDANA_FILE, size=13*fontZoom) im_drawer.rectangle( xy=((canvas.size[0]-bootOffset, yZero-bootHeightThresh), - (canvas.size[0]-bootOffset-15*zoom,yZero)), + (canvas.size[0]-bootOffset-15*zoom, yZero)), fill = YELLOW, outline=BLACK) im_drawer.line( xy=((canvas.size[0]-bootOffset+4, yZero), (canvas.size[0]-bootOffset, yZero)), fill=BLACK) TEXT_Y_DISPLACEMENT = -8 - im_drawer.text(xy=(canvas.size[0]-bootOffset+10,yZero+TEXT_Y_DISPLACEMENT), text='0%', + im_drawer.text(xy=(canvas.size[0]-bootOffset+10, yZero+TEXT_Y_DISPLACEMENT), text='0%', font=bootScaleFont, fill=BLACK) for item in bootScale: @@ -763,10 +763,10 @@ class DisplayMappingResults(object): continue bootY = yZero-bootHeightThresh*item/highestPercent im_drawer.line( - xy=((canvas.size[0]-bootOffset+4,bootY), - (canvas.size[0]-bootOffset,bootY)), + xy=((canvas.size[0]-bootOffset+4, bootY), + (canvas.size[0]-bootOffset, bootY)), fill=BLACK) - im_drawer.text(xy=(canvas.size[0]-bootOffset+10,bootY+TEXT_Y_DISPLACEMENT), + im_drawer.text(xy=(canvas.size[0]-bootOffset+10, bootY+TEXT_Y_DISPLACEMENT), text='%2.1f'%item, font=bootScaleFont, fill=BLACK) if self.legendChecked: @@ -775,7 +775,7 @@ class DisplayMappingResults(object): smallLabelFont = ImageFont.truetype(font=TREBUC_FILE, size=12*fontZoom) leftOffset = xLeftOffset+(nCol-1)*200 im_drawer.rectangle( - xy=((leftOffset,startPosY-6), (leftOffset+12,startPosY+6)), + xy=((leftOffset, startPosY-6), (leftOffset+12, startPosY+6)), fill=YELLOW, outline=BLACK) im_drawer.text(xy=(leftOffset+ 20, startPosY+TEXT_Y_DISPLACEMENT), text='Frequency of the Peak LRS', @@ -872,7 +872,7 @@ class DisplayMappingResults(object): TEXT_Y_DISPLACEMENT = -8 im_drawer.text( text="Sequence Site", - xy=(leftOffset+15,startPosY+TEXT_Y_DISPLACEMENT), font=smallLabelFont, + xy=(leftOffset+15, startPosY+TEXT_Y_DISPLACEMENT), font=smallLabelFont, fill=self.TOP_RIGHT_INFO_COLOR) def drawSNPTrackNew(self, canvas, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None): @@ -922,7 +922,7 @@ class DisplayMappingResults(object): def drawMultiTraitName(self, fd, canvas, gifmap, showLocusForm, offset= (40, 120, 80, 10), zoom = 1): nameWidths = [] yPaddingTop = 10 - colorFont=ImageFont.truetype(font=TREBUC_FILE,size=12) + colorFont=ImageFont.truetype(font=TREBUC_FILE, size=12) if len(self.qtlresults) >20 and self.selectedChr > -1: rightShift = 20 rightShiftStep = 60 @@ -941,20 +941,20 @@ class DisplayMappingResults(object): rightShift += rightShiftStep name = thisTrait.displayName() - nameWidth, nameHeight = im_drawer.textsize(name,font=colorFont) + nameWidth, nameHeight = im_drawer.textsize(name, font=colorFont) nameWidths.append(nameWidth) im_drawer.rectangle( - xy=((rightShift,yPaddingTop+kstep*15), - (rectWidth+rightShift,yPaddingTop+10+kstep*15)), + xy=((rightShift, yPaddingTop+kstep*15), + (rectWidth+rightShift, yPaddingTop+10+kstep*15)), fill=thisLRSColor, outline=BLACK) im_drawer.text( - text=name,xy=(rectWidth+2+rightShift,yPaddingTop+10+kstep*15), - font=colorFont,fill=BLACK) + text=name, xy=(rectWidth+2+rightShift, yPaddingTop+10+kstep*15), + font=colorFont, fill=BLACK) if thisTrait.db: - COORDS = "%d,%d,%d,%d" %(rectWidth+2+rightShift,yPaddingTop+kstep*15,rectWidth+2+rightShift+nameWidth,yPaddingTop+10+kstep*15,) + COORDS = "%d,%d,%d,%d" %(rectWidth+2+rightShift, yPaddingTop+kstep*15, rectWidth+2+rightShift+nameWidth, yPaddingTop+10+kstep*15,) HREF= "javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm, thisTrait.db.name, thisTrait.name) - Areas = HT.Area(shape='rect',coords=COORDS,href=HREF) + Areas = HT.Area(shape='rect', coords=COORDS, href=HREF) gifmap.areas.append(Areas) def drawLegendPanel(self, canvas, offset= (40, 120, 80, 10), zoom = 1): @@ -968,80 +968,80 @@ class DisplayMappingResults(object): if zoom == 2: fontZoom = 1.5 - labelFont=ImageFont.truetype(font=TREBUC_FILE,size=12*fontZoom) + labelFont=ImageFont.truetype(font=TREBUC_FILE, size=12*fontZoom) startPosY = 15 stepPosY = 12*fontZoom if self.manhattan_plot != True: im_drawer.line( - xy=((xLeftOffset,startPosY),(xLeftOffset+32,startPosY)), + xy=((xLeftOffset, startPosY), (xLeftOffset+32, startPosY)), fill=self.LRS_COLOR, width=2) im_drawer.text( - text=self.LRS_LOD, xy=(xLeftOffset+40,startPosY+TEXT_Y_DISPLACEMENT), - font=labelFont,fill=BLACK) + text=self.LRS_LOD, xy=(xLeftOffset+40, startPosY+TEXT_Y_DISPLACEMENT), + font=labelFont, fill=BLACK) startPosY += stepPosY if self.additiveChecked: startPosX = xLeftOffset im_drawer.line( - xy=((startPosX,startPosY),(startPosX+17,startPosY)), + xy=((startPosX, startPosY), (startPosX+17, startPosY)), fill=self.ADDITIVE_COLOR_POSITIVE, width=2) im_drawer.line( - xy=((startPosX+18,startPosY),(startPosX+32,startPosY)), + xy=((startPosX+18, startPosY), (startPosX+32, startPosY)), fill=self.ADDITIVE_COLOR_NEGATIVE, width=2) im_drawer.text( - text='Additive Effect',xy=(startPosX+40,startPosY+TEXT_Y_DISPLACEMENT), - font=labelFont,fill=BLACK) + text='Additive Effect', xy=(startPosX+40, startPosY+TEXT_Y_DISPLACEMENT), + font=labelFont, fill=BLACK) if self.genotype.type == 'intercross' and self.dominanceChecked: startPosX = xLeftOffset startPosY += stepPosY im_drawer.line( - xy=((startPosX,startPosY),(startPosX+17,startPosY)), + xy=((startPosX, startPosY), (startPosX+17, startPosY)), fill=self.DOMINANCE_COLOR_POSITIVE, width=4) im_drawer.line( - xy=((startPosX+18,startPosY),(startPosX+35,startPosY)), + xy=((startPosX+18, startPosY), (startPosX+35, startPosY)), fill=self.DOMINANCE_COLOR_NEGATIVE, width=4) im_drawer.text( - text='Dominance Effect', xy=(startPosX+42,startPosY+5), - font=labelFont,fill=BLACK) + text='Dominance Effect', xy=(startPosX+42, startPosY+5), + font=labelFont, fill=BLACK) if self.haplotypeAnalystChecked: startPosY += stepPosY startPosX = xLeftOffset im_drawer.line( - xy=((startPosX,startPosY),(startPosX+17,startPosY)), + xy=((startPosX, startPosY), (startPosX+17, startPosY)), fill=self.HAPLOTYPE_POSITIVE, width=4) im_drawer.line( - xy=((startPosX+18,startPosY),(startPosX+35,startPosY)), + xy=((startPosX+18, startPosY), (startPosX+35, startPosY)), fill=self.HAPLOTYPE_NEGATIVE, width=4) im_drawer.line( - xy=((startPosX+36,startPosY),(startPosX+53,startPosY)), + xy=((startPosX+36, startPosY), (startPosX+53, startPosY)), fill=self.HAPLOTYPE_HETEROZYGOUS, width=4) im_drawer.line( - xy=((startPosX+54,startPosY),(startPosX+67,startPosY)), + xy=((startPosX+54, startPosY), (startPosX+67, startPosY)), fill=self.HAPLOTYPE_RECOMBINATION, width=4) im_drawer.text( text='Haplotypes (Pat, Mat, Het, Unk)', - xy=(startPosX+76,startPosY+5),font=labelFont,fill=BLACK) + xy=(startPosX+76, startPosY+5), font=labelFont, fill=BLACK) if self.permChecked and self.nperm > 0: startPosY += stepPosY startPosX = xLeftOffset im_drawer.line( - xy=((startPosX, startPosY),( startPosX + 32, startPosY)), + xy=((startPosX, startPosY), ( startPosX + 32, startPosY)), fill=self.SIGNIFICANT_COLOR, width=self.SIGNIFICANT_WIDTH) im_drawer.line( - xy=((startPosX, startPosY + stepPosY),( startPosX + 32, startPosY + stepPosY)), + xy=((startPosX, startPosY + stepPosY), ( startPosX + 32, startPosY + stepPosY)), fill=self.SUGGESTIVE_COLOR, width=self.SUGGESTIVE_WIDTH) im_drawer.text( - text='Significant %s = %2.2f' % (self.LRS_LOD,self.significant), - xy=(xLeftOffset+42,startPosY+TEXT_Y_DISPLACEMENT),font=labelFont,fill=BLACK) + text='Significant %s = %2.2f' % (self.LRS_LOD, self.significant), + xy=(xLeftOffset+42, startPosY+TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK) im_drawer.text( text='Suggestive %s = %2.2f' % (self.LRS_LOD, self.suggestive), - xy=(xLeftOffset+42,startPosY + TEXT_Y_DISPLACEMENT +stepPosY),font=labelFont, + xy=(xLeftOffset+42, startPosY + TEXT_Y_DISPLACEMENT +stepPosY), font=labelFont, fill=BLACK) - labelFont = ImageFont.truetype(font=VERDANA_FILE,size=12*fontZoom) + labelFont = ImageFont.truetype(font=VERDANA_FILE, size=12*fontZoom) labelColor = BLACK if self.dataset.type == "Publish" or self.dataset.type == "Geno": dataset_label = self.dataset.fullname @@ -1109,22 +1109,22 @@ class DisplayMappingResults(object): im_drawer.textsize(string2, font=labelFont)[0]) im_drawer.text( text=identification, - xy=(canvas.size[0] - xRightOffset-d,20*fontZoom),font=labelFont, + xy=(canvas.size[0] - xRightOffset-d, 20*fontZoom), font=labelFont, fill=labelColor) else: d = 4+ max( im_drawer.textsize(string1, font=labelFont)[0], im_drawer.textsize(string2, font=labelFont)[0]) im_drawer.text( - text=string1,xy=(canvas.size[0] - xRightOffset-d,35*fontZoom), - font=labelFont,fill=labelColor) + text=string1, xy=(canvas.size[0] - xRightOffset-d, 35*fontZoom), + font=labelFont, fill=labelColor) im_drawer.text( - text=string2,xy=(canvas.size[0] - xRightOffset-d,50*fontZoom), - font=labelFont,fill=labelColor) + text=string2, xy=(canvas.size[0] - xRightOffset-d, 50*fontZoom), + font=labelFont, fill=labelColor) if string3 != '': im_drawer.text( - text=string3,xy=(canvas.size[0] - xRightOffset-d,65*fontZoom), - font=labelFont,fill=labelColor) + text=string3, xy=(canvas.size[0] - xRightOffset-d, 65*fontZoom), + font=labelFont, fill=labelColor) def drawGeneBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None): @@ -1345,7 +1345,7 @@ class DisplayMappingResults(object): labelText = "3'" im_drawer.text( text=labelText, - xy=(utrEndPix+2,geneYLocation+self.EACH_GENE_HEIGHT), + xy=(utrEndPix+2, geneYLocation+self.EACH_GENE_HEIGHT), font=ImageFont.truetype(font=ARIAL_FILE, size=2)) #draw the genes as rectangles @@ -1357,7 +1357,7 @@ class DisplayMappingResults(object): COORDS = "%d, %d, %d, %d" %(geneStartPix, geneYLocation, geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT)) # NL: 06-02-2011 Rob required to display NCBI info in a new window - gifmap.areas.append(HT.Area(shape='rect',coords=COORDS,href=HREF, title=TITLE,target="_blank")) + gifmap.areas.append(HT.Area(shape='rect', coords=COORDS, href=HREF, title=TITLE, target="_blank")) ## BEGIN HaplotypeAnalyst def drawHaplotypeBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None): @@ -1490,7 +1490,7 @@ class DisplayMappingResults(object): counter = counter + 1 if item.name == samplelist[k]: ind = counter - maxind=max(ind,maxind) + maxind=max(ind, maxind) # lines if (oldgeno[k] == -1 and _geno == -1): @@ -1523,7 +1523,7 @@ class DisplayMappingResults(object): COORDS = "%d, %d, %d, %d" %(geneStartPix, geneYLocation+ind*self.EACH_GENE_HEIGHT, geneEndPix+1, (geneYLocation + ind*self.EACH_GENE_HEIGHT)) TITLE = "Strain: %s, marker (%s) \n Position %2.3f Mb." % (samplelist[k], _chr[j].name, float(txStart)) HREF = '' - gifmap.areas.append(HT.Area(shape='rect',coords=COORDS,href=HREF, title=TITLE)) + gifmap.areas.append(HT.Area(shape='rect', coords=COORDS, href=HREF, title=TITLE)) # if there are no more markers in a chromosome, the plotRight value calculated above will be before the plotWidth # resulting in some empty space on the right side of the plot area. This draws an "unknown" bar from plotRight to the edge. @@ -1642,14 +1642,14 @@ class DisplayMappingResults(object): WEBQTL_HREF = "javascript:rangeView('%s', %f, %f)" % (self.selectedChr - 1, max(0, (calBase-webqtlZoomWidth))/1000000.0, (calBase+webqtlZoomWidth)/1000000.0) WEBQTL_TITLE = "Click to view this section of the genome in WebQTL" - gifmap.areas.append(HT.Area(shape='rect',coords=WEBQTL_COORDS,href=WEBQTL_HREF, title=WEBQTL_TITLE)) + gifmap.areas.append(HT.Area(shape='rect', coords=WEBQTL_COORDS, href=WEBQTL_HREF, title=WEBQTL_TITLE)) im_drawer.rectangle( xy=((xBrowse1, paddingTop), (xBrowse2, (paddingTop + self.BAND_HEIGHT))), outline=self.CLICKABLE_WEBQTL_REGION_COLOR, fill=self.CLICKABLE_WEBQTL_REGION_COLOR) im_drawer.line( - xy=((xBrowse1, paddingTop),( xBrowse1, (paddingTop + self.BAND_HEIGHT))), + xy=((xBrowse1, paddingTop), ( xBrowse1, (paddingTop + self.BAND_HEIGHT))), fill=self.CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR) if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat": @@ -1659,14 +1659,14 @@ class DisplayMappingResults(object): else: PHENOGEN_HREF = "https://phenogen.org/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases) PHENOGEN_TITLE = "Click to view this section of the genome in PhenoGen" - gifmap.areas.append(HT.Area(shape='rect',coords=PHENOGEN_COORDS,href=PHENOGEN_HREF, title=PHENOGEN_TITLE)) + gifmap.areas.append(HT.Area(shape='rect', coords=PHENOGEN_COORDS, href=PHENOGEN_HREF, title=PHENOGEN_TITLE)) im_drawer.rectangle( xy=((xBrowse1, phenogenPaddingTop), (xBrowse2, (phenogenPaddingTop+self.BAND_HEIGHT))), outline=self.CLICKABLE_PHENOGEN_REGION_COLOR, fill=self.CLICKABLE_PHENOGEN_REGION_COLOR) im_drawer.line( - xy=((xBrowse1, phenogenPaddingTop),( xBrowse1, (phenogenPaddingTop+self.BAND_HEIGHT))), + xy=((xBrowse1, phenogenPaddingTop), ( xBrowse1, (phenogenPaddingTop+self.BAND_HEIGHT))), fill=self.CLICKABLE_PHENOGEN_REGION_OUTLINE_COLOR) UCSC_COORDS = "%d, %d, %d, %d" %(xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop+self.BAND_HEIGHT)) @@ -1675,7 +1675,7 @@ class DisplayMappingResults(object): else: UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d" % (self._ucscDb, self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases) UCSC_TITLE = "Click to view this section of the genome in the UCSC Genome Browser" - gifmap.areas.append(HT.Area(shape='rect',coords=UCSC_COORDS,href=UCSC_HREF, title=UCSC_TITLE)) + gifmap.areas.append(HT.Area(shape='rect', coords=UCSC_COORDS, href=UCSC_HREF, title=UCSC_TITLE)) im_drawer.rectangle( xy=((xBrowse1, ucscPaddingTop), (xBrowse2, (ucscPaddingTop+self.BAND_HEIGHT))), @@ -1692,7 +1692,7 @@ class DisplayMappingResults(object): else: ENSEMBL_HREF = "http://www.ensembl.org/Rattus_norvegicus/contigview?chr=%s&start=%d&end=%d" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases) ENSEMBL_TITLE = "Click to view this section of the genome in the Ensembl Genome Browser" - gifmap.areas.append(HT.Area(shape='rect',coords=ENSEMBL_COORDS,href=ENSEMBL_HREF, title=ENSEMBL_TITLE)) + gifmap.areas.append(HT.Area(shape='rect', coords=ENSEMBL_COORDS, href=ENSEMBL_HREF, title=ENSEMBL_TITLE)) im_drawer.rectangle( xy=((xBrowse1, ensemblPaddingTop), (xBrowse2, (ensemblPaddingTop+self.BAND_HEIGHT))), @@ -1789,8 +1789,8 @@ class DisplayMappingResults(object): continue Xc = xLeftOffset + plotXScale*(_Mb - startMb) if counter % NUM_MINOR_TICKS == 0: # Draw a MAJOR mark, not just a minor tick mark - im_drawer.line(xy=((Xc,yZero), - (Xc,yZero+xMajorTickHeight)), + im_drawer.line(xy=((Xc, yZero), + (Xc, yZero+xMajorTickHeight)), fill=xAxisTickMarkColor, width=X_MAJOR_TICK_THICKNESS) # Draw the MAJOR tick mark labelStr = str(formatStr % _Mb) # What Mbase location to put on the label @@ -1800,8 +1800,8 @@ class DisplayMappingResults(object): text=labelStr, font=MBLabelFont, fill=xAxisLabelColor) else: - im_drawer.line(xy=((Xc,yZero), - (Xc,yZero+xMinorTickHeight)), + im_drawer.line(xy=((Xc, yZero), + (Xc, yZero+xMinorTickHeight)), fill=xAxisTickMarkColor, width=X_MINOR_TICK_THICKNESS) # Draw the MINOR tick mark @@ -1834,7 +1834,7 @@ class DisplayMappingResults(object): text="Megabases", xy=( xLeftOffset+(plotWidth-im_drawer.textsize( - "Megabases",font=megabaseLabelFont)[0])/2, + "Megabases", font=megabaseLabelFont)[0])/2, strYLoc+MBLabelFont.font.height+10*(zoom%2)), font=megabaseLabelFont, fill=BLACK) pass @@ -1889,7 +1889,7 @@ class DisplayMappingResults(object): for j, ChrInfo in enumerate(ChrAInfo): preLpos = -1 for i, item in enumerate(ChrInfo): - Lname,Lpos = item + Lname, Lpos = item if Lpos != preLpos: offsetA += stepA differ = 1 @@ -1903,17 +1903,17 @@ class DisplayMappingResults(object): Zorder = 0 if differ: im_drawer.line( - xy=((startPosX+Lpos,yZero),(xLeftOffset+offsetA,\ + xy=((startPosX+Lpos, yZero), (xLeftOffset+offsetA,\ yZero+25)), fill=lineColor) im_drawer.line( - xy=((xLeftOffset+offsetA,yZero+25),(xLeftOffset+offsetA,\ + xy=((xLeftOffset+offsetA, yZero+25), (xLeftOffset+offsetA,\ yZero+40+Zorder*(LRectWidth+3))), fill=lineColor) rectColor = ORANGE else: im_drawer.line( - xy=((xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)-3),(\ + xy=((xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)-3), (\ xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3))), fill=lineColor) rectColor = DEEPPINK @@ -1921,9 +1921,9 @@ class DisplayMappingResults(object): xy=((xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)), (xLeftOffset+offsetA-LRectHeight, yZero+40+Zorder*(LRectWidth+3)+LRectWidth)), - outline=rectColor,fill=rectColor,width = 0) + outline=rectColor, fill=rectColor, width = 0) COORDS="%d,%d,%d,%d"%(xLeftOffset+offsetA-LRectHeight, yZero+40+Zorder*(LRectWidth+3),\ - xLeftOffset+offsetA,yZero+40+Zorder*(LRectWidth+3)+LRectWidth) + xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)+LRectWidth) HREF="/show_trait?trait_id=%s&dataset=%s" % (Lname, self.dataset.group.name+"Geno") #HREF="javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm,fd.RISet+"Geno", Lname) Areas=HT.Area(shape='rect', coords=COORDS, href=HREF, target="_blank", title="Locus : " + Lname) @@ -1931,7 +1931,7 @@ class DisplayMappingResults(object): ##piddle bug if j == 0: im_drawer.line( - xy=((startPosX,yZero),(startPosX,yZero+40)), + xy=((startPosX, yZero), (startPosX, yZero+40)), fill=lineColor) startPosX += (self.ChrLengthDistList[j]+self.GraphInterval)*plotXScale @@ -1943,7 +1943,7 @@ class DisplayMappingResults(object): strYLoc + MBLabelFont.font.height+ 10*(zoom%2)), font=centimorganLabelFont, fill=BLACK) - im_drawer.line(xy=((xLeftOffset,yZero), (xLeftOffset+plotWidth,yZero)), + im_drawer.line(xy=((xLeftOffset, yZero), (xLeftOffset+plotWidth, yZero)), fill=BLACK, width=X_AXIS_THICKNESS) # Draw the X axis itself @@ -2079,7 +2079,7 @@ class DisplayMappingResults(object): LRS_LOD_Max = 0.000001 yTopOffset + 30*(zoom - 1) yLRS = yZero - (item/LRS_LOD_Max) * LRSHeightThresh - im_drawer.line(xy=((xLeftOffset,yLRS), (xLeftOffset-4,yLRS)), + im_drawer.line(xy=((xLeftOffset, yLRS), (xLeftOffset-4, yLRS)), fill=self.LRS_COLOR, width=1*zoom) if all_int: scaleStr = "%d" % item @@ -2127,8 +2127,8 @@ class DisplayMappingResults(object): else: sugg_title = "Suggestive LOD = %0.2f" % (self.suggestive/4.61) sig_title = "Significant LOD = %0.2f" % (self.significant/4.61) - Areas1 = HT.Area(shape='rect',coords=sugg_coords,title=sugg_title) - Areas2 = HT.Area(shape='rect',coords=sig_coords,title=sig_title) + Areas1 = HT.Area(shape='rect', coords=sugg_coords, title=sugg_title) + Areas2 = HT.Area(shape='rect', coords=sig_coords, title=sig_title) gifmap.areas.append(Areas1) gifmap.areas.append(Areas2) @@ -2316,7 +2316,7 @@ class DisplayMappingResults(object): im_drawer.text( text="5", xy=( - Xc-im_drawer.textsize("5",font=symbolFont)[0]/2+1, + Xc-im_drawer.textsize("5", font=symbolFont)[0]/2+1, Yc-4), fill=point_color, font=symbolFont) else: @@ -2383,8 +2383,8 @@ class DisplayMappingResults(object): ) else: im_drawer.line( - xy=((Xc0,yZero-(Yc0-yZero)), - (Xc,yZero-(Yc-yZero))), + xy=((Xc0, yZero-(Yc0-yZero)), + (Xc, yZero-(Yc-yZero))), fill=minusColor, width=lineWidth #, clipX=(xLeftOffset, xLeftOffset + plotWidth) ) @@ -2471,8 +2471,8 @@ class DisplayMappingResults(object): ###draw additive scale if not self.multipleInterval and self.additiveChecked: - additiveScaleFont=ImageFont.truetype(font=VERDANA_FILE,size=16*zoom) - additiveScale = Plot.detScaleOld(0,additiveMax) + additiveScaleFont=ImageFont.truetype(font=VERDANA_FILE, size=16*zoom) + additiveScale = Plot.detScaleOld(0, additiveMax) additiveStep = (additiveScale[1]-additiveScale[0])/additiveScale[2] additiveAxisList = Plot.frange(0, additiveScale[1], additiveStep) addPlotScale = AdditiveHeightThresh/additiveMax @@ -2482,18 +2482,18 @@ class DisplayMappingResults(object): for item in additiveAxisList: additiveY = yZero - item*addPlotScale im_drawer.line( - xy=((xLeftOffset + plotWidth,additiveY), - (xLeftOffset+4+ plotWidth,additiveY)), + xy=((xLeftOffset + plotWidth, additiveY), + (xLeftOffset+4+ plotWidth, additiveY)), fill=self.ADDITIVE_COLOR_POSITIVE, width=1*zoom) scaleStr = "%2.3f" % item im_drawer.text( text=scaleStr, - xy=(xLeftOffset + plotWidth +6,additiveY+TEXT_Y_DISPLACEMENT), - font=additiveScaleFont,fill=self.ADDITIVE_COLOR_POSITIVE) + xy=(xLeftOffset + plotWidth +6, additiveY+TEXT_Y_DISPLACEMENT), + font=additiveScaleFont, fill=self.ADDITIVE_COLOR_POSITIVE) im_drawer.line( - xy=((xLeftOffset+plotWidth,additiveY), - (xLeftOffset+plotWidth,yZero)), + xy=((xLeftOffset+plotWidth, additiveY), + (xLeftOffset+plotWidth, yZero)), fill=self.ADDITIVE_COLOR_POSITIVE, width=1*zoom) im_drawer.line( @@ -2553,7 +2553,7 @@ class DisplayMappingResults(object): chrFontZoom = 2 else: chrFontZoom = 1 - chrLabelFont=ImageFont.truetype(font=VERDANA_FILE,size=24*chrFontZoom) + chrLabelFont=ImageFont.truetype(font=VERDANA_FILE, size=24*chrFontZoom) for i, _chr in enumerate(self.genotype): if (i % 2 == 0): @@ -2575,10 +2575,10 @@ class DisplayMappingResults(object): TEXT_Y_DISPLACEMENT = 0 im_drawer.text(xy=(chrStartPix, yTopOffset + TEXT_Y_DISPLACEMENT), text=_chr.name, font=chrLabelFont, fill=BLACK) - COORDS = "%d,%d,%d,%d" %(chrStartPix, yTopOffset, chrEndPix,yTopOffset +20) + COORDS = "%d,%d,%d,%d" %(chrStartPix, yTopOffset, chrEndPix, yTopOffset +20) #add by NL 09-03-2010 - HREF = "javascript:chrView(%d,%s);" % (i,self.ChrLengthMbList) + HREF = "javascript:chrView(%d,%s);" % (i, self.ChrLengthMbList) #HREF = "javascript:changeView(%d,%s);" % (i,self.ChrLengthMbList) Areas = HT.Area(shape='rect', coords=COORDS, href=HREF) gifmap.areas.append(Areas) @@ -2720,7 +2720,7 @@ class DisplayMappingResults(object): else: chr_as_int = int(theGO["Chromosome"]) - 1 if refGene: - literatureCorrelationString = str(self.getLiteratureCorrelation(self.cursor,refGene,theGO['GeneID']) or "N/A") + literatureCorrelationString = str(self.getLiteratureCorrelation(self.cursor, refGene, theGO['GeneID']) or "N/A") this_row = [selectCheck.__str__(), str(tableIterationsCnt), @@ -2820,8 +2820,8 @@ class DisplayMappingResults(object): lCorr = None try: query = 'SELECT Value FROM LCorrRamin3 WHERE GeneId1 = %s and GeneId2 = %s' - for x,y in [(geneId1,geneId2),(geneId2,geneId1)]: - cursor.execute(query,(x,y)) + for x, y in [(geneId1, geneId2), (geneId2, geneId1)]: + cursor.execute(query, (x, y)) lCorr = cursor.fetchone() if lCorr: lCorr = lCorr[0] diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py index d4ee6fe6..2f282adc 100644 --- a/wqflask/wqflask/marker_regression/plink_mapping.py +++ b/wqflask/wqflask/marker_regression/plink_mapping.py @@ -54,7 +54,7 @@ def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''): for i, sample in enumerate(ped_sample_list): try: value = vals[i] - value = str(value).replace('value=','') + value = str(value).replace('value=', '') value = value.strip() except: value = -9999 @@ -78,7 +78,7 @@ def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''): # get strain name from ped file in order def get_samples_from_ped_file(dataset): - ped_file= open("{}{}.ped".format(flat_files('mapping'), dataset.group.name),"r") + ped_file= open("{}{}.ped".format(flat_files('mapping'), dataset.group.name), "r") line = ped_file.readline() sample_list=[] @@ -155,7 +155,7 @@ def parse_plink_output(output_filename, species): # output: lineList list ####################################################### def build_line_list(line=None): - line_list = string.split(string.strip(line),' ')# irregular number of whitespaces between columns + line_list = string.split(string.strip(line), ' ')# irregular number of whitespaces between columns line_list = [item for item in line_list if item !=''] line_list = list(map(string.strip, line_list)) diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index 145dbc77..1e6dff57 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -707,7 +707,7 @@ def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples): perm_strata_strings.append(combined_string) - d = dict([(y,x+1) for x,y in enumerate(sorted(set(perm_strata_strings)))]) + d = dict([(y, x+1) for x, y in enumerate(sorted(set(perm_strata_strings)))]) list_to_numbers = [d[x] for x in perm_strata_strings] perm_strata = list_to_numbers diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index 5b3946e3..c07a7670 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -53,7 +53,7 @@ views.py). search = self.search_terms self.original_search_string = self.search_terms # check for dodgy search terms - rx = re.compile(r'.*\W(href|http|sql|select|update)\W.*',re.IGNORECASE) + rx = re.compile(r'.*\W(href|http|sql|select|update)\W.*', re.IGNORECASE) if rx.match(search): logger.info("Regex failed search") self.search_term_exists = False diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py index 21ba7f63..f17e825e 100644 --- a/wqflask/wqflask/show_trait/SampleList.py +++ b/wqflask/wqflask/show_trait/SampleList.py @@ -57,7 +57,7 @@ class SampleList(object): sample = webqtlCaseData.webqtlCaseData(name=sample_name) sample.extra_info = {} - if self.dataset.group.name == 'AXBXA' and sample_name in ('AXB18/19/20','AXB13/14','BXA8/17'): + if self.dataset.group.name == 'AXBXA' and sample_name in ('AXB18/19/20', 'AXB13/14', 'BXA8/17'): sample.extra_info['url'] = "/mouseCross.html#AXB/BXA" sample.extra_info['css_class'] = "fs12" diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py index a871e91a..232cb8da 100644 --- a/wqflask/wqflask/user_manager.py +++ b/wqflask/wqflask/user_manager.py @@ -867,7 +867,7 @@ def forgot_password_submit(): email_address = params['email_address'] next_page = None if email_address != "": - logger.debug("Wants to send password E-mail to ",email_address) + logger.debug("Wants to send password E-mail to ", email_address) user_details = get_user_by_unique_column("email_address", email_address) if user_details: ForgotPasswordEmail(user_details["email_address"]) diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 394a9e28..92c20fc7 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -55,7 +55,7 @@ from wqflask.ctl import ctl_analysis from wqflask.snp_browser import snp_browser from utility import temp_data -from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL,GN_VERSION,JS_TWITTER_POST_FETCHER_PATH,JS_GUIX_PATH, CSS_PATH +from utility.tools import SQL_URI, TEMPDIR, USE_REDIS, USE_GN_SERVER, GN_SERVER_URL, GN_VERSION, JS_TWITTER_POST_FETCHER_PATH, JS_GUIX_PATH, CSS_PATH from utility.helper_functions import get_species_groups from utility.authentication_tools import check_resource_availability from utility.redis_tools import get_redis_conn @@ -133,10 +133,10 @@ def handle_bad_request(e): list = [fn for fn in os.listdir("./wqflask/static/gif/error") if fn.endswith(".gif") ] animation = random.choice(list) - resp = make_response(render_template("error.html",message=err_msg,stack=formatted_lines,error_image=animation,version=GN_VERSION)) + resp = make_response(render_template("error.html", message=err_msg, stack=formatted_lines, error_image=animation, version=GN_VERSION)) # logger.error("Set cookie %s with %s" % (err_msg, animation)) - resp.set_cookie(err_msg[:32],animation) + resp.set_cookie(err_msg[:32], animation) return resp @app.route("/authentication_needed") @@ -257,7 +257,7 @@ def docedit(): @app.route('/generated/') def generated_file(filename): logger.info(request.url) - return send_from_directory(GENERATED_IMAGE_DIR,filename) + return send_from_directory(GENERATED_IMAGE_DIR, filename) @app.route("/help") def help(): -- cgit v1.2.3 From 09cb4a05526c73229428401f356251bbfe8bf1cd Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 20 Aug 2020 15:39:50 +0300 Subject: Add backward support for urllib * wqflask/base/trait.py: Remove unused imports * wqflask/db/call.py (Bench): Add urllib2 fallback for python2 --- wqflask/base/trait.py | 3 +-- wqflask/db/call.py | 11 +++++++++-- 2 files changed, 10 insertions(+), 4 deletions(-) (limited to 'wqflask') diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 05b272c3..a19b66f7 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -6,7 +6,6 @@ import resource import codecs import requests import random -import urllib.request, urllib.parse, urllib.error from base import webqtlConfig from base.webqtlCaseData import webqtlCaseData @@ -607,4 +606,4 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): else: raise KeyError(repr(trait.name)+' information is not found in the database.') - return trait \ No newline at end of file + return trait diff --git a/wqflask/db/call.py b/wqflask/db/call.py index 3b8f782e..0971d2a2 100644 --- a/wqflask/db/call.py +++ b/wqflask/db/call.py @@ -3,7 +3,10 @@ from flask import g import string -import urllib.request, urllib.error, urllib.parse +try: # Python2 support + import urllib.request, urllib.error, urllib.parse +except: + import urllib2 import json from utility.tools import USE_GN_SERVER, LOG_SQL, GN_SERVER_URL from utility.benchmark import Bench @@ -59,7 +62,11 @@ def gn_server(path): """ with Bench("GN_SERVER", LOG_SQL): - res = urllib.request.urlopen(GN_SERVER_URL+path) + res = () + try: + res = urllib.request.urlopen(GN_SERVER_URL+path) + except: + res = urllib2.urlopen(GN_SERVER_URL+path) rest = res.read() res2 = json.loads(rest) logger.debug(res2) -- cgit v1.2.3 From 7f623509a4afded47eb8580451c146487d2ef662 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 20 Aug 2020 15:41:18 +0300 Subject: Disable python2 QTLReaper * wqflask/base/data_set.py: Remove usage of "reaper" to load datasets --- wqflask/base/data_set.py | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) (limited to 'wqflask') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 06e1c551..43beec26 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -34,7 +34,6 @@ from utility import webqtlUtil from db import webqtlDatabaseFunction from base import species from base import webqtlConfig -import reaper from flask import Flask, g import os import math @@ -456,12 +455,7 @@ class DatasetGroup(object): full_filename = str(locate(self.genofile, 'genotype')) else: full_filename = str(locate(self.name + '.geno', 'genotype')) - - if use_reaper: - genotype_1 = reaper.Dataset() - genotype_1.read(full_filename) - else: - genotype_1 = gen_geno_ob.genotype(full_filename) + genotype_1 = gen_geno_ob.genotype(full_filename) if genotype_1.type == "group" and self.parlist: genotype_2 = genotype_1.add( -- cgit v1.2.3 From 1f4fb6b24f3508d80be1f07cd62e38ac9385ef41 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 20 Aug 2020 16:35:17 +0300 Subject: Handle module renames in the standard library Run: ``` 2to3-3.8 -f imports -w . && \ 2to3-3.8 -f imports2 -w . ``` See: and --- wqflask/base/data_set.py | 2 +- wqflask/maintenance/gen_select_dataset.py | 4 ++-- wqflask/maintenance/quantile_normalize.py | 4 ++-- wqflask/maintenance/set_resource_defaults.py | 4 ++-- wqflask/utility/svg.py | 16 ++++++++-------- wqflask/wqflask/api/router.py | 14 +++++++------- wqflask/wqflask/collect.py | 2 +- .../wqflask/comparison_bar_chart/comparison_bar_chart.py | 2 +- wqflask/wqflask/correlation/show_corr_results.py | 2 +- wqflask/wqflask/correlation_matrix/show_corr_matrix.py | 2 +- wqflask/wqflask/export_traits.py | 4 ++-- wqflask/wqflask/heatmap/heatmap.py | 4 ++-- .../wqflask/marker_regression/display_mapping_results.py | 4 ++-- wqflask/wqflask/marker_regression/run_mapping.py | 2 +- wqflask/wqflask/network_graph/network_graph.py | 2 +- wqflask/wqflask/show_trait/show_trait.py | 2 +- wqflask/wqflask/user_manager.py | 2 +- wqflask/wqflask/views.py | 12 ++++++------ 18 files changed, 42 insertions(+), 42 deletions(-) (limited to 'wqflask') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 43beec26..8151a29d 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -44,7 +44,7 @@ import codecs import json import requests import gzip -import cPickle as pickle +import pickle as pickle import itertools from redis import Redis diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index d12b328f..fd65a52a 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -50,7 +50,7 @@ from utility.tools import locate, locate_ignore_error, TEMPDIR, SQL_URI import MySQLdb import simplejson as json -import urlparse +import urllib.parse #import sqlalchemy as sa @@ -66,7 +66,7 @@ from pprint import pformat as pf def parse_db_uri(): """Converts a database URI to the db name, host name, user name, and password""" - parsed_uri = urlparse.urlparse(SQL_URI) + parsed_uri = urllib.parse.urlparse(SQL_URI) db_conn_info = dict( db = parsed_uri.path[1:], diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py index 43edfd13..4d6e03bf 100644 --- a/wqflask/maintenance/quantile_normalize.py +++ b/wqflask/maintenance/quantile_normalize.py @@ -6,7 +6,7 @@ sys.path.insert(0, './') import MySQLdb -import urlparse +import urllib.parse import numpy as np import pandas as pd @@ -22,7 +22,7 @@ from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT, SQL_URI def parse_db_uri(): """Converts a database URI to the db name, host name, user name, and password""" - parsed_uri = urlparse.urlparse(SQL_URI) + parsed_uri = urllib.parse.urlparse(SQL_URI) db_conn_info = dict( db = parsed_uri.path[1:], diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py index d53a255b..abd5416c 100644 --- a/wqflask/maintenance/set_resource_defaults.py +++ b/wqflask/maintenance/set_resource_defaults.py @@ -34,7 +34,7 @@ Redis = get_redis_conn() import MySQLdb -import urlparse +import urllib.parse from utility.logger import getLogger logger = getLogger(__name__) @@ -42,7 +42,7 @@ logger = getLogger(__name__) def parse_db_uri(): """Converts a database URI to the db name, host name, user name, and password""" - parsed_uri = urlparse.urlparse(SQL_URI) + parsed_uri = urllib.parse.urlparse(SQL_URI) db_conn_info = dict( db = parsed_uri.path[1:], diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py index 19eda0ce..b92cc2d1 100644 --- a/wqflask/utility/svg.py +++ b/wqflask/utility/svg.py @@ -957,8 +957,8 @@ class drawing: # Voeg een element toe aan de grafiek toe. if use_dom_implementation==0: def toXml(self, filename='',compress=False): - import cStringIO - xml=cStringIO.StringIO() + import io + xml=io.StringIO() xml.write("\n") xml.write(" 1: - memory_file = StringIO.StringIO() + memory_file = io.StringIO() with ZipFile(memory_file, mode='w', compression=ZIP_DEFLATED) as zf: for the_file in file_list: zf.writestr(the_file[0], the_file[1]) @@ -460,7 +460,7 @@ def export_perm_data(): ["#Comment: Results sorted from low to high peak linkage"] ] - buff = StringIO.StringIO() + buff = io.StringIO() writer = csv.writer(buff) writer.writerows(the_rows) for item in perm_info['perm_data']: -- cgit v1.2.3 From ab78dd757a7d11375e32637158ddcffc029a3113 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Sun, 23 Aug 2020 15:28:10 +0300 Subject: Remove unused imports --- wqflask/wqflask/correlation/show_corr_results.py | 13 +------------ wqflask/wqflask/news.py | 3 --- 2 files changed, 1 insertion(+), 15 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 65360040..233a3a03 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -20,22 +20,11 @@ from __future__ import absolute_import, print_function, division -import sys - -import string -import pickle -import os -import time -import pp -import math import collections -import resource import json - import scipy import numpy import rpy2.robjects as ro # R Objects -import rpy2.rinterface as ri from rpy2.robjects.packages import importr utils = importr("utils") @@ -648,4 +637,4 @@ def get_header_fields(data_type, corr_method): 'N', 'Sample p(r)'] - return header_fields \ No newline at end of file + return header_fields diff --git a/wqflask/wqflask/news.py b/wqflask/wqflask/news.py index 8bc6b889..20319756 100644 --- a/wqflask/wqflask/news.py +++ b/wqflask/wqflask/news.py @@ -1,7 +1,4 @@ from __future__ import absolute_import, print_function, division -import sys -reload(sys) -sys.setdefaultencoding('utf8') from flask import g class News(object): -- cgit v1.2.3 From 666a423b0b2f8cf98b9e70ed3dcf1c6dc3896b1d Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Sun, 23 Aug 2020 15:28:41 +0300 Subject: Use Python3 string methods * wqflask/utility/webqtlUtil.py (genRandStr): Replace "string.letters" with "string.ascii_letters". --- wqflask/utility/webqtlUtil.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'wqflask') diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py index 77cc3416..d4979011 100644 --- a/wqflask/utility/webqtlUtil.py +++ b/wqflask/utility/webqtlUtil.py @@ -64,7 +64,7 @@ ParInfo ={ # Accessory Functions ######################################### -def genRandStr(prefix = "", length=8, chars=string.letters+string.digits): +def genRandStr(prefix = "", length=8, chars=string.ascii_letters+string.digits): from random import choice _str = prefix[:] for i in range(length): @@ -110,4 +110,4 @@ def hasAccessToConfidentialPhenotypeTrait(privilege, userName, authorized_users) AuthorizedUsersList=list(map(string.strip, string.split(authorized_users, ','))) if AuthorizedUsersList.__contains__(userName): access_to_confidential_phenotype_trait = 1 - return access_to_confidential_phenotype_trait \ No newline at end of file + return access_to_confidential_phenotype_trait -- cgit v1.2.3 From 239fc74198f4dd0388d01b41bc3a3278aed5973b Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 26 Aug 2020 01:33:04 +0300 Subject: Remove unused imports --- .../comparison_bar_chart/comparison_bar_chart.py | 18 ----------- wqflask/wqflask/correlation/show_corr_results.py | 12 ++----- .../wqflask/correlation_matrix/show_corr_matrix.py | 11 ------- wqflask/wqflask/heatmap/heatmap.py | 37 +++------------------- wqflask/wqflask/network_graph/network_graph.py | 20 ++---------- 5 files changed, 9 insertions(+), 89 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py index 3e5daa50..16832621 100644 --- a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py +++ b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py @@ -19,34 +19,16 @@ # This module is used by GeneNetwork project (www.genenetwork.org) from __future__ import absolute_import, print_function, division - -import sys -# sys.path.append(".") Never do this in a webserver! - -import string -import pickle -import os -import time -import pp -import math -import collections -import resource - - from pprint import pformat as pf from base.trait import create_trait from base import data_set from utility import webqtlUtil, helper_functions, corr_result_helpers -from db import webqtlDatabaseFunction import utility.webqtlUtil #this is for parallel computing only. from wqflask.correlation import correlation_functions -from utility.benchmark import Bench from MySQLdb import escape_string as escape -from pprint import pformat as pf - from flask import Flask, g diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 233a3a03..5ced30b6 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -29,24 +29,16 @@ import rpy2.robjects as ro # R Objects from rpy2.robjects.packages import importr utils = importr("utils") -from pprint import pformat as pf - -from base import webqtlConfig -from utility.THCell import THCell -from utility.TDCell import TDCell -from base.trait import create_trait from base import data_set from utility import webqtlUtil, helper_functions, corr_result_helpers, hmac from db import webqtlDatabaseFunction -import utility.webqtlUtil #this is for parallel computing only. +import utility.webqtlUtil #this is for parallel computing only. from wqflask.correlation import correlation_functions from utility.benchmark import Bench import utility.webqtlUtil -from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string - +from utility.type_checking import is_str, get_float, get_int, get_string from MySQLdb import escape_string as escape -from pprint import pformat as pf from flask import Flask, g diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index ea786289..bd5aca1f 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -20,19 +20,8 @@ from __future__ import absolute_import, print_function, division -import sys -# sys.path.append(".") Never do this in a webserver! - -import string -import pickle -import os import datetime -import time -import pp import math -import collections -import resource - import numpy as np import scipy diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py index 4fdc1f13..1f1cdb90 100644 --- a/wqflask/wqflask/heatmap/heatmap.py +++ b/wqflask/wqflask/heatmap/heatmap.py @@ -1,46 +1,19 @@ from __future__ import absolute_import, print_function, division -import sys -# sys.path.append(".") Never in a running webserver - import string -import pickle import os -import datetime -import time -import pp -import math import random -import collections -import resource - -import scipy -import numpy as np - -from pprint import pformat as pf - -from base.trait import GeneralTrait -from base import data_set from base import species from base import webqtlConfig from utility import helper_functions -from utility import Plot, Bunch -from utility import temp_data -from utility.tools import flat_files, REAPER_COMMAND, TEMPDIR - -from MySQLdb import escape_string as escape - -import pickle as pickle -import simplejson as json - -from pprint import pformat as pf +from utility.tools import flat_files, REAPER_COMMAND, TEMPDIR from redis import Redis -Redis = Redis() - from flask import Flask, g - from utility.logger import getLogger + +Redis = Redis() + logger = getLogger(__name__ ) class Heatmap(object): @@ -205,4 +178,4 @@ def parse_reaper_output(gwa_filename): marker['additive'] = float(line.split("\t")[6]) marker_obs.append(marker) - return marker_obs \ No newline at end of file + return marker_obs diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py index 7916651f..2a4c4a93 100644 --- a/wqflask/wqflask/network_graph/network_graph.py +++ b/wqflask/wqflask/network_graph/network_graph.py @@ -20,27 +20,11 @@ from __future__ import absolute_import, print_function, division -import sys - -import string -import pickle -import os -import time -import pp -import math -import collections -import resource - import scipy - import simplejson as json - -from rpy2.robjects.packages import importr -import rpy2.robjects as robjects - from pprint import pformat as pf -from utility.THCell import THCell + from utility.TDCell import TDCell from base.trait import create_trait from base import data_set @@ -218,4 +202,4 @@ class NetworkGraph(object): trait_ob = create_trait(dataset=dataset_ob, name=trait_name, cellid=None) - self.trait_list.append((trait_ob, dataset_ob)) \ No newline at end of file + self.trait_list.append((trait_ob, dataset_ob)) -- cgit v1.2.3 From 3335bb967e59da17d104624be971e4a3e98e07c8 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 26 Aug 2020 01:33:43 +0300 Subject: Update corestats import * wqflask/utility/Plot.py: import corestats from the utility module. --- wqflask/utility/Plot.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py index 7d9d7649..48a5c7ba 100644 --- a/wqflask/utility/Plot.py +++ b/wqflask/utility/Plot.py @@ -32,7 +32,7 @@ from PIL import ImageFont from math import * -import corestats +import utility.corestats as corestats from base import webqtlConfig from utility.pillow_utils import draw_rotated_text import utility.logger -- cgit v1.2.3 From 5305c6b0080b36c3ad0865677b613dd970991d7f Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 26 Aug 2020 17:30:29 +0300 Subject: Replace python2-htmlgen with python-htmlgen * wqflask/wqflask/marker_regression/display_mapping_results.py: Use python-htmlgen --- .../marker_regression/display_mapping_results.py | 74 ++++++++++++++-------- 1 file changed, 49 insertions(+), 25 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 255e3b74..ccdafa14 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -35,7 +35,7 @@ import json from flask import Flask, g -from htmlgen import HTMLgen2 as HT +import htmlgen as HT from base import webqtlConfig from base.GeneralObject import GeneralObject @@ -88,35 +88,60 @@ class HtmlGenWrapper: """Wrapper Methods for HTML gen""" @staticmethod def create_image_tag(**kwargs): - return HT.Image(**kwargs) + image = HT.Image("", "") + for key, value in list(kwargs.items()): + image.set_attribute(key, value) + return image @staticmethod def create_form_tag(**kwargs): - return HT.Form(**kwargs) + form = HT.Form("POST", "") # Default method is POST + + for key, value in list(kwargs.items()): + if key == "submit": + form.append(value) + continue + form.set_attribute(key.replace("cgi", "action"), str(value)) + return form @staticmethod def create_p_tag(**kwargs): - return HT.Paragraph(**kwargs) + paragraph = HT.Paragraph() + for key, value in list(kwargs.items()): + paragraph.set_attribute(key, value) + return paragraph @staticmethod def create_br_tag(): - return HT.BR() + return HT.VoidElement("br") @staticmethod def create_input_tag(**kwargs): - return HT.Input(**kwargs) + input_ = HT.Input() + for key, value in list(kwargs.items()): + input_.set_attribute(key.lower().replace("_", ""), value) + return input_ @staticmethod def create_area_tag(**kwargs): - return HT.Area(**kwargs) + area = HT.VoidElement("area") + for key, value in list(kwargs.items()): + area.set_attribute(key, value) + return area @staticmethod def create_link_tag(href, content, **kwargs): - return HT.Href(href, content, **kwargs) + link = HT.Link(href, content) + for key, value in list(kwargs.items()): + link.set_attribute(key, value) + return link @staticmethod def create_map_tag(**kwargs): - return HT.Map(**kwargs) + map_ = HT.Element("map") + for key, value in list(kwargs.items()): + map_.set_attribute(key, value) + return map_ class DisplayMappingResults(object): @@ -554,7 +579,6 @@ class DisplayMappingResults(object): src="/image/{}.png".format(self.filename), border="0", usemap='#WebQTLImageMap' ) - self.intImg = intImg #Scales plot differently for high resolution if self.draw2X: @@ -575,12 +599,12 @@ class DisplayMappingResults(object): cgi=os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name=showLocusForm, - submit=HtmlGenWrapper.create_input_tag(type='hidden')) + submit=HtmlGenWrapper.create_input_tag(type_='hidden')) hddn = {'FormID':'showDatabase', 'ProbeSetID':'_','database':fd.RISet+"Geno",'CellID':'_', 'RISet':fd.RISet, 'incparentsf1':'ON'} for key in hddn.keys(): showLocusForm.append(HtmlGenWrapper.create_input_tag( - name=key, value=hddn[key], type='hidden')) + name=key, value=hddn[key], type_='hidden')) showLocusForm.append(intImg) else: showLocusForm = intImg @@ -1002,7 +1026,7 @@ class DisplayMappingResults(object): COORDS = "%d,%d,%d,%d" %(rectWidth+2+rightShift, yPaddingTop+kstep*15, rectWidth+2+rightShift+nameWidth, yPaddingTop+10+kstep*15,) HREF= "javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm, thisTrait.db.name, thisTrait.name) Areas = HtmlGenWrapper.create_area_tag(shape='rect', coords=COORDS, href=HREF) - gifmap.areas.append(Areas) ### TODO + gifmap.append(Areas) ### TODO def drawLegendPanel(self, canvas, offset= (40, 120, 80, 10), zoom = 1): im_drawer = ImageDraw.Draw(canvas) @@ -1404,7 +1428,7 @@ class DisplayMappingResults(object): COORDS = "%d, %d, %d, %d" %(geneStartPix, geneYLocation, geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT)) # NL: 06-02-2011 Rob required to display NCBI info in a new window - gifmap.areas.append( + gifmap.append( HtmlGenWrapper.create_area_tag( shape='rect', coords=COORDS, @@ -1578,7 +1602,7 @@ class DisplayMappingResults(object): COORDS = "%d, %d, %d, %d" %(geneStartPix, geneYLocation+ind*self.EACH_GENE_HEIGHT, geneEndPix+1, (geneYLocation + ind*self.EACH_GENE_HEIGHT)) TITLE = "Strain: %s, marker (%s) \n Position %2.3f Mb." % (samplelist[k], _chr[j].name, float(txStart)) HREF = '' - gifmap.areas.append( + gifmap.append( HtmlGenWrapper.create_area_tag( shape='rect', coords=COORDS, @@ -1702,7 +1726,7 @@ class DisplayMappingResults(object): WEBQTL_HREF = "javascript:rangeView('%s', %f, %f)" % (self.selectedChr - 1, max(0, (calBase-webqtlZoomWidth))/1000000.0, (calBase+webqtlZoomWidth)/1000000.0) WEBQTL_TITLE = "Click to view this section of the genome in WebQTL" - gifmap.areas.append( + gifmap.append( HtmlGenWrapper.create_area_tag( shape='rect', coords=WEBQTL_COORDS, @@ -1724,7 +1748,7 @@ class DisplayMappingResults(object): else: PHENOGEN_HREF = "https://phenogen.org/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases) PHENOGEN_TITLE = "Click to view this section of the genome in PhenoGen" - gifmap.areas.append( + gifmap.append( HtmlGenWrapper.create_area_tag( shape='rect', coords=PHENOGEN_COORDS, @@ -1745,7 +1769,7 @@ class DisplayMappingResults(object): else: UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d" % (self._ucscDb, self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases) UCSC_TITLE = "Click to view this section of the genome in the UCSC Genome Browser" - gifmap.areas.append( + gifmap.append( HtmlGenWrapper.create_area_tag( shape='rect', coords=UCSC_COORDS, @@ -1767,7 +1791,7 @@ class DisplayMappingResults(object): else: ENSEMBL_HREF = "http://www.ensembl.org/Rattus_norvegicus/contigview?chr=%s&start=%d&end=%d" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases) ENSEMBL_TITLE = "Click to view this section of the genome in the Ensembl Genome Browser" - gifmap.areas.append(HtmlGenWrapper.create_area_tag( + gifmap.append(HtmlGenWrapper.create_area_tag( shape='rect', coords=ENSEMBL_COORDS, href=ENSEMBL_HREF, @@ -2011,7 +2035,7 @@ class DisplayMappingResults(object): href=HREF, target="_blank", title="Locus : {}".format(Lname)) - gifmap.areas.append(Areas) + gifmap.append(Areas) ##piddle bug if j == 0: im_drawer.line( @@ -2227,8 +2251,8 @@ class DisplayMappingResults(object): shape='rect', coords=sig_coords, title=sig_title) - gifmap.areas.append(Areas1) - gifmap.areas.append(Areas2) + gifmap.append(Areas1) + gifmap.append(Areas2) start_pos_x += (chr_length_dist+self.GraphInterval)*plotXScale return start_pos_x @@ -2682,7 +2706,7 @@ class DisplayMappingResults(object): shape='rect', coords=COORDS, href=HREF) - gifmap.areas.append(Areas) + gifmap.append(Areas) startPosX += (self.ChrLengthDistList[i]+self.GraphInterval)*plotXScale return plotXScale @@ -2768,7 +2792,7 @@ class DisplayMappingResults(object): this_row = [] #container for the cells of each row selectCheck = HtmlGenWrapper.create_input_tag( - type="checkbox", + type_="checkbox", name="selectCheck", value=theGO["GeneSymbol"], Class="checkbox trait_checkbox") # checkbox for each row @@ -2887,7 +2911,7 @@ class DisplayMappingResults(object): for gIndex, theGO in enumerate(geneCol): this_row = [] # container for the cells of each row selectCheck = str(HtmlGenWrapper.create_input_tag( - type="checkbox", + type_="checkbox", name="selectCheck", Class="checkbox trait_checkbox")) # checkbox for each row -- cgit v1.2.3 From 6486bc57651f074245ae0bf786f9e92460d73fef Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 26 Aug 2020 17:31:17 +0300 Subject: Fix failing tests that use python2-htmlgen * wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py: Fix tests. --- .../test_display_mapping_results.py | 91 ++++++++++++---------- 1 file changed, 48 insertions(+), 43 deletions(-) (limited to 'wqflask') diff --git a/wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py b/wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py index 6f791df1..8ae0f09f 100644 --- a/wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py +++ b/wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py @@ -1,6 +1,6 @@ import unittest -from htmlgen import HTMLgen2 as HT +import htmlgen as HT from wqflask.marker_regression.display_mapping_results import ( DisplayMappingResults, HtmlGenWrapper @@ -26,9 +26,9 @@ class TestHtmlGenWrapper(unittest.TestCase): width="10", height="13", usemap="#webqtlmap")), - ("""""") + ("""random""") ) def test_create_form(self): @@ -37,7 +37,7 @@ class TestHtmlGenWrapper(unittest.TestCase): cgi="/testing/", enctype='multipart/form-data', name="formName", - submit=HT.Input(type='hidden') + submit=HtmlGenWrapper.create_input_tag(type_='hidden', name='Default_Name') ) test_image = HtmlGenWrapper.create_image_tag( src="test.png", @@ -49,10 +49,10 @@ class TestHtmlGenWrapper(unittest.TestCase): ) self.assertEqual( str(test_form).replace("\n", ""), - ("""
""")) + ("""
""")) hddn = { 'FormID': 'showDatabase', 'ProbeSetID': '_', @@ -62,21 +62,26 @@ class TestHtmlGenWrapper(unittest.TestCase): 'incparentsf1': 'ON' } for key in hddn.keys(): - test_form.append(HT.Input(name=key, value=hddn[key], - type='hidden')) + test_form.append( + HtmlGenWrapper.create_input_tag( + name=key, + value=hddn[key], + type_='hidden')) test_form.append(test_image) + self.assertEqual(str(test_form).replace("\n", ""), ( - """
""" - """""" - """""" - """""" - """""" - """""" - """""" - """random""" - """
""")) + """
""" + """""" + """""" + """""" + """""" + """""" + """""" + """""" + """random""" + """
""")) def test_create_paragraph(self): """Test HT.Paragraph method""" @@ -89,48 +94,48 @@ class TestHtmlGenWrapper(unittest.TestCase): ) self.assertEqual( str(test_p_element), - """

""" + """

""" ) - test_p_element.append(HT.BR()) + test_p_element.append(HtmlGenWrapper.create_br_tag()) test_p_element.append(par_text) self.assertEqual( str(test_p_element), - """


{}

""".format(par_text) + """


{}

""".format(par_text) ) def test_create_br_tag(self): """Test HT.BR() method""" self.assertEqual(str(HtmlGenWrapper.create_br_tag()), - "
") + "
") def test_create_input_tag(self): """Test HT.Input method""" self.assertEqual( str(HtmlGenWrapper.create_input_tag( - type="hidden", + type_="hidden", name="name", value="key", Class="trait trait_")).replace("\n", ""), - ("""""")) + ("""""")) def test_create_map_tag(self): """Test HT.Map method""" self.assertEqual(str(HtmlGenWrapper.create_map_tag( name="WebqTLImageMap")).replace("\n", ""), - """""") - gifmap = HtmlGenWrapper.create_map_tag(areas=[]) - gifmap.areas.append(HT.Area(shape="rect", - coords='1 2 3', href='#area1')) - gifmap.areas.append(HT.Area(shape="rect", - coords='1 2 3', href='#area2')) + """""") + gifmap = HtmlGenWrapper.create_map_tag(name="test") + gifmap.append(HtmlGenWrapper.create_area_tag(shape="rect", + coords='1 2 3', href='#area1')) + gifmap.append(HtmlGenWrapper.create_area_tag(shape="rect", + coords='1 2 3', href='#area2')) self.assertEqual( str(gifmap).replace("\n", ""), - ("""""" - """""" - """""" - """""")) + ("""""" + """""" + """""" + """""")) def test_create_area_tag(self): """Test HT.Area method""" @@ -140,12 +145,12 @@ class TestHtmlGenWrapper(unittest.TestCase): coords="1 2", href="http://test.com", title="Some Title")).replace("\n", ""), - ("""""")) + ("""""")) def test_create_link_tag(self): """Test HT.HREF method""" self.assertEqual( str(HtmlGenWrapper.create_link_tag( "www.test.com", "test", target="_blank")).replace("\n", ""), - """test""") + """test""") -- cgit v1.2.3 From 133db0e8dbc5a0812dc1f06402f2b788aecaef20 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 26 Aug 2020 17:36:23 +0300 Subject: Replace calls to "basestring with "str"" See: --- wqflask/utility/helper_functions.py | 2 +- wqflask/wqflask/collect.py | 2 +- wqflask/wqflask/show_trait/show_trait.py | 2 +- wqflask/wqflask/snp_browser/snp_browser.py | 4 ++-- 4 files changed, 5 insertions(+), 5 deletions(-) (limited to 'wqflask') diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py index 9a4a235a..107c9ec6 100644 --- a/wqflask/utility/helper_functions.py +++ b/wqflask/utility/helper_functions.py @@ -34,7 +34,7 @@ def get_species_dataset_trait(self, start_vars): #self.genotype = self.dataset.group.genotype def get_trait_db_obs(self, trait_db_list): - if isinstance(trait_db_list, basestring): + if isinstance(trait_db_list, str): trait_db_list = trait_db_list.split(",") self.trait_list = [] diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py index d77567f8..06c00930 100644 --- a/wqflask/wqflask/collect.py +++ b/wqflask/wqflask/collect.py @@ -38,7 +38,7 @@ from utility.logger import getLogger logger = getLogger(__name__) def process_traits(unprocessed_traits): - if isinstance(unprocessed_traits, basestring): + if isinstance(unprocessed_traits, str): unprocessed_traits = unprocessed_traits.split(",") traits = set() for trait in unprocessed_traits: diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 738aa28a..6a74cada 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -372,7 +372,7 @@ class ShowTrait(object): this_group = self.dataset.group.name # We're checking a string here! - assert isinstance(this_group, basestring), "We need a string type thing here" + assert isinstance(this_group, str), "We need a string type thing here" if this_group[:3] == 'BXD' and this_group != "BXD-Harvested": this_group = 'BXD' diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py index b18bfc62..b3d26caf 100644 --- a/wqflask/wqflask/snp_browser/snp_browser.py +++ b/wqflask/wqflask/snp_browser/snp_browser.py @@ -477,7 +477,7 @@ class SnpBrowser(object): the_bases = [] for j, item in enumerate(allele_value_list): - if item and isinstance(item, basestring): + if item and isinstance(item, str): this_base = [str(item), base_color_dict[item]] else: this_base = "" @@ -612,7 +612,7 @@ class SnpBrowser(object): this_allele_list = [] for item in self.allele_list: - if item and isinstance(item, basestring) and (item.lower() not in this_allele_list) and (item != "-"): + if item and isinstance(item, str) and (item.lower() not in this_allele_list) and (item != "-"): this_allele_list.append(item.lower()) total_allele_count = len(this_allele_list) -- cgit v1.2.3 From 94f97127a9e451c7adb36613d090a612601b9d01 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 26 Aug 2020 17:38:13 +0300 Subject: Rename "unicode" to "str" See: --- wqflask/base/data_set.py | 4 ++-- wqflask/base/trait.py | 10 +++++----- wqflask/wqflask/model.py | 6 +++--- wqflask/wqflask/user_manager.py | 2 +- wqflask/wqflask/user_session.py | 2 +- 5 files changed, 12 insertions(+), 12 deletions(-) (limited to 'wqflask') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 8151a29d..39a8a2ed 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -1044,9 +1044,9 @@ class MrnaAssayDataSet(DataSet): # XZ, 12/08/2008: description # XZ, 06/05/2009: Rob asked to add probe target description - description_string = unicode( + description_string = str( str(this_trait.description).strip(codecs.BOM_UTF8), 'utf-8') - target_string = unicode( + target_string = str( str(this_trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8') if len(description_string) > 1 and description_string != 'None': diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index a19b66f7..09c41fa7 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -490,9 +490,9 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): else: trait.description_display = "" - trait.abbreviation = unicode(str(trait.abbreviation).strip(codecs.BOM_UTF8), 'utf-8', errors="replace") - trait.description_display = unicode(str(trait.description_display).strip(codecs.BOM_UTF8), 'utf-8', errors="replace") - trait.authors = unicode(str(trait.authors).strip(codecs.BOM_UTF8), 'utf-8', errors="replace") + trait.abbreviation = str(str(trait.abbreviation).strip(codecs.BOM_UTF8), 'utf-8', errors="replace") + trait.description_display = str(str(trait.description_display).strip(codecs.BOM_UTF8), 'utf-8', errors="replace") + trait.authors = str(str(trait.authors).strip(codecs.BOM_UTF8), 'utf-8', errors="replace") if not trait.year.isdigit(): trait.pubmed_text = "N/A" @@ -503,8 +503,8 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % trait.pubmed_id if dataset.type == 'ProbeSet' and dataset.group: - description_string = unicode(str(trait.description).strip(codecs.BOM_UTF8), 'utf-8') - target_string = unicode(str(trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8') + description_string = str(str(trait.description).strip(codecs.BOM_UTF8), 'utf-8') + target_string = str(str(trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8') if len(description_string) > 1 and description_string != 'None': description_display = description_string diff --git a/wqflask/wqflask/model.py b/wqflask/wqflask/model.py index 38117a8e..a135761c 100644 --- a/wqflask/wqflask/model.py +++ b/wqflask/wqflask/model.py @@ -18,7 +18,7 @@ from wqflask.database import Base, init_db class User(Base): __tablename__ = "user" - id = Column(Unicode(36), primary_key=True, default=lambda: unicode(uuid.uuid4())) + id = Column(Unicode(36), primary_key=True, default=lambda: str(uuid.uuid4())) email_address = Column(Unicode(50), unique=True, nullable=False) # Todo: Turn on strict mode for Mysql @@ -120,7 +120,7 @@ class User(Base): class Login(Base): __tablename__ = "login" - id = Column(Unicode(36), primary_key=True, default=lambda: unicode(uuid.uuid4())) + id = Column(Unicode(36), primary_key=True, default=lambda: str(uuid.uuid4())) user = Column(Unicode(36), ForeignKey('user.id')) timestamp = Column(DateTime(), default=lambda: datetime.datetime.utcnow()) ip_address = Column(Unicode(39)) @@ -138,7 +138,7 @@ class Login(Base): class UserCollection(Base): __tablename__ = "user_collection" - id = Column(Unicode(36), primary_key=True, default=lambda: unicode(uuid.uuid4())) + id = Column(Unicode(36), primary_key=True, default=lambda: str(uuid.uuid4())) user = Column(Unicode(36), ForeignKey('user.id')) # I'd prefer this to not have a length, but for the index below it needs one diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py index 56d1c084..3c41e2b8 100644 --- a/wqflask/wqflask/user_manager.py +++ b/wqflask/wqflask/user_manager.py @@ -252,7 +252,7 @@ class UserSession(object): def add_collection(self, collection_name, traits): """Add collection into ElasticSearch""" - collection_dict = {'id': unicode(uuid.uuid4()), + collection_dict = {'id': str(uuid.uuid4()), 'name': collection_name, 'created_timestamp': datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'), 'changed_timestamp': datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'), diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py index 3aa2c151..71c31c57 100644 --- a/wqflask/wqflask/user_session.py +++ b/wqflask/wqflask/user_session.py @@ -184,7 +184,7 @@ class UserSession(object): def add_collection(self, collection_name, traits): """Add collection into Redis""" - collection_dict = {'id': unicode(uuid.uuid4()), + collection_dict = {'id': str(uuid.uuid4()), 'name': collection_name, 'created_timestamp': datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'), 'changed_timestamp': datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'), -- cgit v1.2.3 From 7717f0d3d4802d115a8b5ace4d379864ba5b1188 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 26 Aug 2020 18:51:54 +0300 Subject: Replace "__cmp__" with "__eq__" magic method * wqflask/base/GeneralObject.py: "__cmp__" is no longer used in python3. See: --- wqflask/base/GeneralObject.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'wqflask') diff --git a/wqflask/base/GeneralObject.py b/wqflask/base/GeneralObject.py index 707569db..0122ee32 100644 --- a/wqflask/base/GeneralObject.py +++ b/wqflask/base/GeneralObject.py @@ -61,5 +61,6 @@ class GeneralObject: s += '%s = %s\n' % (key, self.__dict__[key]) return s - def __cmp__(self, other): - return len(list(self.__dict__.keys())).__cmp__(len(list(other.__dict__.keys()))) + def __eq__(self, other): + return (len(list(self.__dict__.keys())) == + len(list(other.__dict__.keys()))) -- cgit v1.2.3 From 303e4b71c2172da5be19c84d4be5a062329ac013 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 26 Aug 2020 19:12:33 +0300 Subject: Remove "from __future__ import new_feature" statements See: --- test/requests/link_checker.py | 1 - test/requests/main_web_functionality.py | 22 ++++++++++++---------- test/requests/mapping_tests.py | 1 - test/requests/navigation_tests.py | 1 - test/requests/test-website.py | 2 +- webtests/browser_run.py | 4 +--- webtests/correlation_matrix_test.py | 2 -- webtests/correlation_test.py | 2 -- webtests/marker_regression_test.py | 2 -- webtests/show_trait_js_test.py | 2 -- webtests/test_runner.py | 4 +--- wqflask/base/data_set.py | 1 - wqflask/base/mrna_assay_tissue_data.py | 4 +--- wqflask/base/species.py | 4 +--- wqflask/base/trait.py | 2 -- wqflask/maintenance/convert_dryad_to_bimbam.py | 3 +-- wqflask/maintenance/convert_geno_to_bimbam.py | 3 +-- wqflask/maintenance/gen_select_dataset.py | 10 +--------- .../maintenance/generate_kinship_from_bimbam.py | 3 +-- .../maintenance/generate_probesetfreeze_file.py | 2 -- wqflask/maintenance/geno_to_json.py | 3 +-- wqflask/maintenance/get_group_samplelists.py | 2 -- wqflask/maintenance/print_benchmark.py | 4 +--- wqflask/maintenance/quantile_normalize.py | 7 +------ wqflask/maintenance/set_resource_defaults.py | 4 +--- wqflask/utility/Plot.py | 2 -- wqflask/utility/after.py | 4 +--- wqflask/utility/authentication_tools.py | 2 -- wqflask/utility/benchmark.py | 2 -- wqflask/utility/chunks.py | 2 -- wqflask/utility/db_tools.py | 2 -- wqflask/utility/gen_geno_ob.py | 4 +--- wqflask/utility/genofile_parser.py | 1 - wqflask/utility/helper_functions.py | 2 -- wqflask/utility/hmac.py | 4 +--- wqflask/utility/redis_tools.py | 4 +--- wqflask/utility/temp_data.py | 1 - wqflask/wqflask/__init__.py | 2 -- wqflask/wqflask/api/correlation.py | 4 +--- wqflask/wqflask/api/gen_menu.py | 2 -- wqflask/wqflask/api/mapping.py | 2 -- wqflask/wqflask/api/router.py | 4 +--- wqflask/wqflask/collect.py | 3 --- .../comparison_bar_chart/comparison_bar_chart.py | 1 - wqflask/wqflask/correlation/corr_scatter_plot.py | 4 +--- .../wqflask/correlation/correlation_functions.py | 4 +--- wqflask/wqflask/correlation/show_corr_results.py | 2 -- .../wqflask/correlation_matrix/show_corr_matrix.py | 2 -- wqflask/wqflask/do_search.py | 2 -- wqflask/wqflask/docs.py | 4 +--- wqflask/wqflask/export_traits.py | 4 +--- wqflask/wqflask/external_tools/send_to_bnw.py | 4 +--- .../wqflask/external_tools/send_to_geneweaver.py | 4 +--- .../wqflask/external_tools/send_to_webgestalt.py | 4 +--- wqflask/wqflask/group_manager.py | 5 +---- wqflask/wqflask/gsearch.py | 2 -- wqflask/wqflask/heatmap/heatmap.py | 2 -- wqflask/wqflask/interval_analyst/GeneUtil.py | 2 -- wqflask/wqflask/marker_regression/run_mapping.py | 4 +--- wqflask/wqflask/model.py | 4 +--- wqflask/wqflask/network_graph/network_graph.py | 2 -- wqflask/wqflask/news.py | 1 - wqflask/wqflask/parser.py | 2 -- wqflask/wqflask/resource_manager.py | 4 +--- wqflask/wqflask/search_results.py | 2 -- wqflask/wqflask/send_mail.py | 2 -- wqflask/wqflask/show_trait/SampleList.py | 2 -- wqflask/wqflask/show_trait/export_trait_data.py | 4 +--- wqflask/wqflask/show_trait/show_trait.py | 2 -- wqflask/wqflask/snp_browser/snp_browser.py | 2 -- wqflask/wqflask/submit_bnw.py | 4 +--- wqflask/wqflask/update_search_results.py | 2 -- wqflask/wqflask/user_login.py | 4 +--- wqflask/wqflask/user_manager.py | 2 -- wqflask/wqflask/user_session.py | 2 -- wqflask/wqflask/views.py | 2 -- 76 files changed, 45 insertions(+), 190 deletions(-) (limited to 'wqflask') diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py index 5e16a5cd..949a33c8 100644 --- a/test/requests/link_checker.py +++ b/test/requests/link_checker.py @@ -1,4 +1,3 @@ -from __future__ import print_function import re import requests from lxml.html import parse diff --git a/test/requests/main_web_functionality.py b/test/requests/main_web_functionality.py index d070dab9..78030307 100644 --- a/test/requests/main_web_functionality.py +++ b/test/requests/main_web_functionality.py @@ -1,9 +1,7 @@ -from __future__ import print_function -import re import requests from lxml.html import parse from link_checker import check_page -from requests.exceptions import ConnectionError + def check_home(url): doc = parse(url).getroot() @@ -11,20 +9,23 @@ def check_home(url): assert(search_button[0].value == "Search") print("OK") + def check_search_page(host): data = dict( - species="mouse" - , group="BXD" - , type="Hippocampus mRNA" - , dataset="HC_M2_0606_P" - , search_terms_or="" - , search_terms_and="MEAN=(15 16) LRS=(23 46)") + species="mouse", + group="BXD", + type="Hippocampus mRNA", + dataset="HC_M2_0606_P", + search_terms_or="", + search_terms_and="MEAN=(15 16) LRS=(23 46)") result = requests.get(host+"/search", params=data) found = result.text.find("records are shown below") assert(found >= 0) assert(result.status_code == 200) print("OK") - check_traits_page(host, "/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P") + check_traits_page(host, ("/show_trait?trait_id=1435395_" + "s_at&dataset=HC_M2_0606_P")) + def check_traits_page(host, traits_url): doc = parse(host+traits_url).getroot() @@ -33,6 +34,7 @@ def check_traits_page(host, traits_url): print("OK") check_page(host, host+traits_url) + def check_main_web_functionality(args_obj, parser): print("") print("Checking main web functionality...") diff --git a/test/requests/mapping_tests.py b/test/requests/mapping_tests.py index 5748a2a3..19b22c21 100644 --- a/test/requests/mapping_tests.py +++ b/test/requests/mapping_tests.py @@ -1,4 +1,3 @@ -from __future__ import print_function import re import copy import json diff --git a/test/requests/navigation_tests.py b/test/requests/navigation_tests.py index eda27324..6b91c1fd 100644 --- a/test/requests/navigation_tests.py +++ b/test/requests/navigation_tests.py @@ -1,4 +1,3 @@ -from __future__ import print_function import re import requests from lxml.html import parse diff --git a/test/requests/test-website.py b/test/requests/test-website.py index f90d1843..8bfb47c2 100755 --- a/test/requests/test-website.py +++ b/test/requests/test-website.py @@ -3,7 +3,7 @@ # env GN2_PROFILE=/home/wrk/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -c ../test/requests/test-website.py http://localhost:5003 # # Mostly to pick up the Guix GN2_PROFILE and python modules -from __future__ import print_function + import argparse from link_checker import check_links from link_checker import check_packaged_js_files diff --git a/webtests/browser_run.py b/webtests/browser_run.py index 2ec299c5..7ee540b7 100644 --- a/webtests/browser_run.py +++ b/webtests/browser_run.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, division, print_function - __all__ = ('sleep', 'testmod', 'test') from doctest import testmod @@ -71,4 +69,4 @@ class Test(object): -test = Test() \ No newline at end of file +test = Test() diff --git a/webtests/correlation_matrix_test.py b/webtests/correlation_matrix_test.py index 8529c265..97114890 100644 --- a/webtests/correlation_matrix_test.py +++ b/webtests/correlation_matrix_test.py @@ -65,8 +65,6 @@ text: 0.608\n71 """ -from __future__ import absolute_import, division, print_function - from browser_run import * testmod() diff --git a/webtests/correlation_test.py b/webtests/correlation_test.py index aad3a69f..311bb847 100644 --- a/webtests/correlation_test.py +++ b/webtests/correlation_test.py @@ -44,8 +44,6 @@ text: 1.000 """ -from __future__ import absolute_import, division, print_function - from browser_run import * testmod() diff --git a/webtests/marker_regression_test.py b/webtests/marker_regression_test.py index c4f76f53..9b4a4acb 100644 --- a/webtests/marker_regression_test.py +++ b/webtests/marker_regression_test.py @@ -48,8 +48,6 @@ text: 11.511 """ -from __future__ import absolute_import, division, print_function - from browser_run import * testmod() diff --git a/webtests/show_trait_js_test.py b/webtests/show_trait_js_test.py index 0fd2c16c..34ffd3b7 100644 --- a/webtests/show_trait_js_test.py +++ b/webtests/show_trait_js_test.py @@ -35,8 +35,6 @@ style: display: none; """ -from __future__ import absolute_import, division, print_function - from browser_run import * testmod() diff --git a/webtests/test_runner.py b/webtests/test_runner.py index ef6d0d69..b5b590a6 100644 --- a/webtests/test_runner.py +++ b/webtests/test_runner.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, division, print_function - import unittest import doctest import glob @@ -25,4 +23,4 @@ def main(): runner.run(suite) if __name__ == '__main__': - main() \ No newline at end of file + main() diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 39a8a2ed..8ac7a279 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -18,7 +18,6 @@ # # This module is used by GeneNetwork project (www.genenetwork.org) -from __future__ import absolute_import, print_function, division from db.call import fetchall, fetchone, fetch1 from utility.logger import getLogger from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists, GN2_BASE_URL diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py index 6fec5dcd..33ce12bd 100644 --- a/wqflask/base/mrna_assay_tissue_data.py +++ b/wqflask/base/mrna_assay_tissue_data.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - import collections from flask import g @@ -92,4 +90,4 @@ class MrnaAssayTissueData(object): else: symbol_values_dict[result.Symbol.lower()].append(result.value) - return symbol_values_dict \ No newline at end of file + return symbol_values_dict diff --git a/wqflask/base/species.py b/wqflask/base/species.py index 6d99af65..e3f1bc4a 100644 --- a/wqflask/base/species.py +++ b/wqflask/base/species.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - import collections from flask import Flask, g @@ -59,4 +57,4 @@ class Chromosomes(object): results = g.db.execute(query).fetchall() for item in results: - self.chromosomes[item.OrderId] = IndChromosome(item.Name, item.Length) \ No newline at end of file + self.chromosomes[item.OrderId] = IndChromosome(item.Name, item.Length) diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 09c41fa7..b20efd2a 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, division, print_function - import os import string import resource diff --git a/wqflask/maintenance/convert_dryad_to_bimbam.py b/wqflask/maintenance/convert_dryad_to_bimbam.py index e833b395..12ce35e9 100644 --- a/wqflask/maintenance/convert_dryad_to_bimbam.py +++ b/wqflask/maintenance/convert_dryad_to_bimbam.py @@ -6,7 +6,6 @@ Convert data dryad files to a BIMBAM _geno and _snps file """ -from __future__ import print_function, division, absolute_import import sys sys.path.append("..") @@ -67,4 +66,4 @@ def convert_dryad_to_bimbam(filename): if __name__=="__main__": input_filename = "/home/zas1024/cfw_data/" + sys.argv[1] + ".txt" - convert_dryad_to_bimbam(input_filename) \ No newline at end of file + convert_dryad_to_bimbam(input_filename) diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py index 528b98cf..d49742f2 100644 --- a/wqflask/maintenance/convert_geno_to_bimbam.py +++ b/wqflask/maintenance/convert_geno_to_bimbam.py @@ -9,7 +9,6 @@ code """ -from __future__ import print_function, division, absolute_import import sys sys.path.append("..") import os @@ -187,4 +186,4 @@ if __name__=="__main__": #convertob = ConvertGenoFile("/home/zas1024/gene/genotype_files/genotypes/SRxSHRSPF2.geno", "/home/zas1024/gene/genotype_files/new_genotypes/SRxSHRSPF2.json") #convertob.convert() ConvertGenoFile.process_all(Old_Geno_Directory, New_Geno_Directory) - #ConvertGenoFiles(Geno_Directory) \ No newline at end of file + #ConvertGenoFiles(Geno_Directory) diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index fd65a52a..544e2fd1 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -30,14 +30,6 @@ It needs to be run manually when database has been changed. Run it as # # This module is used by GeneNetwork project (www.genenetwork.org) -from __future__ import print_function, division - -#from flask import config -# -#cdict = {} -#config = config.Config(cdict).from_envvar('WQFLASK_SETTINGS') -#print("cdict is:", cdict) - import sys # NEW: Note we prepend the current path - otherwise a guix instance of GN2 may be used instead @@ -319,4 +311,4 @@ def _test_it(): if __name__ == '__main__': Conn = MySQLdb.Connect(**parse_db_uri()) Cursor = Conn.cursor() - main() \ No newline at end of file + main() diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py index b53f5dda..60257b28 100644 --- a/wqflask/maintenance/generate_kinship_from_bimbam.py +++ b/wqflask/maintenance/generate_kinship_from_bimbam.py @@ -8,7 +8,6 @@ and uses GEMMA to generate their corresponding kinship/relatedness matrix file """ -from __future__ import print_function, division, absolute_import import sys sys.path.append("..") import os @@ -58,4 +57,4 @@ if __name__=="__main__": Bimbam_Directory = """/export/local/home/zas1024/genotype_files/genotype/bimbam/""" GenerateKinshipMatrices.process_all(Geno_Directory, Bimbam_Directory) - #./gemma -g /home/zas1024/genotype_files/genotype/bimbam/BXD_geno.txt -p /home/zas1024/genotype_files/genotype/bimbam/BXD_pheno.txt -gk 1 -o BXD \ No newline at end of file + #./gemma -g /home/zas1024/genotype_files/genotype/bimbam/BXD_geno.txt -p /home/zas1024/genotype_files/genotype/bimbam/BXD_pheno.txt -gk 1 -o BXD diff --git a/wqflask/maintenance/generate_probesetfreeze_file.py b/wqflask/maintenance/generate_probesetfreeze_file.py index 4231cc7c..b1e41e9a 100644 --- a/wqflask/maintenance/generate_probesetfreeze_file.py +++ b/wqflask/maintenance/generate_probesetfreeze_file.py @@ -1,7 +1,5 @@ #!/usr/bin/python -from __future__ import absolute_import, print_function, division - import sys # sys.path.insert(0, "..") - why? diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py index 9579812a..7e7fd241 100644 --- a/wqflask/maintenance/geno_to_json.py +++ b/wqflask/maintenance/geno_to_json.py @@ -9,7 +9,6 @@ code """ -from __future__ import print_function, division, absolute_import import sys sys.path.append("..") import os @@ -194,4 +193,4 @@ if __name__=="__main__": ConvertGenoFile.process_all(Old_Geno_Directory, New_Geno_Directory) #ConvertGenoFiles(Geno_Directory) - #process_csv(Input_File, Output_File) \ No newline at end of file + #process_csv(Input_File, Output_File) diff --git a/wqflask/maintenance/get_group_samplelists.py b/wqflask/maintenance/get_group_samplelists.py index fb22898a..3f9d0278 100644 --- a/wqflask/maintenance/get_group_samplelists.py +++ b/wqflask/maintenance/get_group_samplelists.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - import os import glob import gzip diff --git a/wqflask/maintenance/print_benchmark.py b/wqflask/maintenance/print_benchmark.py index ae327cf3..b24ce4f1 100644 --- a/wqflask/maintenance/print_benchmark.py +++ b/wqflask/maintenance/print_benchmark.py @@ -1,7 +1,5 @@ #!/usr/bin/python -from __future__ import absolute_import, print_function, division - import time from pprint import pformat as pf @@ -40,4 +38,4 @@ def new_main(): print(pf(TheCounter.Counters)) if __name__ == '__main__': - new_main() \ No newline at end of file + new_main() diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py index 4d6e03bf..701b2b50 100644 --- a/wqflask/maintenance/quantile_normalize.py +++ b/wqflask/maintenance/quantile_normalize.py @@ -1,10 +1,5 @@ -from __future__ import absolute_import, print_function, division - import sys sys.path.insert(0, './') - - - import MySQLdb import urllib.parse @@ -126,4 +121,4 @@ if __name__ == '__main__': } ) - print(response) \ No newline at end of file + print(response) diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py index abd5416c..4177c124 100644 --- a/wqflask/maintenance/set_resource_defaults.py +++ b/wqflask/maintenance/set_resource_defaults.py @@ -16,8 +16,6 @@ To run: """ -from __future__ import print_function, division - import sys import json @@ -163,4 +161,4 @@ def main(): if __name__ == '__main__': Conn = MySQLdb.Connect(**parse_db_uri()) Cursor = Conn.cursor() - main() \ No newline at end of file + main() diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py index 48a5c7ba..61f408d2 100644 --- a/wqflask/utility/Plot.py +++ b/wqflask/utility/Plot.py @@ -24,8 +24,6 @@ # # Last updated by GeneNetwork Core Team 2010/10/20 -from __future__ import print_function - from PIL import ImageColor from PIL import ImageDraw from PIL import ImageFont diff --git a/wqflask/utility/after.py b/wqflask/utility/after.py index b628a0a4..06091ecb 100644 --- a/wqflask/utility/after.py +++ b/wqflask/utility/after.py @@ -1,5 +1,3 @@ -from __future__ import print_function, division, absolute_import - """ See: http://flask.pocoo.org/docs/patterns/deferredcallbacks/#deferred-callbacks @@ -13,4 +11,4 @@ def after_this_request(f): if not hasattr(g, 'after_request_callbacks'): g.after_request_callbacks = [] g.after_request_callbacks.append(f) - return f \ No newline at end of file + return f diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py index bc03eb55..0e499180 100644 --- a/wqflask/utility/authentication_tools.py +++ b/wqflask/utility/authentication_tools.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - import json import requests diff --git a/wqflask/utility/benchmark.py b/wqflask/utility/benchmark.py index 221e5151..ea5a0ab6 100644 --- a/wqflask/utility/benchmark.py +++ b/wqflask/utility/benchmark.py @@ -1,5 +1,3 @@ -from __future__ import print_function, division, absolute_import - import collections import inspect import time diff --git a/wqflask/utility/chunks.py b/wqflask/utility/chunks.py index d91b9bf4..9a7db102 100644 --- a/wqflask/utility/chunks.py +++ b/wqflask/utility/chunks.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - import math import time diff --git a/wqflask/utility/db_tools.py b/wqflask/utility/db_tools.py index 4034f39c..92bde505 100644 --- a/wqflask/utility/db_tools.py +++ b/wqflask/utility/db_tools.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - from MySQLdb import escape_string as escape def create_in_clause(items): diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py index ae42f834..81085ffe 100644 --- a/wqflask/utility/gen_geno_ob.py +++ b/wqflask/utility/gen_geno_ob.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, division, print_function - import utility.logger logger = utility.logger.getLogger(__name__ ) @@ -178,4 +176,4 @@ class Locus(object): if allele in list(geno_table.keys()): self.genotype.append(geno_table[allele]) else: #ZS: Some genotype appears that isn't specified in the metadata, make it unknown - self.genotype.append("U") \ No newline at end of file + self.genotype.append("U") diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py index af306731..0b736176 100644 --- a/wqflask/utility/genofile_parser.py +++ b/wqflask/utility/genofile_parser.py @@ -1,7 +1,6 @@ # CTL analysis for GN2 # Author / Maintainer: Danny Arends -from __future__ import print_function, division, absolute_import import sys import os import glob diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py index 107c9ec6..7eb7f013 100644 --- a/wqflask/utility/helper_functions.py +++ b/wqflask/utility/helper_functions.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - from base import data_set from base.trait import create_trait from base.species import TheSpecies diff --git a/wqflask/utility/hmac.py b/wqflask/utility/hmac.py index b08be97e..73e28790 100644 --- a/wqflask/utility/hmac.py +++ b/wqflask/utility/hmac.py @@ -1,5 +1,3 @@ -from __future__ import print_function, division, absolute_import - import hmac import hashlib @@ -37,4 +35,4 @@ def url_for_hmac(endpoint, **values): return url + combiner + "hm=" + hm app.jinja_env.globals.update(url_for_hmac=url_for_hmac, - data_hmac=data_hmac) \ No newline at end of file + data_hmac=data_hmac) diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py index 1377a564..13ac5cfe 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -1,5 +1,3 @@ -from __future__ import print_function, division, absolute_import - import uuid import simplejson as json import datetime @@ -306,4 +304,4 @@ def change_resource_owner(resource_id, new_owner_id): the_resource['owner_id'] = new_owner_id Redis.delete("resource") - Redis.hset("resources", resource_id, json.dumps(the_resource)) \ No newline at end of file + Redis.hset("resources", resource_id, json.dumps(the_resource)) diff --git a/wqflask/utility/temp_data.py b/wqflask/utility/temp_data.py index 2f2726c6..4144ae00 100644 --- a/wqflask/utility/temp_data.py +++ b/wqflask/utility/temp_data.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division, absolute_import from redis import Redis import simplejson as json diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py index d729aef5..e73f833f 100644 --- a/wqflask/wqflask/__init__.py +++ b/wqflask/wqflask/__init__.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, division, print_function - import sys import jinja2 diff --git a/wqflask/wqflask/api/correlation.py b/wqflask/wqflask/api/correlation.py index eb05645e..7da13121 100644 --- a/wqflask/wqflask/api/correlation.py +++ b/wqflask/wqflask/api/correlation.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, division, print_function - import collections import scipy @@ -234,4 +232,4 @@ def init_corr_params(start_vars): 'return_count' : return_count } - return corr_params \ No newline at end of file + return corr_params diff --git a/wqflask/wqflask/api/gen_menu.py b/wqflask/wqflask/api/gen_menu.py index 41966f78..1dcafe1f 100644 --- a/wqflask/wqflask/api/gen_menu.py +++ b/wqflask/wqflask/api/gen_menu.py @@ -1,5 +1,3 @@ -from __future__ import print_function, division - from flask import g diff --git a/wqflask/wqflask/api/mapping.py b/wqflask/wqflask/api/mapping.py index 92c27c9b..d59a69df 100644 --- a/wqflask/wqflask/api/mapping.py +++ b/wqflask/wqflask/api/mapping.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, division, print_function - import string from base import data_set diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py index 5f9b81b8..acf7ce4a 100644 --- a/wqflask/wqflask/api/router.py +++ b/wqflask/wqflask/api/router.py @@ -1,7 +1,5 @@ # GN2 API -from __future__ import absolute_import, division, print_function - import os, io, csv, json, datetime, requests, yaml import zlib from zipfile import ZipFile, ZIP_DEFLATED @@ -966,4 +964,4 @@ def get_group_id(group_name): if group_id: return group_id[0] else: - return None \ No newline at end of file + return None diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py index 06c00930..15383603 100644 --- a/wqflask/wqflask/collect.py +++ b/wqflask/wqflask/collect.py @@ -1,6 +1,3 @@ -from __future__ import print_function, division, absolute_import - - import os import hashlib import datetime diff --git a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py index 16832621..92de6073 100644 --- a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py +++ b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py @@ -18,7 +18,6 @@ # # This module is used by GeneNetwork project (www.genenetwork.org) -from __future__ import absolute_import, print_function, division from pprint import pformat as pf from base.trait import create_trait diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py index 57a8d85f..929cd2c9 100644 --- a/wqflask/wqflask/correlation/corr_scatter_plot.py +++ b/wqflask/wqflask/correlation/corr_scatter_plot.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - import math from flask import g @@ -130,4 +128,4 @@ def get_intercept_coords(slope, intercept, x_range, y_range): intercept_coords.append([x1, y1]) intercept_coords.append([x2, y2]) - return intercept_coords \ No newline at end of file + return intercept_coords diff --git a/wqflask/wqflask/correlation/correlation_functions.py b/wqflask/wqflask/correlation/correlation_functions.py index abaa212f..b883e361 100644 --- a/wqflask/wqflask/correlation/correlation_functions.py +++ b/wqflask/wqflask/correlation/correlation_functions.py @@ -24,8 +24,6 @@ # # Last updated by NL 2011/03/23 -from __future__ import absolute_import, print_function, division - import math import rpy2.robjects import string @@ -114,4 +112,4 @@ def get_trait_symbol_and_tissue_values(symbol_list=None): tissue_data = MrnaAssayTissueData(gene_symbols=symbol_list) if len(tissue_data.gene_symbols): - return tissue_data.get_symbol_values_pairs() \ No newline at end of file + return tissue_data.get_symbol_values_pairs() diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 5ced30b6..e5b87c6a 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -18,8 +18,6 @@ # # This module is used by GeneNetwork project (www.genenetwork.org) -from __future__ import absolute_import, print_function, division - import collections import json import scipy diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index bd5aca1f..7b4bda31 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -18,8 +18,6 @@ # # This module is used by GeneNetwork project (www.genenetwork.org) -from __future__ import absolute_import, print_function, division - import datetime import math import numpy as np diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index cc9c1860..de8e1e78 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -1,5 +1,3 @@ -from __future__ import print_function, division - import string import requests import json diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py index 78407e22..8628b81d 100644 --- a/wqflask/wqflask/docs.py +++ b/wqflask/wqflask/docs.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - import codecs from flask import g @@ -42,4 +40,4 @@ def update_text(start_vars): sql = "UPDATE Docs SET content='{0}' WHERE entry='{1}';".format(content, start_vars['entry_type']) g.db.execute(sql) except: - pass \ No newline at end of file + pass diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py index 2f4e9aac..3a886537 100644 --- a/wqflask/wqflask/export_traits.py +++ b/wqflask/wqflask/export_traits.py @@ -1,5 +1,3 @@ -from __future__ import print_function, division - import csv import xlsxwriter import io @@ -140,4 +138,4 @@ def sort_traits_by_group(trait_list=[]): traits_by_group[trait.dataset.group.name].append(trait) - return traits_by_group \ No newline at end of file + return traits_by_group diff --git a/wqflask/wqflask/external_tools/send_to_bnw.py b/wqflask/wqflask/external_tools/send_to_bnw.py index 68efd10d..efa17f05 100644 --- a/wqflask/wqflask/external_tools/send_to_bnw.py +++ b/wqflask/wqflask/external_tools/send_to_bnw.py @@ -18,8 +18,6 @@ # # This module is used by GeneNetwork project (www.genenetwork.org) -from __future__ import absolute_import, print_function, division - from base.trait import GeneralTrait from utility import helper_functions, corr_result_helpers @@ -69,4 +67,4 @@ class SendToBNW(object): if has_none: continue self.form_value += ",".join(str(cell) for cell in row) - self.form_value += ";" \ No newline at end of file + self.form_value += ";" diff --git a/wqflask/wqflask/external_tools/send_to_geneweaver.py b/wqflask/wqflask/external_tools/send_to_geneweaver.py index 9844bab4..93164233 100644 --- a/wqflask/wqflask/external_tools/send_to_geneweaver.py +++ b/wqflask/wqflask/external_tools/send_to_geneweaver.py @@ -18,8 +18,6 @@ # # This module is used by GeneNetwork project (www.genenetwork.org) -from __future__ import absolute_import, print_function, division - import string from flask import Flask, g @@ -109,4 +107,4 @@ def test_chip(trait_list): chip_name = '%s_NA' % result[0] return chip_name - return chip_name \ No newline at end of file + return chip_name diff --git a/wqflask/wqflask/external_tools/send_to_webgestalt.py b/wqflask/wqflask/external_tools/send_to_webgestalt.py index 30ca024f..b255ba95 100644 --- a/wqflask/wqflask/external_tools/send_to_webgestalt.py +++ b/wqflask/wqflask/external_tools/send_to_webgestalt.py @@ -18,8 +18,6 @@ # # This module is used by GeneNetwork project (www.genenetwork.org) -from __future__ import absolute_import, print_function, division - import string from flask import Flask, g @@ -123,4 +121,4 @@ def gen_gene_id_list(trait_list): trait_name_list.append(trait.name) retrieve_trait_info(trait, trait.dataset) gene_id_list.append(str(trait.geneid)) - return trait_name_list, gene_id_list \ No newline at end of file + return trait_name_list, gene_id_list diff --git a/wqflask/wqflask/group_manager.py b/wqflask/wqflask/group_manager.py index 24848ed8..e6079c3e 100644 --- a/wqflask/wqflask/group_manager.py +++ b/wqflask/wqflask/group_manager.py @@ -1,6 +1,3 @@ - -from __future__ import print_function, division, absolute_import - from flask import (Flask, g, render_template, url_for, request, make_response, redirect, flash) @@ -142,4 +139,4 @@ def send_group_invites(group_id, user_email_list = [], user_type="members"): else: send_verification_email(user_details, template_name = "email/group_verification.txt", key_prefix = "verification_code", subject = "You've been invited to join a GeneNetwork user group") -#@app.route() \ No newline at end of file +#@app.route() diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py index c65a1415..6d797a29 100644 --- a/wqflask/wqflask/gsearch.py +++ b/wqflask/wqflask/gsearch.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - import json from flask import Flask, g diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py index 1f1cdb90..cca5a4fc 100644 --- a/wqflask/wqflask/heatmap/heatmap.py +++ b/wqflask/wqflask/heatmap/heatmap.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - import string import os import random diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py index a39e5d0f..17c8ccbf 100644 --- a/wqflask/wqflask/interval_analyst/GeneUtil.py +++ b/wqflask/wqflask/interval_analyst/GeneUtil.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - import string from flask import Flask, g diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index 67512bc6..7ae84b16 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - from base.trait import GeneralTrait from base import data_set #import create_dataset @@ -711,4 +709,4 @@ def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples): list_to_numbers = [d[x] for x in perm_strata_strings] perm_strata = list_to_numbers - return perm_strata \ No newline at end of file + return perm_strata diff --git a/wqflask/wqflask/model.py b/wqflask/wqflask/model.py index a135761c..772f74e4 100644 --- a/wqflask/wqflask/model.py +++ b/wqflask/wqflask/model.py @@ -1,5 +1,3 @@ -from __future__ import print_function, division, absolute_import - import uuid import datetime @@ -168,4 +166,4 @@ def display_collapsible(number): def user_uuid(): """Unique cookie for a user""" - user_uuid = request.cookies.get('user_uuid') \ No newline at end of file + user_uuid = request.cookies.get('user_uuid') diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py index 2a4c4a93..70e5dd58 100644 --- a/wqflask/wqflask/network_graph/network_graph.py +++ b/wqflask/wqflask/network_graph/network_graph.py @@ -18,8 +18,6 @@ # # This module is used by GeneNetwork project (www.genenetwork.org) -from __future__ import absolute_import, print_function, division - import scipy import simplejson as json from pprint import pformat as pf diff --git a/wqflask/wqflask/news.py b/wqflask/wqflask/news.py index 20319756..0675ec4b 100644 --- a/wqflask/wqflask/news.py +++ b/wqflask/wqflask/news.py @@ -1,4 +1,3 @@ -from __future__ import absolute_import, print_function, division from flask import g class News(object): diff --git a/wqflask/wqflask/parser.py b/wqflask/wqflask/parser.py index 1ca5ecff..472dd30e 100644 --- a/wqflask/wqflask/parser.py +++ b/wqflask/wqflask/parser.py @@ -17,8 +17,6 @@ be acceptable.] """ -from __future__ import print_function, division - import re from pprint import pformat as pf diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py index 6b3e00fb..e883d5da 100644 --- a/wqflask/wqflask/resource_manager.py +++ b/wqflask/wqflask/resource_manager.py @@ -1,5 +1,3 @@ -from __future__ import print_function, division, absolute_import - import json from flask import (Flask, g, render_template, url_for, request, make_response, @@ -131,4 +129,4 @@ def get_group_names(group_masks): this_mask['name'] = group_name group_masks_with_names[group_id] = this_mask - return group_masks_with_names \ No newline at end of file + return group_masks_with_names diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index c07a7670..f6c677a8 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - import re import uuid from math import * diff --git a/wqflask/wqflask/send_mail.py b/wqflask/wqflask/send_mail.py index bf5d0dd8..86e8a558 100644 --- a/wqflask/wqflask/send_mail.py +++ b/wqflask/wqflask/send_mail.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, division, print_function - import datetime import time diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py index f17e825e..6fcf7cec 100644 --- a/wqflask/wqflask/show_trait/SampleList.py +++ b/wqflask/wqflask/show_trait/SampleList.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - from flask import Flask, g from base import webqtlCaseData diff --git a/wqflask/wqflask/show_trait/export_trait_data.py b/wqflask/wqflask/show_trait/export_trait_data.py index 68c3ad7d..2d76b935 100644 --- a/wqflask/wqflask/show_trait/export_trait_data.py +++ b/wqflask/wqflask/show_trait/export_trait_data.py @@ -1,5 +1,3 @@ -from __future__ import print_function, division - import simplejson as json from pprint import pformat as pf @@ -71,4 +69,4 @@ def cmp_samples(a, b): else: return 1 else: - return -1 \ No newline at end of file + return -1 diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 6a74cada..e93b0289 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - import string import os import datetime diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py index b3d26caf..0db7e1fe 100644 --- a/wqflask/wqflask/snp_browser/snp_browser.py +++ b/wqflask/wqflask/snp_browser/snp_browser.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - from flask import Flask, g, url_for import string diff --git a/wqflask/wqflask/submit_bnw.py b/wqflask/wqflask/submit_bnw.py index 59e60dfd..a0e84c8c 100644 --- a/wqflask/wqflask/submit_bnw.py +++ b/wqflask/wqflask/submit_bnw.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - from base.trait import GeneralTrait from base import data_set from utility import helper_functions @@ -8,4 +6,4 @@ import utility.logger logger = utility.logger.getLogger(__name__ ) def get_bnw_input(start_vars): - logger.debug("BNW VARS:", start_vars) \ No newline at end of file + logger.debug("BNW VARS:", start_vars) diff --git a/wqflask/wqflask/update_search_results.py b/wqflask/wqflask/update_search_results.py index 68bea9d6..672f95b1 100644 --- a/wqflask/wqflask/update_search_results.py +++ b/wqflask/wqflask/update_search_results.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - import json from flask import Flask, g diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py index 04672b45..10cb7319 100644 --- a/wqflask/wqflask/user_login.py +++ b/wqflask/wqflask/user_login.py @@ -1,5 +1,3 @@ -from __future__ import print_function, division, absolute_import - import os import hashlib import datetime @@ -470,4 +468,4 @@ def register(): @app.errorhandler(401) def unauthorized(error): - return redirect(url_for('login')) \ No newline at end of file + return redirect(url_for('login')) diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py index 3c41e2b8..24191a15 100644 --- a/wqflask/wqflask/user_manager.py +++ b/wqflask/wqflask/user_manager.py @@ -1,5 +1,3 @@ -from __future__ import print_function, division, absolute_import - import os import hashlib import datetime diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py index 71c31c57..c1f38396 100644 --- a/wqflask/wqflask/user_session.py +++ b/wqflask/wqflask/user_session.py @@ -1,5 +1,3 @@ -from __future__ import print_function, division, absolute_import - import datetime import time import uuid diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 83d5202e..b0489e64 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -2,8 +2,6 @@ # # Main routing table for GN2 -from __future__ import absolute_import, division, print_function - import traceback # for error page import os # for error gifs import random # for random error gif -- cgit v1.2.3 From 24bed3fc4f3a69c24074e9c5829a46b66702cbbf Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 26 Aug 2020 22:01:03 +0300 Subject: Remove debug statement * wqflask/wqflask/views.py(search_page): "debugf" raises an error since the first arg is expected to be an int --- wqflask/wqflask/views.py | 2 -- 1 file changed, 2 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index b0489e64..0224da4a 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -206,8 +206,6 @@ def search_page(): result = the_search.__dict__ valid_search = result['search_term_exists'] - logger.debugf("result", result) - if USE_REDIS and valid_search: Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL)) Redis.expire(key, 60*60) -- cgit v1.2.3 From 357ca458695fbc60c97de3d1cdf89034a8722bc5 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 27 Aug 2020 01:18:11 +0300 Subject: Replace "string.split" & "string.join" with python's inbuilt methods --- scripts/maintenance/readProbeSetMean_v7.py | 20 ++++++++++---------- scripts/maintenance/readProbeSetSE_v7.py | 14 +++++++------- wqflask/base/data_set.py | 2 +- wqflask/base/trait.py | 14 +++++++------- wqflask/utility/webqtlUtil.py | 4 ++-- wqflask/wqflask/external_tools/send_to_geneweaver.py | 2 +- wqflask/wqflask/external_tools/send_to_webgestalt.py | 2 +- wqflask/wqflask/interval_analyst/GeneUtil.py | 4 ++-- .../marker_regression/display_mapping_results.py | 2 +- wqflask/wqflask/marker_regression/plink_mapping.py | 6 +++--- wqflask/wqflask/show_trait/show_trait.py | 4 ++-- wqflask/wqflask/snp_browser/snp_browser.py | 12 ++++++------ 12 files changed, 43 insertions(+), 43 deletions(-) (limited to 'wqflask') diff --git a/scripts/maintenance/readProbeSetMean_v7.py b/scripts/maintenance/readProbeSetMean_v7.py index a540796a..43f084f4 100755 --- a/scripts/maintenance/readProbeSetMean_v7.py +++ b/scripts/maintenance/readProbeSetMean_v7.py @@ -60,15 +60,15 @@ print('Checking if each line have same number of members') GeneList = [] isCont = 1 header = fp.readline() -header = string.split(string.strip(header), '\t') -header = list(map(string.strip, header)) +header = header.strip().split('\t') +header = [x.strip() for x in header] nfield = len(header) line = fp.readline() kj = 0 while line: - line2 = string.split(string.strip(line), '\t') - line2 = list(map(string.strip, line2)) + line2 = line.strip().split('\t') + line2 = [x.strip() for x in line2] if len(line2) != nfield: print(("Error : " + line)) isCont = 0 @@ -98,8 +98,8 @@ print('Checking if each strain exist in database') isCont = 1 fp.seek(0) header = fp.readline() -header = string.split(string.strip(header), '\t') -header = list(map(string.strip, header)) +header = header.strip().split('\t') +header = [x.strip() for x in header] header = list(map(translateAlias, header)) header = header[dataStart:] Ids = [] @@ -126,8 +126,8 @@ print('Check if each ProbeSet exist in database') ##---- find PID is name or target ----## line = fp.readline() line = fp.readline() -line2 = string.split(string.strip(line), '\t') -line2 = list(map(string.strip, line2)) +line2 = line.strip().split('\t') +line2 = [x.strip() for x in line2] PId = line2[0] db.execute('select Id from ProbeSet where Name="%s" and ChipId=%d' % @@ -222,8 +222,8 @@ kj = 0 values1 = [] values2 = [] while line: - line2 = string.split(string.strip(line), '\t') - line2 = list(map(string.strip, line2)) + line2 = line.strip().split('\t') + line2 = [x.strip() for x in line2] PId = line2[0] recordId = NameIds[PId] diff --git a/scripts/maintenance/readProbeSetSE_v7.py b/scripts/maintenance/readProbeSetSE_v7.py index 20a846a4..edd9e7b0 100755 --- a/scripts/maintenance/readProbeSetSE_v7.py +++ b/scripts/maintenance/readProbeSetSE_v7.py @@ -71,14 +71,14 @@ print('Checking if each line have same number of members') GeneList = [] isCont = 1 header = fp.readline() -header = string.split(string.strip(header), '\t') +header = header.strip().split('\t') header = list(map(string.strip, header)) nfield = len(header) line = fp.readline() kj = 0 while line: - line2 = string.split(string.strip(line), '\t') + line2 = line.strip().split('\t') line2 = list(map(string.strip, line2)) if len(line2) != nfield: isCont = 0 @@ -109,7 +109,7 @@ print('Checking if each strain exist in database') isCont = 1 fp.seek(0) header = fp.readline() -header = string.split(string.strip(header), '\t') +header = header.strip().split('\t') header = list(map(string.strip, header)) header = list(map(translateAlias, header)) header = header[dataStart:] @@ -137,8 +137,8 @@ print('Check if each ProbeSet exist in database') ##---- find PID is name or target ----## line = fp.readline() line = fp.readline() -line2 = string.split(string.strip(line), '\t') -line2 = list(map(string.strip, line2)) +line2 = line.strip().split('\t') +line2 = [x.strip() for x in line2] PId = line2[0] db.execute('select Id from ProbeSet where Name="%s" and ChipId=%d' % @@ -217,8 +217,8 @@ line = fp.readline() kj = 0 while line: - line2 = string.split(string.strip(line), '\t') - line2 = list(map(string.strip, line2)) + line2 = line.strip().split('\t') + line2 = [x.strip() for x in line2] CellId = line2[0] if CellId not in ProbeNameId: diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 8ac7a279..ce017fb4 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -697,7 +697,7 @@ class DataSet(object): else: query = "SELECT {}.Name,".format(escape(dataset_type)) data_start_pos = 1 - query += string.join(temp, ', ') + query += ', '.join(temp) query += ' FROM ({}, {}XRef, {}Freeze) '.format(*mescape(dataset_type, self.type, self.type)) diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index b20efd2a..2fd5d725 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -150,8 +150,8 @@ class GeneralTrait(object): alias = 'Not available' if getattr(self, "alias", None): - alias = string.replace(self.alias, ";", " ") - alias = string.join(string.split(alias), ", ") + alias = self.alias.replace(";", " ") + alias = ", ".join(alias.split()) return alias @@ -437,7 +437,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): #XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name # to avoid the problem of same marker name from different species. elif dataset.type == 'Geno': - display_fields_string = string.join(dataset.display_fields, ',Geno.') + display_fields_string = ',Geno.'.join(dataset.display_fields) display_fields_string = 'Geno.' + display_fields_string query = """ SELECT %s @@ -456,8 +456,8 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): query = """SELECT %s FROM %s WHERE Name = %s""" logger.sql(query) trait_info = g.db.execute(query, - (string.join(dataset.display_fields, ','), - dataset.type, trait.name)).fetchone() + ','.join(dataset.display_fields), + dataset.type, trait.name).fetchone() if trait_info: trait.haveinfo = True @@ -501,8 +501,8 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % trait.pubmed_id if dataset.type == 'ProbeSet' and dataset.group: - description_string = str(str(trait.description).strip(codecs.BOM_UTF8), 'utf-8') - target_string = str(str(trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8') + description_string = trait.description + target_string = trait.probe_target_description if len(description_string) > 1 and description_string != 'None': description_display = description_string diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py index d4979011..5681fadf 100644 --- a/wqflask/utility/webqtlUtil.py +++ b/wqflask/utility/webqtlUtil.py @@ -107,7 +107,7 @@ def hasAccessToConfidentialPhenotypeTrait(privilege, userName, authorized_users) if webqtlConfig.USERDICT[privilege] > webqtlConfig.USERDICT['user']: access_to_confidential_phenotype_trait = 1 else: - AuthorizedUsersList=list(map(string.strip, string.split(authorized_users, ','))) - if AuthorizedUsersList.__contains__(userName): + AuthorizedUsersList=[x.strip() for x in authorized_users.split(',')] + if userName in AuthorizedUsersList: access_to_confidential_phenotype_trait = 1 return access_to_confidential_phenotype_trait diff --git a/wqflask/wqflask/external_tools/send_to_geneweaver.py b/wqflask/wqflask/external_tools/send_to_geneweaver.py index 93164233..4c958a88 100644 --- a/wqflask/wqflask/external_tools/send_to_geneweaver.py +++ b/wqflask/wqflask/external_tools/send_to_geneweaver.py @@ -55,7 +55,7 @@ class SendToGeneWeaver(object): 'client': "genenetwork", 'species': species_name, 'idtype': self.chip_name, - 'list': string.join(trait_name_list, ","), + 'list': ",".join(trait_name_list), } def get_trait_name_list(trait_list): diff --git a/wqflask/wqflask/external_tools/send_to_webgestalt.py b/wqflask/wqflask/external_tools/send_to_webgestalt.py index b255ba95..2f068792 100644 --- a/wqflask/wqflask/external_tools/send_to_webgestalt.py +++ b/wqflask/wqflask/external_tools/send_to_webgestalt.py @@ -47,7 +47,7 @@ class SendToWebGestalt(object): id_type = "entrezgene" self.hidden_vars = { - 'gene_list' : string.join(gene_id_list, "\n"), + 'gene_list' : "\n".join(gene_id_list), 'id_type' : "entrezgene", 'ref_set' : "genome", 'enriched_database_category' : "geneontology", diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py index 17c8ccbf..d0dd7aea 100644 --- a/wqflask/wqflask/interval_analyst/GeneUtil.py +++ b/wqflask/wqflask/interval_analyst/GeneUtil.py @@ -31,7 +31,7 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'): Chromosome = '%s' AND ((TxStart > %f and TxStart <= %f) OR (TxEnd > %f and TxEnd <= %f)) ORDER BY txStart - """ % (string.join(fetchFields, ", "), + """ % (", ".join(fetchFields), speciesId, chrName, startMb, endMb, startMb, endMb)).fetchall() @@ -66,7 +66,7 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'): othSpec, othSpecId = item newdict2 = {} - resultsOther = g.db.execute("SELECT %s FROM GeneList WHERE SpeciesId = %d AND geneSymbol= '%s' LIMIT 1" % (string.join(fetchFields, ", "), + resultsOther = g.db.execute("SELECT %s FROM GeneList WHERE SpeciesId = %d AND geneSymbol= '%s' LIMIT 1" % (", ".join(fetchFields), othSpecId, newdict["GeneSymbol"])).fetchone() diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index ccdafa14..dfaa1562 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -454,7 +454,7 @@ class DisplayMappingResults(object): Chr_Length.Name in (%s) Order by Chr_Length.OrderId - """ % (self.dataset.group.name, string.join(["'%s'" % X[0] for X in self.ChrList[1:]], ", "))) + """ % (self.dataset.group.name, ", ".join(["'%s'" % X[0] for X in self.ChrList[1:]]))) self.ChrLengthMbList = [x[0]/1000000.0 for x in self.ChrLengthMbList] self.ChrLengthMbSum = reduce(lambda x, y:x+y, self.ChrLengthMbList, 0.0) diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py index 2f282adc..6c38c34f 100644 --- a/wqflask/wqflask/marker_regression/plink_mapping.py +++ b/wqflask/wqflask/marker_regression/plink_mapping.py @@ -83,7 +83,7 @@ def get_samples_from_ped_file(dataset): sample_list=[] while line: - lineList = string.split(string.strip(line), '\t') + lineList = line.strip().split('\t') lineList = list(map(string.strip, lineList)) sample_name = lineList[0] @@ -155,8 +155,8 @@ def parse_plink_output(output_filename, species): # output: lineList list ####################################################### def build_line_list(line=None): - line_list = string.split(string.strip(line), ' ')# irregular number of whitespaces between columns + line_list = line.strip().split(' ')# irregular number of whitespaces between columns line_list = [item for item in line_list if item !=''] line_list = list(map(string.strip, line_list)) - return line_list \ No newline at end of file + return line_list diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index e93b0289..88cd7dca 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -229,8 +229,8 @@ class ShowTrait(object): hddn = OrderedDict() if self.dataset.group.allsamples: - hddn['allsamples'] = string.join(self.dataset.group.allsamples, ' ') - hddn['primary_samples'] = string.join(self.primary_sample_names, ',') + hddn['allsamples'] = ''.join(self.dataset.group.allsamples) + hddn['primary_samples'] = ''.join(self.primary_sample_names) hddn['trait_id'] = self.trait_id hddn['trait_display_name'] = self.this_trait.display_name hddn['dataset'] = self.dataset.name diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py index 0db7e1fe..2df71b12 100644 --- a/wqflask/wqflask/snp_browser/snp_browser.py +++ b/wqflask/wqflask/snp_browser/snp_browser.py @@ -456,7 +456,7 @@ class SnpBrowser(object): function_list = [] if function_details: - function_list = string.split(string.strip(function_details), ",") + function_list = function_details.strip().split(",") function_list = list(map(string.strip, function_list)) function_list[0] = function_list[0].title() function_details = ", ".join(item for item in function_list) @@ -722,11 +722,11 @@ def get_effect_details_by_category(effect_name = None, effect_value = None): new_codon_group_list = ['Start Gained'] codon_effect_group_list = ['Start Lost', 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous'] - effect_detail_list = string.split(string.strip(effect_value), '|') + effect_detail_list = effect_value.strip().split('|') effect_detail_list = list(map(string.strip, effect_detail_list)) for index, item in enumerate(effect_detail_list): - item_list = string.split(string.strip(item), ',') + item_list = item.strip().split(',') item_list = list(map(string.strip, item_list)) gene_id = item_list[0] @@ -746,13 +746,13 @@ def get_effect_details_by_category(effect_name = None, effect_value = None): if effect_name in new_codon_group_list: new_codon = item_list[6] tmp_list = [biotype, new_codon] - function_detail_list.append(string.join(tmp_list, ", ")) + function_detail_list.append(", ".join(tmp_list)) elif effect_name in codon_effect_group_list: old_new_AA = item_list[6] old_new_codon = item_list[7] codon_num = item_list[8] tmp_list = [biotype, old_new_AA, old_new_codon, codon_num] - function_detail_list.append(string.join(tmp_list, ", ")) + function_detail_list.append(", ".join(tmp_list)) else: function_detail_list.append(biotype) @@ -852,7 +852,7 @@ def get_gene_id_name_dict(species_id, gene_name_list): if len(gene_name_list) == 0: return "" gene_name_str_list = ["'" + gene_name + "'" for gene_name in gene_name_list] - gene_name_str = string.join(gene_name_str_list, ",") + gene_name_str = ",".join(gene_name_str_list) query = """ SELECT -- cgit v1.2.3 From 958972339e6c244ebedaf494bf43ca1eecabe6c4 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 27 Aug 2020 01:22:14 +0300 Subject: Remove unused imports --- wqflask/base/mrna_assay_tissue_data.py | 1 - wqflask/base/species.py | 5 ----- wqflask/runserver.py | 9 --------- wqflask/wqflask/correlation_matrix/show_corr_matrix.py | 4 ---- wqflask/wqflask/do_search.py | 2 +- wqflask/wqflask/network_graph/network_graph.py | 5 ----- 6 files changed, 1 insertion(+), 25 deletions(-) (limited to 'wqflask') diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py index 33ce12bd..12f18f71 100644 --- a/wqflask/base/mrna_assay_tissue_data.py +++ b/wqflask/base/mrna_assay_tissue_data.py @@ -7,7 +7,6 @@ from utility import Bunch from MySQLdb import escape_string as escape -from pprint import pformat as pf from utility.logger import getLogger logger = getLogger(__name__ ) diff --git a/wqflask/base/species.py b/wqflask/base/species.py index e3f1bc4a..2771d116 100644 --- a/wqflask/base/species.py +++ b/wqflask/base/species.py @@ -2,11 +2,6 @@ import collections from flask import Flask, g -#from MySQLdb import escape_string as escape - -from utility import Bunch - -from pprint import pformat as pf from utility.logger import getLogger logger = getLogger(__name__ ) diff --git a/wqflask/runserver.py b/wqflask/runserver.py index 15572d97..58d79589 100644 --- a/wqflask/runserver.py +++ b/wqflask/runserver.py @@ -11,25 +11,16 @@ from wqflask import app import logging -import utility.logger -logger = utility.logger.getLogger(__name__ ) - -import signal -signal.signal(signal.SIGPIPE, signal.SIG_DFL) BLUE = '\033[94m' GREEN = '\033[92m' BOLD = '\033[1m' ENDC = '\033[0m' -from utility.startup_config import app_config - app_config() werkzeug_logger = logging.getLogger('werkzeug') -from utility.tools import WEBSERVER_MODE, SERVER_PORT - if WEBSERVER_MODE == 'DEBUG': app.run(host='0.0.0.0', port=SERVER_PORT, diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index 7b4bda31..dac4037e 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -47,10 +47,6 @@ import utility.webqtlUtil #this is for parallel computing only. from wqflask.correlation import correlation_functions from utility.benchmark import Bench -from MySQLdb import escape_string as escape - -from pprint import pformat as pf - from flask import Flask, g, url_for import utility.logger diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index de8e1e78..7e71f7d7 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -8,7 +8,6 @@ from MySQLdb import escape_string as escape from pprint import pformat as pf import sys -# sys.path.append("..") Never in a running webserver from db import webqtlDatabaseFunction from utility.tools import GN2_BASE_URL @@ -17,6 +16,7 @@ import logging from utility.logger import getLogger logger = getLogger(__name__) + class DoSearch(object): """Parent class containing parameters/functions used for all searches""" diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py index 70e5dd58..cfefe4ec 100644 --- a/wqflask/wqflask/network_graph/network_graph.py +++ b/wqflask/wqflask/network_graph/network_graph.py @@ -31,11 +31,6 @@ from utility.tools import GN2_BRANCH_URL from db import webqtlDatabaseFunction import utility.webqtlUtil #this is for parallel computing only. from wqflask.correlation import correlation_functions -from utility.benchmark import Bench - -from MySQLdb import escape_string as escape - -from pprint import pformat as pf from flask import Flask, g -- cgit v1.2.3 From 391c1681eaeabfdbe65a64a1bb8b05beca30141e Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 27 Aug 2020 01:23:29 +0300 Subject: Add global method to convert binary string to plain string * wqflask/utility/db_tools.py: escape_string returns a binary string which introduces a bug when composing sql query string. The escaped strings have to be converted to plain text. --- wqflask/utility/db_tools.py | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) (limited to 'wqflask') diff --git a/wqflask/utility/db_tools.py b/wqflask/utility/db_tools.py index 92bde505..6e19778f 100644 --- a/wqflask/utility/db_tools.py +++ b/wqflask/utility/db_tools.py @@ -1,4 +1,5 @@ -from MySQLdb import escape_string as escape +from MySQLdb import escape_string as escape_ + def create_in_clause(items): """Create an in clause for mysql""" @@ -6,8 +7,11 @@ def create_in_clause(items): in_clause = '( {} )'.format(in_clause) return in_clause + def mescape(*items): """Multiple escape""" - escaped = [escape(str(item)) for item in items] - #print("escaped is:", escaped) - return escaped + return [escape_(str(item)).decode('utf8') for item in items] + + +def escape(string_): + return escape_(string_).decode('utf8') -- cgit v1.2.3 From 5992562296aabdd51bc3575f36d16d1c245d9d1f Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 27 Aug 2020 01:26:20 +0300 Subject: Remove redundant methods which are defined elsewhere * wqflask/base/data_set.py: Delete "create_in_clause", and "mescape" which are defined in "utility.db_tools" --- wqflask/base/data_set.py | 18 +++--------------- 1 file changed, 3 insertions(+), 15 deletions(-) (limited to 'wqflask') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index ce017fb4..07704e4c 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -23,7 +23,9 @@ from utility.logger import getLogger from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists, GN2_BASE_URL from db.gn_server import menu_main from pprint import pformat as pf -from MySQLdb import escape_string as escape +from utility.db_tools import escape +from utility.db_tools import mescape +from utility.db_tools import create_in_clause from maintenance import get_group_samplelists from utility.tools import locate, locate_ignore_error, flat_files from utility import gen_geno_ob @@ -204,20 +206,6 @@ def create_datasets_list(): return datasets -def create_in_clause(items): - """Create an in clause for mysql""" - in_clause = ', '.join("'{}'".format(x) for x in mescape(*items)) - in_clause = '( {} )'.format(in_clause) - return in_clause - - -def mescape(*items): - """Multiple escape""" - escaped = [escape(str(item)) for item in items] - #logger.debug("escaped is:", escaped) - return escaped - - class Markers(object): """Todo: Build in cacheing so it saves us reading the same file more than once""" -- cgit v1.2.3 From 2697301045266b40f571eeb2f9c7d8eb220552b4 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 27 Aug 2020 01:28:08 +0300 Subject: Replace mysqldb's "escape" with the one from utils.db_tools Mysqldb's escape returns a binary string. Use utils.db_tools which adds an extra step of converting the binary string to a string. --- wqflask/base/mrna_assay_tissue_data.py | 2 +- wqflask/base/trait.py | 2 +- wqflask/wqflask/api/correlation.py | 2 +- wqflask/wqflask/correlation/show_corr_results.py | 2 +- wqflask/wqflask/do_search.py | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) (limited to 'wqflask') diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py index 12f18f71..f1929518 100644 --- a/wqflask/base/mrna_assay_tissue_data.py +++ b/wqflask/base/mrna_assay_tissue_data.py @@ -5,7 +5,7 @@ from flask import g from utility import db_tools from utility import Bunch -from MySQLdb import escape_string as escape +from utility.db_tools import escape from utility.logger import getLogger diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 2fd5d725..e3507ae1 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -19,7 +19,7 @@ Redis = get_redis_conn() from wqflask import app import simplejson as json -from MySQLdb import escape_string as escape +from utility.db_tools import escape from pprint import pformat as pf from flask import Flask, g, request, url_for, redirect, make_response, render_template diff --git a/wqflask/wqflask/api/correlation.py b/wqflask/wqflask/api/correlation.py index 7da13121..f5b50dcd 100644 --- a/wqflask/wqflask/api/correlation.py +++ b/wqflask/wqflask/api/correlation.py @@ -2,7 +2,7 @@ import collections import scipy -from MySQLdb import escape_string as escape +from utility.db_tools import escape from flask import g diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index e5b87c6a..91146e5b 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -35,7 +35,7 @@ from wqflask.correlation import correlation_functions from utility.benchmark import Bench import utility.webqtlUtil from utility.type_checking import is_str, get_float, get_int, get_string -from MySQLdb import escape_string as escape +from utility.db_tools import escape from flask import Flask, g diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 7e71f7d7..00636563 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -4,7 +4,7 @@ import json from flask import Flask, g -from MySQLdb import escape_string as escape +from utility.db_tools import escape from pprint import pformat as pf import sys -- cgit v1.2.3 From 3095a738e883d1526d7f9cb35d50ace062616a06 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 27 Aug 2020 01:29:23 +0300 Subject: Remove comment block --- wqflask/wqflask/parser.py | 16 ---------------- 1 file changed, 16 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/parser.py b/wqflask/wqflask/parser.py index 472dd30e..76fae54b 100644 --- a/wqflask/wqflask/parser.py +++ b/wqflask/wqflask/parser.py @@ -76,22 +76,6 @@ def parse(pstring): logger.debug("* items are:", pf(items) + "\n") return(items) - #def encregexp(self,str): - # if not str: - # return [] - # else: - # wildcardkeyword = str.strip() - # wildcardkeyword = string.replace(wildcardkeyword,',',' ') - # wildcardkeyword = string.replace(wildcardkeyword,';',' ') - # wildcardkeyword = wildcardkeyword.split() - # NNN = len(wildcardkeyword) - # for i in range(NNN): - # keyword = wildcardkeyword[i] - # keyword = string.replace(keyword,"*",".*") - # keyword = string.replace(keyword,"?",".") - # wildcardkeyword[i] = keyword#'[[:<:]]'+ keyword+'[[:>:]]' - # return wildcardkeyword - if __name__ == '__main__': parse("foo=[3 2 1]") -- cgit v1.2.3 From c030e128508b17896dbef3ba9794698195cafc04 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 27 Aug 2020 01:30:09 +0300 Subject: Apply pep-8 formatting --- wqflask/runserver.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'wqflask') diff --git a/wqflask/runserver.py b/wqflask/runserver.py index 58d79589..b48ceee1 100644 --- a/wqflask/runserver.py +++ b/wqflask/runserver.py @@ -12,10 +12,10 @@ from wqflask import app import logging -BLUE = '\033[94m' +BLUE = '\033[94m' GREEN = '\033[92m' -BOLD = '\033[1m' -ENDC = '\033[0m' +BOLD = '\033[1m' +ENDC = '\033[0m' app_config() @@ -38,7 +38,7 @@ elif WEBSERVER_MODE == 'DEV': threaded=False, processes=0, use_reloader=True) -else: # staging/production modes +else: # staging/production modes app.run(host='0.0.0.0', port=SERVER_PORT, debug=False, -- cgit v1.2.3 From 869da13b92e70fa0769cd1a49e15b03e2c9d0550 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 27 Aug 2020 01:31:33 +0300 Subject: Fix failing tests --- wqflask/tests/base/test_data_set.py | 71 +++++++++++++++++++++++------- wqflask/tests/base/test_general_object.py | 9 ++-- wqflask/tests/wqflask/api/test_gen_menu.py | 6 +++ 3 files changed, 66 insertions(+), 20 deletions(-) (limited to 'wqflask') diff --git a/wqflask/tests/base/test_data_set.py b/wqflask/tests/base/test_data_set.py index 94780a5d..e6000e56 100644 --- a/wqflask/tests/base/test_data_set.py +++ b/wqflask/tests/base/test_data_set.py @@ -4,7 +4,7 @@ import unittest import mock from wqflask import app -from data import gen_menu_json +from .data import gen_menu_json from base.data_set import DatasetType @@ -59,9 +59,14 @@ class TestDataSetTypes(unittest.TestCase): self.assertEqual(data_set("BXDGeno"), "Geno") self.assertEqual(data_set("BXDPublish"), "Publish") self.assertEqual(data_set("HLC_0311"), "ProbeSet") + redis_mock.set.assert_called_once_with( "dataset_structure", - '{"BXDGeno": "Geno", "BXDPublish": "Publish", "HLCPublish": "Publish", "HLC_0311": "ProbeSet", "HC_M2_0606_P": "ProbeSet"}') + ('{"HLC_0311": "ProbeSet", ' + '"HLCPublish": "Publish", ' + '"BXDGeno": "Geno", ' + '"HC_M2_0606_P": "ProbeSet", ' + '"BXDPublish": "Publish"}')) @mock.patch('base.data_set.g') def test_set_dataset_key_mrna(self, db_mock): @@ -74,8 +79,17 @@ class TestDataSetTypes(unittest.TestCase): self.assertEqual(data_set("Test"), "ProbeSet") redis_mock.set.assert_called_once_with( "dataset_structure", - '{"Aging-Brain-UCIPublish": "Publish", "AKXDGeno": "Geno", "B139_K_1206_M": "ProbeSet", "AD-cases-controls-MyersGeno": "Geno", "AD-cases-controls-MyersPublish": "Publish", "All Phenotypes": "Publish", "Test": "ProbeSet", "AXBXAPublish": "Publish", "B139_K_1206_R": "ProbeSet", "AXBXAGeno": "Geno"}') - expected_db_call = """""" + ('{"AD-cases-controls-MyersGeno": "Geno", ' + '"AD-cases-controls-MyersPublish": "Publish", ' + '"AKXDGeno": "Geno", ' + '"AXBXAGeno": "Geno", ' + '"AXBXAPublish": "Publish", ' + '"Aging-Brain-UCIPublish": "Publish", ' + '"All Phenotypes": "Publish", ' + '"B139_K_1206_M": "ProbeSet", ' + '"B139_K_1206_R": "ProbeSet", ' + '"Test": "ProbeSet"}')) + db_mock.db.execute.assert_called_with( ("SELECT ProbeSetFreeze.Id FROM ProbeSetFreeze " + "WHERE ProbeSetFreeze.Name = \"Test\" ") @@ -92,13 +106,21 @@ class TestDataSetTypes(unittest.TestCase): self.assertEqual(data_set("Test"), "Publish") redis_mock.set.assert_called_once_with( "dataset_structure", - '{"Aging-Brain-UCIPublish": "Publish", "AKXDGeno": "Geno", "B139_K_1206_M": "ProbeSet", "AD-cases-controls-MyersGeno": "Geno", "AD-cases-controls-MyersPublish": "Publish", "All Phenotypes": "Publish", "Test": "Publish", "AXBXAPublish": "Publish", "B139_K_1206_R": "ProbeSet", "AXBXAGeno": "Geno"}') - expected_db_call = """""" + ('{"AD-cases-controls-MyersGeno": "Geno", ' + '"AD-cases-controls-MyersPublish": "Publish", ' + '"AKXDGeno": "Geno", ' + '"AXBXAGeno": "Geno", ' + '"AXBXAPublish": "Publish", ' + '"Aging-Brain-UCIPublish": "Publish", ' + '"All Phenotypes": "Publish", ' + '"B139_K_1206_M": "ProbeSet", ' + '"B139_K_1206_R": "ProbeSet", ' + '"Test": "Publish"}')) db_mock.db.execute.assert_called_with( - ("SELECT InfoFiles.GN_AccesionId " + - "FROM InfoFiles, PublishFreeze, InbredSet " + + ("SELECT InfoFiles.GN_AccesionId " + "FROM InfoFiles, PublishFreeze, InbredSet " "WHERE InbredSet.Name = 'Test' AND " - "PublishFreeze.InbredSetId = InbredSet.Id AND " + + "PublishFreeze.InbredSetId = InbredSet.Id AND " "InfoFiles.InfoPageName = PublishFreeze.Name") ) @@ -111,10 +133,20 @@ class TestDataSetTypes(unittest.TestCase): data_set = DatasetType(redis_mock) data_set.set_dataset_key("other_pheno", "Test") self.assertEqual(data_set("Test"), "Publish") + redis_mock.set.assert_called_once_with( "dataset_structure", - '{"Aging-Brain-UCIPublish": "Publish", "AKXDGeno": "Geno", "B139_K_1206_M": "ProbeSet", "AD-cases-controls-MyersGeno": "Geno", "AD-cases-controls-MyersPublish": "Publish", "All Phenotypes": "Publish", "Test": "Publish", "AXBXAPublish": "Publish", "B139_K_1206_R": "ProbeSet", "AXBXAGeno": "Geno"}') - expected_db_call = """""" + ('{"AD-cases-controls-MyersGeno": "Geno", ' + '"AD-cases-controls-MyersPublish": "Publish", ' + '"AKXDGeno": "Geno", ' + '"AXBXAGeno": "Geno", ' + '"AXBXAPublish": "Publish", ' + '"Aging-Brain-UCIPublish": "Publish", ' + '"All Phenotypes": "Publish", ' + '"B139_K_1206_M": "ProbeSet", ' + '"B139_K_1206_R": "ProbeSet", ' + '"Test": "Publish"}')) + db_mock.db.execute.assert_called_with( ("SELECT PublishFreeze.Name " + "FROM PublishFreeze, InbredSet " + @@ -133,8 +165,17 @@ class TestDataSetTypes(unittest.TestCase): self.assertEqual(data_set("Test"), "Geno") redis_mock.set.assert_called_once_with( "dataset_structure", - '{"Aging-Brain-UCIPublish": "Publish", "AKXDGeno": "Geno", "B139_K_1206_M": "ProbeSet", "AD-cases-controls-MyersGeno": "Geno", "AD-cases-controls-MyersPublish": "Publish", "All Phenotypes": "Publish", "Test": "Geno", "AXBXAPublish": "Publish", "B139_K_1206_R": "ProbeSet", "AXBXAGeno": "Geno"}') - expected_db_call = """""" + ('{"AD-cases-controls-MyersGeno": "Geno", ' + '"AD-cases-controls-MyersPublish": "Publish", ' + '"AKXDGeno": "Geno", ' + '"AXBXAGeno": "Geno", ' + '"AXBXAPublish": "Publish", ' + '"Aging-Brain-UCIPublish": "Publish", ' + '"All Phenotypes": "Publish", ' + '"B139_K_1206_M": "ProbeSet", ' + '"B139_K_1206_R": "ProbeSet", ' + '"Test": "Geno"}')) + db_mock.db.execute.assert_called_with( - ("SELECT GenoFreeze.Id FROM GenoFreeze WHERE GenoFreeze.Name = \"Test\" ") - ) + ("SELECT GenoFreeze.Id FROM " + "GenoFreeze WHERE GenoFreeze.Name = \"Test\" ")) diff --git a/wqflask/tests/base/test_general_object.py b/wqflask/tests/base/test_general_object.py index c7701021..00fd3c72 100644 --- a/wqflask/tests/base/test_general_object.py +++ b/wqflask/tests/base/test_general_object.py @@ -17,9 +17,9 @@ class TestGeneralObjectTests(unittest.TestCase): def test_object_dict(self): """Test whether the base class is printed properly""" test_obj = GeneralObject("a", name="test", value=1) - self.assertEqual(str(test_obj), "value = 1\nname = test\n") + self.assertEqual(str(test_obj), "name = test\nvalue = 1\n") self.assertEqual( - repr(test_obj), "value = 1\nname = test\ncontents = ['a']\n") + repr(test_obj), "contents = ['a']\nname = test\nvalue = 1\n") self.assertEqual(len(test_obj), 2) self.assertEqual(test_obj["value"], 1) test_obj["test"] = 1 @@ -36,6 +36,5 @@ class TestGeneralObjectTests(unittest.TestCase): test_obj1 = GeneralObject("a", name="test", value=1) test_obj2 = GeneralObject("b", name="test2", value=2) test_obj3 = GeneralObject("a", name="test", x=1, y=2) - self.assertTrue(test_obj1 == test_obj2 ) - self.assertFalse(test_obj1 == test_obj3 ) - + self.assertTrue(test_obj1 == test_obj2) + self.assertFalse(test_obj1 == test_obj3) diff --git a/wqflask/tests/wqflask/api/test_gen_menu.py b/wqflask/tests/wqflask/api/test_gen_menu.py index 239484aa..bf41054d 100644 --- a/wqflask/tests/wqflask/api/test_gen_menu.py +++ b/wqflask/tests/wqflask/api/test_gen_menu.py @@ -2,6 +2,7 @@ import unittest import mock +from wqflask import app from wqflask.api.gen_menu import gen_dropdown_json from wqflask.api.gen_menu import get_species from wqflask.api.gen_menu import get_groups @@ -17,6 +18,8 @@ class TestGenMenu(unittest.TestCase): """Tests for the gen_menu module""" def setUp(self): + self.app_context = app.app_context() + self.app_context.push() self.test_group = { 'mouse': [ ['H_T1', @@ -67,6 +70,9 @@ class TestGenMenu(unittest.TestCase): } } + def tearDown(self): + self.app_context.pop() + @mock.patch('wqflask.api.gen_menu.g') def test_get_species(self, db_mock): """Test that assertion is raised when dataset and dataset_name -- cgit v1.2.3 From 46443ec8d2cdfd7c60358a889d90a90e4f7daaf4 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 27 Aug 2020 01:32:34 +0300 Subject: Replace string arguments to "hmac.new" with bytearray See: --- wqflask/utility/hmac.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/utility/hmac.py b/wqflask/utility/hmac.py index 73e28790..aa21c741 100644 --- a/wqflask/utility/hmac.py +++ b/wqflask/utility/hmac.py @@ -10,7 +10,7 @@ def hmac_creation(stringy): secret = app.config['SECRET_HMAC_CODE'] - hmaced = hmac.new(secret, stringy, hashlib.sha1) + hmaced = hmac.new(bytearray(secret, 'utf8'), bytearray(stringy, 'utf8'), hashlib.sha1) hm = hmaced.hexdigest() # ZS: Leaving the below comment here to ask Pjotr about # "Conventional wisdom is that you don't lose much in terms of security if you throw away up to half of the output." -- cgit v1.2.3 From d5fc56b802f2195dfdad3f6c3e20a3832aa95567 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 27 Aug 2020 01:34:09 +0300 Subject: Import "reduce" without a try block * wqflask/wqflask/correlation_matrix/show_corr_matrix.py: Import 'reduce' --- wqflask/wqflask/correlation_matrix/show_corr_matrix.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index dac4037e..49ba9e5d 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -29,10 +29,8 @@ import rpy2.robjects as robjects from pprint import pformat as pf from utility.redis_tools import get_redis_conn -try: # Only import this for Python3 - from functools import reduce -except: - pass +from functools import reduce + Redis = get_redis_conn() THIRTY_DAYS = 60 * 60 * 24 * 30 -- cgit v1.2.3 From 83b8880088572eb11110b3b873c04148112be3b9 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 27 Aug 2020 01:35:30 +0300 Subject: Convert sibling imports to relative imports See: --- wqflask/runserver.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'wqflask') diff --git a/wqflask/runserver.py b/wqflask/runserver.py index b48ceee1..a81d62b8 100644 --- a/wqflask/runserver.py +++ b/wqflask/runserver.py @@ -7,8 +7,9 @@ # # /sbin/iptables -A INPUT -p tcp -i eth0 -s ! 71.236.239.43 --dport 5003 -j DROP -from wqflask import app - +from .wqflask import app +from .utility.startup_config import app_config +from .utility.tools import WEBSERVER_MODE, SERVER_PORT import logging -- cgit v1.2.3 From 3d5cc150fb5927edb759c52a52cae8533bc22252 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 27 Aug 2020 03:13:43 +0300 Subject: Replace dict.iteritems() with dict.items() "iteritems()" got omitted in python3.X --- wqflask/wqflask/templates/admin/manage_resource.html | 2 +- wqflask/wqflask/templates/loading.html | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/templates/admin/manage_resource.html b/wqflask/wqflask/templates/admin/manage_resource.html index 0b12eaae..33a37594 100644 --- a/wqflask/wqflask/templates/admin/manage_resource.html +++ b/wqflask/wqflask/templates/admin/manage_resource.html @@ -65,7 +65,7 @@ - {% for key, value in group_masks.iteritems() %} + {% for key, value in group_masks.items() %} {{ value.name }} {{ value.data }} diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html index 15ab4080..9b335dfe 100644 --- a/wqflask/wqflask/templates/loading.html +++ b/wqflask/wqflask/templates/loading.html @@ -1,7 +1,7 @@ Loading {{ start_vars.tool_used }} Results
- {% for key, value in start_vars.iteritems() %} + {% for key, value in start_vars.items() %} {% endfor %}
@@ -44,4 +44,4 @@ $("#loading_form").attr("action", "{{ start_vars.form_url }}"); setTimeout(function(){ $("#loading_form").submit()}, 350); - \ No newline at end of file + -- cgit v1.2.3 From e102c7c0a7d1ad3c305ed8db0d19fa12cfa5cb38 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 27 Aug 2020 03:19:23 +0300 Subject: Remove relative imports * wqflask/runserver.py: Relative imports leads to import errors. --- wqflask/runserver.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'wqflask') diff --git a/wqflask/runserver.py b/wqflask/runserver.py index a81d62b8..df957bd9 100644 --- a/wqflask/runserver.py +++ b/wqflask/runserver.py @@ -7,9 +7,9 @@ # # /sbin/iptables -A INPUT -p tcp -i eth0 -s ! 71.236.239.43 --dport 5003 -j DROP -from .wqflask import app -from .utility.startup_config import app_config -from .utility.tools import WEBSERVER_MODE, SERVER_PORT +from wqflask import app +from utility.startup_config import app_config +from utility.tools import WEBSERVER_MODE, SERVER_PORT import logging -- cgit v1.2.3 From 1e030b2543c22a8148f39657b5921724d9512d40 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 27 Aug 2020 03:22:06 +0300 Subject: Remove python2 string processing to utf-8 * wqflask/base/trait.py: Remove python2 codecs.BOM_UTF8 methods. * wqflask/wqflask/search_results.py: Remove utf-8 decode method on string. --- wqflask/base/trait.py | 4 ---- wqflask/wqflask/search_results.py | 2 +- 2 files changed, 1 insertion(+), 5 deletions(-) (limited to 'wqflask') diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index e3507ae1..6950cf11 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -488,10 +488,6 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): else: trait.description_display = "" - trait.abbreviation = str(str(trait.abbreviation).strip(codecs.BOM_UTF8), 'utf-8', errors="replace") - trait.description_display = str(str(trait.description_display).strip(codecs.BOM_UTF8), 'utf-8', errors="replace") - trait.authors = str(str(trait.authors).strip(codecs.BOM_UTF8), 'utf-8', errors="replace") - if not trait.year.isdigit(): trait.pubmed_text = "N/A" else: diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index f6c677a8..0de14f15 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -115,7 +115,7 @@ views.py). trait_dict['hmac'] = hmac.data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name)) if this_trait.dataset.type == "ProbeSet": trait_dict['symbol'] = this_trait.symbol - trait_dict['description'] = this_trait.description_display.decode('utf-8', 'replace') + trait_dict['description'] = this_trait.description_display trait_dict['location'] = this_trait.location_repr trait_dict['mean'] = "N/A" trait_dict['additive'] = "N/A" -- cgit v1.2.3 From c6c80dde5cfb03c73b61523950af0ca6d208aea4 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 27 Aug 2020 03:25:06 +0300 Subject: Update imports * wqflask/wqflask/api/router.py: Break imports into separate lines and remove unused ones. --- wqflask/wqflask/api/router.py | 17 ++++++++++++----- 1 file changed, 12 insertions(+), 5 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py index acf7ce4a..8e59ef27 100644 --- a/wqflask/wqflask/api/router.py +++ b/wqflask/wqflask/api/router.py @@ -1,14 +1,21 @@ # GN2 API -import os, io, csv, json, datetime, requests, yaml -import zlib +import os +import io +import csv +import json +import datetime +import requests + from zipfile import ZipFile, ZIP_DEFLATED -import io import flask -from flask import g, Response, request, make_response, render_template, send_from_directory, jsonify, redirect, send_file -import sqlalchemy +from flask import g +from flask import request +from flask import make_response +from flask import send_file + from wqflask import app from wqflask.api import correlation, mapping, gen_menu -- cgit v1.2.3 From b46faf479e129801f4bec2457444b5341e8aeabf Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 27 Aug 2020 03:26:36 +0300 Subject: Add a check for a "uuid" object * wqflask/wqflask/views.py(json_default_handler): Check for "uuid.UUID" instance to avoid TypeError. --- wqflask/wqflask/views.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 0224da4a..557ff523 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -930,8 +930,8 @@ def json_default_handler(obj): if hasattr(obj, 'isoformat'): return obj.isoformat() # Handle integer keys for dictionaries - elif isinstance(obj, int): - return str(int) + elif isinstance(obj, int) or isinstance(obj, uuid.UUID): + return str(obj) # Handle custom objects if hasattr(obj, '__dict__'): return obj.__dict__ -- cgit v1.2.3 From 70dbeeb5832711ed5271434e482c18bc7ea095b8 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 27 Aug 2020 03:28:43 +0300 Subject: Add check for empty group_code when adding a new resource * wqflask/utility/authentication_tools.py(add_new_resource): If group_code is "None", an error is thrown when you try to: `group_code + "_" + str(trait_id)` --- wqflask/utility/authentication_tools.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'wqflask') diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py index 0e499180..73c39399 100644 --- a/wqflask/utility/authentication_tools.py +++ b/wqflask/utility/authentication_tools.py @@ -49,7 +49,10 @@ def add_new_resource(dataset, trait_id=None): } if dataset.type == "Publish": - resource_ob['name'] = get_group_code(dataset) + "_" + str(trait_id) + group_code = get_group_code(dataset) + if group_code is None: + group_code = "" + resource_ob['name'] = group_code + "_" + str(trait_id) resource_ob['data'] = { 'dataset': dataset.id, 'trait' : trait_id @@ -74,7 +77,6 @@ def add_new_resource(dataset, trait_id=None): def get_group_code(dataset): results = g.db.execute("SELECT InbredSetCode from InbredSet where Name='{}'".format(dataset.group.name)).fetchone() - return results[0] def check_admin(resource_id=None): -- cgit v1.2.3 From 90475fed0b2d1bd192a641bd417f6dfef79653d0 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Mon, 31 Aug 2020 20:34:31 +0300 Subject: Remove typo at beginning of line * wqflask/utility/authentication_tools.py: Remove accidental char at beginning of line. --- wqflask/utility/authentication_tools.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py index 68bbb276..c52ebafa 100644 --- a/wqflask/utility/authentication_tools.py +++ b/wqflask/utility/authentication_tools.py @@ -88,7 +88,7 @@ def check_admin(resource_id=None): response = json.loads(requests.get(the_url).content)['admin'] except: resource_info = get_resource_info(resource_id) -l response = resource_info['default_mask']['admin'] + response = resource_info['default_mask']['admin'] if 'edit-admins' in response: return "edit-admins" -- cgit v1.2.3 From f4a8789a5f28e1527d4c801b40176f47aa44146c Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 17 Sep 2020 17:16:28 +0300 Subject: Apply pep8 * wqflask/base/trait.py: Apply pep8. * wqflask/utility/authentication_tools.py: Ditto. --- wqflask/base/trait.py | 192 +++++++++++++++++++------------- wqflask/utility/authentication_tools.py | 32 ++++-- 2 files changed, 134 insertions(+), 90 deletions(-) (limited to 'wqflask') diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 6950cf11..548ccc4c 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -1,36 +1,30 @@ -import os -import string -import resource -import codecs import requests -import random +import simplejson as json +from wqflask import app from base import webqtlConfig from base.webqtlCaseData import webqtlCaseData from base.data_set import create_dataset -from db import webqtlDatabaseFunction -from utility import webqtlUtil from utility import hmac from utility.authentication_tools import check_resource_availability -from utility.tools import GN2_BASE_URL, GN_VERSION -from utility.redis_tools import get_redis_conn, get_resource_id, get_resource_info -Redis = get_redis_conn() +from utility.tools import GN2_BASE_URL +from utility.redis_tools import get_redis_conn, get_resource_id -from wqflask import app - -import simplejson as json from utility.db_tools import escape -from pprint import pformat as pf -from flask import Flask, g, request, url_for, redirect, make_response, render_template +from flask import g, request, url_for from utility.logger import getLogger -logger = getLogger(__name__ ) + +logger = getLogger(__name__) + +Redis = get_redis_conn() + def create_trait(**kw): - assert bool(kw.get('dataset')) != bool(kw.get('dataset_name')), "Needs dataset ob. or name"; + assert bool(kw.get('dataset')) != bool( + kw.get('dataset_name')), "Needs dataset ob. or name" - permitted = True if kw.get('name'): if kw.get('dataset_name'): if kw.get('dataset_name') != "Temp": @@ -40,18 +34,23 @@ def create_trait(**kw): if kw.get('dataset_name') != "Temp": if dataset.type == 'Publish': - permissions = check_resource_availability(dataset, kw.get('name')) + permissions = check_resource_availability( + dataset, kw.get('name')) else: permissions = check_resource_availability(dataset) if "view" in permissions['data']: the_trait = GeneralTrait(**kw) if the_trait.dataset.type != "Temp": - the_trait = retrieve_trait_info(the_trait, the_trait.dataset, get_qtl_info=kw.get('get_qtl_info')) + the_trait = retrieve_trait_info( + the_trait, + the_trait.dataset, + get_qtl_info=kw.get('get_qtl_info')) return the_trait else: return None + class GeneralTrait(object): """ Trait class defines a trait in webqtl, can be either Microarray, @@ -61,12 +60,17 @@ class GeneralTrait(object): def __init__(self, get_qtl_info=False, get_sample_info=True, **kw): # xor assertion - assert bool(kw.get('dataset')) != bool(kw.get('dataset_name')), "Needs dataset ob. or name"; - self.name = kw.get('name') # Trait ID, ProbeSet ID, Published ID, etc. + assert bool(kw.get('dataset')) != bool( + kw.get('dataset_name')), "Needs dataset ob. or name" + # Trait ID, ProbeSet ID, Published ID, etc. + self.name = kw.get('name') if kw.get('dataset_name'): if kw.get('dataset_name') == "Temp": temp_group = self.name.split("_")[2] - self.dataset = create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = temp_group) + self.dataset = create_dataset( + dataset_name="Temp", + dataset_type="Temp", + group_name=temp_group) else: self.dataset = create_dataset(kw.get('dataset_name')) else: @@ -74,7 +78,8 @@ class GeneralTrait(object): self.cellid = kw.get('cellid') self.identification = kw.get('identification', 'un-named trait') self.haveinfo = kw.get('haveinfo', False) - self.sequence = kw.get('sequence') # Blat sequence, available for ProbeSet + # Blat sequence, available for ProbeSet + self.sequence = kw.get('sequence') self.data = kw.get('data', {}) self.view = True @@ -100,9 +105,10 @@ class GeneralTrait(object): elif len(name2) == 3: self.dataset, self.name, self.cellid = name2 - # Todo: These two lines are necessary most of the time, but perhaps not all of the time - # So we could add a simple if statement to short-circuit this if necessary - if get_sample_info != False: + # Todo: These two lines are necessary most of the time, but + # perhaps not all of the time So we could add a simple if + # statement to short-circuit this if necessary + if get_sample_info is not False: self = retrieve_sample_data(self, self.dataset) def export_informative(self, include_variance=0): @@ -116,13 +122,13 @@ class GeneralTrait(object): the_vars = [] sample_aliases = [] for sample_name, sample_data in list(self.data.items()): - if sample_data.value != None: - if not include_variance or sample_data.variance != None: + if sample_data.value is not None: + if not include_variance or sample_data.variance is not None: samples.append(sample_name) vals.append(sample_data.value) the_vars.append(sample_data.variance) sample_aliases.append(sample_data.name2) - return samples, vals, the_vars, sample_aliases + return samples, vals, the_vars, sample_aliases @property def description_fmt(self): @@ -161,12 +167,17 @@ class GeneralTrait(object): alias = 'Not available' if self.symbol: - human_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.upper()) - mouse_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.capitalize()) - other_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.lower()) + human_response = requests.get( + GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.upper()) + mouse_response = requests.get( + GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.capitalize()) + other_response = requests.get( + GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.lower()) if human_response and mouse_response and other_response: - alias_list = json.loads(human_response.content) + json.loads(mouse_response.content) + json.loads(other_response.content) + alias_list = json.loads(human_response.content) + json.loads( + mouse_response.content) + \ + json.loads(other_response.content) filtered_aliases = [] seen = set() @@ -180,33 +191,34 @@ class GeneralTrait(object): return alias - @property def location_fmt(self): '''Return a text formatted location - While we're at it we set self.location in case we need it later (do we?) + While we're at it we set self.location in case we need it + later (do we?) ''' if self.chr and self.mb: - self.location = 'Chr %s @ %s Mb' % (self.chr, self.mb) + self.location = 'Chr %s @ %s Mb' % (self.chr, self.mb) elif self.chr: self.location = 'Chr %s @ Unknown position' % (self.chr) else: self.location = 'Not available' fmt = self.location - ##XZ: deal with direction + # XZ: deal with direction if self.strand_probe == '+': fmt += (' on the plus strand ') elif self.strand_probe == '-': fmt += (' on the minus strand ') return fmt - + + def retrieve_sample_data(trait, dataset, samplelist=None): - if samplelist == None: + if samplelist is None: samplelist = [] if dataset.type == "Temp": @@ -222,16 +234,19 @@ def retrieve_sample_data(trait, dataset, samplelist=None): all_samples_ordered = dataset.group.all_samples_ordered() for i, item in enumerate(results): try: - trait.data[all_samples_ordered[i]] = webqtlCaseData(all_samples_ordered[i], float(item)) + trait.data[all_samples_ordered[i]] = webqtlCaseData( + all_samples_ordered[i], float(item)) except: pass else: for item in results: name, value, variance, num_cases, name2 = item if not samplelist or (samplelist and name in samplelist): - trait.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases) + # name, value, variance, num_cases) + trait.data[name] = webqtlCaseData(*item) return trait + @app.route("/trait/get_sample_data") def get_sample_data(): params = request.args @@ -247,7 +262,8 @@ def get_sample_data(): trait_dict['group'] = trait_ob.dataset.group.name trait_dict['tissue'] = trait_ob.dataset.tissue trait_dict['species'] = trait_ob.dataset.group.species - trait_dict['url'] = url_for('show_trait_page', trait_id = trait, dataset = dataset) + trait_dict['url'] = url_for( + 'show_trait_page', trait_id=trait, dataset=dataset) trait_dict['description'] = trait_ob.description_display if trait_ob.dataset.type == "ProbeSet": trait_dict['symbol'] = trait_ob.symbol @@ -257,22 +273,27 @@ def get_sample_data(): trait_dict['pubmed_link'] = trait_ob.pubmed_link trait_dict['pubmed_text'] = trait_ob.pubmed_text - return json.dumps([trait_dict, {key: value.value for key, value in list(trait_ob.data.items()) }]) + return json.dumps([trait_dict, {key: value.value for + key, value in list( + trait_ob.data.items())}]) else: return None - + + def jsonable(trait): """Return a dict suitable for using as json Actual turning into json doesn't happen here though""" - dataset = create_dataset(dataset_name = trait.dataset.name, dataset_type = trait.dataset.type, group_name = trait.dataset.group.name) - + dataset = create_dataset(dataset_name=trait.dataset.name, + dataset_type=trait.dataset.type, + group_name=trait.dataset.group.name) + if dataset.type == "ProbeSet": return dict(name=trait.name, symbol=trait.symbol, dataset=dataset.name, - dataset_name = dataset.shortname, + dataset_name=dataset.shortname, description=trait.description_display, mean=trait.mean, location=trait.location_repr, @@ -284,7 +305,7 @@ def jsonable(trait): if trait.pubmed_id: return dict(name=trait.name, dataset=dataset.name, - dataset_name = dataset.shortname, + dataset_name=dataset.shortname, description=trait.description_display, abbreviation=trait.abbreviation, authors=trait.authors, @@ -297,7 +318,7 @@ def jsonable(trait): else: return dict(name=trait.name, dataset=dataset.name, - dataset_name = dataset.shortname, + dataset_name=dataset.shortname, description=trait.description_display, abbreviation=trait.abbreviation, authors=trait.authors, @@ -309,19 +330,20 @@ def jsonable(trait): elif dataset.type == "Geno": return dict(name=trait.name, dataset=dataset.name, - dataset_name = dataset.shortname, + dataset_name=dataset.shortname, location=trait.location_repr ) else: return dict() + def jsonable_table_row(trait, dataset_name, index): """Return a list suitable for json and intended to be displayed in a table Actual turning into json doesn't happen here though""" dataset = create_dataset(dataset_name) - + if dataset.type == "ProbeSet": if trait.mean == "": mean = "N/A" @@ -333,11 +355,13 @@ def jsonable_table_row(trait, dataset_name, index): additive = "%.3f" % round(float(trait.additive), 2) return ['', index, - ''+str(trait.name)+'', + ''+str(trait.name)+'', trait.symbol, trait.description_display, trait.location_repr, - mean, + mean, trait.LRS_score_repr, trait.LRS_location_repr, additive] @@ -349,7 +373,9 @@ def jsonable_table_row(trait, dataset_name, index): if trait.pubmed_id: return ['', index, - ''+str(trait.name)+'', + ''+str(trait.name)+'', trait.description_display, trait.authors, '' + trait.pubmed_text + '', @@ -359,7 +385,9 @@ def jsonable_table_row(trait, dataset_name, index): else: return ['', index, - ''+str(trait.name)+'', + ''+str(trait.name)+'', trait.description_display, trait.authors, trait.pubmed_text, @@ -369,7 +397,9 @@ def jsonable_table_row(trait, dataset_name, index): elif dataset.type == "Geno": return ['', index, - ''+str(trait.name)+'', + ''+str(trait.name)+'', trait.location_repr] else: return dict() @@ -380,14 +410,16 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): resource_id = get_resource_id(dataset, trait.name) if dataset.type == 'Publish': - the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view".format(resource_id, g.user_session.user_id) + the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view".format( + resource_id, g.user_session.user_id) else: - the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(resource_id, g.user_session.user_id, trait.name) + the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view&trait={}".format( + resource_id, g.user_session.user_id, trait.name) try: response = requests.get(the_url).content trait_info = json.loads(response) - except: #ZS: I'm assuming the trait is viewable if the try fails for some reason; it should never reach this point unless the user has privileges, since that's dealt with in create_trait + except: # ZS: I'm assuming the trait is viewable if the try fails for some reason; it should never reach this point unless the user has privileges, since that's dealt with in create_trait if dataset.type == 'Publish': query = """ SELECT @@ -416,8 +448,8 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): logger.sql(query) trait_info = g.db.execute(query).fetchone() - #XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name - #XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms. + # XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name + # XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms. elif dataset.type == 'ProbeSet': display_fields_string = ', ProbeSet.'.join(dataset.display_fields) display_fields_string = 'ProbeSet.' + display_fields_string @@ -430,11 +462,11 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): ProbeSetFreeze.Name = '%s' AND ProbeSet.Name = '%s' """ % (escape(display_fields_string), - escape(dataset.name), - escape(str(trait.name))) + escape(dataset.name), + escape(str(trait.name))) logger.sql(query) trait_info = g.db.execute(query).fetchone() - #XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name + # XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name # to avoid the problem of same marker name from different species. elif dataset.type == 'Geno': display_fields_string = ',Geno.'.join(dataset.display_fields) @@ -448,11 +480,11 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): GenoFreeze.Name = '%s' AND Geno.Name = '%s' """ % (escape(display_fields_string), - escape(dataset.name), - escape(trait.name)) + escape(dataset.name), + escape(trait.name)) logger.sql(query) trait_info = g.db.execute(query).fetchone() - else: #Temp type + else: # Temp type query = """SELECT %s FROM %s WHERE Name = %s""" logger.sql(query) trait_info = g.db.execute(query, @@ -462,7 +494,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): if trait_info: trait.haveinfo = True for i, field in enumerate(dataset.display_fields): - holder = trait_info[i] + holder = trait_info[i] setattr(trait, field, holder) if dataset.type == 'Publish': @@ -475,9 +507,9 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): description = trait.post_publication_description - #If the dataset is confidential and the user has access to confidential - #phenotype traits, then display the pre-publication description instead - #of the post-publication description + # If the dataset is confidential and the user has access to confidential + # phenotype traits, then display the pre-publication description instead + # of the post-publication description if trait.confidential: trait.abbreviation = trait.pre_publication_abbreviation trait.description_display = trait.pre_publication_description @@ -514,15 +546,17 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): trait.location_repr = 'N/A' if trait.chr and trait.mb: - trait.location_repr = 'Chr%s: %.6f' % (trait.chr, float(trait.mb)) + trait.location_repr = 'Chr%s: %.6f' % ( + trait.chr, float(trait.mb)) elif dataset.type == "Geno": trait.location_repr = 'N/A' if trait.chr and trait.mb: - trait.location_repr = 'Chr%s: %.6f' % (trait.chr, float(trait.mb)) + trait.location_repr = 'Chr%s: %.6f' % ( + trait.chr, float(trait.mb)) if get_qtl_info: - #LRS and its location + # LRS and its location trait.LRS_score_repr = "N/A" trait.LRS_location_repr = "N/A" trait.locus = trait.locus_chr = trait.locus_mb = trait.lrs = trait.pvalue = trait.additive = "" @@ -594,10 +628,12 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): trait.locus = trait.lrs = trait.additive = "" if (dataset.type == 'Publish' or dataset.type == "ProbeSet") and trait.locus_chr != "" and trait.locus_mb != "": - trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (trait.locus_chr, float(trait.locus_mb)) + trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % ( + trait.locus_chr, float(trait.locus_mb)) if trait.lrs != "": trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs else: - raise KeyError(repr(trait.name)+' information is not found in the database.') - + raise KeyError(repr(trait.name) + + ' information is not found in the database.') + return trait diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py index 390ad75a..ce0c0749 100644 --- a/wqflask/utility/authentication_tools.py +++ b/wqflask/utility/authentication_tools.py @@ -1,30 +1,37 @@ import json import requests -from base import data_set, webqtlConfig - -from utility import hmac -from utility.redis_tools import get_redis_conn, get_resource_info, get_resource_id, add_resource -Redis = get_redis_conn() +from flask import g +from base import webqtlConfig -logger = logging.getLogger(__name__) +from utility.redis_tools import (get_redis_conn, + get_resource_info, + get_resource_id, + add_resource) +Redis = get_redis_conn() def check_resource_availability(dataset, trait_id=None): - # At least for now assume temporary entered traits are accessible if type(dataset) == str or dataset.type == "Temp": return webqtlConfig.DEFAULT_PRIVILEGES resource_id = get_resource_id(dataset, trait_id) - if resource_id: # ZS: This should never be false, but it's technically possible if a non-Temp dataset somehow had a type other than Publish/ProbeSet/Geno + # ZS: This should never be false, but it's technically possible if + # a non-Temp dataset somehow had a type other than + # Publish/ProbeSet/Geno + if resource_id: resource_info = get_resource_info(resource_id) - if not resource_info: # ZS: If resource isn't already in redis, add it with default privileges + + # ZS: If resource isn't already in redis, add it with default + # privileges + if not resource_info: resource_info = add_new_resource(dataset, trait_id) - # ZS: Check if super-user - we should probably come up with some way to integrate this into the proxy + # ZS: Check if super-user - we should probably come up with some + # way to integrate this into the proxy if g.user_session.user_id in Redis.smembers("super_users"): return webqtlConfig.SUPER_PRIVILEGES @@ -76,8 +83,9 @@ def add_new_resource(dataset, trait_id=None): def get_group_code(dataset): - results = g.db.execute("SELECT InbredSetCode from InbredSet where Name='{}'".format( - dataset.group.name)).fetchone() + results = g.db.execute( + "SELECT InbredSetCode from InbredSet where Name='{}'".format( + dataset.group.name)).fetchone() if results[0]: return results[0] else: -- cgit v1.2.3 From 16faa26e52b1f0191595e16550d553907d2f9d67 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 17 Sep 2020 17:21:30 +0300 Subject: Fix errors in tests * wqflask/tests/utility/test_authentication_tools.py test_check_resource_availability_non_default_mask): Mock flask's global 'g' variable properly. * wqflask/tests/base/test_trait.py: Ditto. * wqflask/tests/utility/test_authentication_tools.py: Ditto. --- wqflask/tests/base/test_trait.py | 9 +++------ wqflask/tests/utility/test_authentication_tools.py | 8 ++------ 2 files changed, 5 insertions(+), 12 deletions(-) (limited to 'wqflask') diff --git a/wqflask/tests/base/test_trait.py b/wqflask/tests/base/test_trait.py index 53b0d440..d333458a 100644 --- a/wqflask/tests/base/test_trait.py +++ b/wqflask/tests/base/test_trait.py @@ -38,9 +38,8 @@ class TestRetrieveTraitInfo(unittest.TestCase): dataset={}) @mock.patch('base.trait.requests.get') - @mock.patch('base.trait.g') + @mock.patch('base.trait.g', mock.Mock()) def test_retrieve_trait_info_with_empty_trait_info(self, - g_mock, requests_mock): """Empty trait info""" requests_mock.return_value = TestNilResponse() @@ -49,9 +48,8 @@ class TestRetrieveTraitInfo(unittest.TestCase): dataset=mock.MagicMock()) @mock.patch('base.trait.requests.get') - @mock.patch('base.trait.g') + @mock.patch('base.trait.g', mock.Mock()) def test_retrieve_trait_info_with_non_empty_trait_info(self, - g_mock, requests_mock): """Test that attributes are set""" mock_dataset = mock.MagicMock() @@ -66,9 +64,8 @@ class TestRetrieveTraitInfo(unittest.TestCase): self.assertEqual(test_trait.d, 4) @mock.patch('base.trait.requests.get') - @mock.patch('base.trait.g') + @mock.patch('base.trait.g', mock.Mock()) def test_retrieve_trait_info_utf8_parsing(self, - g_mock, requests_mock): """Test that utf-8 strings are parsed correctly""" utf_8_string = "test_string" diff --git a/wqflask/tests/utility/test_authentication_tools.py b/wqflask/tests/utility/test_authentication_tools.py index 99c74245..ef94eabc 100644 --- a/wqflask/tests/utility/test_authentication_tools.py +++ b/wqflask/tests/utility/test_authentication_tools.py @@ -38,17 +38,15 @@ class TestCheckResourceAvailability(unittest.TestCase): """Test methods related to checking the resource availability""" @mock.patch('utility.authentication_tools.add_new_resource') @mock.patch('utility.authentication_tools.Redis') - @mock.patch('utility.authentication_tools.g') + @mock.patch('utility.authentication_tools.g', mock.Mock()) @mock.patch('utility.authentication_tools.get_resource_id') def test_check_resource_availability_default_mask( self, resource_id_mock, - g_mock, redis_mock, add_new_resource_mock): """Test the resource availability with default mask""" resource_id_mock.return_value = 1 - g_mock.return_value = mock.Mock() redis_mock.smembers.return_value = [] test_dataset = mock.MagicMock() type(test_dataset).type = mock.PropertyMock(return_value="Test") @@ -58,18 +56,16 @@ class TestCheckResourceAvailability(unittest.TestCase): @mock.patch('utility.authentication_tools.requests.get') @mock.patch('utility.authentication_tools.add_new_resource') @mock.patch('utility.authentication_tools.Redis') - @mock.patch('utility.authentication_tools.g') + @mock.patch('utility.authentication_tools.g', TestUserSession()) @mock.patch('utility.authentication_tools.get_resource_id') def test_check_resource_availability_non_default_mask( self, resource_id_mock, - g_mock, redis_mock, add_new_resource_mock, requests_mock): """Test the resource availability with default mask""" resource_id_mock.return_value = 1 - g_mock.return_value = mock.Mock() redis_mock.smembers.return_value = [] add_new_resource_mock.return_value = {"default_mask": 2} requests_mock.return_value = TestResponse() -- cgit v1.2.3 From 6064148eb2b723a308f0d29595a75ab64f47e1e2 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 17 Sep 2020 17:34:11 +0300 Subject: Replace string arguments to "hmac.new" with bytearray Same as: https://github.com/genenetwork/genenetwork2/pull/422/commits/46443ec8d2cdfd7c60358a889d90a90e4f7daaf4 --- wqflask/utility/hmac.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/utility/hmac.py b/wqflask/utility/hmac.py index 10387bb0..6623f69a 100644 --- a/wqflask/utility/hmac.py +++ b/wqflask/utility/hmac.py @@ -10,7 +10,9 @@ def hmac_creation(stringy): """Helper function to create the actual hmac""" secret = app.config['SECRET_HMAC_CODE'] - hmaced = hmac.new(secret, stringy, hashlib.sha1) + hmaced = hmac.new(bytearray(secret, "utf-8"), + bytearray(stringy, "utf-8"), + hashlib.sha1) hm = hmaced.hexdigest() # ZS: Leaving the below comment here to ask Pjotr about # "Conventional wisdom is that you don't lose much in terms of security if you throw away up to half of the output." -- cgit v1.2.3 From bfb5fab5ac57934f7a6bd54938188fa0d2669ad7 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 17 Sep 2020 21:16:28 +0300 Subject: Convert "target_string" to a str type * wqflask/base/trait.py (retrieve_trait_info): Convert "target_string" to a str, otherwise an exception will be thrown if it's None. --- wqflask/base/trait.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'wqflask') diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 548ccc4c..c37a8325 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -538,8 +538,8 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): description_display = trait.symbol if (len(description_display) > 1 and description_display != 'N/A' and - len(target_string) > 1 and target_string != 'None'): - description_display = description_display + '; ' + target_string.strip() + len(str(target_string)) > 1 and target_string != 'None'): + description_display = description_display + '; ' + str(target_string).strip() # Save it for the jinja2 template trait.description_display = description_display -- cgit v1.2.3 From 7f94f657e51bbf9a7a1064b12a7d67b53a14eb11 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Sat, 26 Sep 2020 01:15:09 +0300 Subject: Fix inconsistent line ending in file * wqflask/wqflask/db_info.py: Replace ^M with proper unix line endings. See --- wqflask/wqflask/db_info.py | 254 ++++++++++++++++++++++----------------------- 1 file changed, 127 insertions(+), 127 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/db_info.py b/wqflask/wqflask/db_info.py index f04e38bf..5f3f5e3f 100644 --- a/wqflask/wqflask/db_info.py +++ b/wqflask/wqflask/db_info.py @@ -1,127 +1,127 @@ -import httplib, urllib2 -import re - -from flask import Flask, g - -from utility.logger import getLogger -logger = getLogger(__name__ ) - -class InfoPage(object): - def __init__(self, start_vars): - self.info = None - self.gn_accession_id = None - if 'gn_accession_id' in start_vars: - self.gn_accession_id = start_vars['gn_accession_id'] - self.info_page_name = start_vars['info_page_name'] - - self.get_info() - self.get_datasets_list() - - def get_info(self, create=False): - query_base = ("SELECT InfoPageName, GN_AccesionId, Species.MenuName, Species.TaxonomyId, Tissue.Name, InbredSet.Name, " + - "GeneChip.GeneChipName, GeneChip.GeoPlatform, AvgMethod.Name, Datasets.DatasetName, Datasets.GeoSeries, " + - "Datasets.PublicationTitle, DatasetStatus.DatasetStatusName, Datasets.Summary, Datasets.AboutCases, " + - "Datasets.AboutTissue, Datasets.AboutDataProcessing, Datasets.Acknowledgment, Datasets.ExperimentDesign, " + - "Datasets.Contributors, Datasets.Citation, Datasets.Notes, Investigators.FirstName, Investigators.LastName, " + - "Investigators.Address, Investigators.City, Investigators.State, Investigators.ZipCode, Investigators.Country, " + - "Investigators.Phone, Investigators.Email, Investigators.Url, Organizations.OrganizationName, " + - "InvestigatorId, DatasetId, DatasetStatusId, Datasets.AboutPlatform, InfoFileTitle, Specifics " + - "FROM InfoFiles " + - "LEFT JOIN Species USING (SpeciesId) " + - "LEFT JOIN Tissue USING (TissueId) " + - "LEFT JOIN InbredSet USING (InbredSetId) " + - "LEFT JOIN GeneChip USING (GeneChipId) " + - "LEFT JOIN AvgMethod USING (AvgMethodId) " + - "LEFT JOIN Datasets USING (DatasetId) " + - "LEFT JOIN Investigators USING (InvestigatorId) " + - "LEFT JOIN Organizations USING (OrganizationId) " + - "LEFT JOIN DatasetStatus USING (DatasetStatusId) WHERE ") - - if self.gn_accession_id: - final_query = query_base + "GN_AccesionId = {}".format(self.gn_accession_id) - results = g.db.execute(final_query).fetchone() - if self.info_page_name and not results: - final_query = query_base + "InfoPageName={}".format(self.info_page_name) - elif self.info_page_name: - final_query = query_base + "InfoPageName={}".format(self.info_page_name) - results = g.db.execute(final_query).fetchone() - else: - raise 'No correct parameter found' - - if results: - self.info = process_query_results(results) - - if (not results or len(results) < 1) and self.info_page_name and create: - insert_sql = "INSERT INTO InfoFiles SET InfoFiles.InfoPageName={}".format(self.info_page_name) - return self.get_info() - - if not self.gn_accession_id and self.info: - self.gn_accession_id = self.info['accession_id'] - if not self.info_page_name and self.info: - self.info_page_name = self.info['info_page_name'] - - def get_datasets_list(self): - self.filelist = [] - try: - response = urllib2.urlopen("http://datafiles.genenetwork.org/download/GN%s" % self.gn_accession_id) - data = response.read() - - matches = re.findall(r".+?", data, re.DOTALL) - for i, match in enumerate(matches): - if i == 0: - continue - cells = re.findall(r".+?", match, re.DOTALL) - full_filename = re.search(r"(.+?)<", cells[2]).group(1).strip() - filedate = "N/A" #ZS: Since we can't get it for now - - self.filelist.append([filename, filedate, filesize]) - except Exception, e: - pass - -def process_query_results(results): - info_ob = { - 'info_page_name': results[0], - 'accession_id': results[1], - 'menu_name': results[2], - 'taxonomy_id': results[3], - 'tissue_name': results[4], - 'group_name': results[5], - 'gene_chip_name': results[6], - 'geo_platform': results[7], - 'avg_method_name': results[8], - 'dataset_name': results[9], - 'geo_series': results[10], - 'publication_title': results[11], - 'dataset_status_name': results[12], - 'dataset_summary': results[13], - 'about_cases': results[14], - 'about_tissue': results[15], - 'about_data_processing': results[16], - 'acknowledgement': results[17], - 'experiment_design': results[18], - 'contributors': results[19], - 'citation': results[20], - 'notes': results[21], - 'investigator_firstname': results[22], - 'investigator_lastname': results[23], - 'investigator_address': results[24], - 'investigator_city': results[25], - 'investigator_state': results[26], - 'investigator_zipcode': results[27], - 'investigator_country': results[28], - 'investigator_phone': results[29], - 'investigator_email': results[30], - 'investigator_url': results[31], - 'organization_name': results[32], - 'investigator_id': results[33], - 'dataset_id': results[34], - 'dataset_status_is': results[35], - 'about_platform': results[36], - 'info_file_title': results[37], - 'specifics': results[38] - } - - return info_ob - \ No newline at end of file +import httplib, urllib2 +import re + +from flask import Flask, g + +from utility.logger import getLogger +logger = getLogger(__name__ ) + +class InfoPage(object): + def __init__(self, start_vars): + self.info = None + self.gn_accession_id = None + if 'gn_accession_id' in start_vars: + self.gn_accession_id = start_vars['gn_accession_id'] + self.info_page_name = start_vars['info_page_name'] + + self.get_info() + self.get_datasets_list() + + def get_info(self, create=False): + query_base = ("SELECT InfoPageName, GN_AccesionId, Species.MenuName, Species.TaxonomyId, Tissue.Name, InbredSet.Name, " + + "GeneChip.GeneChipName, GeneChip.GeoPlatform, AvgMethod.Name, Datasets.DatasetName, Datasets.GeoSeries, " + + "Datasets.PublicationTitle, DatasetStatus.DatasetStatusName, Datasets.Summary, Datasets.AboutCases, " + + "Datasets.AboutTissue, Datasets.AboutDataProcessing, Datasets.Acknowledgment, Datasets.ExperimentDesign, " + + "Datasets.Contributors, Datasets.Citation, Datasets.Notes, Investigators.FirstName, Investigators.LastName, " + + "Investigators.Address, Investigators.City, Investigators.State, Investigators.ZipCode, Investigators.Country, " + + "Investigators.Phone, Investigators.Email, Investigators.Url, Organizations.OrganizationName, " + + "InvestigatorId, DatasetId, DatasetStatusId, Datasets.AboutPlatform, InfoFileTitle, Specifics " + + "FROM InfoFiles " + + "LEFT JOIN Species USING (SpeciesId) " + + "LEFT JOIN Tissue USING (TissueId) " + + "LEFT JOIN InbredSet USING (InbredSetId) " + + "LEFT JOIN GeneChip USING (GeneChipId) " + + "LEFT JOIN AvgMethod USING (AvgMethodId) " + + "LEFT JOIN Datasets USING (DatasetId) " + + "LEFT JOIN Investigators USING (InvestigatorId) " + + "LEFT JOIN Organizations USING (OrganizationId) " + + "LEFT JOIN DatasetStatus USING (DatasetStatusId) WHERE ") + + if self.gn_accession_id: + final_query = query_base + "GN_AccesionId = {}".format(self.gn_accession_id) + results = g.db.execute(final_query).fetchone() + if self.info_page_name and not results: + final_query = query_base + "InfoPageName={}".format(self.info_page_name) + elif self.info_page_name: + final_query = query_base + "InfoPageName={}".format(self.info_page_name) + results = g.db.execute(final_query).fetchone() + else: + raise 'No correct parameter found' + + if results: + self.info = process_query_results(results) + + if (not results or len(results) < 1) and self.info_page_name and create: + insert_sql = "INSERT INTO InfoFiles SET InfoFiles.InfoPageName={}".format(self.info_page_name) + return self.get_info() + + if not self.gn_accession_id and self.info: + self.gn_accession_id = self.info['accession_id'] + if not self.info_page_name and self.info: + self.info_page_name = self.info['info_page_name'] + + def get_datasets_list(self): + self.filelist = [] + try: + response = urllib2.urlopen("http://datafiles.genenetwork.org/download/GN%s" % self.gn_accession_id) + data = response.read() + + matches = re.findall(r".+?", data, re.DOTALL) + for i, match in enumerate(matches): + if i == 0: + continue + cells = re.findall(r".+?", match, re.DOTALL) + full_filename = re.search(r"(.+?)<", cells[2]).group(1).strip() + filedate = "N/A" #ZS: Since we can't get it for now + + self.filelist.append([filename, filedate, filesize]) + except Exception, e: + pass + +def process_query_results(results): + info_ob = { + 'info_page_name': results[0], + 'accession_id': results[1], + 'menu_name': results[2], + 'taxonomy_id': results[3], + 'tissue_name': results[4], + 'group_name': results[5], + 'gene_chip_name': results[6], + 'geo_platform': results[7], + 'avg_method_name': results[8], + 'dataset_name': results[9], + 'geo_series': results[10], + 'publication_title': results[11], + 'dataset_status_name': results[12], + 'dataset_summary': results[13], + 'about_cases': results[14], + 'about_tissue': results[15], + 'about_data_processing': results[16], + 'acknowledgement': results[17], + 'experiment_design': results[18], + 'contributors': results[19], + 'citation': results[20], + 'notes': results[21], + 'investigator_firstname': results[22], + 'investigator_lastname': results[23], + 'investigator_address': results[24], + 'investigator_city': results[25], + 'investigator_state': results[26], + 'investigator_zipcode': results[27], + 'investigator_country': results[28], + 'investigator_phone': results[29], + 'investigator_email': results[30], + 'investigator_url': results[31], + 'organization_name': results[32], + 'investigator_id': results[33], + 'dataset_id': results[34], + 'dataset_status_is': results[35], + 'about_platform': results[36], + 'info_file_title': results[37], + 'specifics': results[38] + } + + return info_ob + -- cgit v1.2.3 From 0dc2401b9f66456315808f4c781dd88417941b01 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Sat, 26 Sep 2020 01:16:58 +0300 Subject: Run 2to3-8 tool through file * wqflask/wqflask/db_info.py: Run: 2to3-3.8 -w wqflask/wqflask/db_info.py --- wqflask/wqflask/db_info.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/db_info.py b/wqflask/wqflask/db_info.py index 5f3f5e3f..45a4c96e 100644 --- a/wqflask/wqflask/db_info.py +++ b/wqflask/wqflask/db_info.py @@ -1,4 +1,4 @@ -import httplib, urllib2 +import http.client, urllib.request, urllib.error, urllib.parse import re from flask import Flask, g @@ -63,7 +63,7 @@ class InfoPage(object): def get_datasets_list(self): self.filelist = [] try: - response = urllib2.urlopen("http://datafiles.genenetwork.org/download/GN%s" % self.gn_accession_id) + response = urllib.request.urlopen("http://datafiles.genenetwork.org/download/GN%s" % self.gn_accession_id) data = response.read() matches = re.findall(r".+?", data, re.DOTALL) @@ -77,7 +77,7 @@ class InfoPage(object): filedate = "N/A" #ZS: Since we can't get it for now self.filelist.append([filename, filedate, filesize]) - except Exception, e: + except Exception as e: pass def process_query_results(results): -- cgit v1.2.3 From 1ac412ce0273081fc8df8296b4d03d46e4922fd8 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Sat, 26 Sep 2020 01:18:40 +0300 Subject: Apply PEP 8 to buffer * wqflask/wqflask/db_info.py: Run pep8 through buffers. Fixes inconsistent use of tabs and spaces in indentation which trips up unittests. --- wqflask/wqflask/db_info.py | 31 +++++++++++++++++++++---------- 1 file changed, 21 insertions(+), 10 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/db_info.py b/wqflask/wqflask/db_info.py index 45a4c96e..f420b472 100644 --- a/wqflask/wqflask/db_info.py +++ b/wqflask/wqflask/db_info.py @@ -1,10 +1,14 @@ -import http.client, urllib.request, urllib.error, urllib.parse +import http.client +import urllib.request +import urllib.error +import urllib.parse import re from flask import Flask, g from utility.logger import getLogger -logger = getLogger(__name__ ) +logger = getLogger(__name__) + class InfoPage(object): def __init__(self, start_vars): @@ -38,12 +42,15 @@ class InfoPage(object): "LEFT JOIN DatasetStatus USING (DatasetStatusId) WHERE ") if self.gn_accession_id: - final_query = query_base + "GN_AccesionId = {}".format(self.gn_accession_id) + final_query = query_base + \ + "GN_AccesionId = {}".format(self.gn_accession_id) results = g.db.execute(final_query).fetchone() if self.info_page_name and not results: - final_query = query_base + "InfoPageName={}".format(self.info_page_name) + final_query = query_base + \ + "InfoPageName={}".format(self.info_page_name) elif self.info_page_name: - final_query = query_base + "InfoPageName={}".format(self.info_page_name) + final_query = query_base + \ + "InfoPageName={}".format(self.info_page_name) results = g.db.execute(final_query).fetchone() else: raise 'No correct parameter found' @@ -52,18 +59,20 @@ class InfoPage(object): self.info = process_query_results(results) if (not results or len(results) < 1) and self.info_page_name and create: - insert_sql = "INSERT INTO InfoFiles SET InfoFiles.InfoPageName={}".format(self.info_page_name) + insert_sql = "INSERT INTO InfoFiles SET InfoFiles.InfoPageName={}".format( + self.info_page_name) return self.get_info() if not self.gn_accession_id and self.info: self.gn_accession_id = self.info['accession_id'] if not self.info_page_name and self.info: - self.info_page_name = self.info['info_page_name'] + self.info_page_name = self.info['info_page_name'] def get_datasets_list(self): self.filelist = [] try: - response = urllib.request.urlopen("http://datafiles.genenetwork.org/download/GN%s" % self.gn_accession_id) + response = urllib.request.urlopen( + "http://datafiles.genenetwork.org/download/GN%s" % self.gn_accession_id) data = response.read() matches = re.findall(r".+?", data, re.DOTALL) @@ -71,10 +80,11 @@ class InfoPage(object): if i == 0: continue cells = re.findall(r".+?", match, re.DOTALL) - full_filename = re.search(r"(.+?)<", cells[2]).group(1).strip() - filedate = "N/A" #ZS: Since we can't get it for now + filedate = "N/A" # ZS: Since we can't get it for now self.filelist.append([filename, filedate, filesize]) except Exception as e: @@ -125,3 +135,4 @@ def process_query_results(results): return info_ob + -- cgit v1.2.3 From f67b0c92af93e3153fe9375e98a139386a4f2fb0 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Sat, 26 Sep 2020 01:21:10 +0300 Subject: Fix failing tests * wqflask/tests/base/test_trait.py: Remove decode function call which is no longer supported in python3. --- wqflask/tests/base/test_trait.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'wqflask') diff --git a/wqflask/tests/base/test_trait.py b/wqflask/tests/base/test_trait.py index 9c3154f3..d333458a 100644 --- a/wqflask/tests/base/test_trait.py +++ b/wqflask/tests/base/test_trait.py @@ -93,6 +93,6 @@ class TestRetrieveTraitInfo(unittest.TestCase): test_trait = retrieve_trait_info(trait=mock_trait, dataset=mock_dataset) self.assertEqual(test_trait.abbreviation, - "ファイルを画面毎に見て行くには、次のコマンドを使います。".decode('utf-8')) + "ファイルを画面毎に見て行くには、次のコマンドを使います。") self.assertEqual(test_trait.authors, - "Jane Doe かいと".decode('utf-8')) + "Jane Doe かいと") -- cgit v1.2.3 From bbcecf8e7d8389b8466fe51dde6538387fdce6b5 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Sat, 26 Sep 2020 01:33:52 +0300 Subject: Fix failing tests by replacing mock with unittest.mock * wqflask/tests/base/test_data_set.py (imports): Run: `find . -type f -name "*py" -print0 | xargs -0 sed -i \ "s|import mock|from unittest import mock|g"` * wqflask/tests/base/test_trait.py(imports): Ditto. * wqflask/tests/utility/test_authentication_tools.py(imports): Ditto. * wqflask/tests/utility/test_hmac.py(imports). Ditto. * wqflask/tests/wqflask/api/test_gen_menu.py: Ditto --- wqflask/tests/base/test_data_set.py | 2 +- wqflask/tests/base/test_trait.py | 2 +- wqflask/tests/utility/test_authentication_tools.py | 2 +- wqflask/tests/utility/test_hmac.py | 2 +- wqflask/tests/wqflask/api/test_gen_menu.py | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) (limited to 'wqflask') diff --git a/wqflask/tests/base/test_data_set.py b/wqflask/tests/base/test_data_set.py index b1de4932..96563a16 100644 --- a/wqflask/tests/base/test_data_set.py +++ b/wqflask/tests/base/test_data_set.py @@ -1,7 +1,7 @@ """Tests for wqflask/base/data_set.py""" import unittest -import mock +from unittest import mock from wqflask import app from .data import gen_menu_json diff --git a/wqflask/tests/base/test_trait.py b/wqflask/tests/base/test_trait.py index d333458a..bf4e88e0 100644 --- a/wqflask/tests/base/test_trait.py +++ b/wqflask/tests/base/test_trait.py @@ -1,7 +1,7 @@ # -*- coding: utf-8 -*- """Tests wqflask/base/trait.py""" import unittest -import mock +from unittest import mock from base.trait import GeneralTrait from base.trait import retrieve_trait_info diff --git a/wqflask/tests/utility/test_authentication_tools.py b/wqflask/tests/utility/test_authentication_tools.py index ef94eabc..5c391be5 100644 --- a/wqflask/tests/utility/test_authentication_tools.py +++ b/wqflask/tests/utility/test_authentication_tools.py @@ -1,6 +1,6 @@ """Tests for authentication tools""" import unittest -import mock +from unittest import mock from utility.authentication_tools import check_resource_availability from utility.authentication_tools import add_new_resource diff --git a/wqflask/tests/utility/test_hmac.py b/wqflask/tests/utility/test_hmac.py index 16b50771..7c61c0a6 100644 --- a/wqflask/tests/utility/test_hmac.py +++ b/wqflask/tests/utility/test_hmac.py @@ -2,7 +2,7 @@ """Test hmac utility functions""" import unittest -import mock +from unittest import mock from utility.hmac import data_hmac from utility.hmac import url_for_hmac diff --git a/wqflask/tests/wqflask/api/test_gen_menu.py b/wqflask/tests/wqflask/api/test_gen_menu.py index bf41054d..84898bd1 100644 --- a/wqflask/tests/wqflask/api/test_gen_menu.py +++ b/wqflask/tests/wqflask/api/test_gen_menu.py @@ -1,6 +1,6 @@ """Test cases for wqflask.api.gen_menu""" import unittest -import mock +from unittest import mock from wqflask import app from wqflask.api.gen_menu import gen_dropdown_json -- cgit v1.2.3 From a8c983a69b12ff32a30d488d7f326915f1aa7d63 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Mon, 28 Sep 2020 18:00:00 +0300 Subject: Fix casting error * wqflask/base/trait.py (retrieve_trait_info): If the description_string or discription_display value return a None object, evaluate to an empty string. Fixes errors related to *len(None)*. --- wqflask/base/trait.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) (limited to 'wqflask') diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 7666348e..03c4b079 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -507,13 +507,14 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): description_string = unicode(str(trait.description).strip(codecs.BOM_UTF8), 'utf-8') target_string = unicode(str(trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8') - if len(description_string) > 1 and description_string != 'None': + if str(description_string or "") != "" and description_string != 'None': description_display = description_string else: description_display = trait.symbol - if (len(description_display) > 1 and description_display != 'N/A' and - len(target_string) > 1 and target_string != 'None'): + if (str(description_display or "") != "" and + description_display != 'N/A' and + str(target_string or "") != "" and target_string != 'None'): description_display = description_display + '; ' + target_string.strip() # Save it for the jinja2 template @@ -607,4 +608,4 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): else: raise KeyError, `trait.name`+' information is not found in the database.' - return trait \ No newline at end of file + return trait -- cgit v1.2.3 From 21ec6863d7f8380d66c39f1ed3b8d9cc0dc86e49 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Mon, 28 Sep 2020 18:34:53 +0300 Subject: Fix failing test * wqflask/tests/base/test_trait.py: Add app_context to test class, otherwise an error related to working outside the app_context is generated. Adding the app_context is required when mocking "Flask.g". --- wqflask/tests/base/test_trait.py | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/tests/base/test_trait.py b/wqflask/tests/base/test_trait.py index 60ebaee0..826ccefd 100644 --- a/wqflask/tests/base/test_trait.py +++ b/wqflask/tests/base/test_trait.py @@ -3,6 +3,7 @@ import unittest from unittest import mock +from wqflask import app from base.trait import GeneralTrait from base.trait import retrieve_trait_info @@ -31,6 +32,14 @@ class MockTrait(GeneralTrait): class TestRetrieveTraitInfo(unittest.TestCase): """Tests for 'retrieve_trait_info'""" + + def setUp(self): + self.app_context = app.app_context() + self.app_context.push() + + def tearDown(self): + self.app_context.pop() + def test_retrieve_trait_info_with_empty_dataset(self): """Test that an exception is raised when dataset is empty""" with self.assertRaises(AssertionError): @@ -104,7 +113,7 @@ class TestRetrieveTraitInfo(unittest.TestCase): resource_id_mock, g_mock, requests_mock): - """Test """ + """Test retrieve trait info when lrs has a value""" resource_id_mock.return_value = 1 g_mock.db.execute.return_value.fetchone = mock.Mock() g_mock.db.execute.return_value.fetchone.side_effect = [ -- cgit v1.2.3 From ce728fa92e02725202bca486e8336b2e1158f4ef Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 29 Sep 2020 15:57:01 +0300 Subject: Add test for process_traits from collections.py * wqflask/tests/wqflask/test_collect.py: Add it. --- wqflask/tests/wqflask/test_collect.py | 73 +++++++++++++++++++++++++++++++++++ 1 file changed, 73 insertions(+) create mode 100644 wqflask/tests/wqflask/test_collect.py (limited to 'wqflask') diff --git a/wqflask/tests/wqflask/test_collect.py b/wqflask/tests/wqflask/test_collect.py new file mode 100644 index 00000000..06609b4c --- /dev/null +++ b/wqflask/tests/wqflask/test_collect.py @@ -0,0 +1,73 @@ +"""Test cases for some methods in collect.py""" + +import unittest +import mock + +from flask import Flask +from wqflask.collect import process_traits + +app = Flask(__name__) + + +class MockSession: + """Helper class for mocking wqflask.collect.g.user_session.logged_in""" + def __init__(self, is_logged_in=False): + self.is_logged_in = is_logged_in + + @property + def logged_in(self): + return self.is_logged_in + + +class MockFlaskG: + """Helper class for mocking wqflask.collect.g.user_session""" + def __init__(self, is_logged_in=False): + self.is_logged_in = is_logged_in + + @property + def user_session(self): + if self.is_logged_in: + return MockSession(is_logged_in=True) + return MockSession() + + +class TestCollect(unittest.TestCase): + + def setUp(self): + self.app_context = app.app_context() + self.app_context.push() + + def tearDown(self): + self.app_context.pop() + + @mock.patch("wqflask.collect.g", MockFlaskG()) + def test_process_traits_with_bytestring(self): + """ + Test that the correct traits are returned when the user is logged + out and bytes are used. + """ + self.assertEqual(process_traits( + b'1452452_at:HC_M2_0606_P:163d04f7db7c9e110de6,' + b'1452447_at:HC_M2_0606_P:eeece8fceb67072debea,' + b'1451401_a_at:HC_M2_0606_P:a043d23b3b3906d8318e,' + b'1429252_at:HC_M2_0606_P:6fa378b349bc9180e8f5'), + set(['1429252_at:HC_M2_0606_P', + '1451401_a_at:HC_M2_0606_P', + '1452447_at:HC_M2_0606_P', + '1452452_at:HC_M2_0606_P'])) + + @mock.patch("wqflask.collect.g", MockFlaskG()) + def test_process_traits_with_normal_string(self): + """ + Test that the correct traits are returned when the user is logged + out and a normal string is used. + """ + self.assertEqual(process_traits( + '1452452_at:HC_M2_0606_P:163d04f7db7c9e110de6,' + '1452447_at:HC_M2_0606_P:eeece8fceb67072debea,' + '1451401_a_at:HC_M2_0606_P:a043d23b3b3906d8318e,' + '1429252_at:HC_M2_0606_P:6fa378b349bc9180e8f5'), + set(['1429252_at:HC_M2_0606_P', + '1451401_a_at:HC_M2_0606_P', + '1452447_at:HC_M2_0606_P', + '1452452_at:HC_M2_0606_P'])) -- cgit v1.2.3 From d6fa2ebf9b3c53daec63e2ccd23feb87335a1e81 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 29 Sep 2020 17:09:11 +0300 Subject: Add check for bytes * wqflask/wqflask/collect.py (process_traits): Check whether the passed "unprocessed_traits" is a byte otherwise an error is generated when bytes(the default) are passed. --- wqflask/wqflask/collect.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py index 15383603..e7dac72a 100644 --- a/wqflask/wqflask/collect.py +++ b/wqflask/wqflask/collect.py @@ -35,7 +35,9 @@ from utility.logger import getLogger logger = getLogger(__name__) def process_traits(unprocessed_traits): - if isinstance(unprocessed_traits, str): + if isinstance(unprocessed_traits, bytes): + unprocessed_traits = unprocessed_traits.decode('utf-8').split(",") + else: # It's a string unprocessed_traits = unprocessed_traits.split(",") traits = set() for trait in unprocessed_traits: -- cgit v1.2.3 From 744d0cd6cd5e2bca98acbec1b8a1eed6986f824e Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 29 Sep 2020 22:59:38 +0300 Subject: Apply pep 8 to buffer * wqflask/wqflask/user_manager.py: Remove some stale comments. (imports): Apply pep-8 and remove unused imports. --- wqflask/wqflask/user_manager.py | 73 +++++++++++++++++++---------------------- 1 file changed, 33 insertions(+), 40 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py index 24191a15..7b25b68e 100644 --- a/wqflask/wqflask/user_manager.py +++ b/wqflask/wqflask/user_manager.py @@ -2,50 +2,62 @@ import os import hashlib import datetime import time -import logging import uuid -import hashlib import hmac import base64 -import urllib.parse - +import redis # used for collections import simplejson as json +import requests -#from redis import StrictRedis -import redis # used for collections -Redis = redis.StrictRedis() +from base.data_set import create_datasets_list -from flask import (Flask, g, render_template, url_for, request, make_response, - redirect, flash, abort) +from flask import g +from flask import render_template +from flask import url_for +from flask import request +from flask import make_response +from flask import redirect +from flask import flash from wqflask import app -from pprint import pformat as pf - -from wqflask import pbkdf2 # password hashing +from wqflask import pbkdf2 # password hashing from wqflask.database import db_session from wqflask import model -from utility import Bunch, Struct, after +from smtplib import SMTP + +from pprint import pformat as pf -import logging +from utility import Bunch +from utility import Struct from utility.logger import getLogger -logger = getLogger(__name__) -from base.data_set import create_datasets_list +from utility.redis_tools import get_user_id +from utility.redis_tools import get_user_by_unique_column +from utility.redis_tools import set_user_attribute +from utility.redis_tools import save_user +from utility.redis_tools import save_verification_code +from utility.redis_tools import check_verification_code +from utility.redis_tools import get_user_collections +from utility.redis_tools import save_collections -import requests +from utility.tools import SMTP_CONNECT +from utility.tools import SMTP_USERNAME +from utility.tools import SMTP_PASSWORD -from utility.redis_tools import get_user_id, get_user_by_unique_column, set_user_attribute, save_user, save_verification_code, check_verification_code, get_user_collections, save_collections -from smtplib import SMTP -from utility.tools import SMTP_CONNECT, SMTP_USERNAME, SMTP_PASSWORD, LOG_SQL_ALCHEMY +logger = getLogger(__name__) + + +Redis = redis.StrictRedis() THREE_DAYS = 60 * 60 * 24 * 3 -#THREE_DAYS = 45 + def timestamp(): return datetime.datetime.utcnow().isoformat() + class AnonUser(object): """Anonymous user handling""" cookie_name = 'anon_user_v1' @@ -228,25 +240,6 @@ class UserSession(object): return len(self.user_collections) -### -# ZS: This is currently not used, but I'm leaving it here commented out because the old "set superuser" code (at the bottom of this file) used it -### -# @property -# def user_ob(self): -# """Actual sqlalchemy record""" -# # Only look it up once if needed, then store it -# # raise "OBSOLETE: use ElasticSearch instead" -# try: -# if LOG_SQL_ALCHEMY: -# logging.getLogger('sqlalchemy.pool').setLevel(logging.DEBUG) -# -# # Already did this before -# return self.db_object -# except AttributeError: -# # Doesn't exist so we'll create it -# self.db_object = model.User.query.get(self.user_id) -# return self.db_object - def add_collection(self, collection_name, traits): """Add collection into ElasticSearch""" -- cgit v1.2.3 From 52ce47b7e1417bfa877ea68d2bcb119fc951d1d1 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 29 Sep 2020 23:13:16 +0300 Subject: Remove undefined variable --- wqflask/wqflask/collect.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py index e7dac72a..9752c8b5 100644 --- a/wqflask/wqflask/collect.py +++ b/wqflask/wqflask/collect.py @@ -124,7 +124,8 @@ def collections_new(): g.user_session.add_traits_to_collection(collection_id, traits) return redirect(url_for('view_collection', uc_id=collection_id)) else: - CauseAnError + # CauseAnError + pass def create_new(collection_name): params = request.args -- cgit v1.2.3 From 475b6e333e6356103592b0983d5efb8e84eb73e7 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 30 Sep 2020 02:09:27 +0300 Subject: Fix import in tests --- wqflask/tests/wqflask/test_collect.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/tests/wqflask/test_collect.py b/wqflask/tests/wqflask/test_collect.py index 06609b4c..9a36132d 100644 --- a/wqflask/tests/wqflask/test_collect.py +++ b/wqflask/tests/wqflask/test_collect.py @@ -1,7 +1,7 @@ """Test cases for some methods in collect.py""" import unittest -import mock +from unittest import mock from flask import Flask from wqflask.collect import process_traits -- cgit v1.2.3 From dce0cd8725e68e6984c8b54a2cc108e4f8c9df7a Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 30 Sep 2020 16:55:25 +0300 Subject: Fix StopIteration error thrown in view collections page * wqflask/wqflask/user_session.py (user_id): Use byte-string when fetching user_id. See: https://github.com/genenetwork/genenetwork2/pull/422#issuecomment-701082458 --- wqflask/wqflask/user_session.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py index c1f38396..9f4c5458 100644 --- a/wqflask/wqflask/user_session.py +++ b/wqflask/wqflask/user_session.py @@ -127,10 +127,10 @@ class UserSession(object): @property def user_id(self): """Shortcut to the user_id""" - if 'user_id' not in self.record: - self.record['user_id'] = str(uuid.uuid4()) + if b'user_id' not in self.record: + self.record[b'user_id'] = str(uuid.uuid4()) - return self.record['user_id'] + return self.record[b'user_id'] @property def redis_user_id(self): -- cgit v1.2.3 From bbc1a53dd0a8a60e8c22f0576be0a2624cb5a3ad Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 30 Sep 2020 17:10:17 +0300 Subject: Apply pep 8 formatting * wqflask/wqflask/correlation/show_corr_results.py [imports]: Apply pep8 and remove unused imports. --- wqflask/wqflask/correlation/show_corr_results.py | 25 ++++++++++++++---------- 1 file changed, 15 insertions(+), 10 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 91146e5b..8e0aa5df 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -23,25 +23,29 @@ import json import scipy import numpy import rpy2.robjects as ro # R Objects +import utility.logger +import utility.webqtlUtil from rpy2.robjects.packages import importr -utils = importr("utils") from base import data_set -from utility import webqtlUtil, helper_functions, corr_result_helpers, hmac -from db import webqtlDatabaseFunction -import utility.webqtlUtil #this is for parallel computing only. +from utility import helper_functions +from utility import corr_result_helpers +from utility import hmac + from wqflask.correlation import correlation_functions from utility.benchmark import Bench -import utility.webqtlUtil -from utility.type_checking import is_str, get_float, get_int, get_string -from utility.db_tools import escape +from utility.type_checking import is_str +from utility.type_checking import get_float +from utility.type_checking import get_int +from utility.type_checking import get_string +from utility.db_tools import escape -from flask import Flask, g +from flask import g -import utility.logger -logger = utility.logger.getLogger(__name__ ) +utils = importr("utils") +logger = utility.logger.getLogger(__name__) METHOD_LIT = "3" METHOD_TISSUE_PEARSON = "4" @@ -51,6 +55,7 @@ TISSUE_METHODS = [METHOD_TISSUE_PEARSON, METHOD_TISSUE_RANK] TISSUE_MOUSE_DB = 1 + class CorrelationResults(object): def __init__(self, start_vars): # get trait list from db (database name) -- cgit v1.2.3 From f0aa59dc9413daceb580938c4d706e8831bf4daa Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 30 Sep 2020 17:11:06 +0300 Subject: Add missing import * wqflask/wqflask/correlation/show_corr_results.py: Add it. --- wqflask/wqflask/correlation/show_corr_results.py | 2 ++ 1 file changed, 2 insertions(+) (limited to 'wqflask') diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 8e0aa5df..e710bacd 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -26,6 +26,8 @@ import rpy2.robjects as ro # R Objects import utility.logger import utility.webqtlUtil +from base.trait import create_trait + from rpy2.robjects.packages import importr from base import data_set -- cgit v1.2.3 From 968bc7d468b2a24ded48b4deeb76b216ddb9a350 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 1 Oct 2020 16:10:41 +0300 Subject: Make object JSON serializable * wqflask/wqflask/search_results.py (SearchResultPage.gen_search_result): Some of the items is self.trait_list are in bytes, and *json.loads* can't serialize bytes into JSON. --- wqflask/wqflask/search_results.py | 4 ++++ 1 file changed, 4 insertions(+) (limited to 'wqflask') diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index aa8f9e8f..ce836ce2 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -149,6 +149,10 @@ views.py). trait_dict['additive'] = "N/A" if this_trait.additive != "": trait_dict['additive'] = '%.3f' % this_trait.additive + # Convert any bytes in dict to a normal utf-8 string + for key in trait_dict.keys(): + if isinstance(trait_dict[key], bytes): + trait_dict[key] = trait_dict[key].decode('utf-8') trait_list.append(trait_dict) self.trait_list = json.dumps(trait_list) -- cgit v1.2.3 From 4aa6c2dc7d6e74316e793f219a6a44411fbef5ac Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 1 Oct 2020 18:16:45 +0300 Subject: Convert trait attributes to utf-8 strings if they were bytes --- wqflask/base/trait.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index d0c79119..24d0476d 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -147,7 +147,8 @@ class GeneralTrait(object): formatted = self.post_publication_description else: formatted = "Not available" - + if isinstance(formatted, bytes): + formatted = formatted.decode("utf-8") return formatted @property @@ -495,6 +496,8 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): trait.haveinfo = True for i, field in enumerate(dataset.display_fields): holder = trait_info[i] + if isinstance(holder, bytes): + holder = holder.decode('utf-8') setattr(trait, field, holder) if dataset.type == 'Publish': -- cgit v1.2.3 From 94c36c8c93bea837a6e277d1dc3a2bc9120f9044 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Fri, 2 Oct 2020 00:39:06 +0300 Subject: Cast "previous_chr" to an int * wqflask/wqflask/marker_regression/gemma_mapping.py (parse_loco_output): Cast "previous_chr" to an int which prevents the error "Python typeerror: ‘>’ not supported between instances of ‘str’ and ‘int’" from being thrown. The error is **only** thrown in Python3. --- wqflask/wqflask/marker_regression/gemma_mapping.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index b858b573..68a8d5ba 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -218,9 +218,9 @@ def parse_loco_output(this_dataset, gwa_output_filename): marker['chr'] = int(line.split("\t")[0][3:]) else: marker['chr'] = int(line.split("\t")[0]) - if marker['chr'] > previous_chr: + if marker['chr'] > int(previous_chr): previous_chr = marker['chr'] - elif marker['chr'] < previous_chr: + elif marker['chr'] < int(previous_chr): break else: marker['chr'] = line.split("\t")[0] -- cgit v1.2.3 From 509bd3b90dcb6ab71f42385d1feccb154a6d5108 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Fri, 2 Oct 2020 00:46:36 +0300 Subject: Remove unnecessary commented out blocks * wqflask/wqflask/show_trait/SampleList.py: See above. --- wqflask/wqflask/show_trait/SampleList.py | 44 -------------------------------- 1 file changed, 44 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py index 6fcf7cec..7a6f1664 100644 --- a/wqflask/wqflask/show_trait/SampleList.py +++ b/wqflask/wqflask/show_trait/SampleList.py @@ -102,7 +102,6 @@ class SampleList(object): self.attributes = {} for attr, values in itertools.groupby(results.fetchall(), lambda row: (row.Id, row.Name)): key, name = attr - #logger.debug("radish: %s - %s" % (key, name)) self.attributes[key] = Bunch() self.attributes[key].name = name self.attributes[key].distinct_values = [item.Value for item in values] @@ -153,49 +152,6 @@ class SampleList(object): """Returns true if SE values exist for any samples, otherwise false""" return any(sample.variance for sample in self.sample_list) - -# def get_transform_vals(dataset, trait): -# es = get_elasticsearch_connection(for_user=False) - -# logger.info("DATASET NAME:", dataset.name) - -# query = '{"bool": {"must": [{"match": {"name": "%s"}}, {"match": {"dataset": "%s"}}]}}' % (trait.name, dataset.name) - -# es_body = { -# "query": { -# "bool": { -# "must": [ -# { -# "match": { -# "name": "%s" % (trait.name) -# } -# }, -# { -# "match": { -# "dataset": "%s" % (dataset.name) -# } -# } -# ] -# } -# } -# } - -# response = es.search( index = "traits", doc_type = "trait", body = es_body ) -# logger.info("THE RESPONSE:", response) -# results = response['hits']['hits'] - -# if len(results) > 0: -# samples = results[0]['_source']['samples'] - -# sample_dict = {} -# for sample in samples: -# sample_dict[sample['name']] = sample['qnorm'] - -# #logger.info("SAMPLE DICT:", sample_dict) -# return sample_dict -# else: -# return None - def natural_sort_key(x): """Get expected results when using as a key for sort - ints or strings are sorted properly""" -- cgit v1.2.3 From 5aee7c35ef27dbfa590dfd30364000840dd0006a Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Fri, 2 Oct 2020 01:04:23 +0300 Subject: Update natural_sort function * wqflask/wqflask/show_trait/SampleList.py (natural_sort): Add new function. (SampleList.get_attributes): Use new sort function to do natural_sort. --- wqflask/wqflask/show_trait/SampleList.py | 24 ++++++++++++++---------- 1 file changed, 14 insertions(+), 10 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py index 7a6f1664..b43b57dc 100644 --- a/wqflask/wqflask/show_trait/SampleList.py +++ b/wqflask/wqflask/show_trait/SampleList.py @@ -1,3 +1,4 @@ +import re from flask import Flask, g from base import webqtlCaseData @@ -105,8 +106,7 @@ class SampleList(object): self.attributes[key] = Bunch() self.attributes[key].name = name self.attributes[key].distinct_values = [item.Value for item in values] - self.attributes[key].distinct_values.sort(key=natural_sort_key) - + natural_sort(self.attributes[key].distinct_values) all_numbers = True for value in self.attributes[key].distinct_values: try: @@ -152,11 +152,15 @@ class SampleList(object): """Returns true if SE values exist for any samples, otherwise false""" return any(sample.variance for sample in self.sample_list) -def natural_sort_key(x): - """Get expected results when using as a key for sort - ints or strings are sorted properly""" - - try: - x = int(x) - except ValueError: - pass - return x + + +def natural_sort(list, key=lambda s:s): + """ + Sort the list into natural alphanumeric order. + """ + def get_alphanum_key_func(key): + convert = lambda text: int(text) if text.isdigit() else text + return lambda s: [convert(c) for c in re.split('([0-9]+)', key(s))] + sort_key = get_alphanum_key_func(key) + list.sort(key=sort_key) + -- cgit v1.2.3 From 5559aeca7989cfe0b454dff018eada6fb69a73a6 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Fri, 2 Oct 2020 02:36:09 +0300 Subject: Replace is_integer with isinstance when checking for an int value --- wqflask/wqflask/marker_regression/display_mapping_results.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 5a7a4614..745b8e78 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -2157,7 +2157,7 @@ class DisplayMappingResults(object): #ZS: Convert to int if all axis values are whole numbers all_int = True for item in LRSAxisList: - if item.is_integer(): + if isinstance(item, int): continue else: all_int = False -- cgit v1.2.3 From a3b9372cc24857ac38a1938bc2a94b2dc96471bb Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Fri, 2 Oct 2020 02:36:56 +0300 Subject: Cast variable properly to avoid type exceptions * wqflask/wqflask/marker_regression/run_mapping.py: See 94c36c8c. --- wqflask/wqflask/marker_regression/run_mapping.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index f42d2315..995923a7 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -409,8 +409,8 @@ class RunMapping(object): self.results_for_browser.append(browser_marker) self.annotations_for_browser.append(annot_marker) - if marker['chr'] > 0 or marker['chr'] == "X" or marker['chr'] == "X/Y": - if marker['chr'] > highest_chr or marker['chr'] == "X" or marker['chr'] == "X/Y": + if str(marker['chr']) > '0' or str(marker['chr']) == "X" or str(marker['chr']) == "X/Y": + if str(marker['chr']) > str(highest_chr) or str(marker['chr']) == "X" or str(marker['chr']) == "X/Y": highest_chr = marker['chr'] if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()): if 'Mb' in marker.keys(): -- cgit v1.2.3 From ea3876a87f5f6ac6e5990514f485213181456bb2 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Fri, 2 Oct 2020 02:41:41 +0300 Subject: Apply PEP 8 formatting --- wqflask/wqflask/show_trait/SampleList.py | 70 ++++++++++++++++---------------- 1 file changed, 35 insertions(+), 35 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py index b43b57dc..dccd1ba8 100644 --- a/wqflask/wqflask/show_trait/SampleList.py +++ b/wqflask/wqflask/show_trait/SampleList.py @@ -1,83 +1,82 @@ import re -from flask import Flask, g +import itertools +import utility.logger +from flask import g from base import webqtlCaseData -from utility import webqtlUtil, Plot, Bunch -from base.trait import GeneralTrait -import numpy as np -from scipy import stats -from pprint import pformat as pf +from utility import Plot +from utility import Bunch -import simplejson as json +from pprint import pformat as pf -import itertools +logger = utility.logger.getLogger(__name__) -import utility.logger -logger = utility.logger.getLogger(__name__ ) class SampleList(object): def __init__(self, dataset, sample_names, this_trait, - sample_group_type = "primary", - header = "Samples"): + sample_group_type="primary", + header="Samples"): self.dataset = dataset self.this_trait = this_trait self.sample_group_type = sample_group_type # primary or other self.header = header - self.sample_list = [] # The actual list + self.sample_list = [] # The actual list self.sample_attribute_values = {} self.get_attributes() - #self.sample_qnorm = get_transform_vals(self.dataset, this_trait) - if self.this_trait and self.dataset: self.get_extra_attribute_values() for counter, sample_name in enumerate(sample_names, 1): sample_name = sample_name.replace("_2nd_", "") - if isinstance(self.this_trait, list): #ZS: self.this_trait will be a list if it is a Temp trait - if counter <= len(self.this_trait) and str(self.this_trait[counter-1]).upper() != 'X': - sample = webqtlCaseData.webqtlCaseData(name=sample_name, value=float(self.this_trait[counter-1])) + # ZS: self.this_trait will be a list if it is a Temp trait + if isinstance(self.this_trait, list): + if (counter <= len(self.this_trait) and + str(self.this_trait[counter-1]).upper() != 'X'): + sample = webqtlCaseData.webqtlCaseData( + name=sample_name, + value=float(self.this_trait[counter-1])) else: sample = webqtlCaseData.webqtlCaseData(name=sample_name) else: - #ZS - If there's no value for the sample/strain, create the sample object (so samples with no value are still displayed in the table) + # ZS - If there's no value for the sample/strain, + # create the sample object (so samples with no value + # are still displayed in the table) try: sample = self.this_trait.data[sample_name] except KeyError: - #logger.debug("No sample %s, let's create it now" % sample_name) sample = webqtlCaseData.webqtlCaseData(name=sample_name) sample.extra_info = {} - if self.dataset.group.name == 'AXBXA' and sample_name in ('AXB18/19/20', 'AXB13/14', 'BXA8/17'): + if (self.dataset.group.name == 'AXBXA' and + sample_name in ('AXB18/19/20', 'AXB13/14', 'BXA8/17')): sample.extra_info['url'] = "/mouseCross.html#AXB/BXA" sample.extra_info['css_class'] = "fs12" sample.this_id = str(counter) - #### For extra attribute columns; currently only used by several datasets - Zach + # For extra attribute columns; currently only used by + # several datasets - Zach if self.sample_attribute_values: - sample.extra_attributes = self.sample_attribute_values.get(sample_name, {}) - #logger.debug("sample.extra_attributes is", pf(sample.extra_attributes)) - + sample.extra_attributes = self.sample_attribute_values.get( + sample_name, {}) self.sample_list.append(sample) - - #logger.debug("attribute vals are", pf(self.sample_attribute_values)) - self.do_outliers() def __repr__(self): return " --> %s" % (pf(self.__dict__)) def do_outliers(self): - values = [sample.value for sample in self.sample_list if sample.value != None] + values = [sample.value for sample in self.sample_list + if sample.value is not None] upper_bound, lower_bound = Plot.find_outliers(values) for sample in self.sample_list: @@ -105,7 +104,8 @@ class SampleList(object): key, name = attr self.attributes[key] = Bunch() self.attributes[key].name = name - self.attributes[key].distinct_values = [item.Value for item in values] + self.attributes[key].distinct_values = [ + item.Value for item in values] natural_sort(self.attributes[key].distinct_values) all_numbers = True for value in self.attributes[key].distinct_values: @@ -138,8 +138,9 @@ class SampleList(object): for item in items: attribute_value = item.Value - #ZS: If it's an int, turn it into one for sorting - #(for example, 101 would be lower than 80 if they're strings instead of ints) + # ZS: If it's an int, turn it into one for sorting + # (for example, 101 would be lower than 80 if + # they're strings instead of ints) try: attribute_value = int(attribute_value) except ValueError: @@ -154,13 +155,12 @@ class SampleList(object): return any(sample.variance for sample in self.sample_list) -def natural_sort(list, key=lambda s:s): +def natural_sort(list, key=lambda s: s): """ Sort the list into natural alphanumeric order. """ def get_alphanum_key_func(key): - convert = lambda text: int(text) if text.isdigit() else text + def convert(text): return int(text) if text.isdigit() else text return lambda s: [convert(c) for c in re.split('([0-9]+)', key(s))] sort_key = get_alphanum_key_func(key) list.sort(key=sort_key) - -- cgit v1.2.3 From 11180abbba8af29499e6eda2c7c408fc4e0eb80a Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Fri, 2 Oct 2020 03:16:18 +0300 Subject: Split author's list into it's own variable * wqflask/wqflask/templates/correlation_page.html: Ditto. Prevents jinja from throwing an error due to compaing a list type with an int. --- wqflask/wqflask/templates/correlation_page.html | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index bb2a697f..435c0b37 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -170,7 +170,8 @@ {% endif %} {% if trait.description_display|length > 70 %}{{ trait.description_display[:70] }}...{% else %}{{ trait.description_display }}{% endif %} {% if trait.authors %} - {% if trait.authors.split(',') > 6 %}{{ trait.authors.split(',')[:6]|join(', ') }}, et al.{% else %}{{ trait.authors }}{% endif %} + {% set authors_list = trait.authors.split(',') %} + {% if authors_list|length > 6 %}{{ authors_list[:6]|join(', ') }}, et al.{% else %}{{ trait.authors }}{% endif %} {% else %} N/A {% endif %} -- cgit v1.2.3 From f0dd46e668a55bd024f5dee4e99cf1215a107c26 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Fri, 2 Oct 2020 03:48:23 +0300 Subject: Ignore utf-8 encoding errors * wqflask/base/trait.py (retrieve_trait_info): Add extra param to ignore errors such as: "utf-8 codec can't decode byte 0xb5 in position 0: invalid start byte" thrown in Python3. --- wqflask/base/trait.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 24d0476d..a493cfbf 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -497,7 +497,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): for i, field in enumerate(dataset.display_fields): holder = trait_info[i] if isinstance(holder, bytes): - holder = holder.decode('utf-8') + holder = holder.decode("utf-8", errors="ignore") setattr(trait, field, holder) if dataset.type == 'Publish': -- cgit v1.2.3 From 4aa138360fd41f9d496e00aa744700cd4d8a53a6 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 7 Oct 2020 15:08:05 +0300 Subject: Apply PEP-8 formatting --- .../wqflask/correlation_matrix/show_corr_matrix.py | 29 ++-- wqflask/wqflask/network_graph/network_graph.py | 100 ++++++------ wqflask/wqflask/wgcna/wgcna_analysis.py | 169 ++++++++++++--------- 3 files changed, 156 insertions(+), 142 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index 49ba9e5d..c0d84aa2 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -22,33 +22,24 @@ import datetime import math import numpy as np import scipy - -from rpy2.robjects.packages import importr import rpy2.robjects as robjects +import utility.webqtlUtil # this is for parallel computing only. +import utility.logger -from pprint import pformat as pf +from base import data_set +from functools import reduce +from rpy2.robjects.packages import importr +from utility import webqtlUtil +from utility import helper_functions +from utility import corr_result_helpers from utility.redis_tools import get_redis_conn -from functools import reduce + +logger = utility.logger.getLogger(__name__) Redis = get_redis_conn() THIRTY_DAYS = 60 * 60 * 24 * 30 -from utility.THCell import THCell -from utility.TDCell import TDCell -from base.trait import GeneralTrait -from base import data_set -from utility import webqtlUtil, helper_functions, corr_result_helpers - -from db import webqtlDatabaseFunction -import utility.webqtlUtil #this is for parallel computing only. -from wqflask.correlation import correlation_functions -from utility.benchmark import Bench - -from flask import Flask, g, url_for - -import utility.logger -logger = utility.logger.getLogger(__name__ ) class CorrelationMatrix(object): diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py index cfefe4ec..723a749f 100644 --- a/wqflask/wqflask/network_graph/network_graph.py +++ b/wqflask/wqflask/network_graph/network_graph.py @@ -1,4 +1,4 @@ -## Copyright (C) University of Tennessee Health Science Center, Memphis, TN. +# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. # # This program is free software: you can redistribute it and/or modify it # under the terms of the GNU Affero General Public License @@ -20,25 +20,19 @@ import scipy import simplejson as json -from pprint import pformat as pf - -from utility.TDCell import TDCell from base.trait import create_trait from base import data_set -from utility import webqtlUtil, helper_functions, corr_result_helpers +from utility import helper_functions +from utility import corr_result_helpers from utility.tools import GN2_BRANCH_URL -from db import webqtlDatabaseFunction -import utility.webqtlUtil #this is for parallel computing only. -from wqflask.correlation import correlation_functions - -from flask import Flask, g class NetworkGraph(object): def __init__(self, start_vars): - trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')] + trait_db_list = [trait.strip() + for trait in start_vars['trait_list'].split(',')] helper_functions.get_trait_db_obs(self, trait_db_list) @@ -66,7 +60,8 @@ class NetworkGraph(object): this_trait_vals.append('') self.sample_data.append(this_trait_vals) - 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) + # 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.lowest_overlap = 8 self.nodes_list = [] self.edges_list = [] @@ -78,9 +73,9 @@ class NetworkGraph(object): this_sample_data = this_trait.data corr_result_row = [] - is_spearman = False #ZS: To determine if it's above or below the diagonal + 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 + 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] @@ -99,20 +94,23 @@ class NetworkGraph(object): this_trait_vals.append(sample_value) target_vals.append(target_sample_value) - this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(this_trait_vals, target_vals) + this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values( + this_trait_vals, target_vals) if num_overlap < self.lowest_overlap: self.lowest_overlap = num_overlap if num_overlap == 0: continue else: - pearson_r, pearson_p = scipy.stats.pearsonr(this_trait_vals, target_vals) + pearson_r, pearson_p = scipy.stats.pearsonr( + this_trait_vals, target_vals) if is_spearman == False: sample_r, sample_p = pearson_r, pearson_p if sample_r == 1: continue else: - sample_r, sample_p = scipy.stats.spearmanr(this_trait_vals, target_vals) + sample_r, sample_p = scipy.stats.spearmanr( + this_trait_vals, target_vals) if -1 <= sample_r < -0.7: color = "#0000ff" @@ -130,44 +128,44 @@ class NetworkGraph(object): color = "#ffa500" width = 2 elif 0.7 <= sample_r <= 1: - color = "#ff0000" - width = 3 + color = "#ff0000" + width = 3 else: color = "#000000" - width = 0 + 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), - 'correlation' : round(sample_r, 3), - 'abs_corr' : abs(round(sample_r, 3)), - 'p_value' : round(sample_p, 3), - 'overlap' : num_overlap, - 'color' : color, - 'width' : width } + 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), + 'correlation': round(sample_r, 3), + 'abs_corr': abs(round(sample_r, 3)), + 'p_value': round(sample_p, 3), + 'overlap': num_overlap, + 'color': color, + 'width': width} - edge_dict = { 'data' : edge_data } + 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, - 'symbol' : this_trait.symbol, - 'geneid' : this_trait.geneid, - 'omim' : this_trait.omim, - 'max_corr' : max_corr } } + node_dict = {'data': {'id': str(this_trait.name) + ":" + str(this_trait.dataset.name), + 'label': this_trait.symbol, + 'symbol': this_trait.symbol, + 'geneid': this_trait.geneid, + 'omim': this_trait.omim, + 'max_corr': max_corr}} elif trait_db[1].type == "Publish": - node_dict = { 'data' : {'id' : str(this_trait.name) + ":" + str(this_trait.dataset.name), - 'label' : this_trait.name, - 'max_corr' : max_corr } } + node_dict = {'data': {'id': str(this_trait.name) + ":" + str(this_trait.dataset.name), + 'label': this_trait.name, + 'max_corr': max_corr}} else: - node_dict = { 'data' : {'id' : str(this_trait.name) + ":" + str(this_trait.dataset.name), - 'label' : this_trait.name, - 'max_corr' : max_corr } } + node_dict = {'data': {'id': str(this_trait.name) + ":" + str(this_trait.dataset.name), + 'label': this_trait.name, + 'max_corr': max_corr}} self.nodes_list.append(node_dict) self.elements = json.dumps(self.nodes_list + self.edges_list) @@ -177,13 +175,13 @@ class NetworkGraph(object): 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 = list(range(len(self.traits))), - rows = list(range(len(self.traits))), - samples = self.all_sample_list, - sample_data = self.sample_data, - elements = self.elements,) + self.js_data = dict(traits=[trait.name for trait in self.traits], + groups=groups, + cols=list(range(len(self.traits))), + rows=list(range(len(self.traits))), + samples=self.all_sample_list, + sample_data=self.sample_data, + elements=self.elements,) def get_trait_db_obs(self, trait_db_list): self.trait_list = [] @@ -193,6 +191,6 @@ class NetworkGraph(object): trait_name, dataset_name = trait_db.split(":") dataset_ob = data_set.create_dataset(dataset_name) trait_ob = create_trait(dataset=dataset_ob, - name=trait_name, - cellid=None) + name=trait_name, + cellid=None) self.trait_list.append((trait_ob, dataset_ob)) diff --git a/wqflask/wqflask/wgcna/wgcna_analysis.py b/wqflask/wqflask/wgcna/wgcna_analysis.py index d79ad6df..0afe7e82 100644 --- a/wqflask/wqflask/wgcna/wgcna_analysis.py +++ b/wqflask/wqflask/wgcna/wgcna_analysis.py @@ -1,122 +1,146 @@ # WGCNA analysis for GN2 # Author / Maintainer: Danny Arends import sys -from numpy import * -import scipy as sp # SciPy import rpy2.robjects as ro # R Objects import rpy2.rinterface as ri +import array +from numpy import * from base.webqtlConfig import GENERATED_IMAGE_DIR -from utility import webqtlUtil # Random number for the image - -import base64 -import array +from rpy2.robjects.packages import importr +from utility import webqtlUtil # Random number for the image from utility import helper_functions -from rpy2.robjects.packages import importr utils = importr("utils") -## Get pointers to some common R functions -r_library = ro.r["library"] # Map the library function -r_options = ro.r["options"] # Map the options function -r_read_csv = ro.r["read.csv"] # Map the read.csv function -r_dim = ro.r["dim"] # Map the dim function -r_c = ro.r["c"] # Map the c function -r_cat = ro.r["cat"] # Map the cat function -r_paste = ro.r["paste"] # Map the paste function -r_unlist = ro.r["unlist"] # Map the unlist function -r_unique = ro.r["unique"] # Map the unique function -r_length = ro.r["length"] # Map the length function -r_unlist = ro.r["unlist"] # Map the unlist function -r_list = ro.r.list # Map the list function -r_matrix = ro.r.matrix # Map the matrix function -r_seq = ro.r["seq"] # Map the seq function -r_table = ro.r["table"] # Map the table function -r_names = ro.r["names"] # Map the names function -r_sink = ro.r["sink"] # Map the sink function -r_is_NA = ro.r["is.na"] # Map the is.na function -r_file = ro.r["file"] # Map the file function -r_png = ro.r["png"] # Map the png function for plotting -r_dev_off = ro.r["dev.off"] # Map the dev.off function +# Get pointers to some common R functions +r_library = ro.r["library"] # Map the library function +r_options = ro.r["options"] # Map the options function +r_read_csv = ro.r["read.csv"] # Map the read.csv function +r_dim = ro.r["dim"] # Map the dim function +r_c = ro.r["c"] # Map the c function +r_cat = ro.r["cat"] # Map the cat function +r_paste = ro.r["paste"] # Map the paste function +r_unlist = ro.r["unlist"] # Map the unlist function +r_unique = ro.r["unique"] # Map the unique function +r_length = ro.r["length"] # Map the length function +r_unlist = ro.r["unlist"] # Map the unlist function +r_list = ro.r.list # Map the list function +r_matrix = ro.r.matrix # Map the matrix function +r_seq = ro.r["seq"] # Map the seq function +r_table = ro.r["table"] # Map the table function +r_names = ro.r["names"] # Map the names function +r_sink = ro.r["sink"] # Map the sink function +r_is_NA = ro.r["is.na"] # Map the is.na function +r_file = ro.r["file"] # Map the file function +r_png = ro.r["png"] # Map the png function for plotting +r_dev_off = ro.r["dev.off"] # Map the dev.off function + class WGCNA(object): def __init__(self): print("Initialization of WGCNA") #log = r_file("/tmp/genenetwork_wcgna.log", open = "wt") - #r_sink(log) # Uncomment the r_sink() commands to log output from stdout/stderr to a file + # r_sink(log) # Uncomment the r_sink() commands to log output from stdout/stderr to a file #r_sink(log, type = "message") - r_library("WGCNA") # Load WGCNA - Should only be done once, since it is quite expensive - r_options(stringsAsFactors = False) + # Load WGCNA - Should only be done once, since it is quite expensive + r_library("WGCNA") + r_options(stringsAsFactors=False) print("Initialization of WGCNA done, package loaded in R session") - self.r_enableWGCNAThreads = ro.r["enableWGCNAThreads"] # Map the enableWGCNAThreads function - self.r_pickSoftThreshold = ro.r["pickSoftThreshold"] # Map the pickSoftThreshold function - self.r_blockwiseModules = ro.r["blockwiseModules"] # Map the blockwiseModules function - self.r_labels2colors = ro.r["labels2colors"] # Map the labels2colors function - self.r_plotDendroAndColors = ro.r["plotDendroAndColors"] # Map the plotDendroAndColors function + # Map the enableWGCNAThreads function + self.r_enableWGCNAThreads = ro.r["enableWGCNAThreads"] + # Map the pickSoftThreshold function + self.r_pickSoftThreshold = ro.r["pickSoftThreshold"] + # Map the blockwiseModules function + self.r_blockwiseModules = ro.r["blockwiseModules"] + # Map the labels2colors function + self.r_labels2colors = ro.r["labels2colors"] + # Map the plotDendroAndColors function + self.r_plotDendroAndColors = ro.r["plotDendroAndColors"] print("Obtained pointers to WGCNA functions") def run_analysis(self, requestform): 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'])) + # Enable multi threading + self.r_enableWGCNAThreads() + self.trait_db_list = [trait.strip() + for trait in requestform['trait_list'].split(',')] + 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 - strains = [] # All the strains we have data for (contains duplicates) - traits = [] # All the traits we have data for (should not contain duplicates) + # All the strains we have data for (contains duplicates) + strains = [] + # All the traits we have data for (should not contain duplicates) + traits = [] for trait in self.trait_list: traits.append(trait[0].name) self.input[trait[0].name] = {} for strain in trait[0].data: strains.append(strain) - self.input[trait[0].name][strain] = trait[0].data[strain].value + self.input[trait[0].name][strain] = trait[0].data[strain].value # Transfer the load data from python to R - uStrainsR = r_unique(ro.Vector(strains)) # Unique strains in R vector + # Unique strains in R vector + uStrainsR = r_unique(ro.Vector(strains)) uTraitsR = r_unique(ro.Vector(traits)) # Unique traits in R vector r_cat("The number of unique strains:", r_length(uStrainsR), "\n") r_cat("The number of unique traits:", r_length(uTraitsR), "\n") # rM is the datamatrix holding all the data in R /rows = strains columns = traits - rM = ro.r.matrix(ri.NA_Real, nrow=r_length(uStrainsR), ncol=r_length(uTraitsR), dimnames = r_list(uStrainsR, uTraitsR)) + rM = ro.r.matrix(ri.NA_Real, nrow=r_length(uStrainsR), ncol=r_length( + uTraitsR), dimnames=r_list(uStrainsR, uTraitsR)) for t in uTraitsR: - trait = t[0] # R uses vectors every single element is a vector + # R uses vectors every single element is a vector + trait = t[0] for s in uStrainsR: - strain = s[0] # R uses vectors every single element is a vector + # R uses vectors every single element is a vector + strain = s[0] #DEBUG: print(trait, strain, " in python: ", self.input[trait].get(strain), "in R:", rM.rx(strain,trait)[0]) - rM.rx[strain, trait] = self.input[trait].get(strain) # Update the matrix location + rM.rx[strain, trait] = self.input[trait].get( + strain) # Update the matrix location sys.stdout.flush() self.results = {} - self.results['nphe'] = r_length(uTraitsR)[0] # Number of phenotypes/traits - self.results['nstr'] = r_length(uStrainsR)[0] # Number of strains + # Number of phenotypes/traits + self.results['nphe'] = r_length(uTraitsR)[0] + self.results['nstr'] = r_length( + uStrainsR)[0] # Number of strains self.results['phenotypes'] = uTraitsR # Traits used - self.results['strains'] = uStrainsR # Strains used in the analysis - self.results['requestform'] = requestform # Store the user specified parameters for the output page + # Strains used in the analysis + self.results['strains'] = uStrainsR + # Store the user specified parameters for the output page + self.results['requestform'] = requestform # Calculate soft threshold if the user specified the SoftThreshold variable 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))) - self.sft = self.r_pickSoftThreshold(rM, powerVector = rpow, verbose = 5) - - 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") - self.results['Power'] = 1 # No power could be estimated - else: - self.results['Power'] = self.sft[0][0] # Use the estimated power + powers = [int(threshold.strip()) + for threshold in requestform['SoftThresholds'].rstrip().split(",")] + rpow = r_unlist(r_c(powers)) + print(("SoftThresholds: {} == {}".format(powers, rpow))) + self.sft = self.r_pickSoftThreshold( + rM, powerVector=rpow, verbose=5) + + 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") + # No power could be estimated + self.results['Power'] = 1 + else: + # Use the estimated power + self.results['Power'] = self.sft[0][0] else: - # The user clicked a button, so no soft threshold selection - self.results['Power'] = requestform.get('Power') # Use the power value the user gives + # The user clicked a button, so no soft threshold selection + # Use the power value the user gives + self.results['Power'] = requestform.get('Power') # Create the block wise modules using WGCNA - network = self.r_blockwiseModules(rM, power = self.results['Power'], TOMType = requestform['TOMtype'], minModuleSize = requestform['MinModuleSize'], verbose = 3) + network = self.r_blockwiseModules( + rM, power=self.results['Power'], TOMType=requestform['TOMtype'], minModuleSize=requestform['MinModuleSize'], verbose=3) # Save the network for the GUI self.results['network'] = network @@ -130,7 +154,8 @@ class WGCNA(object): self.results['imgloc'] = GENERATED_IMAGE_DIR + self.results['imgurl'] r_png(self.results['imgloc'], width=1000, height=600, type='cairo-png') mergedColors = self.r_labels2colors(network[1]) - self.r_plotDendroAndColors(network[5][0], mergedColors, "Module colors", dendroLabels = False, hang = 0.03, addGuide = True, guideHang = 0.05) + self.r_plotDendroAndColors(network[5][0], mergedColors, "Module colors", + dendroLabels=False, hang=0.03, addGuide=True, guideHang=0.05) r_dev_off() sys.stdout.flush() @@ -146,11 +171,11 @@ class WGCNA(object): print("Processing WGCNA output") template_vars = {} template_vars["input"] = self.input - template_vars["powers"] = self.sft[1:] # Results from the soft threshold analysis + # Results from the soft threshold analysis + template_vars["powers"] = self.sft[1:] template_vars["results"] = self.results self.render_image(results) sys.stdout.flush() - #r_sink(type = "message") # This restores R output to the stdout/stderr - #r_sink() # We should end the Rpy session more or less + # r_sink(type = "message") # This restores R output to the stdout/stderr + # r_sink() # We should end the Rpy session more or less return(dict(template_vars)) - -- cgit v1.2.3 From ef11f5e40ec0b8ef90a00b9d98d81cca2ff5d8d9 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 7 Oct 2020 15:58:14 +0300 Subject: Convert cmp function into a key function * wqflask/wqflask/correlation_matrix/show_corr_matrix.py (sortEigenVectors): Convert the comparison function into a key function. See: https://docs.python.org/3/howto/sorting.html#the-old-way-using-the-cmp-parameter --- wqflask/wqflask/correlation_matrix/show_corr_matrix.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index c0d84aa2..f24b9f7f 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -28,6 +28,7 @@ import utility.logger from base import data_set from functools import reduce +from functools import cmp_to_key from rpy2.robjects.packages import importr from utility import webqtlUtil @@ -268,7 +269,7 @@ def sortEigenVectors(vector): for item in eigenValues: combines.append([eigenValues[i], eigenVectors[i]]) i += 1 - combines.sort(webqtlUtil.cmpEigenValue) + sorted(combines, key=cmp_to_key(webqtlUtil.cmpEigenValue)) A = [] B = [] for item in combines: -- cgit v1.2.3 From 65846e5b05841b7c31a37298b49b99bb77d48a31 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 8 Oct 2020 22:37:07 +0300 Subject: Update base64 conversion * wqflask/wqflask/wgcna/wgcna_analysis.py (WGCNA.render_image): Use Python3's base64 library from the stdlib to perform conversion. * wqflask/wqflask/ctl/ctl_analysis.py (CTL.loadImage): Ditto. --- wqflask/wqflask/ctl/ctl_analysis.py | 2 +- wqflask/wqflask/wgcna/wgcna_analysis.py | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py index e58a7b87..2a2124ca 100644 --- a/wqflask/wqflask/ctl/ctl_analysis.py +++ b/wqflask/wqflask/ctl/ctl_analysis.py @@ -194,7 +194,7 @@ class CTL(object): def loadImage(self, path, name): imgfile = open(self.results[path], 'rb') imgdata = imgfile.read() - imgB64 = imgdata.encode("base64") + imgB64 = base64.b64encode(imgdata) bytesarray = array.array('B', imgB64) self.results[name] = bytesarray diff --git a/wqflask/wqflask/wgcna/wgcna_analysis.py b/wqflask/wqflask/wgcna/wgcna_analysis.py index 0afe7e82..35fb3ec0 100644 --- a/wqflask/wqflask/wgcna/wgcna_analysis.py +++ b/wqflask/wqflask/wgcna/wgcna_analysis.py @@ -1,5 +1,6 @@ # WGCNA analysis for GN2 # Author / Maintainer: Danny Arends +import base64 import sys import rpy2.robjects as ro # R Objects import rpy2.rinterface as ri @@ -163,8 +164,8 @@ class WGCNA(object): print(("pre-loading imgage results:", self.results['imgloc'])) imgfile = open(self.results['imgloc'], 'rb') imgdata = imgfile.read() - imgB64 = imgdata.encode("base64") bytesarray = array.array('B', imgB64) + imgB64 = base64.b64encode(imgdata) self.results['imgdata'] = bytesarray def process_results(self, results): -- cgit v1.2.3 From dca0dab44a40faecd39ad7a176674fd4389b1903 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 8 Oct 2020 22:39:52 +0300 Subject: Use built-in array as a named import * wqflask/wqflask/wgcna/wgcna_analysis.py (WGCNA.render_image): Use named import method. This is a workaround for using explicitly using "array" which conflicts with something else in the namespace. --- wqflask/wqflask/wgcna/wgcna_analysis.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/wgcna/wgcna_analysis.py b/wqflask/wqflask/wgcna/wgcna_analysis.py index 35fb3ec0..93742daf 100644 --- a/wqflask/wqflask/wgcna/wgcna_analysis.py +++ b/wqflask/wqflask/wgcna/wgcna_analysis.py @@ -4,8 +4,8 @@ import base64 import sys import rpy2.robjects as ro # R Objects import rpy2.rinterface as ri -import array +from array import array as arr from numpy import * from base.webqtlConfig import GENERATED_IMAGE_DIR from rpy2.robjects.packages import importr @@ -164,8 +164,8 @@ class WGCNA(object): print(("pre-loading imgage results:", self.results['imgloc'])) imgfile = open(self.results['imgloc'], 'rb') imgdata = imgfile.read() - bytesarray = array.array('B', imgB64) imgB64 = base64.b64encode(imgdata) + bytesarray = arr('B', imgB64) self.results['imgdata'] = bytesarray def process_results(self, results): -- cgit v1.2.3 From 8db56f2472aa8d2549ff9fb2045f257c0388f6cc Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Fri, 9 Oct 2020 01:03:15 +0300 Subject: Replace "ncores" with "nthreads" param to r_CTLscan --- wqflask/wqflask/ctl/ctl_analysis.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py index 2a2124ca..6ffba28f 100644 --- a/wqflask/wqflask/ctl/ctl_analysis.py +++ b/wqflask/wqflask/ctl/ctl_analysis.py @@ -143,7 +143,7 @@ class CTL(object): #r_write_table(rPheno, "~/outputGN/pheno.csv") # Perform the CTL scan - res = self.r_CTLscan(rGeno, rPheno, strategy = strategy, nperm = nperm, parametric = parametric, ncores = 6) + res = self.r_CTLscan(rGeno, rPheno, strategy = strategy, nperm = nperm, parametric = parametric, nthreads=6) # Get significant interactions significant = self.r_CTLsignificant(res, significance = significance) -- cgit v1.2.3 From f604c81a5cf501c39bf195159a5b1c70a97195dc Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Fri, 9 Oct 2020 01:04:03 +0300 Subject: Replace string concat("+") with python3's f-string --- wqflask/wqflask/ctl/ctl_analysis.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py index 6ffba28f..72b4f3a3 100644 --- a/wqflask/wqflask/ctl/ctl_analysis.py +++ b/wqflask/wqflask/ctl/ctl_analysis.py @@ -186,8 +186,8 @@ class CTL(object): self.addNode(gtT) self.addEdge(gtS, gtT, significant, x) - significant[0][x] = gtS.symbol + " (" + gtS.name + ")" # Update the trait name for the displayed table - significant[2][x] = gtT.symbol + " (" + gtT.name + ")" # Update the trait name for the displayed table + significant[0][x] = "{} ({})".format(gtS.symbol, gtS.name) # Update the trait name for the displayed table + significant[2][x] = "{} ({})".format(gtT.symbol, gtT.name) # Update the trait name for the displayed table self.elements = json.dumps(self.nodes_list + self.edges_list) -- cgit v1.2.3 From 4e786c530d231718773cb629d3cac7449314c151 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Fri, 9 Oct 2020 01:38:10 +0300 Subject: Update base64 conversion --- wqflask/wqflask/views.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 7fdc62e5..e8d17613 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -164,7 +164,7 @@ def tmp_page(img_path): logger.info("initial_start_vars:", initial_start_vars) imgfile = open(GENERATED_IMAGE_DIR + img_path, 'rb') imgdata = imgfile.read() - imgB64 = imgdata.encode("base64") + imgB64 = base64.b64encode(imgdata) bytesarray = array.array('B', imgB64) return render_template("show_image.html", img_base64 = bytesarray ) @@ -790,7 +790,7 @@ def mapping_results_page(): logger.info("initial_start_vars:", initial_start_vars) imgfile = open(TEMPDIR + img_path, 'rb') imgdata = imgfile.read() - imgB64 = imgdata.encode("base64") + imgB64 = base64.b64encode(imgdata) bytesarray = array.array('B', imgB64) result['pair_scan_array'] = bytesarray rendered_template = render_template("pair_scan_results.html", **result) -- cgit v1.2.3 From 16cd94dfa0e892576f1c566948b775b954f7f508 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Fri, 9 Oct 2020 03:04:30 +0300 Subject: Fix export function on traits and analysis page * wqflask/wqflask/views.py (export_trait_excel): Write data as bytes instead of strings. See: https://stackoverflow.com/questions/32075135/python-3-in-memory-zipfile-error-string-argument-expected-got-bytes * wqflask/wqflask/show_trait/export_trait_data.py: Convert cmp function into a key function. --- wqflask/wqflask/show_trait/export_trait_data.py | 4 ++-- wqflask/wqflask/views.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/show_trait/export_trait_data.py b/wqflask/wqflask/show_trait/export_trait_data.py index 2d76b935..f2132966 100644 --- a/wqflask/wqflask/show_trait/export_trait_data.py +++ b/wqflask/wqflask/show_trait/export_trait_data.py @@ -1,7 +1,7 @@ import simplejson as json from pprint import pformat as pf - +from functools import cmp_to_key from base.trait import create_trait from base import data_set @@ -46,7 +46,7 @@ def get_export_metadata(trait_id, dataset_name): def dict_to_sorted_list(dictionary): sorted_list = [item for item in list(dictionary.items())] - sorted_list = sorted(sorted_list, cmp=cmp_samples) + sorted_list = sorted(sorted_list, key=cmp_to_key(cmp_samples)) sorted_values = [item[1] for item in sorted_list] return sorted_values diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index e8d17613..c37be418 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -376,7 +376,7 @@ def export_trait_excel(): logger.info("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data))) - buff = io.StringIO() + buff = io.BytesIO() workbook = xlsxwriter.Workbook(buff, {'in_memory': True}) worksheet = workbook.add_worksheet() for i, row in enumerate(sample_data): -- cgit v1.2.3 From 1c987139736be4f855c49f4a2f9ce4abc497d9e2 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Mon, 12 Oct 2020 14:29:00 +0300 Subject: Wrap args of print statements correctly using braces * wqflask/wqflask/wgcna/wgcna_analysis.py: Update print statements by wrapping then in "()". Run: "2to3-3.8 -w wqflask/wqflask/wgcna/wgcna_analysis.py" --- wqflask/wqflask/wgcna/wgcna_analysis.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/wgcna/wgcna_analysis.py b/wqflask/wqflask/wgcna/wgcna_analysis.py index c6e03ec5..6bf75216 100644 --- a/wqflask/wqflask/wgcna/wgcna_analysis.py +++ b/wqflask/wqflask/wgcna/wgcna_analysis.py @@ -69,8 +69,8 @@ class WGCNA(object): self.r_enableWGCNAThreads() 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 contains the phenotype values we need to send to R @@ -125,14 +125,14 @@ class WGCNA(object): 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") # No power could be estimated self.results['Power'] = 1 else: -- cgit v1.2.3 From 2b782327281dc9ca586d1303a44418f8d42f76dd Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 13 Oct 2020 16:32:11 -0500 Subject: Changed styling in show_trait.html to use CSS instead * wqflask/wqflask/static/new/css/main.css - Added CSS for min-height in table cells with checkboxes, since this would apply to all tables throughout the site * wqflask/wqflask/static/new/css/show_trait.css - Added CSS for styling that was previous in show_trait.html * wqflask/wqflask/templates/show_trait.html - Replaced directly styling with classes --- wqflask/wqflask/static/new/css/main.css | 4 ++ wqflask/wqflask/static/new/css/show_trait.css | 32 ++++++++++++- wqflask/wqflask/templates/show_trait.html | 69 ++++++++++----------------- 3 files changed, 61 insertions(+), 44 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/static/new/css/main.css b/wqflask/wqflask/static/new/css/main.css index 097cd997..d5fb8a61 100644 --- a/wqflask/wqflask/static/new/css/main.css +++ b/wqflask/wqflask/static/new/css/main.css @@ -33,4 +33,8 @@ .collapsing { overflow: hidden!important; } +} + +.checkbox { + min-height: 20px; } \ No newline at end of file diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css index 92deab20..a9e85ee7 100644 --- a/wqflask/wqflask/static/new/css/show_trait.css +++ b/wqflask/wqflask/static/new/css/show_trait.css @@ -35,8 +35,13 @@ table.dataTable thead th, table.dataTable tfoot { padding: 4px 18px 4px 10px; } +/* Header for a column with a numeric value that should be right-aligned */ +table.dataTable thead th div.numeric_header { + text-align: right; +} + table.dataTable tbody td { - padding: 4px 15px 2px 10px; + padding: 2px 15px 0px 10px; } table.dataTable.cell-border tbody th, table.dataTable.cell-border tbody td { @@ -51,4 +56,29 @@ table.dataTable.cell-border tbody tr td:first-child { .glyphicon { position: relative; top: 2px; +} + +.trait_page_main_div { + min-width: 700px; +} + +table.dataTable tbody td.column_name-Checkbox { + padding: 3px 0px 0px 9px; + text-align: center; +} + +table.dataTable tbody td.column_name-Index { + padding: 2px 4px 0px 2px; + text-align: right; +} + +/* the column with +/- in it that appears in the table when there's an SE column */ +table.dataTable tbody td.column_name-PlusMinus { + padding-left: 2px; + padding-right: 2px; + text-align: center; +} + +table.dataTable tbody td.column_name-Value, table.dataTable tbody td.column_name-SE, table.dataTable tbody td.column_name-num_cases { + text-align: right; } \ No newline at end of file diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index ea881917..3d34b331 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -37,7 +37,7 @@ -
+
@@ -237,30 +237,22 @@ if (data.outlier) { $(row).addClass("outlier"); } - $('td', row).eq(0).attr("align", "center"); - $('td', row).eq(0).attr("style", "padding: 2px 0px 0px 2px;"); + $('td', row).eq(0).addClass("column_name-Checkbox") $('td', row).eq(1).addClass("column_name-Index") - $('td', row).eq(1).attr("align", "right"); - $('td', row).eq(1).attr("style", "padding: 2px 4px 0px 2px;"); $('td', row).eq(2).addClass("column_name-Sample") $('td', row).eq(3).addClass("column_name-Value") - $('td', row).eq(3).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;"); {% if sample_groups[0].se_exists() %} - $('td', row).eq(4).attr("align", "center"); - $('td', row).eq(4).attr("style", "padding-left: 2px; padding-right: 2px;"); - $('td', row).eq(5).addClass("column_name-SE") - $('td', row).eq(5).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;"); + $('td', row).eq(4).addClass("column_name-PlusMinus") + $('td', row).eq(5).addClass("column_name-SE value_column") {% if has_num_cases %} $('td', row).eq(6).addClass("column_name-num_cases") - $('td', row).eq(6).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;"); {% endif %} {% else %} {% if has_num_cases %} $('td', row).eq(4).addClass("column_name-num_cases") - $('td', row).eq(4).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;"); {% endif %} {% endif %} {% if sample_groups[0].attributes|length > 0 %} {% for attribute in sample_groups[0].attributes|sort() %} $('td', row).eq(attribute_start_pos + {{ loop.index }}).addClass("column_name-{{ sample_groups[0].attributes[attribute].name }}") - $('td', row).eq(attribute_start_pos + {{ loop.index }}).attr("style", "text-align: {{ sample_groups[0].attributes[attribute].alignment }}; padding-top: 2px; padding-bottom: 0px;") + $('td', row).eq(attribute_start_pos + {{ loop.index }}).attr("style", "text-align: {{ sample_groups[0].attributes[attribute].alignment }};") {% endfor %} {% endif %} }, @@ -271,7 +263,7 @@ 'orderDataType': "dom-checkbox", 'searchable' : false, 'render': function(data, type, row, meta) { - return '' + return '' } }, { @@ -289,15 +281,15 @@ } }, { - 'title': "
Value
", + 'title': "
Value
", 'orderDataType': "dom-input", 'type': "cust-txt", 'data': null, 'render': function(data, type, row, meta) { if (data.value == null) { - return '' + return '' } else { - return '' + return '' } } }{% if sample_groups[0].se_exists() %}, @@ -311,28 +303,28 @@ } }, { - 'title': "
SE
", + 'title': "
SE
", 'orderDataType': "dom-input", 'type': "cust-txt", 'data': null, 'render': function(data, type, row, meta) { if (data.variance == null) { - return '' + return '' } else { - return '' + return '' } } }{% endif %}{% if has_num_cases %}, { - 'title': "
N
", + 'title': "
N
", 'orderDataType': "dom-input", 'type': "cust-txt", 'data': null, 'render': function(data, type, row, meta) { if (data.num_cases == null || data.num_cases == undefined) { - return '' + return '' } else { - return '' + return '' } } }{% endif %}{% if sample_groups[0].attributes|length > 0 %}{% for attribute in sample_groups[0].attributes|sort() %}, @@ -387,25 +379,16 @@ if (data.outlier) { $(row).addClass("outlier"); } - $('td', row).eq(0).attr("align", "center"); - $('td', row).eq(0).attr("style", "padding: 2px 0px 0px 2px;"); $('td', row).eq(1).addClass("column_name-Index") - $('td', row).eq(1).attr("align", "right"); - $('td', row).eq(1).attr("style", "padding: 2px 4px 0px 2px;"); $('td', row).eq(2).addClass("column_name-Sample") $('td', row).eq(3).addClass("column_name-Value") - $('td', row).eq(3).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;"); {% if sample_groups[1].se_exists() %} - $('td', row).eq(4).attr("align", "center"); - $('td', row).eq(4).attr("style", "padding-left: 2px; padding-right: 2px;"); + $('td', row).eq(4).addClass("column_name-PlusMinus") $('td', row).eq(5).addClass("column_name-SE") - $('td', row).eq(5).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;"); {% if has_num_cases %} $('td', row).eq(6).addClass("column_name-num_cases") - $('td', row).eq(6).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;"); {% endif %} {% else %} {% if has_num_cases %} $('td', row).eq(4).addClass("column_name-num_cases") - $('td', row).eq(4).attr("style", "text-align: right; padding-top: 2px; padding-bottom: 0px;"); {% endif %} {% endif %} {% if sample_groups[1].attributes|length > 0 %} {% for attribute in sample_groups[1].attributes|sort() %} @@ -421,7 +404,7 @@ 'orderDataType': "dom-checkbox", 'searchable' : false, 'render': function(data, type, row, meta) { - return '' + return '' } }, { @@ -439,15 +422,15 @@ } }, { - 'title': "
Value
", + 'title': "
Value
", 'orderDataType': "dom-input", 'type': "cust-txt", 'data': null, 'render': function(data, type, row, meta) { if (data.value == null) { - return '' + return '' } else { - return '' + return '' } } }{% if sample_groups[1].se_exists() %}, @@ -461,28 +444,28 @@ } }, { - 'title': "
SE
", + 'title': "
SE
", 'orderDataType': "dom-input", 'type': "cust-txt", 'data': null, 'render': function(data, type, row, meta) { if (data.variance == null) { - return '' + return '' } else { - return '' + return '' } } }{% endif %}{% if has_num_cases %}, { - 'title': "
N
", + 'title': "
N
", 'orderDataType': "dom-input", 'type': "cust-txt", 'data': null, 'render': function(data, type, row, meta) { if (data.num_cases == null) { - return '' + return '' } else { - return '' + return '' } } }{% endif %}{% if sample_groups[1].attributes|length > 0 %}{% for attribute in sample_groups[1].attributes|sort() %}, -- cgit v1.2.3 From 794b176384dbe5a8c837a913f9a86f4d36adadcd Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 13 Oct 2020 16:41:32 -0500 Subject: Added styling from show_trait_details.html to show_trait.css * wqflask/wqflask/static/new/css/show_trait.css - Added the bottom margin styling for the div containing the buttons * wqflask/wqflask/templates/show_trait_details.html - Removed some unnecessary styling and moved the styling for .btn_toolbar to show_trait.css --- wqflask/wqflask/static/new/css/show_trait.css | 4 ++++ wqflask/wqflask/templates/show_trait_details.html | 12 ++++++------ 2 files changed, 10 insertions(+), 6 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css index a9e85ee7..671b3cf7 100644 --- a/wqflask/wqflask/static/new/css/show_trait.css +++ b/wqflask/wqflask/static/new/css/show_trait.css @@ -81,4 +81,8 @@ table.dataTable tbody td.column_name-PlusMinus { table.dataTable tbody td.column_name-Value, table.dataTable tbody td.column_name-SE, table.dataTable tbody td.column_name-num_cases { text-align: right; +} + +.btn_toolbar { + margin-bottom:15px; } \ No newline at end of file diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html index 4aced50c..d2999eef 100644 --- a/wqflask/wqflask/templates/show_trait_details.html +++ b/wqflask/wqflask/templates/show_trait_details.html @@ -1,20 +1,20 @@ - +
- + {% if this_trait.dataset.type == 'Publish' %} - + - + - + @@ -213,7 +213,7 @@ {% endif %}
GroupGroup {{ this_trait.dataset.group.species[0]|upper }}{{ this_trait.dataset.group.species[1:] }}: {{ this_trait.dataset.group.name }} group
Phenotype
{{ this_trait.description_fmt }}
{{ this_trait.description_fmt }}
Authors
{{ this_trait.authors }}
{{ this_trait.authors }}
Title
{{ this_trait.title }}
{{ this_trait.title }}
Journal
-
+
{% if this_trait.dataset.type == 'ProbeSet' or this_trait.dataset.type == 'Geno' %} -- cgit v1.2.3 From c32766556222b9f8167496268bc4011f77b60138 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 14 Oct 2020 14:43:23 -0500 Subject: Moved show_trait_statistics.html styling to show_trait.css and fixed a minor issue where not all figures had "Select Group:" before the group selection drop-down * wqflask/wqflask/static/new/css/show_trait.css - Moved styling from show_trait_statistic.html here * wqflask/wqflask/templates/show_trait_statistics.html - Replaced styling with classes, removed some unnecessary/unused styling, and added some missing label text --- wqflask/wqflask/static/new/css/show_trait.css | 14 +- .../wqflask/templates/show_trait_statistics.html | 247 ++++++++++----------- 2 files changed, 131 insertions(+), 130 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css index 671b3cf7..ade7128c 100644 --- a/wqflask/wqflask/static/new/css/show_trait.css +++ b/wqflask/wqflask/static/new/css/show_trait.css @@ -83,6 +83,18 @@ table.dataTable tbody td.column_name-Value, table.dataTable tbody td.column_name text-align: right; } -.btn_toolbar { +div.btn_toolbar { margin-bottom:15px; +} + +div.padding-20 { + padding: 20px; +} + +table.left-float { + float: left; +} + +div.margin-b-40 { + margin-bottom:40px; } \ No newline at end of file diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html index 7bdb3ef9..f7d93447 100644 --- a/wqflask/wqflask/templates/show_trait_statistics.html +++ b/wqflask/wqflask/templates/show_trait_statistics.html @@ -1,148 +1,137 @@
-
- - -
-
-
-
-
-
-
-
- {% if sample_groups|length != 1 %} - -

- {% endif %} -
-
-
-
+
+ +
+
+
+
- {% if num_values < 256 %} -
-
- {% if sample_groups|length != 1 %} - - {% endif %} - {% if sample_groups[0].attributes %} -
- -
- {% endif %} -
- - -
- -
-
-
+
+
+
+ {% if sample_groups|length != 1 %} + Select Group: + +

+ {% endif %} +
+
- {% endif %} -
-
- {% if sample_groups|length != 1 %} - Select Group: - + {% for group, pretty_group in sample_group_types.items() %} + + {% endfor %} + + {% endif %} + {% if sample_groups[0].attributes %} +
+ -
-
- {% endif %} - -
-
-
-
-
- More about Normal Probability Plots and more - about interpreting these plots from the glossary -
-
- -
-
-
-
+ {% endif %} +
+ +
-
-
-
-
+
+
-
- -
- - +
+ {% endif %} +
+
+ {% if sample_groups|length != 1 %} + Select Group: + +
+
+ {% endif %} + +
+
-
-
+
+
+ More about Normal Probability Plots and more + about interpreting these plots from the glossary
+
+
+
+
+
+
+
+
+
+
+
+
+ + +
+
+
+
+
- +
-
-- cgit v1.2.3 From fa79f3b05688a59cdf1c46170b63ebdd6e2ebf4b Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 14 Oct 2020 14:50:32 -0500 Subject: Changed a couple class names because it's probably dumb to include the pixels in the name since that might change later * wqflask/wqflask/static/new/css/show_trait.css - Changed a couple class names * wqflask/wqflask/templates/show_trait_statistics.html - Changed a couple class names --- wqflask/wqflask/static/new/css/show_trait.css | 4 ++-- wqflask/wqflask/templates/show_trait_statistics.html | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css index ade7128c..68aa34e2 100644 --- a/wqflask/wqflask/static/new/css/show_trait.css +++ b/wqflask/wqflask/static/new/css/show_trait.css @@ -87,7 +87,7 @@ div.btn_toolbar { margin-bottom:15px; } -div.padding-20 { +div.stats_form_div { padding: 20px; } @@ -95,6 +95,6 @@ table.left-float { float: left; } -div.margin-b-40 { +div.scatterplot_btn_div { margin-bottom:40px; } \ No newline at end of file diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html index f7d93447..7f50b7bc 100644 --- a/wqflask/wqflask/templates/show_trait_statistics.html +++ b/wqflask/wqflask/templates/show_trait_statistics.html @@ -27,12 +27,12 @@
-
+
-
+
{% if sample_groups|length != 1 %} Select Group: -- cgit v1.2.3 From 64158e2ff7df3f7d177a4a3a0b8d7ff9c8f7cfe5 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 14 Oct 2020 17:26:45 -0500 Subject: Converted show_trait_calculate_correlations.html to use CSS instead of styling in the template * wqflask/wqflask/static/new/css/show_trait.css - Added styling for elements in show_trait_calculate_correlations.html and changed a few existing class names to be more reasonable * wqflask/wqflask/templates/show_trait.html - Changed the class name for the main div * wqflask/wqflask/templates/show_trait_calculate_correlations.html - Substituted direct styling with CSS and changing some styling to make the correlation method descriptions keep a reasonable width and position * wqflask/wqflask/templates/show_trait_statistics.html - Changed some class names to be better --- wqflask/wqflask/static/new/css/show_trait.css | 57 +++- wqflask/wqflask/templates/show_trait.html | 2 +- .../show_trait_calculate_correlations.html | 295 ++++++++++----------- .../wqflask/templates/show_trait_statistics.html | 10 +- 4 files changed, 202 insertions(+), 162 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css index 68aa34e2..f20b840e 100644 --- a/wqflask/wqflask/static/new/css/show_trait.css +++ b/wqflask/wqflask/static/new/css/show_trait.css @@ -1,17 +1,17 @@ tr .outlier { - background-color: #ffff99; + background-color: #ffff99; } table.dataTable tbody tr.selected { - background-color: #ffee99; + background-color: #ffee99; } #bar_chart_container { - overflow-x:scroll; + overflow-x:scroll; } div.sample_group { - overflow: auto; # needed because it contains float dataTable wrapper + overflow: auto; # needed because it contains float dataTable wrapper } .js-plotly-plot .plotly .modebar { @@ -58,7 +58,7 @@ table.dataTable.cell-border tbody tr td:first-child { top: 2px; } -.trait_page_main_div { +.showtrait-main-div { min-width: 700px; } @@ -83,11 +83,12 @@ table.dataTable tbody td.column_name-Value, table.dataTable tbody td.column_name text-align: right; } -div.btn_toolbar { +div.btn-toolbar { margin-bottom:15px; } -div.stats_form_div { +/* div containing the form options for each segment of the trait page - correlations, statistics, mapping, etc */ +div.section-form-div { padding: 20px; } @@ -95,6 +96,46 @@ table.left-float { float: left; } -div.scatterplot_btn_div { +div.scatterplot-btn-div { margin-bottom:40px; +} + +div.correlation-main { + min-width: 1200px; +} + +div.correlation-options { + min-width: 700px; +} + +.min-expr-field { + width: 70px; +} + +span.p-range-container { + display: inline; +} + +div.p-range-slider { + width: 200px; + margin-left: 15px; +} + +span.p-range-lower { + margin-top: 5px; + font: 400 12px Arial; + color: #888; + display: inline-block; +} + +span.p-range-upper { + font: 400 12px Arial; + color: #888; + display: inline-block; + margin: 5px 0px 0px 170px; +} + +.corr-location { + width: 50px; + display: inline; } \ No newline at end of file diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index 3d34b331..599cef42 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -37,7 +37,7 @@ -
+
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html index 9420c9c6..00fdfc21 100644 --- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html +++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html @@ -1,149 +1,148 @@ -
-
-
- -
- -
- -
-
- -
- -
- -
-
- -
- -
- -
-
- -
- -
- -
-
- -
- -
- -
-
- {% if dataset.type != "Publish" %} -
- -
- -
-
-
- -
- - Chr:     - Mb:  to  - -
-
-
- {% endif %} -
- -
- - - -
- -                                     - - -
-
- -
- -
- -
-
+
+
+
+ +
+ +
+ +
+
+ +
+ +
+ +
+
+ +
+ +
+ +
+
+ +
+ +
+ +
+
+ +
+ +
+ +
+
+ {% if dataset.type != "Publish" %} +
+ +
+ +
+
+
+ +
+ + Chr:     + Mb:  to  + +
+
+
+ {% endif %} +
+ +
+ + + +
+ + + +
+
+ +
+ +
+ +
+
+
-
-
- - The Sample Correlation - is computed - between trait data and any - other traits in the sample database selected above. Use - Spearman - Rank - when the sample size is small (<20) or when there are influential outliers. - - - -
-
\ No newline at end of file +
+ + The Sample Correlation + is computed + between trait data and any + other traits in the sample database selected above. Use + Spearman + Rank + when the sample size is small (<20) or when there are influential outliers. + + + +
+
\ No newline at end of file diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html index 7f50b7bc..4f347d4e 100644 --- a/wqflask/wqflask/templates/show_trait_statistics.html +++ b/wqflask/wqflask/templates/show_trait_statistics.html @@ -27,12 +27,12 @@
-
+
-
+
{% if sample_groups|length != 1 %} Select Group: @@ -84,7 +84,7 @@
{% endif %}
-
+
{% if sample_groups|length != 1 %} Select Group: {% endif %} Yes   No -
@@ -338,22 +328,6 @@
- -
-- cgit v1.2.3 From 9d94339ea0fe9f04d1f5f5fcb70c743ab720086e Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 15 Oct 2020 14:04:53 -0500 Subject: Replaced styling from show_trait_transform_and_filter.html with CSS * wqflask/wqflask/static/new/css/show_trait.css - Added styles for elements in show_trait_transform_and_filter.html * wqflask/wqflask/templates/show_trait_transform_and_filter.html - Replaced styling in template with classes --- wqflask/wqflask/static/new/css/show_trait.css | 13 ++++++++++ .../templates/show_trait_transform_and_filter.html | 28 +++++++++++----------- 2 files changed, 27 insertions(+), 14 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css index f20b840e..f9c3dcd9 100644 --- a/wqflask/wqflask/static/new/css/show_trait.css +++ b/wqflask/wqflask/static/new/css/show_trait.css @@ -138,4 +138,17 @@ span.p-range-upper { .corr-location { width: 50px; display: inline; +} + +div.block-by-index-div { + margin-bottom: 10px; +} + +div.block-by-attribute-div { + margin-top:10px; + margin-bottom:10px; +} + +div.normalize-div { + margin-top:10px; } \ No newline at end of file diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html index b4118b04..3956a34f 100644 --- a/wqflask/wqflask/templates/show_trait_transform_and_filter.html +++ b/wqflask/wqflask/templates/show_trait_transform_and_filter.html @@ -5,7 +5,7 @@ needed.

-
+
{% for attribute in sample_groups[0].attributes %} @@ -47,18 +47,18 @@
-
- - +
+ +
    {% for mapping_method in dataset.group.mapping_names %} {% if mapping_method == "GEMMA" %} -
  • +
  • GEMMA
    • {% elif mapping_method == "R/qtl" %} -
  • +
  • R/qtl
    • {% elif mapping_method == "QTLReaper" %} -
  • +
  • Haley-Knott Regression
    • {% endif %} {% endfor %} -
{% for mapping_method in dataset.group.mapping_names %} {% if mapping_method == "GEMMA" %}
-
+
- -
- {% for item in chr_list %} {% endfor %} @@ -41,8 +38,8 @@
{% if genofiles and genofiles|length>0 %}
- -
+ +
+ +
+
- -
+ +
-
- - Select covariate(s) from a collection -
-
+ +
{% if g.user_session.num_collections < 1 %} No collections available. Please add traits to a collection to use them as covariates. {% else %} -
- - +
+ +
- + {% endif %}
-
+
@@ -97,20 +91,20 @@
{% elif mapping_method == "QTLReaper" %}
-
+
- -
-
- -
- {% for item in chr_list %} {% endfor %} @@ -119,9 +113,9 @@
{% if genofiles and genofiles|length>0 %}
- -
- {% for item in scales_in_geno[genofiles[0]['location']] %} {% endfor %} @@ -129,8 +123,8 @@
- -
+ +
+ +
+
- -
- -
-
-
- -
- {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %} - - {% else %} - - {% endif %} - Yes   No -
-
- -
- -
+ +
-
+
@@ -221,11 +194,11 @@
{% elif mapping_method == "R/qtl" %}
-
+
- -
- {% for item in chr_list %} {% endfor %} @@ -234,9 +207,9 @@
{% if genofiles and genofiles|length > 0 %}
- -
- {% for item in scales_in_geno[genofiles[0]['location']] %} {% endfor %} @@ -244,8 +217,8 @@
- -
+ +
{% if sample_groups[0].attributes|length > 0 %}
- -
+ +
{% endif %}
- -
- {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %} - - {% else %} - - {% endif %} - - + +
+ + +
- -
+ +
@@ -319,8 +288,8 @@
-
-
- {% for mapping_method in dataset.group.mapping_names %} - {% if mapping_method == "GEMMA" %} -
GEMMA
-
Maps traits with correction for kinship among samples using a linear mixed model method, and also allows users to fit multiple covariates such as sex, age, treatment, and genetic markers (PMID: 2453419, and GitHub code). GEMMA incorporates the Leave One Chromosome Out (LOCO) method to ensure that the correction for kinship does not remove useful genetic variance near each marker. Markers can be filtered to include only those with minor allele frequencies (MAF) above a threshold. The default MAF is 0.05.
- {% elif mapping_method == "R/qtl" %} -
R/qtl (version 1.44.9
-
The original R/qtl mapping package that supports classic experimental crosses including 4-parent F2 intercrosses (e.g., NIA ITP UM-HET3). R/qtl is ideal for populations that do not have complex kinship or admixture (PMID: 12724300). Both R/qtl as implemented here, and R/qtl2 (PMID: 30591514) are available as R suites.
- {% elif mapping_method == "QTLReaper" %} -
Haley-Knott Regression
-
Fast linear mapping method (PMID 16718932) works well with F2 intercrosses and backcrosses, but that is not recommended for complex or admixed populations (e.g., GWAS or heterogeneous stock studies) or for advanced intercrosses, recombinant inbred families, or diallel crosses. Interactive plots in GeneNetwork have relied on the fast HK mapping for two decades and we still use this method for mapping omics data sets and computing genome-wide permutation threshold (QTL Reaper code).
- {% endif %} - {% endfor %} -
-