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 --- wqflask/maintenance/gen_select_dataset.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'wqflask/maintenance/gen_select_dataset.py') 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]) -- 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/maintenance/gen_select_dataset.py') 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 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/maintenance/gen_select_dataset.py') 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 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/maintenance/gen_select_dataset.py') 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