diff options
Diffstat (limited to 'wqflask/utility')
| -rw-r--r-- | wqflask/utility/Plot.py | 251 | ||||
| -rw-r--r-- | wqflask/utility/TDCell.py | 6 | ||||
| -rw-r--r-- | wqflask/utility/THCell.py | 8 | ||||
| -rw-r--r-- | wqflask/utility/__init__.py | 10 | ||||
| -rw-r--r-- | wqflask/utility/after.py | 1 | ||||
| -rw-r--r-- | wqflask/utility/authentication_tools.py | 1 | ||||
| -rw-r--r-- | wqflask/utility/benchmark.py | 14 | ||||
| -rw-r--r-- | wqflask/utility/chunks.py | 2 | ||||
| -rw-r--r-- | wqflask/utility/corestats.py | 9 | ||||
| -rw-r--r-- | wqflask/utility/elasticsearch_tools.py | 19 | ||||
| -rw-r--r-- | wqflask/utility/external.py | 3 | ||||
| -rw-r--r-- | wqflask/utility/gen_geno_ob.py | 29 | ||||
| -rw-r--r-- | wqflask/utility/genofile_parser.py | 151 | ||||
| -rw-r--r-- | wqflask/utility/helper_functions.py | 2 | ||||
| -rw-r--r-- | wqflask/utility/logger.py | 38 | ||||
| -rw-r--r-- | wqflask/utility/pillow_utils.py | 6 | ||||
| -rw-r--r-- | wqflask/utility/redis_tools.py | 9 | ||||
| -rw-r--r-- | wqflask/utility/startup_config.py | 15 | ||||
| -rw-r--r-- | wqflask/utility/svg.py | 723 | ||||
| -rw-r--r-- | wqflask/utility/temp_data.py | 3 | ||||
| -rw-r--r-- | wqflask/utility/tools.py | 148 | ||||
| -rw-r--r-- | wqflask/utility/type_checking.py | 11 | ||||
| -rw-r--r-- | wqflask/utility/webqtlUtil.py | 65 |
23 files changed, 853 insertions, 671 deletions
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py index 61f408d2..9b2c6735 100644 --- a/wqflask/utility/Plot.py +++ b/wqflask/utility/Plot.py @@ -34,7 +34,7 @@ import utility.corestats as corestats from base import webqtlConfig from utility.pillow_utils import draw_rotated_text import utility.logger -logger = utility.logger.getLogger(__name__ ) +logger = utility.logger.getLogger(__name__) # ---- Define common colours ---- # BLUE = ImageColor.getrgb("blue") @@ -47,6 +47,7 @@ COUR_FILE = "./wqflask/static/fonts/courbd.ttf" TAHOMA_FILE = "./wqflask/static/fonts/tahoma.ttf" # ---- END: FONT FILES ---- # + def cformat(d, rank=0): 'custom string format' strD = "%2.6f" % d @@ -68,22 +69,24 @@ def cformat(d, rank=0): strD = '0.0' return strD + def frange(start, end=None, inc=1.0): "A faster range-like function that does accept float increments..." if end == None: end = start + 0.0 start = 0.0 else: - start += 0.0 # force it to be a float + start += 0.0 # force it to be a float count = int((end - start) / inc) if start + count * inc != end: - # Need to adjust the count. AFAICT, it always comes up one short. + # Need to adjust the count. AFAICT, it always comes up one short. count += 1 L = [start] * count for i in range(1, count): L[i] = start + i * inc return L + def find_outliers(vals): """Calculates the upper and lower bounds of a set of sample/case values @@ -119,154 +122,163 @@ def find_outliers(vals): # parameter: data is either object returned by reaper permutation function (called by MarkerRegressionPage.py) # or the first object returned by direct (pair-scan) permu function (called by DirectPlotPage.py) -def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLabel=None, YLabel=None, title=None, offset= (60, 20, 40, 40), zoom = 1): + + +def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLabel=None, YLabel=None, title=None, offset=(60, 20, 40, 40), zoom=1): im_drawer = ImageDraw.Draw(canvas) xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset plotWidth = canvas.size[0] - xLeftOffset - xRightOffset plotHeight = canvas.size[1] - yTopOffset - yBottomOffset - if plotHeight<=0 or plotWidth<=0: - return + if plotHeight <= 0 or plotWidth <= 0: + return if len(data) < 2: - return + return max_D = max(data) min_D = min(data) - #add by NL 06-20-2011: fix the error: when max_D is infinite, log function in detScale will go wrong - if max_D == float('inf') or max_D>webqtlConfig.MAXLRS: - max_D=webqtlConfig.MAXLRS #maximum LRS value + # add by NL 06-20-2011: fix the error: when max_D is infinite, log function in detScale will go wrong + if max_D == float('inf') or max_D > webqtlConfig.MAXLRS: + max_D = webqtlConfig.MAXLRS # maximum LRS value xLow, xTop, stepX = detScale(min_D, max_D) - #reduce data - #ZS: Used to determine number of bins for permutation output - step = ceil((xTop-xLow)/50.0) + # reduce data + # ZS: Used to determine number of bins for permutation output + step = ceil((xTop - xLow) / 50.0) j = xLow dataXY = [] Count = [] while j <= xTop: - dataXY.append(j) - Count.append(0) - j += step + dataXY.append(j) + Count.append(0) + j += step for i, item in enumerate(data): - if item == float('inf') or item>webqtlConfig.MAXLRS: - item = webqtlConfig.MAXLRS #maximum LRS value - j = int((item-xLow)/step) - Count[j] += 1 + if item == float('inf') or item > webqtlConfig.MAXLRS: + item = webqtlConfig.MAXLRS # maximum LRS value + 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) - yScale = plotHeight/(yTop-yLow) - barWidth = xScale*step + # draw data + xScale = plotWidth / (xTop - xLow) + yScale = plotHeight / (yTop - yLow) + barWidth = xScale * step for i, count in enumerate(Count): - if count: - xc = (dataXY[i]-xLow)*xScale+xLeftOffset - yc =-(count-yLow)*yScale+yTopOffset+plotHeight - im_drawer.rectangle( - xy=((xc+2, yc), (xc+barWidth-2, yTopOffset+plotHeight)), - outline=barColor, fill=barColor) - - #draw drawing region + if count: + xc = (dataXY[i] - xLow) * xScale + xLeftOffset + yc = -(count - yLow) * yScale + yTopOffset + plotHeight + im_drawer.rectangle( + xy=((xc + 2, yc), (xc + barWidth - 2, yTopOffset + plotHeight)), + outline=barColor, fill=barColor) + + # draw drawing region im_drawer.rectangle( - xy=((xLeftOffset, yTopOffset), (xLeftOffset+plotWidth, yTopOffset+plotHeight)) + xy=((xLeftOffset, yTopOffset), + (xLeftOffset + plotWidth, yTopOffset + plotHeight)) ) - #draw scale - 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)), - 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) - 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) - strY = "%d" %y - im_drawer.text( - text=strY, - 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) + # draw scale + 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)), + 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) + 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) + strY = "%d" % y + im_drawer.text( + text=strY, + 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) if XLabel: - im_drawer.text( - text=XLabel, - xy=(xLeftOffset+( - plotWidth-im_drawer.textsize(XLabel, font=labelFont)[0])/2.0, - yTopOffset+plotHeight+yBottomOffset-10), - font=labelFont, fill=labelColor) + im_drawer.text( + text=XLabel, + xy=(xLeftOffset + ( + plotWidth - im_drawer.textsize(XLabel, font=labelFont)[0]) / 2.0, + yTopOffset + plotHeight + yBottomOffset - 10), + 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), + yTopOffset + plotHeight - ( + plotHeight - im_drawer.textsize( + 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, - 20), - font=labelFont, fill=labelColor) + im_drawer.text( + text=title, + xy=(xLeftOffset + (plotWidth - im_drawer.textsize( + title, font=labelFont)[0]) / 2.0, + 20), + font=labelFont, fill=labelColor) # This function determines the scale of the plot + + def detScaleOld(min, max): - if min>=max: + if min >= max: return None elif min == -1.0 and max == 1.0: return [-1.2, 1.2, 12] else: - a=max-min - b=floor(log10(a)) - 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)] - -def detScale(min=0,max=0): - - if min>=max: + a = max - min + b = floor(log10(a)) + 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)] + + +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] else: - a=max-min + a = max - min if max != 0: - max += 0.1*a + max += 0.1 * a if min != 0: - if min > 0 and min < 0.1*a: + if min > 0 and min < 0.1 * a: min = 0.0 else: - min -= 0.1*a - a=max-min - b=floor(log10(a)) - c=pow(10.0, b) - low=c*floor(min/c) - high=c*ceil(max/c) - n = round((high-low)/c) + min -= 0.1 * a + a = max - min + b = floor(log10(a)) + c = pow(10.0, b) + low = c * floor(min / c) + high = c * ceil(max / c) + n = round((high - low) / c) div = 2.0 while n < 5 or n > 15: if n < 5: @@ -274,23 +286,27 @@ def detScale(min=0,max=0): else: c *= div if div == 2.0: - div =5.0 + div = 5.0 else: - div =2.0 - low=c*floor(min/c) - high=c*ceil(max/c) - n = round((high-low)/c) + div = 2.0 + low = c * floor(min / c) + high = c * ceil(max / c) + n = round((high - low) / c) return [low, high, n] + def bluefunc(x): - return 1.0 / (1.0 + exp(-10*(x-0.6))) + return 1.0 / (1.0 + exp(-10 * (x - 0.6))) + def redfunc(x): - return 1.0 / (1.0 + exp(10*(x-0.5))) + 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 @@ -303,26 +319,27 @@ def colorSpectrum(n=100): return [ImageColor.getrgb("rgb(100%,0%,0%)"), ImageColor.getrgb("rgb(0%,100%,0%)"), ImageColor.getrgb("rgb(0%,0%,100%)")] - N = n*multiple - out = [None]*N; + N = n * multiple + out = [None] * N for i in range(N): - x = float(i)/N + x = float(i) / N out[i] = ImageColor.getrgb("rgb({}%,{}%,{}%".format( - *[int(i*100) for i in ( + *[int(i * 100) for i in ( redfunc(x), greenfunc(x), bluefunc(x))])) out2 = [out[0]] - step = N/float(n-1) + step = N / float(n - 1) j = 0 - for i in range(n-2): + for i in range(n - 2): j += step out2.append(out[int(j)]) out2.append(out[-1]) return out2 + def _test(): import doctest doctest.testmod() -if __name__=="__main__": +if __name__ == "__main__": _test() diff --git a/wqflask/utility/TDCell.py b/wqflask/utility/TDCell.py index 8de8e050..4b0f4b1d 100644 --- a/wqflask/utility/TDCell.py +++ b/wqflask/utility/TDCell.py @@ -33,9 +33,9 @@ class TDCell: def __init__(self, html="", text="", val=0.0): - self.html = html #html, for web page - self.text = text #text value, for output to a text file - self.val = val #sort by value + self.html = html # html, for web page + self.text = text # text value, for output to a text file + self.val = val # sort by value def __str__(self): return self.text diff --git a/wqflask/utility/THCell.py b/wqflask/utility/THCell.py index dde221b5..f533dcb8 100644 --- a/wqflask/utility/THCell.py +++ b/wqflask/utility/THCell.py @@ -33,10 +33,10 @@ class THCell: def __init__(self, html="", text="", sort=1, idx=-1): - self.html = html #html, for web page - self.text = text #Column text value - self.sort = sort #0: not sortable, 1: yes - self.idx = idx #sort by value + self.html = html # html, for web page + self.text = text # Column text value + self.sort = sort # 0: not sortable, 1: yes + self.idx = idx # sort by value def __str__(self): return self.text diff --git a/wqflask/utility/__init__.py b/wqflask/utility/__init__.py index df926884..25273fa0 100644 --- a/wqflask/utility/__init__.py +++ b/wqflask/utility/__init__.py @@ -2,10 +2,12 @@ from pprint import pformat as pf # Todo: Move these out of __init__ + class Bunch: """Like a dictionary but using object notation""" - def __init__(self, **kw): - self.__dict__ = kw + + def __init__(self, **kw): + self.__dict__ = kw def __repr__(self): return pf(self.__dict__) @@ -30,6 +32,4 @@ class Struct: def __repr__(self): return '{%s}' % str(', '.join('%s : %s' % (k, repr(v)) for - (k, v) in list(self.__dict__.items()))) - - + (k, v) in list(self.__dict__.items()))) diff --git a/wqflask/utility/after.py b/wqflask/utility/after.py index 06091ecb..2b560e48 100644 --- a/wqflask/utility/after.py +++ b/wqflask/utility/after.py @@ -7,6 +7,7 @@ from flask import g from wqflask import app + def after_this_request(f): if not hasattr(g, 'after_request_callbacks'): g.after_request_callbacks = [] diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py index 672b36d5..57dbf8ba 100644 --- a/wqflask/utility/authentication_tools.py +++ b/wqflask/utility/authentication_tools.py @@ -11,6 +11,7 @@ from utility.redis_tools import (get_redis_conn, add_resource) Redis = get_redis_conn() + def check_resource_availability(dataset, trait_id=None): # At least for now assume temporary entered traits are accessible if type(dataset) == str or dataset.type == "Temp": diff --git a/wqflask/utility/benchmark.py b/wqflask/utility/benchmark.py index 91ea91e8..6ece2f21 100644 --- a/wqflask/utility/benchmark.py +++ b/wqflask/utility/benchmark.py @@ -4,7 +4,8 @@ import time from utility.tools import LOG_BENCH from utility.logger import getLogger -logger = getLogger(__name__ ) +logger = getLogger(__name__) + class Bench: entries = collections.OrderedDict() @@ -18,7 +19,8 @@ class Bench: if self.name: logger.debug("Starting benchmark: %s" % (self.name)) else: - logger.debug("Starting benchmark at: %s [%i]" % (inspect.stack()[1][3], inspect.stack()[1][2])) + logger.debug("Starting benchmark at: %s [%i]" % ( + inspect.stack()[1][3], inspect.stack()[1][2])) self.start_time = time.time() def __exit__(self, type, value, traceback): @@ -32,14 +34,16 @@ class Bench: logger.info(" %s took: %f seconds" % (name, (time_taken))) if self.name: - Bench.entries[self.name] = Bench.entries.get(self.name, 0) + time_taken + Bench.entries[self.name] = Bench.entries.get( + self.name, 0) + time_taken @classmethod def report(cls): - total_time = sum((time_taken for time_taken in list(cls.entries.values()))) + total_time = sum( + (time_taken for time_taken in list(cls.entries.values()))) print("\nTiming report\n") for name, time_taken in list(cls.entries.items()): - percent = int(round((time_taken/total_time) * 100)) + percent = int(round((time_taken / total_time) * 100)) print("[{}%] {}: {}".format(percent, name, time_taken)) print() diff --git a/wqflask/utility/chunks.py b/wqflask/utility/chunks.py index 9a7db102..484b5de6 100644 --- a/wqflask/utility/chunks.py +++ b/wqflask/utility/chunks.py @@ -26,6 +26,6 @@ def divide_into_chunks(the_list, number_chunks): chunks = [] for counter in range(0, length, chunksize): - chunks.append(the_list[counter:counter+chunksize]) + chunks.append(the_list[counter:counter + chunksize]) return chunks diff --git a/wqflask/utility/corestats.py b/wqflask/utility/corestats.py index 67ca3ad3..da0a21db 100644 --- a/wqflask/utility/corestats.py +++ b/wqflask/utility/corestats.py @@ -15,7 +15,9 @@ import sys -#ZS: Should switch to using some third party library for this; maybe scipy has an equivalent +# ZS: Should switch to using some third party library for this; maybe scipy has an equivalent + + class Stats: def __init__(self, sequence): @@ -63,7 +65,8 @@ class Stats: if len(self.sequence) < 1: value = None elif (percentile >= 100): - sys.stderr.write('ERROR: percentile must be < 100. you supplied: %s\n'% percentile) + sys.stderr.write( + 'ERROR: percentile must be < 100. you supplied: %s\n' % percentile) value = None else: element_idx = int(len(self.sequence) * (percentile / 100.0)) @@ -80,4 +83,4 @@ class Stats: # stats = corestats.Stats(sequence) # print stats.avg() # print stats.percentile(90) -# -------------------------------------------
\ No newline at end of file +# ------------------------------------------- diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py index a5580811..eae3ba03 100644 --- a/wqflask/utility/elasticsearch_tools.py +++ b/wqflask/utility/elasticsearch_tools.py @@ -47,11 +47,14 @@ logger = getLogger(__name__) from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT + def test_elasticsearch_connection(): - es = Elasticsearch(['http://'+ELASTICSEARCH_HOST+":"+str(ELASTICSEARCH_PORT)+'/'], verify_certs=True) + es = Elasticsearch(['http://' + ELASTICSEARCH_HOST + \ + ":" + str(ELASTICSEARCH_PORT) + '/'], verify_certs=True) if not es.ping(): logger.warning("Elasticsearch is DOWN") + def get_elasticsearch_connection(for_user=True): """Return a connection to ES. Returns None on failure""" logger.info("get_elasticsearch_connection") @@ -77,6 +80,7 @@ def get_elasticsearch_connection(for_user=True): return es + def setup_users_index(es_connection): if es_connection: index_settings = { @@ -85,20 +89,24 @@ def setup_users_index(es_connection): "type": "keyword"}}} es_connection.indices.create(index='users', ignore=400) - es_connection.indices.put_mapping(body=index_settings, index="users", doc_type="local") + es_connection.indices.put_mapping( + body=index_settings, index="users", doc_type="local") + def get_user_by_unique_column(es, column_name, column_value, index="users", doc_type="local"): return get_item_by_unique_column(es, column_name, column_value, index=index, doc_type=doc_type) + def save_user(es, user, user_id): es_save_data(es, "users", "local", user, user_id) + def get_item_by_unique_column(es, column_name, column_value, index, doc_type): item_details = None try: response = es.search( - index = index, doc_type = doc_type, body = { - "query": { "match": { column_name: column_value } } + index=index, doc_type=doc_type, body={ + "query": {"match": {column_name: column_value}} }) if len(response["hits"]["hits"]) > 0: item_details = response["hits"]["hits"][0]["_source"] @@ -106,7 +114,8 @@ def get_item_by_unique_column(es, column_name, column_value, index, doc_type): pass return item_details + def es_save_data(es, index, doc_type, data_item, data_id,): from time import sleep es.create(index, doc_type, body=data_item, id=data_id) - sleep(1) # Delay 1 second to allow indexing + sleep(1) # Delay 1 second to allow indexing diff --git a/wqflask/utility/external.py b/wqflask/utility/external.py index 50afea08..805d2ffe 100644 --- a/wqflask/utility/external.py +++ b/wqflask/utility/external.py @@ -4,6 +4,7 @@ import os import sys import subprocess + def shell(command): if subprocess.call(command, shell=True) != 0: - raise Exception("ERROR: failed on "+command) + raise Exception("ERROR: failed on " + command) diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py index 0a381c9b..e619b7b6 100644 --- a/wqflask/utility/gen_geno_ob.py +++ b/wqflask/utility/gen_geno_ob.py @@ -1,5 +1,6 @@ import utility.logger -logger = utility.logger.getLogger(__name__ ) +logger = utility.logger.getLogger(__name__) + class genotype: """ @@ -18,7 +19,7 @@ class genotype: self.filler = False self.mb_exists = False - #ZS: This is because I'm not sure if some files switch the column that contains Mb/cM positions; might be unnecessary + # ZS: This is because I'm not sure if some files switch the column that contains Mb/cM positions; might be unnecessary self.cm_column = 2 self.mb_column = 3 @@ -36,14 +37,16 @@ class genotype: return len(self.chromosomes) def read_rdata_output(self, qtl_results): - #ZS: This is necessary because R/qtl requires centimorgan marker positions, which it normally gets from the .geno file, but that doesn't exist for HET3-ITP (which only has RData), so it needs to read in the marker cM positions from the results - self.chromosomes = [] #ZS: Overwriting since the .geno file's contents are just placeholders + # ZS: This is necessary because R/qtl requires centimorgan marker positions, which it normally gets from the .geno file, but that doesn't exist for HET3-ITP (which only has RData), so it needs to read in the marker cM positions from the results + # ZS: Overwriting since the .geno file's contents are just placeholders + self.chromosomes = [] - this_chr = "" #ZS: This is so it can track when the chromosome changes as it iterates through markers + this_chr = "" # ZS: This is so it can track when the chromosome changes as it iterates through markers chr_ob = None for marker in qtl_results: locus = Locus(self) - if (str(marker['chr']) != this_chr) and this_chr != "X": #ZS: This is really awkward but works as a temporary fix + # ZS: This is really awkward but works as a temporary fix + if (str(marker['chr']) != this_chr) and this_chr != "X": if this_chr != "": self.chromosomes.append(chr_ob) this_chr = str(marker['chr']) @@ -68,7 +71,7 @@ class genotype: with open(filename, 'r') as geno_file: lines = geno_file.readlines() - this_chr = "" #ZS: This is so it can track when the chromosome changes as it iterates through markers + this_chr = "" # ZS: This is so it can track when the chromosome changes as it iterates through markers chr_ob = None for line in lines: if line[0] == "#": @@ -119,6 +122,7 @@ class genotype: self.chromosomes.append(chr_ob) + class Chr: def __init__(self, name, geno_ob): self.name = name @@ -140,8 +144,9 @@ class Chr: def add_marker(self, marker_row): self.loci.append(Locus(self.geno_ob, marker_row)) + class Locus: - def __init__(self, geno_ob, marker_row = None): + def __init__(self, geno_ob, marker_row=None): self.chr = None self.name = None self.cM = None @@ -153,9 +158,11 @@ class Locus: try: self.cM = float(marker_row[geno_ob.cm_column]) except: - self.cM = float(marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else 0 + self.cM = float( + marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else 0 try: - self.Mb = float(marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else None + self.Mb = float( + marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else None except: self.Mb = self.cM @@ -175,5 +182,5 @@ class Locus: for allele in marker_row[start_pos:]: 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 + else: # ZS: Some genotype appears that isn't specified in the metadata, make it unknown self.genotype.append("U") diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py index f8e96d19..86d9823e 100644 --- a/wqflask/utility/genofile_parser.py +++ b/wqflask/utility/genofile_parser.py @@ -12,88 +12,89 @@ import simplejson as json from pprint import pformat as pf + class Marker: - def __init__(self): - self.name = None - self.chr = None - self.cM = None - self.Mb = None - self.genotypes = [] + def __init__(self): + self.name = None + self.chr = None + self.cM = None + self.Mb = None + self.genotypes = [] class ConvertGenoFile: - def __init__(self, input_file): - self.mb_exists = False - self.cm_exists = False - self.markers = [] - - self.latest_row_pos = None - self.latest_col_pos = None + def __init__(self, input_file): + self.mb_exists = False + self.cm_exists = False + self.markers = [] - self.latest_row_value = None - self.latest_col_value = None - self.input_fh = open(input_file) - print("!!!!!!!!!!!!!!!!PARSER!!!!!!!!!!!!!!!!!!") - self.haplotype_notation = { - '@mat': "1", - '@pat': "2", - '@het': "-999", - '@unk': "-999" - } - self.configurations = {} + self.latest_row_pos = None + self.latest_col_pos = None - def process_rows(self): - for self.latest_row_pos, row in enumerate(self.input_fh): - self.latest_row_value = row - # Take care of headers - if not row.strip(): - continue - if row.startswith('#'): - continue - if row.startswith('Chr'): - if 'Mb' in row.split(): - self.mb_exists = True - if 'cM' in row.split(): - self.cm_exists = True - skip = 2 + self.cm_exists + self.mb_exists - self.individuals = row.split()[skip:] - continue - if row.startswith('@'): - key, _separater, value = row.partition(':') - key = key.strip() - value = value.strip() - if key in self.haplotype_notation: - self.configurations[value] = self.haplotype_notation[key] - continue - if not len(self.configurations): - raise EmptyConfigurations - yield row + self.latest_row_value = None + self.latest_col_value = None + self.input_fh = open(input_file) + print("!!!!!!!!!!!!!!!!PARSER!!!!!!!!!!!!!!!!!!") + self.haplotype_notation = { + '@mat': "1", + '@pat': "2", + '@het': "-999", + '@unk': "-999" + } + self.configurations = {} - def process_csv(self): - for row in self.process_rows(): - row_items = row.split("\t") + def process_rows(self): + for self.latest_row_pos, row in enumerate(self.input_fh): + self.latest_row_value = row + # Take care of headers + if not row.strip(): + continue + if row.startswith('#'): + continue + if row.startswith('Chr'): + if 'Mb' in row.split(): + self.mb_exists = True + if 'cM' in row.split(): + self.cm_exists = True + skip = 2 + self.cm_exists + self.mb_exists + self.individuals = row.split()[skip:] + continue + if row.startswith('@'): + key, _separater, value = row.partition(':') + key = key.strip() + value = value.strip() + if key in self.haplotype_notation: + self.configurations[value] = self.haplotype_notation[key] + continue + if not len(self.configurations): + raise EmptyConfigurations + yield row - this_marker = Marker() - this_marker.name = row_items[1] - this_marker.chr = row_items[0] - if self.cm_exists and self.mb_exists: - this_marker.cM = row_items[2] - this_marker.Mb = row_items[3] - genotypes = row_items[4:] - elif self.cm_exists: - this_marker.cM = row_items[2] - genotypes = row_items[3:] - elif self.mb_exists: - this_marker.Mb = row_items[2] - genotypes = row_items[3:] - else: - genotypes = row_items[2:] - for item_count, genotype in enumerate(genotypes): - if genotype.upper().strip() in self.configurations: - this_marker.genotypes.append(self.configurations[genotype.upper().strip()]) - else: - print("WARNING:", genotype.upper()) - this_marker.genotypes.append("NA") - self.markers.append(this_marker.__dict__) + def process_csv(self): + for row in self.process_rows(): + row_items = row.split("\t") + this_marker = Marker() + this_marker.name = row_items[1] + this_marker.chr = row_items[0] + if self.cm_exists and self.mb_exists: + this_marker.cM = row_items[2] + this_marker.Mb = row_items[3] + genotypes = row_items[4:] + elif self.cm_exists: + this_marker.cM = row_items[2] + genotypes = row_items[3:] + elif self.mb_exists: + this_marker.Mb = row_items[2] + genotypes = row_items[3:] + else: + genotypes = row_items[2:] + for item_count, genotype in enumerate(genotypes): + if genotype.upper().strip() in self.configurations: + this_marker.genotypes.append( + self.configurations[genotype.upper().strip()]) + else: + print("WARNING:", genotype.upper()) + this_marker.genotypes.append("NA") + self.markers.append(this_marker.__dict__) diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py index 12fd6be5..ecc075ae 100644 --- a/wqflask/utility/helper_functions.py +++ b/wqflask/utility/helper_functions.py @@ -39,7 +39,7 @@ def get_trait_db_obs(self, trait_db_list): for trait in trait_db_list: data, _separator, hmac_string = trait.rpartition(':') data = data.strip() - assert hmac_string==hmac.hmac_creation(data), "Data tampering?" + assert hmac_string == hmac.hmac_creation(data), "Data tampering?" trait_name, dataset_name = data.split(":")[:2] if dataset_name == "Temp": dataset_ob = data_set.create_dataset( diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py index e904eb94..d706e32a 100644 --- a/wqflask/utility/logger.py +++ b/wqflask/utility/logger.py @@ -35,6 +35,7 @@ import datetime from utility.tools import LOG_LEVEL, LOG_LEVEL_DEBUG, LOG_SQL + class GNLogger: """A logger class with some additional functionality, such as multiple parameter logging, SQL logging, timing, colors, and lazy @@ -49,14 +50,14 @@ class GNLogger: """Set the undelying log level""" self.logger.setLevel(value) - def debug(self,*args): + def debug(self, *args): """Call logging.debug for multiple args. Use (lazy) debugf and level=num to filter on LOG_LEVEL_DEBUG. """ self.collect(self.logger.debug, *args) - def debug20(self,*args): + def debug20(self, *args): """Call logging.debug for multiple args. Use level=num to filter on LOG_LEVEL_DEBUG (NYI). @@ -65,29 +66,29 @@ LOG_LEVEL_DEBUG (NYI). if self.logger.getEffectiveLevel() < 20: self.collect(self.logger.debug, *args) - def info(self,*args): + def info(self, *args): """Call logging.info for multiple args""" self.collect(self.logger.info, *args) - def warning(self,*args): + def warning(self, *args): """Call logging.warning for multiple args""" self.collect(self.logger.warning, *args) # self.logger.warning(self.collect(*args)) - def error(self,*args): + def error(self, *args): """Call logging.error for multiple args""" now = datetime.datetime.utcnow() time_str = now.strftime('%H:%M:%S UTC %Y%m%d') - l = [time_str]+list(args) + l = [time_str] + list(args) self.collect(self.logger.error, *l) - def infof(self,*args): + 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) - def debugf(self,level=0,*args): + def debugf(self, level=0, *args): """Call logging.debug for multiple args lazily and handle LOG_LEVEL_DEBUG correctly @@ -97,7 +98,7 @@ LOG_LEVEL_DEBUG (NYI). if self.logger.getEffectiveLevel() < 20: self.collectf(self.logger.debug, *args) - def sql(self, sqlcommand, fun = None): + def sql(self, sqlcommand, fun=None): """Log SQL command, optionally invoking a timed fun""" if LOG_SQL: caller = stack()[1][3] @@ -110,11 +111,11 @@ LOG_LEVEL_DEBUG (NYI). self.info(result) return result - def collect(self,fun,*args): + def collect(self, fun, *args): """Collect arguments and use fun to output""" - out = "."+stack()[2][3] + out = "." + stack()[2][3] for a in args: - if len(out)>1: + if len(out) > 1: out += ": " if isinstance(a, str): out = out + a @@ -122,11 +123,11 @@ LOG_LEVEL_DEBUG (NYI). out = out + pf(a, width=160) fun(out) - def collectf(self,fun,*args): + def collectf(self, fun, *args): """Collect arguments and use fun to output one by one""" - out = "."+stack()[2][3] + out = "." + stack()[2][3] for a in args: - if len(out)>1: + if len(out) > 1: out += ": " if isfunction(a): out += a() @@ -139,7 +140,9 @@ LOG_LEVEL_DEBUG (NYI). # Get the module logger. You can override log levels at the # module level -def getLogger(name, level = None): + + +def getLogger(name, level=None): gnlogger = GNLogger(name) logger = gnlogger.logger @@ -148,5 +151,6 @@ def getLogger(name, level = None): else: logger.setLevel(LOG_LEVEL) - logger.info("Log level of "+name+" set to "+logging.getLevelName(logger.getEffectiveLevel())) + logger.info("Log level of " + name + " set to " + \ + logging.getLevelName(logger.getEffectiveLevel())) return gnlogger diff --git a/wqflask/utility/pillow_utils.py b/wqflask/utility/pillow_utils.py index c486abba..5713e155 100644 --- a/wqflask/utility/pillow_utils.py +++ b/wqflask/utility/pillow_utils.py @@ -3,12 +3,14 @@ from PIL import Image, ImageColor, ImageDraw, ImageFont from utility.tools import TEMPDIR import utility.logger -logger = utility.logger.getLogger(__name__ ) +logger = utility.logger.getLogger(__name__) BLACK = ImageColor.getrgb("black") WHITE = ImageColor.getrgb("white") # def draw_rotated_text(canvas: Image, text: str, font: ImageFont, xy: tuple, fill: ImageColor=BLACK, angle: int=-90): + + def draw_rotated_text(canvas, text, font, xy, fill=BLACK, angle=-90): # type: (Image, str, ImageFont, tuple, ImageColor, int) """Utility function draw rotated text""" @@ -20,6 +22,8 @@ def draw_rotated_text(canvas, text, font, xy, fill=BLACK, angle=-90): canvas.paste(im=tmp_img2, box=tuple([int(i) for i in xy])) # def draw_open_polygon(canvas: Image, xy: tuple, fill: ImageColor=WHITE, outline: ImageColor=BLACK): + + def draw_open_polygon(canvas, xy, fill=None, outline=BLACK, width=0): # type: (Image, tuple, ImageColor, ImageColor) draw_ctx = ImageDraw.Draw(canvas) diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py index 8052035f..96a4be12 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -133,8 +133,10 @@ def get_user_groups(user_id): for key in groups_list: try: group_ob = json.loads(groups_list[key]) - group_admins = set([this_admin.encode('utf-8') if this_admin else None for this_admin in group_ob['admins']]) - group_members = set([this_member.encode('utf-8') if this_member else None for this_member in group_ob['members']]) + group_admins = set([this_admin.encode( + 'utf-8') if this_admin else None for this_admin in group_ob['admins']]) + group_members = set([this_member.encode( + 'utf-8') if this_member else None for this_member in group_ob['members']]) if user_id in group_admins: admin_group_ids.append(group_ob['id']) elif user_id in group_members: @@ -203,7 +205,8 @@ def get_groups_like_unique_column(column_name, column_value): if column_value in group_info[column_name]: matched_groups.append(group_info) else: - matched_groups.append(load_json_from_redis(group_list, column_value)) + matched_groups.append( + load_json_from_redis(group_list, column_value)) return matched_groups diff --git a/wqflask/utility/startup_config.py b/wqflask/utility/startup_config.py index f1aaebb6..6ef759e0 100644 --- a/wqflask/utility/startup_config.py +++ b/wqflask/utility/startup_config.py @@ -3,12 +3,13 @@ from wqflask import app from utility.tools import WEBSERVER_MODE, show_settings, get_setting_int, get_setting, get_setting_bool import utility.logger -logger = utility.logger.getLogger(__name__ ) +logger = utility.logger.getLogger(__name__) -BLUE = '\033[94m' +BLUE = '\033[94m' GREEN = '\033[92m' -BOLD = '\033[1m' -ENDC = '\033[0m' +BOLD = '\033[1m' +ENDC = '\033[0m' + def app_config(): app.config['SESSION_TYPE'] = 'filesystem' @@ -27,7 +28,8 @@ def app_config(): port = get_setting_int("SERVER_PORT") if get_setting_bool("USE_GN_SERVER"): - print(("GN2 API server URL is ["+BLUE+get_setting("GN_SERVER_URL")+ENDC+"]")) + print( + ("GN2 API server URL is [" + BLUE + get_setting("GN_SERVER_URL") + ENDC + "]")) import requests page = requests.get(get_setting("GN_SERVER_URL")) if page.status_code != 200: @@ -36,4 +38,5 @@ 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 b92cc2d1..eddb97da 100644 --- a/wqflask/utility/svg.py +++ b/wqflask/utility/svg.py @@ -172,7 +172,7 @@ def _viewboxlist(a): """formats a tuple""" s = '' for e in a: - s += str(e)+' ' + s += str(e) + ' ' return s @@ -189,7 +189,7 @@ class pathdata: def __init__(self, x=None, y=None): self.path = [] if x is not None and y is not None: - self.path.append('M '+str(x)+' '+str(y)) + self.path.append('M ' + str(x) + ' ' + str(y)) def closepath(self): """ends the path""" @@ -197,79 +197,83 @@ class pathdata: def move(self, x, y): """move to absolute""" - self.path.append('M '+str(x)+' '+str(y)) + self.path.append('M ' + str(x) + ' ' + str(y)) def relmove(self, x, y): """move to relative""" - self.path.append('m '+str(x)+' '+str(y)) + self.path.append('m ' + str(x) + ' ' + str(y)) def line(self, x, y): """line to absolute""" - self.path.append('L '+str(x)+' '+str(y)) + self.path.append('L ' + str(x) + ' ' + str(y)) def relline(self, x, y): """line to relative""" - self.path.append('l '+str(x)+' '+str(y)) + self.path.append('l ' + str(x) + ' ' + str(y)) def hline(self, x): """horizontal line to absolute""" - self.path.append('H'+str(x)) + self.path.append('H' + str(x)) def relhline(self, x): """horizontal line to relative""" - self.path.append('h'+str(x)) + self.path.append('h' + str(x)) def vline(self, y): """verical line to absolute""" - self.path.append('V'+str(y)) + self.path.append('V' + str(y)) def relvline(self, y): """vertical line to relative""" - self.path.append('v'+str(y)) + self.path.append('v' + str(y)) def bezier(self, x1, y1, x2, y2, x, y): """bezier with xy1 and xy2 to xy absolut""" - self.path.append('C'+str(x1)+','+str(y1)+' '+str(x2) + - ','+str(y2)+' '+str(x)+','+str(y)) + self.path.append('C' + str(x1) + ',' + str(y1) + ' ' + str(x2) + + ',' + str(y2) + ' ' + str(x) + ',' + str(y)) def relbezier(self, x1, y1, x2, y2, x, y): """bezier with xy1 and xy2 to xy relative""" - self.path.append('c'+str(x1)+','+str(y1)+' '+str(x2) + - ','+str(y2)+' '+str(x)+','+str(y)) + self.path.append('c' + str(x1) + ',' + str(y1) + ' ' + str(x2) + + ',' + str(y2) + ' ' + str(x) + ',' + str(y)) def smbezier(self, x2, y2, x, y): """smooth bezier with xy2 to xy absolut""" - self.path.append('S'+str(x2)+','+str(y2)+' '+str(x)+','+str(y)) + self.path.append('S' + str(x2) + ',' + str(y2) + \ + ' ' + str(x) + ',' + str(y)) def relsmbezier(self, x2, y2, x, y): """smooth bezier with xy2 to xy relative""" - self.path.append('s'+str(x2)+','+str(y2)+' '+str(x)+','+str(y)) + self.path.append('s' + str(x2) + ',' + str(y2) + \ + ' ' + str(x) + ',' + str(y)) def qbezier(self, x1, y1, x, y): """quadratic bezier with xy1 to xy absolut""" - self.path.append('Q'+str(x1)+','+str(y1)+' '+str(x)+','+str(y)) + self.path.append('Q' + str(x1) + ',' + str(y1) + \ + ' ' + str(x) + ',' + str(y)) def relqbezier(self, x1, y1, x, y): """quadratic bezier with xy1 to xy relative""" - self.path.append('q'+str(x1)+','+str(y1)+' '+str(x)+','+str(y)) + self.path.append('q' + str(x1) + ',' + str(y1) + \ + ' ' + str(x) + ',' + str(y)) def smqbezier(self, x, y): """smooth quadratic bezier to xy absolut""" - self.path.append('T'+str(x)+','+str(y)) + self.path.append('T' + str(x) + ',' + str(y)) def relsmqbezier(self, x, y): """smooth quadratic bezier to xy relative""" - self.path.append('t'+str(x)+','+str(y)) + self.path.append('t' + str(x) + ',' + str(y)) def ellarc(self, rx, ry, xrot, laf, sf, x, y): """elliptival arc with rx and ry rotating with xrot using large-arc-flag and sweep-flag to xy absolut""" - self.path.append('A'+str(rx)+','+str(ry)+' '+str(xrot) + - ' '+str(laf)+' '+str(sf)+' '+str(x)+' '+str(y)) + self.path.append('A' + str(rx) + ',' + str(ry) + ' ' + str(xrot) + + ' ' + str(laf) + ' ' + str(sf) + ' ' + str(x) + ' ' + str(y)) def relellarc(self, rx, ry, xrot, laf, sf, x, y): """elliptival arc with rx and ry rotating with xrot using large-arc-flag and sweep-flag to xy relative""" - self.path.append('a'+str(rx)+','+str(ry)+' '+str(xrot) + - ' '+str(laf)+' '+str(sf)+' '+str(x)+' '+str(y)) + self.path.append('a' + str(rx) + ',' + str(ry) + ' ' + str(xrot) + + ' ' + str(laf) + ' ' + str(sf) + ' ' + str(x) + ' ' + str(y)) def __repr__(self): return ' '.join(self.path) @@ -312,36 +316,36 @@ class SVGelement: self.elements.append(SVGelement) def toXml(self, level, f): - f.write('\t'*level) - f.write('<'+self.type) + f.write('\t' * level) + f.write('<' + self.type) for attkey in list(self.attributes.keys()): - f.write(' '+_escape(str(attkey))+'=' + - _quoteattr(str(self.attributes[attkey]))) + f.write(' ' + _escape(str(attkey)) + '=' + + _quoteattr(str(self.attributes[attkey]))) if self.namespace: - f.write(' xmlns="' + _escape(str(self.namespace)) + - '" xmlns:xlink="http://www.w3.org/1999/xlink"') + f.write(' xmlns="' + _escape(str(self.namespace)) + + '" xmlns:xlink="http://www.w3.org/1999/xlink"') if self.elements or self.text or self.cdata: f.write('>') if self.elements: f.write('\n') for element in self.elements: - element.toXml(level+1, f) + element.toXml(level + 1, f) if self.cdata: - f.write('\n'+'\t'*(level+1)+'<![CDATA[') + f.write('\n' + '\t' * (level + 1) + '<![CDATA[') for line in self.cdata.splitlines(): - f.write('\n'+'\t'*(level+2)+line) - f.write('\n'+'\t'*(level+1)+']]>\n') + f.write('\n' + '\t' * (level + 2) + line) + f.write('\n' + '\t' * (level + 1) + ']]>\n') if self.text: if isinstance(self.text, type('')): # If the text is only text f.write(_escape(str(self.text))) else: # If the text is a spannedtext class f.write(str(self.text)) if self.elements: - f.write('\t'*level+'</'+self.type+'>\n') + f.write('\t' * level + '</' + self.type + '>\n') elif self.text: - f.write('</'+self.type+'>\n') + f.write('</' + self.type + '>\n') elif self.cdata: - f.write('\t'*level+'</'+self.type+'>\n') + f.write('\t' * level + '</' + self.type + '>\n') else: f.write('/>\n') @@ -447,38 +451,41 @@ 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) - if x!=None: - self.attributes['x']=x - if y!=None: - self.attributes['y']=y - if fill!=None: - self.attributes['fill']=fill - if stroke!=None: - self.attributes['stroke']=stroke - if stroke_width!=None: - self.attributes['stroke-width']=stroke_width + SVGelement.__init__( + self, 'rect', {'width': width, 'height': height}, **args) + if x != None: + self.attributes['x'] = x + if y != None: + self.attributes['y'] = y + if fill != None: + self.attributes['fill'] = fill + if stroke != None: + self.attributes['stroke'] = stroke + if stroke_width != None: + self.attributes['stroke-width'] = stroke_width + class ellipse(SVGelement): """e=ellipse(rx,ry,x,y,fill,stroke,stroke_width,**args) an ellipse is defined as a center and a x and y radius. """ - def __init__(self,cx=None,cy=None,rx=None,ry=None,fill=None,stroke=None,stroke_width=None,**args): - if rx==None or ry== None: + + def __init__(self, cx=None, cy=None, rx=None, ry=None, fill=None, stroke=None, stroke_width=None, **args): + if rx == None or ry == None: raise ValueError('both rx and ry are required') - SVGelement.__init__(self, 'ellipse', {'rx':rx,'ry':ry}, **args) - if cx!=None: - self.attributes['cx']=cx - if cy!=None: - self.attributes['cy']=cy - if fill!=None: - self.attributes['fill']=fill - if stroke!=None: - self.attributes['stroke']=stroke - if stroke_width!=None: - self.attributes['stroke-width']=stroke_width + SVGelement.__init__(self, 'ellipse', {'rx': rx, 'ry': ry}, **args) + if cx != None: + self.attributes['cx'] = cx + if cy != None: + self.attributes['cy'] = cy + if fill != None: + self.attributes['fill'] = fill + if stroke != None: + self.attributes['stroke'] = stroke + if stroke_width != None: + self.attributes['stroke-width'] = stroke_width class circle(SVGelement): @@ -486,20 +493,22 @@ class circle(SVGelement): The circle creates an element using a x, y and radius values eg """ - def __init__(self,cx=None,cy=None,r=None,fill=None,stroke=None,stroke_width=None,**args): - if r==None: + + 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) - if cx!=None: - self.attributes['cx']=cx - if cy!=None: - self.attributes['cy']=cy - if fill!=None: - self.attributes['fill']=fill - if stroke!=None: - self.attributes['stroke']=stroke - if stroke_width!=None: - self.attributes['stroke-width']=stroke_width + SVGelement.__init__(self, 'circle', {'r': r}, **args) + if cx != None: + self.attributes['cx'] = cx + if cy != None: + self.attributes['cy'] = cy + if fill != None: + self.attributes['fill'] = fill + if stroke != None: + self.attributes['stroke'] = stroke + if stroke_width != None: + self.attributes['stroke-width'] = stroke_width + class point(circle): """p=point(x,y,color) @@ -507,72 +516,83 @@ class point(circle): A point is defined as a circle with a size 1 radius. It may be more efficient to use a very small rectangle if you use many points because a circle is difficult to render. """ - def __init__(self,x,y,fill='black',**args): + + def __init__(self, x, y, fill='black', **args): circle.__init__(self, x, y, 1, fill, **args) + class line(SVGelement): """l=line(x1,y1,x2,y2,stroke,stroke_width,**args) 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): + + def __init__(self, x1=None, y1=None, x2=None, y2=None, stroke=None, stroke_width=None, **args): SVGelement.__init__(self, 'line', **args) - if x1!=None: - self.attributes['x1']=x1 - if y1!=None: - self.attributes['y1']=y1 - if x2!=None: - self.attributes['x2']=x2 - if y2!=None: - self.attributes['y2']=y2 - if stroke_width!=None: - self.attributes['stroke-width']=stroke_width - if stroke!=None: - self.attributes['stroke']=stroke + if x1 != None: + self.attributes['x1'] = x1 + if y1 != None: + self.attributes['y1'] = y1 + if x2 != None: + self.attributes['x2'] = x2 + if y2 != None: + self.attributes['y2'] = y2 + if stroke_width != None: + self.attributes['stroke-width'] = stroke_width + if stroke != None: + self.attributes['stroke'] = stroke + class polyline(SVGelement): """pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args) 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) - if fill!=None: - self.attributes['fill']=fill - if stroke_width!=None: - self.attributes['stroke-width']=stroke_width - if stroke!=None: - self.attributes['stroke']=stroke + + def __init__(self, points, fill=None, stroke=None, stroke_width=None, **args): + SVGelement.__init__(self, 'polyline', { + 'points': _xypointlist(points)}, **args) + if fill != None: + self.attributes['fill'] = fill + if stroke_width != None: + self.attributes['stroke-width'] = stroke_width + if stroke != None: + self.attributes['stroke'] = stroke + class polygon(SVGelement): """pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args) 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) - if fill!=None: - self.attributes['fill']=fill - if stroke_width!=None: - self.attributes['stroke-width']=stroke_width - if stroke!=None: - self.attributes['stroke']=stroke + + def __init__(self, points, fill=None, stroke=None, stroke_width=None, **args): + SVGelement.__init__( + self, 'polygon', {'points': _xypointlist(points)}, **args) + if fill != None: + self.attributes['fill'] = fill + if stroke_width != None: + self.attributes['stroke-width'] = stroke_width + if stroke != None: + self.attributes['stroke'] = stroke + class path(SVGelement): """p=path(path,fill,stroke,stroke_width,**args) 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) - if stroke!=None: - self.attributes['stroke']=stroke - if fill!=None: - self.attributes['fill']=fill - if stroke_width!=None: - self.attributes['stroke-width']=stroke_width - if id!=None: - self.attributes['id']=id + + def __init__(self, pathdata, fill=None, stroke=None, stroke_width=None, id=None, **args): + SVGelement.__init__(self, 'path', {'d': str(pathdata)}, **args) + if stroke != None: + self.attributes['stroke'] = stroke + if fill != None: + self.attributes['fill'] = fill + if stroke_width != None: + self.attributes['stroke-width'] = stroke_width + if id != None: + self.attributes['id'] = id class text(SVGelement): @@ -580,20 +600,21 @@ 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): + + def __init__(self, x=None, y=None, text=None, font_size=None, font_family=None, text_anchor=None, **args): SVGelement.__init__(self, 'text', **args) - if x!=None: - self.attributes['x']=x - if y!=None: - self.attributes['y']=y - if font_size!=None: - self.attributes['font-size']=font_size - if font_family!=None: - self.attributes['font-family']=font_family - if text!=None: - self.text=text - if text_anchor!=None: - self.attributes['text-anchor']=text_anchor + if x != None: + self.attributes['x'] = x + if y != None: + self.attributes['y'] = y + if font_size != None: + self.attributes['font-size'] = font_size + if font_family != None: + self.attributes['font-family'] = font_family + if text != None: + self.text = text + if text_anchor != None: + self.attributes['text-anchor'] = text_anchor class textpath(SVGelement): @@ -601,10 +622,12 @@ 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) - if text!=None: - self.text=text + + def __init__(self, link, text=None, **args): + SVGelement.__init__(self, 'textPath', {'xlink:href': link}, **args) + if text != None: + self.text = text + class pattern(SVGelement): """p=pattern(x,y,width,height,patternUnits,**args) @@ -613,18 +636,20 @@ class pattern(SVGelement): graphic object which can be replicated ("tiled") at fixed intervals 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): + + def __init__(self, x=None, y=None, width=None, height=None, patternUnits=None, **args): SVGelement.__init__(self, 'pattern', **args) - if x!=None: - self.attributes['x']=x - if y!=None: - self.attributes['y']=y - if width!=None: - self.attributes['width']=width - if height!=None: - self.attributes['height']=height - if patternUnits!=None: - self.attributes['patternUnits']=patternUnits + if x != None: + self.attributes['x'] = x + if y != None: + self.attributes['y'] = y + if width != None: + self.attributes['width'] = width + if height != None: + self.attributes['height'] = height + if patternUnits != None: + self.attributes['patternUnits'] = patternUnits + class title(SVGelement): """t=title(text,**args) @@ -632,10 +657,12 @@ class title(SVGelement): a title is a text element. The text is displayed in the title bar add at least one to the root svg element """ - def __init__(self,text=None,**args): + + def __init__(self, text=None, **args): SVGelement.__init__(self, 'title', **args) - if text!=None: - self.text=text + if text != None: + self.text = text + class description(SVGelement): """d=description(text,**args) @@ -643,10 +670,12 @@ class description(SVGelement): a description can be added to any element and is used for a tooltip Add this element before adding other elements. """ - def __init__(self,text=None,**args): + + def __init__(self, text=None, **args): SVGelement.__init__(self, 'desc', **args) - if text!=None: - self.text=text + if text != None: + self.text = text + class lineargradient(SVGelement): """lg=lineargradient(x1,y1,x2,y2,id,**args) @@ -654,18 +683,20 @@ class lineargradient(SVGelement): defines a lineargradient using two xy pairs. stop elements van be added to define the gradient colors. """ - def __init__(self,x1=None,y1=None,x2=None,y2=None,id=None,**args): + + def __init__(self, x1=None, y1=None, x2=None, y2=None, id=None, **args): SVGelement.__init__(self, 'linearGradient', **args) - if x1!=None: - self.attributes['x1']=x1 - if y1!=None: - self.attributes['y1']=y1 - if x2!=None: - self.attributes['x2']=x2 - if y2!=None: - self.attributes['y2']=y2 - if id!=None: - self.attributes['id']=id + if x1 != None: + self.attributes['x1'] = x1 + if y1 != None: + self.attributes['y1'] = y1 + if x2 != None: + self.attributes['x2'] = x2 + if y2 != None: + self.attributes['y2'] = y2 + if id != None: + self.attributes['id'] = id + class radialgradient(SVGelement): """rg=radialgradient(cx,cy,r,fx,fy,id,**args) @@ -673,38 +704,43 @@ class radialgradient(SVGelement): defines a radial gradient using a outer circle which are defined by a cx,cy and r and by using a focalpoint. 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): + + def __init__(self, cx=None, cy=None, r=None, fx=None, fy=None, id=None, **args): SVGelement.__init__(self, 'radialGradient', **args) - if cx!=None: - self.attributes['cx']=cx - if cy!=None: - self.attributes['cy']=cy - if r!=None: - self.attributes['r']=r - if fx!=None: - self.attributes['fx']=fx - if fy!=None: - self.attributes['fy']=fy - if id!=None: - self.attributes['id']=id + if cx != None: + self.attributes['cx'] = cx + if cy != None: + self.attributes['cy'] = cy + if r != None: + self.attributes['r'] = r + if fx != None: + self.attributes['fx'] = fx + if fy != None: + self.attributes['fy'] = fy + if id != None: + self.attributes['id'] = id + class stop(SVGelement): """st=stop(offset,stop_color,**args) Puts a stop color at the specified radius """ - def __init__(self,offset,stop_color=None,**args): - SVGelement.__init__(self, 'stop', {'offset':offset}, **args) - if stop_color!=None: - self.attributes['stop-color']=stop_color + + def __init__(self, offset, stop_color=None, **args): + SVGelement.__init__(self, 'stop', {'offset': offset}, **args) + if stop_color != None: + self.attributes['stop-color'] = stop_color + class style(SVGelement): """st=style(type,cdata=None,**args) 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) + + def __init__(self, type, cdata=None, **args): + SVGelement.__init__(self, 'style', {'type': type}, cdata=cdata, **args) class image(SVGelement): @@ -712,22 +748,26 @@ class image(SVGelement): adds an image to the drawing. Supported formats are .png, .jpg and .svg. """ - def __init__(self,url,x=None,y=None,width=None,height=None,**args): - if width==None or height==None: + + 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) - if x!=None: - self.attributes['x']=x - if y!=None: - self.attributes['y']=y + SVGelement.__init__( + self, 'image', {'xlink:href': url, 'width': width, 'height': height}, **args) + if x != None: + self.attributes['x'] = x + if y != None: + self.attributes['y'] = y + class cursor(SVGelement): """c=cursor(url,**args) defines a custom cursor for a element or a drawing """ - def __init__(self,url,**args): - SVGelement.__init__(self, 'cursor', {'xlink:href':url}, **args) + + def __init__(self, url, **args): + SVGelement.__init__(self, 'cursor', {'xlink:href': url}, **args) class marker(SVGelement): @@ -736,20 +776,22 @@ class marker(SVGelement): defines a marker which can be used as an endpoint for a line or other pathtypes 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): + + def __init__(self, id=None, viewBox=None, refx=None, refy=None, markerWidth=None, markerHeight=None, **args): SVGelement.__init__(self, 'marker', **args) - if id!=None: - self.attributes['id']=id - if viewBox!=None: - self.attributes['viewBox']=_viewboxlist(viewBox) - if refx!=None: - self.attributes['refX']=refx - if refy!=None: - self.attributes['refY']=refy - if markerWidth!=None: - self.attributes['markerWidth']=markerWidth - if markerHeight!=None: - self.attributes['markerHeight']=markerHeight + if id != None: + self.attributes['id'] = id + if viewBox != None: + self.attributes['viewBox'] = _viewboxlist(viewBox) + if refx != None: + self.attributes['refX'] = refx + if refy != None: + self.attributes['refY'] = refy + if markerWidth != None: + self.attributes['markerWidth'] = markerWidth + if markerHeight != None: + self.attributes['markerHeight'] = markerHeight + class group(SVGelement): """g=group(id,**args) @@ -757,10 +799,12 @@ class group(SVGelement): a group is defined by an id and is used to contain elements g.addElement(SVGelement) """ - def __init__(self,id=None,**args): + + def __init__(self, id=None, **args): SVGelement.__init__(self, 'g', **args) - if id!=None: - self.attributes['id']=id + if id != None: + self.attributes['id'] = id + class symbol(SVGelement): """sy=symbol(id,viewbox,**args) @@ -771,21 +815,24 @@ class symbol(SVGelement): sy.addElement(SVGelement) """ - def __init__(self,id=None,viewBox=None,**args): + def __init__(self, id=None, viewBox=None, **args): SVGelement.__init__(self, 'symbol', **args) - if id!=None: - self.attributes['id']=id - if viewBox!=None: - self.attributes['viewBox']=_viewboxlist(viewBox) + if id != None: + self.attributes['id'] = id + if viewBox != None: + self.attributes['viewBox'] = _viewboxlist(viewBox) + class defs(SVGelement): """d=defs(**args) container for defining elements """ - def __init__(self,**args): + + def __init__(self, **args): SVGelement.__init__(self, 'defs', **args) + class switch(SVGelement): """sw=switch(**args) @@ -793,7 +840,8 @@ class switch(SVGelement): requiredFeatures, requiredExtensions and systemLanguage. Refer to the SVG specification for details. """ - def __init__(self,**args): + + def __init__(self, **args): SVGelement.__init__(self, 'switch', **args) @@ -802,17 +850,18 @@ 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) - if x!=None: - self.attributes['x']=x - if y!=None: - self.attributes['y']=y - if width!=None: - self.attributes['width']=width - if height!=None: - self.attributes['height']=height + def __init__(self, link, x=None, y=None, width=None, height=None, **args): + SVGelement.__init__(self, 'use', {'xlink:href': link}, **args) + if x != None: + self.attributes['x'] = x + if y != None: + self.attributes['y'] = y + + if width != None: + self.attributes['width'] = width + if height != None: + self.attributes['height'] = height class link(SVGelement): @@ -821,17 +870,21 @@ class link(SVGelement): a link is defined by a hyperlink. add elements which have to be linked a.addElement(SVGelement) """ - def __init__(self,link='',**args): - SVGelement.__init__(self, 'a', {'xlink:href':link}, **args) + + def __init__(self, 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): + + def __init__(self, id=None, **args): SVGelement.__init__(self, 'view', **args) - if id!=None: - self.attributes['id']=id + if id != None: + self.attributes['id'] = id + class script(SVGelement): """sc=script(type,type,cdata,**args) @@ -839,78 +892,94 @@ class script(SVGelement): adds a script element which contains CDATA to the SVG drawing """ - def __init__(self,type,cdata=None,**args): - SVGelement.__init__(self, 'script', {'type':type}, cdata=cdata, **args) + + def __init__(self, type, cdata=None, **args): + SVGelement.__init__( + self, 'script', {'type': type}, cdata=cdata, **args) + class animate(SVGelement): """an=animate(attribute,from,to,during,**args) animates an attribute. """ - def __init__(self,attribute,fr=None,to=None,dur=None,**args): - SVGelement.__init__(self, 'animate', {'attributeName':attribute}, **args) - if fr!=None: - self.attributes['from']=fr - if to!=None: - self.attributes['to']=to - if dur!=None: - self.attributes['dur']=dur + + def __init__(self, attribute, fr=None, to=None, dur=None, **args): + SVGelement.__init__( + self, 'animate', {'attributeName': attribute}, **args) + if fr != None: + self.attributes['from'] = fr + if to != None: + self.attributes['to'] = to + if dur != None: + self.attributes['dur'] = dur + class animateMotion(SVGelement): """an=animateMotion(pathdata,dur,**args) animates a SVGelement over the given path in dur seconds """ - def __init__(self,pathdata,dur,**args): + + def __init__(self, pathdata, dur, **args): SVGelement.__init__(self, 'animateMotion', **args) - if pathdata!=None: - self.attributes['path']=str(pathdata) - if dur!=None: - self.attributes['dur']=dur + if pathdata != None: + self.attributes['path'] = str(pathdata) + if dur != None: + self.attributes['dur'] = dur + class animateTransform(SVGelement): """antr=animateTransform(type,from,to,dur,**args) 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) + + def __init__(self, type=None, fr=None, to=None, dur=None, **args): + SVGelement.__init__(self, 'animateTransform', { + 'attributeName': 'transform'}, **args) # As far as I know the attributeName is always transform - if type!=None: - self.attributes['type']=type - if fr!=None: - self.attributes['from']=fr - if to!=None: - self.attributes['to']=to - if dur!=None: - self.attributes['dur']=dur + if type != None: + self.attributes['type'] = type + if fr != None: + self.attributes['from'] = fr + if to != None: + self.attributes['to'] = to + if dur != None: + self.attributes['dur'] = dur + + class animateColor(SVGelement): """ac=animateColor(attribute,type,from,to,dur,**args) 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) - if type!=None: - self.attributes['type']=type - if fr!=None: - self.attributes['from']=fr - if to!=None: - self.attributes['to']=to - if dur!=None: - self.attributes['dur']=dur + + def __init__(self, attribute, type=None, fr=None, to=None, dur=None, **args): + SVGelement.__init__(self, 'animateColor', { + 'attributeName': attribute}, **args) + if type != None: + self.attributes['type'] = type + if fr != None: + self.attributes['from'] = fr + if to != None: + self.attributes['to'] = to + if dur != None: + self.attributes['dur'] = dur + + class set(SVGelement): """st=set(attribute,to,during,**args) sets an attribute to a value for a """ - def __init__(self,attribute,to=None,dur=None,**args): - SVGelement.__init__(self, 'set', {'attributeName':attribute}, **args) - if to!=None: - self.attributes['to']=to - if dur!=None: - self.attributes['dur']=dur + def __init__(self, attribute, to=None, dur=None, **args): + SVGelement.__init__(self, 'set', {'attributeName': attribute}, **args) + if to != None: + self.attributes['to'] = to + if dur != None: + self.attributes['dur'] = dur class svg(SVGelement): @@ -928,15 +997,17 @@ class svg(SVGelement): d.setSVG(s) d.toXml() """ - def __init__(self,viewBox=None, width=None, height=None,**args): + + def __init__(self, viewBox=None, width=None, height=None, **args): SVGelement.__init__(self, 'svg', **args) - if viewBox!=None: - self.attributes['viewBox']=_viewboxlist(viewBox) - if width!=None: - self.attributes['width']=width - if height!=None: - self.attributes['height']=height - self.namespace="http://www.w3.org/2000/svg" + if viewBox != None: + self.attributes['viewBox'] = _viewboxlist(viewBox) + if width != None: + self.attributes['width'] = width + if height != None: + self.attributes['height'] = height + self.namespace = "http://www.w3.org/2000/svg" + class drawing: """d=drawing() @@ -950,29 +1021,32 @@ class drawing: """ def __init__(self, entity={}): - self.svg=None + self.svg = None self.entity = entity + def setSVG(self, svg): - self.svg=svg + self.svg = svg # Voeg een element toe aan de grafiek toe. - if use_dom_implementation==0: - def toXml(self, filename='',compress=False): + if use_dom_implementation == 0: + def toXml(self, filename='', compress=False): import io - xml=io.StringIO() + xml = io.StringIO() xml.write("<?xml version='1.0' encoding='UTF-8'?>\n") - xml.write("<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.0//EN\" \"http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd\"") + xml.write( + "<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.0//EN\" \"http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd\"") if self.entity: xml.write(" [\n") for item in list(self.entity.keys()): - xml.write("<!ENTITY %s \"%s\">\n" % (item, self.entity[item])) + xml.write("<!ENTITY %s \"%s\">\n" % + (item, self.entity[item])) xml.write("]") xml.write(">\n") self.svg.toXml(0, xml) if not filename: if compress: import gzip - f=io.StringIO() - zf=gzip.GzipFile(fileobj=f, mode='wb') + f = io.StringIO() + zf = gzip.GzipFile(fileobj=f, mode='wb') zf.write(xml.getvalue()) zf.close() f.seek(0) @@ -980,57 +1054,62 @@ class drawing: else: return xml.getvalue() else: - if filename[-4:]=='svgz': + 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() else: - def toXml(self,filename='',compress=False): + def toXml(self, filename='', compress=False): """drawing.toXml() ---->to the screen drawing.toXml(filename)---->to the file 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): """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) + e = root.createElement(element.type) if element.text: - textnode=root.createTextNode(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])) + # in element.attributes is supported from python 2.2 + for attribute in list(element.attributes.keys()): + 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 io - xml=io.StringIO() + xml = io.StringIO() PrettyPrint(root, xml) if compress: import gzip - f=io.StringIO() - zf=gzip.GzipFile(fileobj=f, mode='wb') + f = io.StringIO() + zf = gzip.GzipFile(fileobj=f, mode='wb') zf.write(xml.getvalue()) zf.close() f.seek(0) @@ -1039,63 +1118,67 @@ class drawing: return xml.getvalue() else: try: - if filename[-4:]=='svgz': + if filename[-4:] == 'svgz': import gzip import io - xml=io.StringIO() + xml = io.StringIO() PrettyPrint(root, xml) - 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=open(filename, 'w') + f = open(filename, 'w') PrettyPrint(root, f) f.close() except: print(("Cannot write SVG file: " + filename)) + def validate(self): try: import xml.parsers.xmlproc.xmlval except: - raise exceptions.ImportError('PyXml is required for validating SVG') - svg=self.toXml() - xv=xml.parsers.xmlproc.xmlval.XMLValidator() + raise exceptions.ImportError( + 'PyXml is required for validating SVG') + svg = self.toXml() + xv = xml.parsers.xmlproc.xmlval.XMLValidator() try: xv.feed(svg) except: raise Exception("SVG is not well formed, see messages above") else: print("SVG well formed") -if __name__=='__main__': - d=drawing() - s=svg((0, 0, 100, 100)) - r=rect(-100, -100, 300, 300, 'cyan') +if __name__ == '__main__': + + d = drawing() + s = svg((0, 0, 100, 100)) + r = rect(-100, -100, 300, 300, 'cyan') s.addElement(r) - t=title('SVGdraw Demo') + t = title('SVGdraw Demo') s.addElement(t) - g=group('animations') - e=ellipse(0, 0, 5, 2) + g = group('animations') + 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) - an.attributes['rotate']='auto-reverse' - an.attributes['repeatCount']="indefinite" + 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) + 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) + c = circle(i, j, 1, 'red', 'black', .5) s.addElement(c) d.setSVG(s) diff --git a/wqflask/utility/temp_data.py b/wqflask/utility/temp_data.py index b2cbd458..07c5a318 100644 --- a/wqflask/utility/temp_data.py +++ b/wqflask/utility/temp_data.py @@ -2,6 +2,7 @@ from redis import Redis import simplejson as json + class TempData: def __init__(self, temp_uuid): @@ -11,7 +12,7 @@ class TempData: def store(self, field, value): self.redis.hset(self.key, field, value) - self.redis.expire(self.key, 60*15) # Expire in 15 minutes + self.redis.expire(self.key, 60 * 15) # Expire in 15 minutes def get_all(self): return self.redis.hgetall(self.key) diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 65df59c3..e28abb48 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -9,16 +9,18 @@ from wqflask import app # Use the standard logger here to avoid a circular dependency import logging -logger = logging.getLogger(__name__ ) +logger = logging.getLogger(__name__) OVERRIDES = {} + def app_set(command_id, value): """Set application wide value""" app.config.setdefault(command_id, value) return value -def get_setting(command_id,guess=None): + +def get_setting(command_id, guess=None): """Resolve a setting from the environment or the global settings in app.config, with valid_path is a function checking whether the path points to an expected directory and returns the full path to @@ -54,7 +56,7 @@ def get_setting(command_id,guess=None): # print("Looking for "+command_id+"\n") command = value(os.environ.get(command_id)) if command is None or command == "": - command = OVERRIDES.get(command_id) # currently not in use + command = OVERRIDES.get(command_id) # currently not in use if command is None: # ---- Check whether setting exists in app command = value(app.config.get(command_id)) @@ -62,16 +64,19 @@ def get_setting(command_id,guess=None): command = value(guess) if command is None or command == "": # print command - raise Exception(command_id+' setting unknown or faulty (update default_settings.py?).') + raise Exception( + command_id + ' setting unknown or faulty (update default_settings.py?).') # print("Set "+command_id+"="+str(command)) return command + def get_setting_bool(id): v = get_setting(id) if v not in [0, False, 'False', 'FALSE', None]: - return True + return True return False + def get_setting_int(id): v = get_setting(id) if isinstance(v, str): @@ -80,69 +85,83 @@ def get_setting_int(id): return 0 return v + def valid_bin(bin): if os.path.islink(bin) or valid_file(bin): return bin return None + def valid_file(fn): if os.path.isfile(fn): return fn return None + def valid_path(dir): if os.path.isdir(dir): return dir return None + def js_path(module=None): """ Find the JS module in the two paths """ - try_gn = get_setting("JS_GN_PATH")+"/"+module + try_gn = get_setting("JS_GN_PATH") + "/" + module if valid_path(try_gn): return try_gn - try_guix = get_setting("JS_GUIX_PATH")+"/"+module + try_guix = get_setting("JS_GUIX_PATH") + "/" + module if valid_path(try_guix): return try_guix - raise "No JS path found for "+module+" (if not in Guix check JS_GN_PATH)" + 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) + def gemma_command(guess=None): return assert_bin(get_setting("GEMMA_COMMAND", guess)) + def gemma_wrapper_command(guess=None): return assert_bin(get_setting("GEMMA_WRAPPER_COMMAND", guess)) + def plink_command(guess=None): return assert_bin(get_setting("PLINK_COMMAND", guess)) + def flat_file_exists(subdir): base = get_setting("GENENETWORK_FILES") - return valid_path(base+"/"+subdir) + return valid_path(base + "/" + subdir) + def flat_files(subdir=None): base = get_setting("GENENETWORK_FILES") if subdir: - return assert_dir(base+"/"+subdir) + return assert_dir(base + "/" + subdir) return assert_dir(base) + def assert_bin(fn): if not valid_bin(fn): - raise Exception("ERROR: can not find binary "+fn) + raise Exception("ERROR: can not find binary " + fn) return fn + def assert_dir(dir): if not valid_path(dir): - raise Exception("ERROR: can not find directory "+dir) + raise Exception("ERROR: can not find directory " + dir) return dir + def assert_writable_dir(dir): try: fn = dir + "/test.txt" - fh = open( fn, 'w' ) + fh = open(fn, 'w') fh.write("I am writing this text to the file\n") fh.close() os.remove(fn) @@ -150,16 +169,19 @@ def assert_writable_dir(dir): raise Exception('Unable to write test.txt to directory ' + dir) return dir + def assert_file(fn): if not valid_file(fn): - raise Exception('Unable to find file '+fn) + raise Exception('Unable to find file ' + fn) return fn + def mk_dir(dir): if not valid_path(dir): os.makedirs(dir) return assert_dir(dir) + def locate(name, subdir=None): """ Locate a static flat file in the GENENETWORK_FILES environment. @@ -168,19 +190,22 @@ def locate(name, subdir=None): """ base = get_setting("GENENETWORK_FILES") if subdir: - base = base+"/"+subdir + base = base + "/" + subdir if valid_path(base): lookfor = base + "/" + name if valid_file(lookfor): - logger.info("Found: file "+lookfor+"\n") + logger.info("Found: file " + lookfor + "\n") return lookfor else: - raise Exception("Can not locate "+lookfor) - if subdir: sys.stderr.write(subdir) - raise Exception("Can not locate "+name+" in "+base) + raise Exception("Can not locate " + lookfor) + if subdir: + sys.stderr.write(subdir) + 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): """ @@ -191,35 +216,38 @@ def locate_ignore_error(name, subdir=None): """ base = get_setting("GENENETWORK_FILES") if subdir: - base = base+"/"+subdir + base = base + "/" + subdir if valid_path(base): lookfor = base + "/" + name if valid_file(lookfor): - logger.debug("Found: file "+name+"\n") + logger.debug("Found: file " + name + "\n") return lookfor - logger.info("WARNING: file "+name+" not found\n") + logger.info("WARNING: file " + name + " not found\n") return None + def tempdir(): """ Get UNIX TMPDIR by default """ return valid_path(get_setting("TMPDIR", "/tmp")) -BLUE = '\033[94m' + +BLUE = '\033[94m' GREEN = '\033[92m' -BOLD = '\033[1m' -ENDC = '\033[0m' +BOLD = '\033[1m' +ENDC = '\033[0m' + def show_settings(): from utility.tools import LOG_LEVEL - print(("Set global log level to "+BLUE+LOG_LEVEL+ENDC)) + print(("Set global log level to " + BLUE + LOG_LEVEL + ENDC)) log_level = getattr(logging, LOG_LEVEL.upper()) logging.basicConfig(level=log_level) logger.info(OVERRIDES) - logger.info(BLUE+"Mr. Mojo Risin 2"+ENDC) + logger.info(BLUE + "Mr. Mojo Risin 2" + ENDC) keylist = list(app.config.keys()) print("runserver.py: ****** Webserver configuration - k,v pairs from app.config ******") keylist.sort() @@ -231,35 +259,35 @@ def show_settings(): # Cached values -GN_VERSION = get_setting('GN_VERSION') -HOME = get_setting('HOME') -SERVER_PORT = get_setting('SERVER_PORT') -WEBSERVER_MODE = get_setting('WEBSERVER_MODE') -GN2_BASE_URL = get_setting('GN2_BASE_URL') -GN2_BRANCH_URL = get_setting('GN2_BRANCH_URL') -GN_SERVER_URL = get_setting('GN_SERVER_URL') -SERVER_PORT = get_setting_int('SERVER_PORT') -SQL_URI = get_setting('SQL_URI') -LOG_LEVEL = get_setting('LOG_LEVEL') -LOG_LEVEL_DEBUG = get_setting_int('LOG_LEVEL_DEBUG') -LOG_SQL = get_setting_bool('LOG_SQL') -LOG_SQL_ALCHEMY = get_setting_bool('LOG_SQL_ALCHEMY') -LOG_BENCH = get_setting_bool('LOG_BENCH') -LOG_FORMAT = "%(message)s" # not yet in use -USE_REDIS = get_setting_bool('USE_REDIS') -USE_GN_SERVER = get_setting_bool('USE_GN_SERVER') - -GENENETWORK_FILES = get_setting('GENENETWORK_FILES') -JS_GUIX_PATH = get_setting('JS_GUIX_PATH') +GN_VERSION = get_setting('GN_VERSION') +HOME = get_setting('HOME') +SERVER_PORT = get_setting('SERVER_PORT') +WEBSERVER_MODE = get_setting('WEBSERVER_MODE') +GN2_BASE_URL = get_setting('GN2_BASE_URL') +GN2_BRANCH_URL = get_setting('GN2_BRANCH_URL') +GN_SERVER_URL = get_setting('GN_SERVER_URL') +SERVER_PORT = get_setting_int('SERVER_PORT') +SQL_URI = get_setting('SQL_URI') +LOG_LEVEL = get_setting('LOG_LEVEL') +LOG_LEVEL_DEBUG = get_setting_int('LOG_LEVEL_DEBUG') +LOG_SQL = get_setting_bool('LOG_SQL') +LOG_SQL_ALCHEMY = get_setting_bool('LOG_SQL_ALCHEMY') +LOG_BENCH = get_setting_bool('LOG_BENCH') +LOG_FORMAT = "%(message)s" # not yet in use +USE_REDIS = get_setting_bool('USE_REDIS') +USE_GN_SERVER = get_setting_bool('USE_GN_SERVER') + +GENENETWORK_FILES = get_setting('GENENETWORK_FILES') +JS_GUIX_PATH = get_setting('JS_GUIX_PATH') assert_dir(JS_GUIX_PATH) -JS_GN_PATH = get_setting('JS_GN_PATH') +JS_GN_PATH = get_setting('JS_GN_PATH') # assert_dir(JS_GN_PATH) GITHUB_CLIENT_ID = get_setting('GITHUB_CLIENT_ID') GITHUB_CLIENT_SECRET = get_setting('GITHUB_CLIENT_SECRET') if GITHUB_CLIENT_ID != 'UNKNOWN' and GITHUB_CLIENT_SECRET: GITHUB_AUTH_URL = "https://github.com/login/oauth/authorize?client_id=" + \ - GITHUB_CLIENT_ID+"&client_secret="+GITHUB_CLIENT_SECRET + GITHUB_CLIENT_ID + "&client_secret=" + GITHUB_CLIENT_SECRET GITHUB_API_URL = get_setting('GITHUB_API_URL') ORCID_CLIENT_ID = get_setting('ORCID_CLIENT_ID') @@ -267,7 +295,8 @@ ORCID_CLIENT_SECRET = get_setting('ORCID_CLIENT_SECRET') ORCID_AUTH_URL = None if ORCID_CLIENT_ID != 'UNKNOWN' and ORCID_CLIENT_SECRET: ORCID_AUTH_URL = "https://orcid.org/oauth/authorize?response_type=code&scope=/authenticate&show_login=true&client_id=" + \ - ORCID_CLIENT_ID+"&client_secret="+ORCID_CLIENT_SECRET + "&redirect_uri=" + GN2_BRANCH_URL + "n/login/orcid_oauth2" + ORCID_CLIENT_ID + "&client_secret=" + ORCID_CLIENT_SECRET + \ + "&redirect_uri=" + GN2_BRANCH_URL + "n/login/orcid_oauth2" ORCID_TOKEN_URL = get_setting('ORCID_TOKEN_URL') ELASTICSEARCH_HOST = get_setting('ELASTICSEARCH_HOST') @@ -279,28 +308,29 @@ 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 +TEMPDIR = tempdir() # defaults to UNIX TMPDIR assert_dir(TEMPDIR) # ---- Handle specific JS modules JS_GUIX_PATH = get_setting("JS_GUIX_PATH") assert_dir(JS_GUIX_PATH) -assert_dir(JS_GUIX_PATH+'/cytoscape-panzoom') +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") +assert_file(JS_TWITTER_POST_FETCHER_PATH + "/js/twitterFetcher_min.js") JS_CYTOSCAPE_PATH = get_setting("JS_CYTOSCAPE_PATH", js_path("cytoscape")) assert_dir(JS_CYTOSCAPE_PATH) -assert_file(JS_CYTOSCAPE_PATH+'/cytoscape.min.js') +assert_file(JS_CYTOSCAPE_PATH + '/cytoscape.min.js') # assert_file(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData") diff --git a/wqflask/utility/type_checking.py b/wqflask/utility/type_checking.py index 6b029317..00f14ba9 100644 --- a/wqflask/utility/type_checking.py +++ b/wqflask/utility/type_checking.py @@ -7,6 +7,7 @@ def is_float(value): except: return False + def is_int(value): try: int(value) @@ -14,6 +15,7 @@ def is_int(value): except: return False + def is_str(value): if value is None: return False @@ -23,19 +25,22 @@ def is_str(value): except: return False -def get_float(vars_obj,name,default=None): + +def get_float(vars_obj, name, default=None): if name in vars_obj: if is_float(vars_obj[name]): return float(vars_obj[name]) return default -def get_int(vars_obj,name,default=None): + +def get_int(vars_obj, name, default=None): if name in vars_obj: if is_int(vars_obj[name]): return float(vars_obj[name]) return default -def get_string(vars_obj,name,default=None): + +def get_string(vars_obj, name, default=None): if name in vars_obj: if not vars_obj[name] is None: return str(vars_obj[name]) diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py index 5681fadf..0cb71567 100644 --- a/wqflask/utility/webqtlUtil.py +++ b/wqflask/utility/webqtlUtil.py @@ -33,44 +33,46 @@ from math import * from base import webqtlConfig # NL, 07/27/2010. moved from webqtlForm.py -#Dict of Parents and F1 information, In the order of [F1, Mat, Pat] -ParInfo ={ -'BXH':['BHF1', 'HBF1', 'C57BL/6J', 'C3H/HeJ'], -'AKXD':['AKF1', 'KAF1', 'AKR/J', 'DBA/2J'], -'BXD':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'], -'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'], -'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'], -'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'], -'HRDP':['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv'] +# Dict of Parents and F1 information, In the order of [F1, Mat, Pat] +ParInfo = { + 'BXH': ['BHF1', 'HBF1', 'C57BL/6J', 'C3H/HeJ'], + 'AKXD': ['AKF1', 'KAF1', 'AKR/J', 'DBA/2J'], + 'BXD': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'], + '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'], + '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'], + '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'], + 'HRDP': ['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv'] } ######################################### # Accessory Functions ######################################### -def genRandStr(prefix = "", length=8, chars=string.ascii_letters+string.digits): + +def genRandStr(prefix="", length=8, chars=string.ascii_letters + string.digits): from random import choice _str = prefix[:] for i in range(length): _str += choice(chars) return _str + def ListNotNull(lst): '''Obsolete - Use built in function any (or all or whatever) @@ -83,14 +85,16 @@ def ListNotNull(lst): return 1 return None -def readLineCSV(line): ### dcrowell July 2008 + +def readLineCSV(line): # dcrowell July 2008 """Parses a CSV string of text and returns a list containing each element as a string. Used by correlationPage""" returnList = line.split('","') - returnList[-1]=returnList[-1][:-2] - returnList[0]=returnList[0][1:] + returnList[-1] = returnList[-1][:-2] + returnList[0] = returnList[0][1:] return returnList + def cmpEigenValue(A, B): try: if A[0] > B[0]: @@ -102,12 +106,13 @@ def cmpEigenValue(A, B): except: return 0 + def hasAccessToConfidentialPhenotypeTrait(privilege, userName, authorized_users): access_to_confidential_phenotype_trait = 0 if webqtlConfig.USERDICT[privilege] > webqtlConfig.USERDICT['user']: access_to_confidential_phenotype_trait = 1 else: - AuthorizedUsersList=[x.strip() for x in authorized_users.split(',')] + AuthorizedUsersList = [x.strip() for x in authorized_users.split(',')] if userName in AuthorizedUsersList: access_to_confidential_phenotype_trait = 1 return access_to_confidential_phenotype_trait |