diff options
Diffstat (limited to 'wqflask/utility')
| -rw-r--r-- | wqflask/utility/Plot.py | 13 | ||||
| -rw-r--r-- | wqflask/utility/__init__.py | 2 | ||||
| -rw-r--r-- | wqflask/utility/after.py | 1 | ||||
| -rw-r--r-- | wqflask/utility/authentication_tools.py | 1 | ||||
| -rw-r--r-- | wqflask/utility/benchmark.py | 1 | ||||
| -rw-r--r-- | wqflask/utility/corestats.py | 2 | ||||
| -rw-r--r-- | wqflask/utility/elasticsearch_tools.py | 7 | ||||
| -rw-r--r-- | wqflask/utility/external.py | 1 | ||||
| -rw-r--r-- | wqflask/utility/gen_geno_ob.py | 3 | ||||
| -rw-r--r-- | wqflask/utility/genofile_parser.py | 1 | ||||
| -rw-r--r-- | wqflask/utility/logger.py | 3 | ||||
| -rw-r--r-- | wqflask/utility/pillow_utils.py | 4 | ||||
| -rw-r--r-- | wqflask/utility/startup_config.py | 1 | ||||
| -rw-r--r-- | wqflask/utility/svg.py | 67 | ||||
| -rw-r--r-- | wqflask/utility/temp_data.py | 1 | ||||
| -rw-r--r-- | wqflask/utility/tools.py | 25 | ||||
| -rw-r--r-- | wqflask/utility/type_checking.py | 5 | ||||
| -rw-r--r-- | wqflask/utility/webqtlUtil.py | 5 |
18 files changed, 141 insertions, 2 deletions
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py index 68c2cb72..d35b2089 100644 --- a/wqflask/utility/Plot.py +++ b/wqflask/utility/Plot.py @@ -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 @@ -68,6 +69,7 @@ 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: @@ -84,6 +86,7 @@ def frange(start, end=None, inc=1.0): L[i] = start + i * inc return L + def find_outliers(vals): """Calculates the upper and lower bounds of a set of sample/case values @@ -119,6 +122,8 @@ 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): im_drawer = ImageDraw.Draw(canvas) xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset @@ -230,6 +235,8 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab font=labelFont, fill=labelColor) # This function determines the scale of the plot + + def detScaleOld(min, max): if min >= max: return None @@ -246,6 +253,7 @@ def detScaleOld(min, max): high = c * ceil(max / c) return [low, high, round((high - low) / c)] + def detScale(min=0, max=0): if min >= max: @@ -283,15 +291,19 @@ def detScale(min=0, max=0): return [low, high, n] + def bluefunc(x): return 1.0 / (1.0 + exp(-10 * (x - 0.6))) + 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) + def colorSpectrum(n=100): multiple = 10 if n == 1: @@ -319,6 +331,7 @@ def colorSpectrum(n=100): out2.append(out[-1]) return out2 + def _test(): import doctest doctest.testmod() diff --git a/wqflask/utility/__init__.py b/wqflask/utility/__init__.py index ec7e72d0..d540c96e 100644 --- a/wqflask/utility/__init__.py +++ b/wqflask/utility/__init__.py @@ -2,8 +2,10 @@ 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 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 3d40a3b8..48ab1dc0 100644 --- a/wqflask/utility/benchmark.py +++ b/wqflask/utility/benchmark.py @@ -6,6 +6,7 @@ from utility.tools import LOG_BENCH from utility.logger import getLogger logger = getLogger(__name__) + class Bench: entries = collections.OrderedDict() diff --git a/wqflask/utility/corestats.py b/wqflask/utility/corestats.py index 15d1cb8d..523280a1 100644 --- a/wqflask/utility/corestats.py +++ b/wqflask/utility/corestats.py @@ -16,6 +16,8 @@ import sys # ZS: Should switch to using some third party library for this; maybe scipy has an equivalent + + class Stats: def __init__(self, sequence): diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py index ae1181e4..9415cef0 100644 --- a/wqflask/utility/elasticsearch_tools.py +++ b/wqflask/utility/elasticsearch_tools.py @@ -47,11 +47,13 @@ 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) 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 +79,7 @@ def get_elasticsearch_connection(for_user=True): return es + def setup_users_index(es_connection): if es_connection: index_settings = { @@ -87,12 +90,15 @@ def setup_users_index(es_connection): es_connection.indices.create(index='users', ignore=400) 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: @@ -106,6 +112,7 @@ 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) diff --git a/wqflask/utility/external.py b/wqflask/utility/external.py index c1bf4043..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) diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py index 9cfa39f9..24604e58 100644 --- a/wqflask/utility/gen_geno_ob.py +++ b/wqflask/utility/gen_geno_ob.py @@ -1,6 +1,7 @@ import utility.logger logger = utility.logger.getLogger(__name__) + class genotype: """ Replacement for reaper.Dataset so we can remove qtlreaper use while still generating mapping output figure @@ -119,6 +120,7 @@ class genotype: self.chromosomes.append(chr_ob) + class Chr: def __init__(self, name, geno_ob): self.name = name @@ -140,6 +142,7 @@ 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): self.chr = None diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py index f8e96d19..94a08c17 100644 --- a/wqflask/utility/genofile_parser.py +++ b/wqflask/utility/genofile_parser.py @@ -12,6 +12,7 @@ import simplejson as json from pprint import pformat as pf + class Marker: def __init__(self): self.name = None diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py index 16912e58..47079818 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 @@ -139,6 +140,8 @@ LOG_LEVEL_DEBUG (NYI). # Get the module logger. You can override log levels at the # module level + + def getLogger(name, level=None): gnlogger = GNLogger(name) logger = gnlogger.logger diff --git a/wqflask/utility/pillow_utils.py b/wqflask/utility/pillow_utils.py index 6e95beb0..5713e155 100644 --- a/wqflask/utility/pillow_utils.py +++ b/wqflask/utility/pillow_utils.py @@ -9,6 +9,8 @@ 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/startup_config.py b/wqflask/utility/startup_config.py index f22f4b14..92f944bc 100644 --- a/wqflask/utility/startup_config.py +++ b/wqflask/utility/startup_config.py @@ -10,6 +10,7 @@ GREEN = '\033[92m' BOLD = '\033[1m' ENDC = '\033[0m' + def app_config(): app.config['SESSION_TYPE'] = 'filesystem' if not app.config.get('SECRET_KEY'): diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py index 4c478c36..f5ef81e1 100644 --- a/wqflask/utility/svg.py +++ b/wqflask/utility/svg.py @@ -459,11 +459,13 @@ class rect(SVGelement): 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: raise ValueError('both rx and ry are required') @@ -486,6 +488,7 @@ 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: raise ValueError('r is required') @@ -501,20 +504,24 @@ class circle(SVGelement): if stroke_width != None: self.attributes['stroke-width'] = stroke_width + class point(circle): """p=point(x,y,color) 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): 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): SVGelement.__init__(self, 'line', **args) if x1 != None: @@ -530,11 +537,13 @@ class line(SVGelement): 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: @@ -544,11 +553,13 @@ class polyline(SVGelement): 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: @@ -558,11 +569,13 @@ class polygon(SVGelement): 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: @@ -580,6 +593,7 @@ 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) if x != None: @@ -601,11 +615,13 @@ 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 + class pattern(SVGelement): """p=pattern(x,y,width,height,patternUnits,**args) @@ -613,6 +629,7 @@ 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): SVGelement.__init__(self, 'pattern', **args) if x != None: @@ -626,34 +643,40 @@ class pattern(SVGelement): if patternUnits != None: self.attributes['patternUnits'] = patternUnits + class title(SVGelement): """t=title(text,**args) 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): SVGelement.__init__(self, 'title', **args) if text != None: self.text = text + class description(SVGelement): """d=description(text,**args) 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): SVGelement.__init__(self, 'desc', **args) if text != None: self.text = text + class lineargradient(SVGelement): """lg=lineargradient(x1,y1,x2,y2,id,**args) 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): SVGelement.__init__(self, 'linearGradient', **args) if x1 != None: @@ -667,12 +690,14 @@ class lineargradient(SVGelement): if id != None: self.attributes['id'] = id + class radialgradient(SVGelement): """rg=radialgradient(cx,cy,r,fx,fy,id,**args) 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): SVGelement.__init__(self, 'radialGradient', **args) if cx != None: @@ -688,21 +713,25 @@ class radialgradient(SVGelement): 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 + 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) @@ -712,6 +741,7 @@ 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: raise ValueError('both height and width are required') @@ -721,11 +751,13 @@ class image(SVGelement): 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) @@ -736,6 +768,7 @@ 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): SVGelement.__init__(self, 'marker', **args) if id != None: @@ -751,17 +784,20 @@ class marker(SVGelement): if markerHeight != None: self.attributes['markerHeight'] = markerHeight + class group(SVGelement): """g=group(id,**args) a group is defined by an id and is used to contain elements g.addElement(SVGelement) """ + def __init__(self, id=None, **args): SVGelement.__init__(self, 'g', **args) if id != None: self.attributes['id'] = id + class symbol(SVGelement): """sy=symbol(id,viewbox,**args) @@ -778,14 +814,17 @@ class symbol(SVGelement): if viewBox != None: self.attributes['viewBox'] = _viewboxlist(viewBox) + class defs(SVGelement): """d=defs(**args) container for defining elements """ + def __init__(self, **args): SVGelement.__init__(self, 'defs', **args) + class switch(SVGelement): """sw=switch(**args) @@ -793,6 +832,7 @@ class switch(SVGelement): requiredFeatures, requiredExtensions and systemLanguage. Refer to the SVG specification for details. """ + def __init__(self, **args): SVGelement.__init__(self, 'switch', **args) @@ -802,6 +842,7 @@ 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) if x != None: @@ -821,32 +862,39 @@ 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) + 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) if id != None: self.attributes['id'] = id + class script(SVGelement): """sc=script(type,type,cdata,**args) 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) + 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: @@ -856,11 +904,13 @@ class animate(SVGelement): 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): SVGelement.__init__(self, 'animateMotion', **args) if pathdata != None: @@ -868,11 +918,13 @@ class animateMotion(SVGelement): 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) # As far as I know the attributeName is always transform @@ -884,11 +936,14 @@ class animateTransform(SVGelement): 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: @@ -899,11 +954,14 @@ class animateColor(SVGelement): 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: @@ -912,7 +970,6 @@ class set(SVGelement): self.attributes['dur'] = dur - class svg(SVGelement): """s=svg(viewbox,width,height,**args) @@ -928,6 +985,7 @@ class svg(SVGelement): d.setSVG(s) d.toXml() """ + def __init__(self, viewBox=None, width=None, height=None, **args): SVGelement.__init__(self, 'svg', **args) if viewBox != None: @@ -938,6 +996,7 @@ class svg(SVGelement): self.attributes['height'] = height self.namespace = "http://www.w3.org/2000/svg" + class drawing: """d=drawing() @@ -952,6 +1011,7 @@ class drawing: def __init__(self, entity={}): self.svg = None self.entity = entity + def setSVG(self, svg): self.svg = svg # Voeg een element toe aan de grafiek toe. @@ -1005,6 +1065,7 @@ class drawing: 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""" @@ -1053,6 +1114,7 @@ class drawing: f.close() except: print(("Cannot write SVG file: " + filename)) + def validate(self): try: import xml.parsers.xmlproc.xmlval @@ -1066,9 +1128,10 @@ class drawing: raise Exception("SVG is not well formed, see messages above") else: print("SVG well formed") -if __name__ == '__main__': +if __name__ == '__main__': + d = drawing() s = svg((0, 0, 100, 100)) r = rect(-100, -100, 300, 300, 'cyan') diff --git a/wqflask/utility/temp_data.py b/wqflask/utility/temp_data.py index 2088ba9a..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): diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 9b751344..4fe4db08 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -13,11 +13,13 @@ 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): """Resolve a setting from the environment or the global settings in app.config, with valid_path is a function checking whether the @@ -66,12 +68,14 @@ def get_setting(command_id, guess=None): # 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 False + def get_setting_int(id): v = get_setting(id) if isinstance(v, str): @@ -80,21 +84,25 @@ 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 @@ -107,38 +115,47 @@ def js_path(module=None): return try_guix 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) + def flat_files(subdir=None): base = get_setting("GENENETWORK_FILES") if 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) return fn + def assert_dir(dir): if not valid_path(dir): raise Exception("ERROR: can not find directory " + dir) return dir + def assert_writable_dir(dir): try: fn = dir + "/test.txt" @@ -150,16 +167,19 @@ 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) 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. @@ -179,9 +199,11 @@ def locate(name, subdir=None): 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) + def locate_ignore_error(name, subdir=None): """ Locate a static flat file in the GENENETWORK_FILES environment. @@ -200,17 +222,20 @@ def locate_ignore_error(name, subdir=None): 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' GREEN = '\033[92m' BOLD = '\033[1m' ENDC = '\033[0m' + def show_settings(): from utility.tools import LOG_LEVEL diff --git a/wqflask/utility/type_checking.py b/wqflask/utility/type_checking.py index 662bf794..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 @@ -23,18 +25,21 @@ def is_str(value): except: return False + 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): 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): if name in vars_obj: if not vars_obj[name] is None: diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py index ed59b0eb..f355a865 100644 --- a/wqflask/utility/webqtlUtil.py +++ b/wqflask/utility/webqtlUtil.py @@ -64,6 +64,7 @@ ParInfo = { # Accessory Functions ######################################### + def genRandStr(prefix="", length=8, chars=string.ascii_letters + string.digits): from random import choice _str = prefix[:] @@ -71,6 +72,7 @@ def genRandStr(prefix="", length=8, chars=string.ascii_letters + string.digits): _str += choice(chars) return _str + def ListNotNull(lst): '''Obsolete - Use built in function any (or all or whatever) @@ -83,6 +85,7 @@ def ListNotNull(lst): return 1 return None + 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""" @@ -91,6 +94,7 @@ def readLineCSV(line): # dcrowell July 2008 returnList[0] = returnList[0][1:] return returnList + def cmpEigenValue(A, B): try: if A[0] > B[0]: @@ -102,6 +106,7 @@ 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']: |