diff options
| author | Arun Isaac | 2023-12-29 18:55:37 +0000 |
|---|---|---|
| committer | Arun Isaac | 2023-12-29 19:01:46 +0000 |
| commit | 204a308be0f741726b9a620d88fbc22b22124c81 (patch) | |
| tree | b3cf66906674020b530c844c2bb4982c8a0e2d39 /wqflask/utility | |
| parent | 83062c75442160427b50420161bfcae2c5c34c84 (diff) | |
| download | genenetwork2-204a308be0f741726b9a620d88fbc22b22124c81.tar.gz | |
Namespace all modules under gn2.
We move all modules under a gn2 directory. This is important for
"correct" packaging and deployment as a Guix service.
Diffstat (limited to 'wqflask/utility')
27 files changed, 0 insertions, 3546 deletions
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py deleted file mode 100644 index df7156b4..00000000 --- a/wqflask/utility/Plot.py +++ /dev/null @@ -1,343 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by GeneNetwork Core Team 2010/10/20 - -from PIL import ImageColor -from PIL import ImageDraw -from PIL import ImageFont - -from math import * - -import utility.corestats as corestats -from base import webqtlConfig -from utility.pillow_utils import draw_rotated_text - - -# ---- Define common colours ---- # -BLUE = ImageColor.getrgb("blue") -BLACK = ImageColor.getrgb("black") -# ---- END: Define common colours ---- # - -# ---- FONT FILES ---- # -VERDANA_FILE = "./wqflask/static/fonts/verdana.ttf" -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 - - if rank == 0: - while strD[-1] in ('0', '.'): - if strD[-1] == '0' and strD[-2] == '.' and len(strD) <= 4: - break - elif strD[-1] == '.': - strD = strD[:-1] - break - else: - strD = strD[:-1] - - else: - strD = strD.split(".")[0] - - if strD == '-0.0': - 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 - count = int((end - start) / inc) - if start + count * inc != end: - # 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 - - - >>> find_outliers([3.504, 5.234, 6.123, 7.234, 3.542, 5.341, 7.852, 4.555, 12.537]) - (11.252500000000001, 0.5364999999999993) - - >>> find_outliers([9,12,15,17,31,50,7,5,6,8]) - (32.0, -8.0) - - If there are no vals, returns None for the upper and lower bounds, - which code that calls it will have to deal with. - >>> find_outliers([]) - (None, None) - - """ - - if vals: - stats = corestats.Stats(vals) - low_hinge = stats.percentile(25) - up_hinge = stats.percentile(75) - hstep = 1.5 * (up_hinge - low_hinge) - - upper_bound = up_hinge + hstep - lower_bound = low_hinge - hstep - - else: - upper_bound = None - lower_bound = None - - return upper_bound, lower_bound - -# 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 - - plotWidth = canvas.size[0] - xLeftOffset - xRightOffset - plotHeight = canvas.size[1] - yTopOffset - yBottomOffset - if plotHeight <= 0 or plotWidth <= 0: - return - - if len(data) < 2: - 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) and min_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) - j = xLow - dataXY = [] - Count = [] - while j <= xTop: - dataXY.append(j) - Count.append(0) - j += step - - for i, item in enumerate(data): - if (item == float('inf') or item > webqtlConfig.MAXLRS) and min_D < webqtlConfig.MAXLRS: - item = webqtlConfig.MAXLRS # maximum LRS value - j = int((item - xLow) / step) - Count[j] += 1 - - yLow, yTop, stepY = detScale(0, max(Count)) - - # 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 - im_drawer.rectangle( - 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) - 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) - - if YLabel: - draw_rotated_text(canvas, text=YLabel, - xy=(19, - 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) - if title: - 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: - 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: - return None - elif min == -1.0 and max == 1.0: - return [-1.2, 1.2, 12] - else: - a = max - min - if max != 0: - max += 0.1 * a - if min != 0: - 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) - div = 2.0 - while n < 5 or n > 15: - if n < 5: - c /= div - else: - c *= div - if div == 2.0: - div = 5.0 - else: - 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))) - - -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: - return [ImageColor.getrgb("rgb(100%,0%,0%)")] - elif n == 2: - return [ImageColor.getrgb("100%,0%,0%)"), - ImageColor.getrgb("rgb(0%,0%,100%)")] - elif n == 3: - 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 - for i in range(N): - x = float(i) / N - out[i] = ImageColor.getrgb("rgb({}%,{}%,{}%".format( - *[int(i * 100) for i in ( - redfunc(x), greenfunc(x), bluefunc(x))])) - out2 = [out[0]] - step = N / float(n - 1) - j = 0 - 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__": - _test() diff --git a/wqflask/utility/TDCell.py b/wqflask/utility/TDCell.py deleted file mode 100644 index 4b0f4b1d..00000000 --- a/wqflask/utility/TDCell.py +++ /dev/null @@ -1,41 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by GeneNetwork Core Team 2010/10/20 - -########################################################## -# -# Table Cell Class -# -########################################################## - - -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 - - def __str__(self): - return self.text diff --git a/wqflask/utility/THCell.py b/wqflask/utility/THCell.py deleted file mode 100644 index f533dcb8..00000000 --- a/wqflask/utility/THCell.py +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by GeneNetwork Core Team 2010/10/20 - -########################################################## -# -# Table Header Class -# -########################################################## - - -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 - - def __str__(self): - return self.text diff --git a/wqflask/utility/__init__.py b/wqflask/utility/__init__.py deleted file mode 100644 index 25273fa0..00000000 --- a/wqflask/utility/__init__.py +++ /dev/null @@ -1,35 +0,0 @@ -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 __repr__(self): - return pf(self.__dict__) - - -class Struct: - '''The recursive class for building and representing objects with. - - From http://stackoverflow.com/a/6573827/1175849 - - ''' - - def __init__(self, obj): - for k, v in list(obj.items()): - if isinstance(v, dict): - setattr(self, k, Struct(v)) - else: - setattr(self, k, v) - - def __getitem__(self, val): - return self.__dict__[val] - - def __repr__(self): - return '{%s}' % str(', '.join('%s : %s' % (k, repr(v)) for - (k, v) in list(self.__dict__.items()))) diff --git a/wqflask/utility/after.py b/wqflask/utility/after.py deleted file mode 100644 index 2b560e48..00000000 --- a/wqflask/utility/after.py +++ /dev/null @@ -1,15 +0,0 @@ -""" -See: http://flask.pocoo.org/docs/patterns/deferredcallbacks/#deferred-callbacks - -""" - -from flask import g - -from wqflask import app - - -def after_this_request(f): - if not hasattr(g, 'after_request_callbacks'): - g.after_request_callbacks = [] - g.after_request_callbacks.append(f) - return f diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py deleted file mode 100644 index 5d00d600..00000000 --- a/wqflask/utility/authentication_tools.py +++ /dev/null @@ -1,150 +0,0 @@ -import json -import requests - -from flask import g -from wqflask.database import database_connection -from base import webqtlConfig - -from utility.redis_tools import (get_redis_conn, - get_resource_info, - get_resource_id, - add_resource) -from utility.tools import get_setting, GN_PROXY_URL - -Redis = get_redis_conn() - -def check_resource_availability(dataset, user_id, trait_id=None): - # At least for now assume temporary entered traits are accessible - if type(dataset) == str or dataset.type == "Temp": - return webqtlConfig.DEFAULT_PRIVILEGES - - resource_id = get_resource_id(dataset, trait_id) - - # ZS: This should never be false, but it's technically possible if - # a non-Temp dataset somehow had a type other than - # Publish/ProbeSet/Geno - if resource_id: - resource_info = get_resource_info(resource_id) - - # If resource isn't already in redis, add it with default - # privileges - if not resource_info: - resource_info = add_new_resource(dataset, trait_id) - - # Check if super-user - we should probably come up with some - # way to integrate this into the proxy - if user_id in Redis.smembers("super_users"): - return webqtlConfig.SUPER_PRIVILEGES - - response = None - the_url = f"{GN_PROXY_URL}available?resource={resource_id}&user={user_id}" - try: - response = json.loads(requests.get(the_url).content) - except: - response = resource_info['default_mask'] - - return response - - -def add_new_resource(dataset, trait_id=None): - resource_ob = { - 'owner_id': "none", # webqtlConfig.DEFAULT_OWNER_ID, - 'default_mask': webqtlConfig.DEFAULT_PRIVILEGES, - 'group_masks': {} - } - - if dataset.type == "Publish": - group_code = get_group_code(dataset) - if group_code is None: - group_code = "" - resource_ob['name'] = group_code + "_" + str(trait_id) - resource_ob['data'] = { - 'dataset': dataset.id, - 'trait': trait_id - } - resource_ob['type'] = 'dataset-publish' - elif dataset.type == "Geno": - resource_ob['name'] = dataset.name - resource_ob['data'] = { - 'dataset': dataset.id - } - resource_ob['type'] = 'dataset-geno' - else: - resource_ob['name'] = dataset.name - resource_ob['data'] = { - 'dataset': dataset.id - } - resource_ob['type'] = 'dataset-probeset' - - resource_info = add_resource(resource_ob, update=False) - - return resource_info - - -def get_group_code(dataset): - with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor: - cursor.execute( - "SELECT InbredSetCode FROM InbredSet WHERE Name=%s", - (dataset.group.name,) - ) - if results := cursor.fetchone(): - return results[0] - return "" - - -def check_admin(resource_id=None): - the_url = GN_PROXY_URL + "available?resource={}&user={}".format( - resource_id, g.user_session.user_id) - try: - response = json.loads(requests.get(the_url).content)['admin'] - except: - resource_info = get_resource_info(resource_id) - response = resource_info['default_mask']['admin'] - - if type(response) is list: - if 'edit-admins' in response: - return 'edit_admins' - elif 'edit-access' in response: - return 'edit-access' - - return response - - -def check_owner(dataset=None, trait_id=None, resource_id=None): - if resource_id: - resource_info = get_resource_info(resource_id) - if g.user_session.user_id == resource_info['owner_id']: - return resource_id - else: - resource_id = get_resource_id(dataset, trait_id) - if resource_id: - resource_info = get_resource_info(resource_id) - if g.user_session.user_id == resource_info['owner_id']: - return resource_id - - return False - - -def check_owner_or_admin(dataset=None, trait_id=None, resource_id=None): - if not resource_id: - if dataset.type == "Temp": - return "not-admin" - else: - resource_id = get_resource_id(dataset, trait_id) - - try: - user_id = g.user_session.user_id.encode('utf-8') - except: - user_id = g.user_session.user_id - - if user_id in Redis.smembers("super_users"): - return "owner" - - resource_info = get_resource_info(resource_id) - if resource_info: - if user_id == resource_info['owner_id']: - return "owner" - else: - return check_admin(resource_id) - - return "not-admin" diff --git a/wqflask/utility/chunks.py b/wqflask/utility/chunks.py deleted file mode 100644 index f6e88cbe..00000000 --- a/wqflask/utility/chunks.py +++ /dev/null @@ -1,30 +0,0 @@ -import math - - -def divide_into_chunks(the_list, number_chunks): - """Divides a list into approximately number_chunks smaller lists - - >>> divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 3) - [[1, 2, 7], [3, 22, 8], [5, 22, 333]] - >>> divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 4) - [[1, 2, 7], [3, 22, 8], [5, 22, 333]] - >>> divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 5) - [[1, 2], [7, 3], [22, 8], [5, 22], [333]] - >>> - - """ - length = len(the_list) - - if length == 0: - return [[]] - - if length <= number_chunks: - number_chunks = length - - chunksize = int(math.ceil(length / number_chunks)) - - chunks = [] - for counter in range(0, length, chunksize): - chunks.append(the_list[counter:counter + chunksize]) - - return chunks diff --git a/wqflask/utility/corestats.py b/wqflask/utility/corestats.py deleted file mode 100644 index da0a21db..00000000 --- a/wqflask/utility/corestats.py +++ /dev/null @@ -1,86 +0,0 @@ -#!/usr/bin/env python - -# corestats.py (COREy STATS) -# Copyright (c) 2006-2007, Corey Goldberg (corey@goldb.org) -# -# statistical calculation class -# for processing numeric sequences -# -# license: GNU LGPL -# -# This library is free software; you can redistribute it and/or -# modify it under the terms of the GNU Lesser General Public -# License as published by the Free Software Foundation; either -# version 2.1 of the License, or (at your option) any later version. - -import sys - -# ZS: Should switch to using some third party library for this; maybe scipy has an equivalent - - -class Stats: - - def __init__(self, sequence): - # sequence of numbers we will process - # convert all items to floats for numerical processing - self.sequence = [float(item) for item in sequence] - - def sum(self): - if len(self.sequence) < 1: - return None - else: - return sum(self.sequence) - - def count(self): - return len(self.sequence) - - def min(self): - if len(self.sequence) < 1: - return None - else: - return min(self.sequence) - - def max(self): - if len(self.sequence) < 1: - return None - else: - return max(self.sequence) - - def avg(self): - if len(self.sequence) < 1: - return None - else: - return sum(self.sequence) / len(self.sequence) - - def stdev(self): - if len(self.sequence) < 1: - return None - else: - avg = self.avg() - sdsq = sum([(i - avg) ** 2 for i in self.sequence]) - stdev = (sdsq / (len(self.sequence) - 1)) ** .5 - return stdev - - def percentile(self, percentile): - if len(self.sequence) < 1: - value = None - elif (percentile >= 100): - 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)) - self.sequence.sort() - value = self.sequence[element_idx] - return value - -# Sample script using this class: -# ------------------------------------------- -# #!/usr/bin/env python -# import corestats -# -# sequence = [1, 2.5, 7, 13.4, 8.0] -# stats = corestats.Stats(sequence) -# print stats.avg() -# print stats.percentile(90) -# ------------------------------------------- diff --git a/wqflask/utility/corr_result_helpers.py b/wqflask/utility/corr_result_helpers.py deleted file mode 100644 index ea3ababf..00000000 --- a/wqflask/utility/corr_result_helpers.py +++ /dev/null @@ -1,42 +0,0 @@ -def normalize_values(a_values, b_values): - """ - Trim two lists of values to contain only the values they both share - - Given two lists of sample values, trim each list so that it contains - only the samples that contain a value in both lists. Also returns - the number of such samples. - - >>> normalize_values([2.3, None, None, 3.2, 4.1, 5], [3.4, 7.2, 1.3, None, 6.2, 4.1]) - ([2.3, 4.1, 5], [3.4, 6.2, 4.1], 3) - - """ - - min_length = min(len(a_values), len(b_values)) - a_new = [] - b_new = [] - for a, b in zip(a_values, b_values): - if not (a == None or b == None): - a_new.append(a) - b_new.append(b) - return a_new, b_new, len(a_new) - - -def common_keys(a_samples, b_samples): - """ - >>> a = dict(BXD1 = 9.113, BXD2 = 9.825, BXD14 = 8.985, BXD15 = 9.300) - >>> b = dict(BXD1 = 9.723, BXD3 = 9.825, BXD14 = 9.124, BXD16 = 9.300) - >>> sorted(common_keys(a, b)) - ['BXD1', 'BXD14'] - """ - return set(a_samples.keys()).intersection(set(b_samples.keys())) - - -def normalize_values_with_samples(a_samples, b_samples): - common_samples = common_keys(a_samples, b_samples) - a_new = {} - b_new = {} - for sample in common_samples: - a_new[sample] = a_samples[sample] - b_new[sample] = b_samples[sample] - - return a_new, b_new, len(a_new) diff --git a/wqflask/utility/db_tools.py b/wqflask/utility/db_tools.py deleted file mode 100644 index 98da33f2..00000000 --- a/wqflask/utility/db_tools.py +++ /dev/null @@ -1,23 +0,0 @@ -from utility.tools import get_setting -from wqflask.database import database_connection - - -def escape_(string): - with database_connection(get_setting("SQL_URI")) as conn: - return conn.escape_string(str(string)) - - -def create_in_clause(items): - """Create an in clause for mysql""" - in_clause = ', '.join("'{}'".format(x) for x in mescape(*items)) - in_clause = '( {} )'.format(in_clause) - return in_clause - - -def mescape(*items): - """Multiple escape""" - return [escape_(str(item)).decode('utf8') for item in items] - - -def escape(string_): - return escape_(string_).decode('utf8') diff --git a/wqflask/utility/external.py b/wqflask/utility/external.py deleted file mode 100644 index 805d2ffe..00000000 --- a/wqflask/utility/external.py +++ /dev/null @@ -1,10 +0,0 @@ -# Call external program - -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/formatting.py b/wqflask/utility/formatting.py deleted file mode 100644 index 1da3e9b7..00000000 --- a/wqflask/utility/formatting.py +++ /dev/null @@ -1,121 +0,0 @@ -def numify(number, singular=None, plural=None): - """Turn a number into a word if less than 13 and optionally add a singular or plural word - - >>> numify(3) - 'three' - - >>> numify(1, 'item', 'items') - 'one item' - - >>> numify(9, 'book', 'books') - 'nine books' - - You can add capitalize to change the capitalization - >>> numify(9, 'book', 'books').capitalize() - 'Nine books' - - Or capitalize every word using title - >>> numify(9, 'book', 'books').title() - 'Nine Books' - - >>> numify(15) - '15' - - >>> numify(0) - '0' - - >>> numify(12334, 'hippopotamus', 'hippopotami') - '12,334 hippopotami' - - """ - num_repr = {0: "zero", - 1: "one", - 2: "two", - 3: "three", - 4: "four", - 5: "five", - 6: "six", - 7: "seven", - 8: "eight", - 9: "nine", - 10: "ten", - 11: "eleven", - 12: "twelve"} - - if number == 1: - word = singular - else: - word = plural - - if number in num_repr: - number = num_repr[number] - elif number > 9999: - number = commify(number) - - if word: - return "%s %s" % (number, word) - else: - return str(number) - - -def commify(n): - """Add commas to an integer n. - - See http://stackoverflow.com/questions/3909457/whats-the-easiest-way-to-add-commas-to-an-integer-in-python - But I (Sam) made some small changes based on http://www.grammarbook.com/numbers/numbers.asp - - >>> commify(1) - '1' - >>> commify(123) - '123' - >>> commify(1234) - '1234' - >>> commify(12345) - '12,345' - >>> commify(1234567890) - '1,234,567,890' - >>> commify(123.0) - '123.0' - >>> commify(1234.5) - '1234.5' - >>> commify(1234.56789) - '1234.56789' - >>> commify(123456.789) - '123,456.789' - >>> commify('%.2f' % 1234.5) - '1234.50' - >>> commify(None) - >>> - - """ - if n is None: - return None - - n = str(n) - - if len(n) <= 4: # Might as well do this early - return n - - if '.' in n: - dollars, cents = n.split('.') - else: - dollars, cents = n, None - - # Don't commify numbers less than 10000 - if len(dollars) <= 4: - return n - - r = [] - for i, c in enumerate(reversed(str(dollars))): - if i and (not (i % 3)): - r.insert(0, ',') - r.insert(0, c) - out = ''.join(r) - if cents: - out += '.' + cents - return out - - -if __name__ == '__main__': - import doctest - doctest.testmod() diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py deleted file mode 100644 index c7a1ea59..00000000 --- a/wqflask/utility/gen_geno_ob.py +++ /dev/null @@ -1,182 +0,0 @@ -class genotype: - """ - Replacement for reaper.Dataset so we can remove qtlreaper use while still generating mapping output figure - """ - - def __init__(self, filename): - self.group = None - self.type = "riset" - self.prgy = [] - self.nprgy = 0 - self.mat = -1 - self.pat = 1 - self.het = 0 - self.unk = "U" - 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 - self.cm_column = 2 - self.mb_column = 3 - - self.chromosomes = [] - - self.read_file(filename) - - def __iter__(self): - return iter(self.chromosomes) - - def __getitem__(self, index): - return self.chromosomes[index] - - def __len__(self): - 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 - # 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 - chr_ob = None - for marker in qtl_results: - locus = Locus(self) - # 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']) - if this_chr == "20": - this_chr = "X" - chr_ob = Chr(this_chr, self) - if 'chr' in marker: - locus.chr = str(marker['chr']) - if 'name' in marker: - locus.name = marker['name'] - if 'Mb' in marker: - locus.Mb = marker['Mb'] - if 'cM' in marker: - locus.cM = marker['cM'] - chr_ob.loci.append(locus) - - self.chromosomes.append(chr_ob) - - return self - - def read_file(self, filename): - 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 - chr_ob = None - for line in lines: - if line[0] == "#": - continue - elif line[0] == "@": - label = line.split(":")[0][1:] - if label == "name": - self.group = line.split(":")[1].strip() - elif label == "filler": - if line.split(":")[1].strip() == "yes": - self.filler = True - elif label == "type": - self.type = line.split(":")[1].strip() - elif label == "mat": - self.mat = line.split(":")[1].strip() - elif label == "pat": - self.pat = line.split(":")[1].strip() - elif label == "het": - self.het = line.split(":")[1].strip() - elif label == "unk": - self.unk = line.split(":")[1].strip() - else: - continue - elif line[:3] == "Chr": - header_row = line.split("\t") - if header_row[2] == "Mb": - self.mb_exists = True - self.mb_column = 2 - self.cm_column = 3 - elif header_row[3] == "Mb": - self.mb_exists = True - self.mb_column = 3 - elif header_row[2] == "cM": - self.cm_column = 2 - - if self.mb_exists: - self.prgy = header_row[4:] - else: - self.prgy = header_row[3:] - self.nprgy = len(self.prgy) - else: - if line.split("\t")[0] != this_chr: - if this_chr != "": - self.chromosomes.append(chr_ob) - this_chr = line.split("\t")[0] - chr_ob = Chr(line.split("\t")[0], self) - chr_ob.add_marker(line.split("\t")) - - self.chromosomes.append(chr_ob) - - -class Chr: - def __init__(self, name, geno_ob): - self.name = name - self.loci = [] - self.mb_exists = geno_ob.mb_exists - self.cm_column = geno_ob.cm_column - self.mb_column = geno_ob.mb_column - self.geno_ob = geno_ob - - def __iter__(self): - return iter(self.loci) - - def __getitem__(self, index): - return self.loci[index] - - def __len__(self): - return len(self.loci) - - 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 - self.name = None - self.cM = None - self.Mb = None - self.genotype = [] - if marker_row: - self.chr = marker_row[0] - self.name = marker_row[1] - 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 - try: - self.Mb = float( - marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else None - except: - self.Mb = self.cM - - geno_table = { - geno_ob.mat: -1, - geno_ob.pat: 1, - geno_ob.het: 0, - geno_ob.unk: "U" - } - - self.genotype = [] - if geno_ob.mb_exists: - start_pos = 4 - else: - start_pos = 3 - - 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 - self.genotype.append("U") diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py deleted file mode 100644 index 86d9823e..00000000 --- a/wqflask/utility/genofile_parser.py +++ /dev/null @@ -1,100 +0,0 @@ -# CTL analysis for GN2 -# Author / Maintainer: Danny Arends <Danny.Arends@gmail.com> - -import sys -import os -import glob -import traceback -import gzip - - -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 = [] - - -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 - - 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_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 - - 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 deleted file mode 100644 index 8b20bd74..00000000 --- a/wqflask/utility/helper_functions.py +++ /dev/null @@ -1,69 +0,0 @@ -from base import data_set -from base.trait import create_trait -from base.species import TheSpecies - -from utility import hmac -from utility.tools import get_setting - -from wqflask.database import database_connection - - -def get_species_dataset_trait(self, start_vars): - if "temp_trait" in list(start_vars.keys()): - if start_vars['temp_trait'] == "True": - self.dataset = data_set.create_dataset( - dataset_name="Temp", - dataset_type="Temp", - group_name=start_vars['group']) - else: - self.dataset = data_set.create_dataset(start_vars['dataset']) - else: - self.dataset = data_set.create_dataset(start_vars['dataset']) - self.species = TheSpecies(dataset=self.dataset) - self.this_trait = create_trait(dataset=self.dataset, - name=start_vars['trait_id'], - cellid=None, - get_qtl_info=True) - -def get_trait_db_obs(self, trait_db_list): - if isinstance(trait_db_list, str): - trait_db_list = trait_db_list.split(",") - - self.trait_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?" - trait_name, dataset_name = data.split(":")[:2] - if dataset_name == "Temp": - dataset_ob = data_set.create_dataset( - dataset_name=dataset_name, dataset_type="Temp", - group_name=trait_name.split("_")[2]) - else: - dataset_ob = data_set.create_dataset(dataset_name) - trait_ob = create_trait(dataset=dataset_ob, - name=trait_name, - cellid=None) - if trait_ob: - self.trait_list.append((trait_ob, dataset_ob)) - - -def get_species_groups(): - """Group each species into a group""" - _menu = {} - species, group_name = None, None - with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor: - cursor.execute( - "SELECT s.MenuName, i.InbredSetName FROM InbredSet i " - "INNER JOIN Species s ON s.SpeciesId = i.SpeciesId " - "ORDER BY i.SpeciesId ASC, i.Name ASC" - ) - for species, group_name in cursor.fetchall(): - if species in _menu: - if _menu.get(species): - _menu = _menu[species].append(group_name) - else: - _menu[species] = [group_name] - return [{"species": key, - "groups": value} for key, value in - list(_menu.items())] diff --git a/wqflask/utility/hmac.py b/wqflask/utility/hmac.py deleted file mode 100644 index 29891677..00000000 --- a/wqflask/utility/hmac.py +++ /dev/null @@ -1,43 +0,0 @@ -import hmac -import hashlib - -from flask import url_for - -from wqflask import app - - -def hmac_creation(stringy): - """Helper function to create the actual hmac""" - - secret = app.config['SECRET_HMAC_CODE'] - hmaced = hmac.new(bytearray(secret, "latin-1"), - bytearray(stringy, "utf-8"), - hashlib.sha1) - hm = hmaced.hexdigest() - # ZS: Leaving the below comment here to ask Pjotr about - # "Conventional wisdom is that you don't lose much in terms of security if you throw away up to half of the output." - # http://www.w3.org/QA/2009/07/hmac_truncation_in_xml_signatu.html - hm = hm[:20] - return hm - - -def data_hmac(stringy): - """Takes arbitrary data string and appends :hmac so we know data hasn't been tampered with""" - return stringy + ":" + hmac_creation(stringy) - - -def url_for_hmac(endpoint, **values): - """Like url_for but adds an hmac at the end to insure the url hasn't been tampered with""" - - url = url_for(endpoint, **values) - - hm = hmac_creation(url) - if '?' in url: - combiner = "&" - else: - combiner = "?" - return url + combiner + "hm=" + hm - - -app.jinja_env.globals.update(url_for_hmac=url_for_hmac, - data_hmac=data_hmac) diff --git a/wqflask/utility/json/__init__.py b/wqflask/utility/json/__init__.py deleted file mode 100644 index b1141a34..00000000 --- a/wqflask/utility/json/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -"""Local JSON utilities.""" - -from .encoders import CustomJSONEncoder diff --git a/wqflask/utility/json/encoders.py b/wqflask/utility/json/encoders.py deleted file mode 100644 index 7c5839ac..00000000 --- a/wqflask/utility/json/encoders.py +++ /dev/null @@ -1,17 +0,0 @@ -"""Custom JSON encoders""" -from uuid import UUID -from json import JSONEncoder - -# Do not use this `__ENCODERS__` variable outside of this module. -__ENCODERS__ = { - UUID: lambda obj: str(obj) -} - -class CustomJSONEncoder(JSONEncoder): - """Custom JSONEncoder class.""" - def default(self, obj): - """Serialise `obj` to a JSON representation.""" - obj_type = type(obj) - if obj_type in __ENCODERS__: - return __ENCODERS__[obj_type](obj) - return JSONEncoder.default(self, obj) diff --git a/wqflask/utility/monads.py b/wqflask/utility/monads.py deleted file mode 100644 index 2d708261..00000000 --- a/wqflask/utility/monads.py +++ /dev/null @@ -1,114 +0,0 @@ -"""Monadic utilities - -This module is a collection of monadic utilities for use in -GeneNetwork. It includes: - -* MonadicDict - monadic version of the built-in dictionary -* MonadicDictCursor - monadic version of MySQLdb.cursors.DictCursor - that returns a MonadicDict instead of the built-in dictionary -""" - -from collections import UserDict -from functools import partial - -from MySQLdb.cursors import DictCursor -from pymonad.maybe import Just, Nothing - -class MonadicDict(UserDict): - """ - Monadic version of the built-in dictionary. - - Keys in this dictionary can be any python object, but values must - be monadic values. - - from pymonad.maybe import Just, Nothing - - Initialize by setting individual keys to monadic values. - >>> d = MonadicDict() - >>> d["foo"] = Just(1) - >>> d["bar"] = Nothing - >>> d - {'foo': 1} - - Initialize by converting a built-in dictionary object. - >>> MonadicDict({"foo": 1}) - {'foo': 1} - >>> MonadicDict({"foo": 1, "bar": None}) - {'foo': 1} - - Initialize from a built-in dictionary object with monadic values. - >>> MonadicDict({"foo": Just(1)}, convert=False) - {'foo': 1} - >>> MonadicDict({"foo": Just(1), "bar": Nothing}, convert=False) - {'foo': 1} - - Get values. For non-existent keys, Nothing is returned. Else, a - Just value is returned. - >>> d["foo"] - Just 1 - >>> d["bar"] - Nothing - - Convert MonadicDict object to a built-in dictionary object. - >>> d.data - {'foo': 1} - >>> type(d) - <class 'utility.monads.MonadicDict'> - >>> type(d.data) - <class 'dict'> - - Delete keys. Deleting non-existent keys does nothing. - >>> del d["bar"] - >>> d - {'foo': 1} - >>> del d["foo"] - >>> d - {} - """ - def __init__(self, d={}, convert=True): - """Initialize monadic dictionary. - - If convert is False, values in dictionary d must be - monadic. If convert is True, values in dictionary d are - converted to monadic values. - """ - if convert: - super().__init__({key:Just(value) for key, value in d.items() - if value is not None}) - else: - super().__init__(d) - def __getitem__(self, key): - """Get key from dictionary. - - If key exists in the dictionary, return a Just value. Else, - return Nothing. - """ - try: - return Just(self.data[key]) - except KeyError: - return Nothing - def __setitem__(self, key, value): - """Set key in dictionary. - - value must be a monadic value---either Nothing or a Just - value. If value is a Just value, set it in the dictionary. If - value is Nothing, do nothing. - """ - value.bind(partial(super().__setitem__, key)) - def __delitem__(self, key): - """Delete key from dictionary. - - If key exists in the dictionary, delete it. Else, do nothing. - """ - try: - super().__delitem__(key) - except KeyError: - pass - - -def sql_query_mdict(conn, query): - """Execute SQL query and return a generator of MonadicDict objects.""" - with conn.cursor(DictCursor) as cursor: - cursor.execute(query) - while (row := cursor.fetchone()): - yield MonadicDict(row) diff --git a/wqflask/utility/pillow_utils.py b/wqflask/utility/pillow_utils.py deleted file mode 100644 index e302df18..00000000 --- a/wqflask/utility/pillow_utils.py +++ /dev/null @@ -1,28 +0,0 @@ -from PIL import Image, ImageColor, ImageDraw, ImageFont - -from utility.tools import TEMPDIR - -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""" - tmp_img = Image.new("RGBA", font.getsize(text), color=(0, 0, 0, 0)) - draw_text = ImageDraw.Draw(tmp_img) - draw_text.text(text=text, xy=(0, 0), font=font, fill=fill) - tmp_img2 = tmp_img.rotate(angle, expand=1) - tmp_img2.save("/{0}/{1}.png".format(TEMPDIR, text), format="png") - 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) - draw_ctx.polygon(xy, fill=fill) - draw_ctx.line(xy, fill=outline, width=width) diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py deleted file mode 100644 index 945efbbd..00000000 --- a/wqflask/utility/redis_tools.py +++ /dev/null @@ -1,285 +0,0 @@ -import uuid -import simplejson as json -import datetime - -import redis # used for collections - -from utility.hmac import hmac_creation - - -def get_redis_conn(): - Redis = redis.StrictRedis(port=6379) - return Redis - - -Redis = get_redis_conn() - - -def is_redis_available(): - try: - Redis.ping() - except: - return False - return True - - -def load_json_from_redis(item_list, column_value): - if type(column_value) == str: - column_value = str.encode(column_value) - try: - return json.loads(item_list[column_value]) - except: - return None - - -def get_user_id(column_name, column_value): - user_list = Redis.hgetall("users") - key_list = [] - for key in user_list: - user_ob = json.loads(user_list[key]) - if column_name in user_ob and user_ob[column_name] == column_value: - return key - - return None - - -def get_user_by_unique_column(column_name, column_value): - item_details = None - - user_list = Redis.hgetall("users") - if column_name != "user_id": - for key in user_list: - user_ob = json.loads(user_list[key]) - if column_name in user_ob and user_ob[column_name] == column_value: - item_details = user_ob - else: - item_details = load_json_from_redis(user_list, column_value) - - return item_details - - -def set_user_attribute(user_id, column_name, column_value): - user_info = json.loads(Redis.hget("users", user_id)) - user_info[column_name] = column_value - - Redis.hset("users", user_id, json.dumps(user_info)) - - -def get_user_collections(user_id): - collections = None - collections = Redis.hget("collections", user_id) - - if collections: - return json.loads(collections) - else: - return [] - - -def save_user(user, user_id): - Redis.hset("users", user_id, json.dumps(user)) - - -def save_collections(user_id, collections_ob): - Redis.hset("collections", user_id, collections_ob) - - -def save_verification_code(user_email, code): - Redis.hset("verification_codes", code, user_email) - - -def check_verification_code(code): - email_address = None - user_details = None - email_address = Redis.hget("verification_codes", code) - - if email_address: - user_details = get_user_by_unique_column( - 'email_address', email_address) - if user_details: - return user_details - else: - return None - else: - return None - - -def get_user_groups(user_id): - # Get the groups where a user is an admin or a member and - # return lists corresponding to those two sets of groups - admin_group_ids = [] # Group IDs where user is an admin - user_group_ids = [] # Group IDs where user is a regular user - groups_list = Redis.hgetall("groups") - for group_id, group_details in groups_list.items(): - try: - _details = json.loads(group_details) - group_admins = set([this_admin if this_admin else None for this_admin in _details['admins']]) - group_members = set([this_member if this_member else None for this_member in _details['members']]) - if user_id in group_admins: - admin_group_ids.append(group_id) - elif user_id in group_members: - user_group_ids.append(group_id) - else: - continue - except: - continue - - admin_groups = [] - user_groups = [] - for the_id in admin_group_ids: - admin_groups.append(get_group_info(the_id)) - for the_id in user_group_ids: - user_groups.append(get_group_info(the_id)) - - return admin_groups, user_groups - - -def get_group_info(group_id): - group_json = Redis.hget("groups", group_id) - group_info = None - if group_json: - group_info = json.loads(group_json) - - return group_info - - -def create_group(admin_user_ids, member_user_ids=[], - group_name="Default Group Name"): - group_id = str(uuid.uuid4()) - new_group = { - "id": group_id, - "admins": admin_user_ids, - "members": member_user_ids, - "name": group_name, - "created_timestamp": datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'), - "changed_timestamp": datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p') - } - - Redis.hset("groups", group_id, json.dumps(new_group)) - - return new_group - - -def delete_group(user_id, group_id): - # ZS: If user is an admin of a group, remove it from the groups hash - group_info = get_group_info(group_id) - if user_id in group_info["admins"]: - Redis.hdel("groups", group_id) - return get_user_groups(user_id) - else: - None - - -# ZS "admins" is just to indicate whether the users should be added to -# the groups admins or regular users set -def add_users_to_group(user_id, group_id, user_emails=[], admins=False): - group_info = get_group_info(group_id) - # ZS: Just to make sure that the user is an admin for the group, - # even though they shouldn't be able to reach this point unless - # they are - if user_id in group_info["admins"]: - if admins: - group_users = set(group_info["admins"]) - else: - group_users = set(group_info["members"]) - - for email in user_emails: - user_id = get_user_id("email_address", email) - group_users.add(user_id) - - if admins: - group_info["admins"] = list(group_users) - else: - group_info["members"] = list(group_users) - - group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime( - '%b %d %Y %I:%M%p') - Redis.hset("groups", group_id, json.dumps(group_info)) - return group_info - else: - return None - - -# ZS: User type is because I assume admins can remove other admins -def remove_users_from_group(user_id, - users_to_remove_ids, - group_id, - user_type="members"): - group_info = get_group_info(group_id) - - if user_id in group_info["admins"]: - users_to_remove_set = set(users_to_remove_ids) - # ZS: Make sure an admin can't remove themselves from a group, - # since I imagine we don't want groups to be able to become - # admin-less - if user_type == "admins" and user_id in users_to_remove_set: - users_to_remove_set.remove(user_id) - group_users = set(group_info[user_type]) - group_users -= users_to_remove_set - group_info[user_type] = list(group_users) - group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime( - '%b %d %Y %I:%M%p') - Redis.hset("groups", group_id, json.dumps(group_info)) - - -def change_group_name(user_id, group_id, new_name): - group_info = get_group_info(group_id) - if user_id in group_info["admins"]: - group_info["name"] = new_name - Redis.hset("groups", group_id, json.dumps(group_info)) - return group_info - else: - return None - - -def get_resources(): - resource_list = Redis.hgetall("resources") - return resource_list - - -def get_resource_id(dataset, trait_id=None): - resource_id = False - if dataset.type == "Publish": - if trait_id: - resource_id = hmac_creation("{}:{}:{}".format( - 'dataset-publish', dataset.id, trait_id)) - elif dataset.type == "ProbeSet": - resource_id = hmac_creation( - "{}:{}".format('dataset-probeset', dataset.id)) - elif dataset.type == "Geno": - resource_id = hmac_creation( - "{}:{}".format('dataset-geno', dataset.id)) - - return resource_id - - -def get_resource_info(resource_id): - resource_info = Redis.hget("resources", resource_id) - if resource_info: - return json.loads(resource_info) - else: - return None - - -def add_resource(resource_info, update=True): - if 'trait' in resource_info['data']: - resource_id = hmac_creation('{}:{}:{}'.format( - str(resource_info['type']), str( - resource_info['data']['dataset']), - str(resource_info['data']['trait']))) - else: - resource_id = hmac_creation('{}:{}'.format( - str(resource_info['type']), str(resource_info['data']['dataset']))) - - if update or not Redis.hexists("resources", resource_id): - Redis.hset("resources", resource_id, json.dumps(resource_info)) - - return resource_info - - -def add_access_mask(resource_id, group_id, access_mask): - the_resource = get_resource_info(resource_id) - the_resource['group_masks'][group_id] = access_mask - - Redis.hset("resources", resource_id, json.dumps(the_resource)) - - return the_resource diff --git a/wqflask/utility/startup_config.py b/wqflask/utility/startup_config.py deleted file mode 100644 index 69cac124..00000000 --- a/wqflask/utility/startup_config.py +++ /dev/null @@ -1,41 +0,0 @@ - -from wqflask import app - -from utility.tools import WEBSERVER_MODE -from utility.tools import show_settings -from utility.tools import get_setting_int -from utility.tools import get_setting -from utility.tools import get_setting_bool - - -BLUE = '\033[94m' -GREEN = '\033[92m' -BOLD = '\033[1m' -ENDC = '\033[0m' - - -def app_config(): - app.config['SESSION_TYPE'] = app.config.get('SESSION_TYPE', 'filesystem') - if not app.config.get('SECRET_KEY'): - import os - app.config['SECRET_KEY'] = str(os.urandom(24)) - mode = WEBSERVER_MODE - if mode in ["DEV", "DEBUG"]: - app.config['TEMPLATES_AUTO_RELOAD'] = True - if mode == "DEBUG": - app.debug = True - - print("==========================================") - show_settings() - - port = get_setting_int("SERVER_PORT") - - if get_setting_bool("USE_GN_SERVER"): - print(f"GN2 API server URL is [{BLUE}GN_SERVER_URL{ENDC}]") - import requests - page = requests.get(get_setting("GN_SERVER_URL")) - if page.status_code != 200: - raise Exception("API server not found!") - print(f"GN2 is running. Visit {BLUE}" - f"[http://localhost:{str(port)}/{ENDC}]" - f"({get_setting('WEBSERVER_URL')})") diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py deleted file mode 100644 index 912cd04c..00000000 --- a/wqflask/utility/svg.py +++ /dev/null @@ -1,1179 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by GeneNetwork Core Team 2010/10/20 - -#!/usr/bin/env python -# Copyright (c) 2002, Fedor Baart & Hans de Wit (Stichting Farmaceutische Kengetallen) -# All rights reserved. -## -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -## -# Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -## -# Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -## -# Neither the name of the Stichting Farmaceutische Kengetallen nor the names of -# its contributors may be used to endorse or promote products derived from this -# software without specific prior written permission. -## -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE -# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL -# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR -# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER -# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, -# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE -# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -# Thanks to Gerald Rosennfellner for his help and useful comments. - -import sys -import exceptions -__doc__ = """Use SVGdraw to generate your SVGdrawings. - -SVGdraw uses an object model drawing and a method toXML to create SVG graphics -by using easy to use classes and methods usualy you start by creating a drawing eg - - d=drawing() - # then you create a SVG root element - s=svg() - # then you add some elements eg a circle and add it to the svg root element - c=circle() - # you can supply attributes by using named arguments. - c=circle(fill='red',stroke='blue') - # or by updating the attributes attribute: - c.attributes['stroke-width']=1 - s.addElement(c) - # then you add the svg root element to the drawing - d.setSVG(s) - # and finaly you xmlify the drawing - d.toXml() - - -this results in the svg source of the drawing, which consists of a circle -on a white background. Its as easy as that;) -This module was created using the SVG specification of www.w3c.org and the -O'Reilly (www.oreilly.com) python books as information sources. A svg viewer -is available from www.adobe.com""" - -__version__ = "1.0" - -# there are two possibilities to generate svg: -# via a dom implementation and directly using <element>text</element> strings -# the latter is way faster (and shorter in coding) -# the former is only used in debugging svg programs -# maybe it will be removed alltogether after a while -# with the following variable you indicate whether to use the dom implementation -# Note that PyXML is required for using the dom implementation. -# It is also possible to use the standard minidom. But I didn't try that one. -# Anyway the text based approach is about 60 times faster than using the full dom implementation. -use_dom_implementation = 0 - - -if use_dom_implementation != 0: - try: - from xml.dom import implementation - from xml.dom.ext import PrettyPrint - except: - raise exceptions.ImportError( - "PyXML is required for using the dom implementation") -# The implementation is used for the creating the XML document. -# The prettyprint module is used for converting the xml document object to a xml file - -sys.setrecursionlimit = 50 -# The recursion limit is set conservative so mistakes like s=svg() s.addElement(s) -# won't eat up too much processor time. - -# the following code is pasted form xml.sax.saxutils -# it makes it possible to run the code without the xml sax package installed -# To make it possible to have <rubbish> in your text elements, it is necessary to escape the texts - - -def _escape(data, entities={}): - """Escape &, <, and > in a string of data. - - You can escape other strings of data by passing a dictionary as - the optional entities parameter. The keys and values must all be - strings; each key will be replaced with its corresponding value. - """ - # data = data.replace("&", "&") - data = data.replace("<", "<") - data = data.replace(">", ">") - for chars, entity in list(entities.items()): - data = data.replace(chars, entity) - return data - - -def _quoteattr(data, entities={}): - """Escape and quote an attribute value. - - Escape &, <, and > in a string of data, then quote it for use as - an attribute value. The \" character will be escaped as well, if - necessary. - - You can escape other strings of data by passing a dictionary as - the optional entities parameter. The keys and values must all be - strings; each key will be replaced with its corresponding value. - """ - data = _escape(data, entities) - if '"' in data: - if "'" in data: - data = '"%s"' % data.replace('"', """) - else: - data = "'%s'" % data - else: - data = '"%s"' % data - return data - - -def _xypointlist(a): - """formats a list of xy pairs""" - s = '' - for e in a: # this could be done more elegant - s += str(e)[1:-1] + ' ' - return s - - -def _viewboxlist(a): - """formats a tuple""" - s = '' - for e in a: - s += str(e) + ' ' - return s - - -def _pointlist(a): - """formats a list of numbers""" - return str(a)[1:-1] - - -class pathdata: - """class used to create a pathdata object which can be used for a path. - although most methods are pretty straightforward it might be useful to look at the SVG specification.""" - # I didn't test the methods below. - - def __init__(self, x=None, y=None): - self.path = [] - if x is not None and y is not None: - self.path.append('M ' + str(x) + ' ' + str(y)) - - def closepath(self): - """ends the path""" - self.path.append('z') - - def move(self, x, y): - """move to absolute""" - self.path.append('M ' + str(x) + ' ' + str(y)) - - def relmove(self, x, y): - """move to relative""" - self.path.append('m ' + str(x) + ' ' + str(y)) - - def line(self, x, y): - """line to absolute""" - self.path.append('L ' + str(x) + ' ' + str(y)) - - def relline(self, x, y): - """line to relative""" - self.path.append('l ' + str(x) + ' ' + str(y)) - - def hline(self, x): - """horizontal line to absolute""" - self.path.append('H' + str(x)) - - def relhline(self, x): - """horizontal line to relative""" - self.path.append('h' + str(x)) - - def vline(self, y): - """verical line to absolute""" - self.path.append('V' + str(y)) - - def relvline(self, y): - """vertical line to relative""" - 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)) - - def relbezier(self, x1, y1, x2, y2, x, y): - """bezier with xy1 and xy2 to xy relative""" - self.path.append('c' + str(x1) + ',' + str(y1) + ' ' + str(x2) - + ',' + str(y2) + ' ' + str(x) + ',' + str(y)) - - def smbezier(self, x2, y2, x, y): - """smooth bezier with xy2 to xy absolut""" - self.path.append('S' + str(x2) + ',' + str(y2) + \ - ' ' + str(x) + ',' + str(y)) - - def relsmbezier(self, x2, y2, x, y): - """smooth bezier with xy2 to xy relative""" - self.path.append('s' + str(x2) + ',' + str(y2) + \ - ' ' + str(x) + ',' + str(y)) - - def qbezier(self, x1, y1, x, y): - """quadratic bezier with xy1 to xy absolut""" - self.path.append('Q' + str(x1) + ',' + str(y1) + \ - ' ' + str(x) + ',' + str(y)) - - def relqbezier(self, x1, y1, x, y): - """quadratic bezier with xy1 to xy relative""" - 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)) - - def relsmqbezier(self, x, y): - """smooth quadratic bezier to xy relative""" - self.path.append('t' + str(x) + ',' + str(y)) - - def ellarc(self, rx, ry, xrot, laf, sf, x, y): - """elliptival arc with rx and ry rotating with xrot using large-arc-flag and sweep-flag to xy absolut""" - self.path.append('A' + str(rx) + ',' + str(ry) + ' ' + str(xrot) - + ' ' + str(laf) + ' ' + str(sf) + ' ' + str(x) + ' ' + str(y)) - - def relellarc(self, rx, ry, xrot, laf, sf, x, y): - """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)) - - def __repr__(self): - return ' '.join(self.path) - - -class SVGelement: - """SVGelement(type,attributes,elements,text,namespace,**args) - Creates a arbitrary svg element and is intended to be subclassed not used on its own. - This element is the base of every svg element it defines a class which resembles - a xml-element. The main advantage of this kind of implementation is that you don't - have to create a toXML method for every different graph object. Every element - consists of a type, attribute, optional subelements, optional text and an optional - namespace. Note the elements==None, if elements = None:self.elements=[] construction. - This is done because if you default to elements=[] every object has a reference - to the same empty list.""" - - def __init__(self, type='', attributes=None, elements=None, text='', namespace='', cdata=None, **args): - self.type = type - if attributes == None: - self.attributes = {} - else: - self.attributes = attributes - if elements == None: - self.elements = [] - else: - self.elements = elements - self.text = text - self.namespace = namespace - self.cdata = cdata - for arg in list(args.keys()): - arg2 = arg.replace("__", ":") - arg2 = arg2.replace("_", "-") - self.attributes[arg2] = args[arg] - - def addElement(self, SVGelement): - """adds an element to a SVGelement - - SVGelement.addElement(SVGelement) - """ - self.elements.append(SVGelement) - - def toXml(self, level, f): - 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]))) - if self.namespace: - 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) - if self.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') - 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') - elif self.text: - f.write('</' + self.type + '>\n') - elif self.cdata: - f.write('\t' * level + '</' + self.type + '>\n') - else: - f.write('/>\n') - - -class tspan(SVGelement): - """ts=tspan(text='',**args) - - a tspan element can be used for applying formatting to a textsection - usage: - ts=tspan('this text is bold') - ts.attributes['font-weight']='bold' - st=spannedtext() - st.addtspan(ts) - t=text(3,5,st) - """ - - def __init__(self, text=None, **args): - SVGelement.__init__(self, 'tspan', **args) - if self.text != None: - self.text = text - - def __repr__(self): - s = "<tspan" - for key, value in list(self.attributes.items()): - s += ' %s="%s"' % (key, value) - s += '>' - s += self.text - s += '</tspan>' - return s - - -class tref(SVGelement): - """tr=tref(link='',**args) - - a tref element can be used for referencing text by a link to its id. - usage: - tr=tref('#linktotext') - st=spannedtext() - st.addtref(tr) - t=text(3,5,st) - """ - - def __init__(self, link, **args): - SVGelement.__init__(self, 'tref', {'xlink:href': link}, **args) - - def __repr__(self): - s = "<tref" - - for key, value in list(self.attributes.items()): - s += ' %s="%s"' % (key, value) - s += '/>' - return s - - -class spannedtext: - """st=spannedtext(textlist=[]) - - a spannedtext can be used for text which consists of text, tspan's and tref's - You can use it to add to a text element or path element. Don't add it directly - to a svg or a group element. - usage: - - ts=tspan('this text is bold') - ts.attributes['font-weight']='bold' - tr=tref('#linktotext') - tr.attributes['fill']='red' - st=spannedtext() - st.addtspan(ts) - st.addtref(tr) - st.addtext('This text is not bold') - t=text(3,5,st) - """ - - def __init__(self, textlist=None): - if textlist == None: - self.textlist = [] - else: - self.textlist = textlist - - def addtext(self, text=''): - self.textlist.append(text) - - def addtspan(self, tspan): - self.textlist.append(tspan) - - def addtref(self, tref): - self.textlist.append(tref) - - def __repr__(self): - s = "" - for element in self.textlist: - s += str(element) - return s - - -class rect(SVGelement): - """r=rect(width,height,x,y,fill,stroke,stroke_width,**args) - - a rectangle is defined by a width and height and a xy pair - """ - - def __init__(self, x=None, y=None, width=None, height=None, fill=None, stroke=None, stroke_width=None, **args): - if width == None or height == None: - raise ValueError('both height and width are required') - - 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: - 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 - - -class circle(SVGelement): - """c=circle(x,y,radius,fill,stroke,stroke_width,**args) - - 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') - 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) - - 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: - 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 - - -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 - - -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 - - -class text(SVGelement): - """t=text(x,y,text,font_size,font_family,**args) - - 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: - 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): - """tp=textpath(text,link,**args) - - 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) - - A pattern is used to fill or stroke an object using a pre-defined - 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: - 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) - - 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: - 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) - - 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: - 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 - - -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) - - -class image(SVGelement): - """im=image(url,width,height,x,y,**args) - - 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') - 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) - - -class marker(SVGelement): - """m=marker(id,viewbox,refX,refY,markerWidth,markerHeight,**args) - - 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: - 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) - - 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) - - defines a symbol which can be used on different places in your graph using - the use element. A symbol is not rendered but you can use 'use' elements to - display it by referencing its id. - sy.addElement(SVGelement) - """ - - 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) - - -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) - - Elements added to a switch element which are "switched" by the attributes - requiredFeatures, requiredExtensions and systemLanguage. - Refer to the SVG specification for details. - """ - - def __init__(self, **args): - SVGelement.__init__(self, 'switch', **args) - - -class use(SVGelement): - """u=use(link,x,y,width,height,**args) - - 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 - - -class link(SVGelement): - """a=link(url,**args) - - 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: - 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): - SVGelement.__init__(self, 'animateMotion', **args) - 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) - # 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 - - -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 - - -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 - - -class svg(SVGelement): - """s=svg(viewbox,width,height,**args) - - a svg or element is the root of a drawing add all elements to a svg element. - You can have different svg elements in one svg file - s.addElement(SVGelement) - - eg - d=drawing() - s=svg((0,0,100,100),'100%','100%') - c=circle(50,50,20) - s.addElement(c) - d.setSVG(s) - d.toXml() - """ - - 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" - - -class drawing: - """d=drawing() - - this is the actual SVG document. It needs a svg element as a root. - Use the addSVG method to set the svg to the root. Use the toXml method to write the SVG - source to the screen or to a file - d=drawing() - d.addSVG(svg) - d.toXml(optionalfilename) - """ - - 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. - if use_dom_implementation == 0: - def toXml(self, filename='', compress=False): - import io - 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\"") - 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("]") - 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') - zf.write(xml.getvalue()) - zf.close() - f.seek(0) - return f.read() - else: - return xml.getvalue() - else: - if filename[-4:] == 'svgz': - import gzip - f = gzip.GzipFile(filename=filename, - mode="wb", compresslevel=9) - f.write(xml.getvalue()) - f.close() - else: - f = file(filename, 'w') - f.write(xml.getvalue()) - f.close() - - else: - 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 ') - - 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) - # 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) - else: - e = root.createElement(element.type) - if element.text: - textnode = root.createTextNode(element.text) - e.appendChild(textnode) - # 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) - elementroot.appendChild(e) - return elementroot - root = appender(self.svg, root) - if not filename: - import io - xml = io.StringIO() - PrettyPrint(root, xml) - if compress: - import gzip - f = io.StringIO() - zf = gzip.GzipFile(fileobj=f, mode='wb') - zf.write(xml.getvalue()) - zf.close() - f.seek(0) - return f.read() - else: - return xml.getvalue() - else: - try: - if filename[-4:] == 'svgz': - import gzip - import io - xml = io.StringIO() - PrettyPrint(root, xml) - f = gzip.GzipFile(filename=filename, - mode='wb', compresslevel=9) - f.write(xml.getvalue()) - f.close() - else: - f = open(filename, 'w') - PrettyPrint(root, f) - f.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() - 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') - s.addElement(r) - - t = title('SVGdraw Demo') - s.addElement(t) - g = group('animations') - e = ellipse(0, 0, 5, 2) - g.addElement(e) - c = circle(0, 0, 1, 'red') - g.addElement(c) - 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" - g.addElement(an) - s.addElement(g) - for i in range(20, 120, 20): - u = use('#animations', i, 0) - s.addElement(u) - for i in range(0, 120, 20): - for j in range(5, 105, 10): - c = circle(i, j, 1, 'red', 'black', .5) - s.addElement(c) - d.setSVG(s) - - print((d.toXml())) diff --git a/wqflask/utility/temp_data.py b/wqflask/utility/temp_data.py deleted file mode 100644 index 07c5a318..00000000 --- a/wqflask/utility/temp_data.py +++ /dev/null @@ -1,25 +0,0 @@ -from redis import Redis - -import simplejson as json - - -class TempData: - - def __init__(self, temp_uuid): - self.temp_uuid = temp_uuid - self.redis = Redis() - self.key = "tempdata:{}".format(self.temp_uuid) - - def store(self, field, value): - self.redis.hset(self.key, field, value) - self.redis.expire(self.key, 60 * 15) # Expire in 15 minutes - - def get_all(self): - return self.redis.hgetall(self.key) - - -if __name__ == "__main__": - redis = Redis() - for key in list(redis.keys()): - for field in redis.hkeys(key): - print("{}.{}={}".format(key, field, redis.hget(key, field))) diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py deleted file mode 100644 index 283b0408..00000000 --- a/wqflask/utility/tools.py +++ /dev/null @@ -1,357 +0,0 @@ -# Tools/paths finder resolves external paths from settings and/or environment -# variables - -import os -import sys -import json -import socket -from pathlib import Path - -from wqflask import app - -# Use the standard logger here to avoid a circular dependency -import logging -logger = logging.getLogger(__name__) - - -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 - path points to an expected directory and returns the full path to - the binary command - - guess = os.environ.get('HOME')+'/pylmm' - valid_path(get_setting('PYLMM_PATH',guess)) - - first tries the environment variable in +id+, next gets the Flask - app setting for the same +id+ and finally does an educated - +guess+. - - In all, the environment overrides the others, next is the flask - setting, then the guess. A valid path to the binary command is - returned. If none is resolved an exception is thrown. - - Note that we do not use the system path. This is on purpose - because it will mess up controlled (reproducible) deployment. The - proper way is to either use the GNU Guix defaults as listed in - etc/default_settings.py or override them yourself by creating a - different settings.py file (or setting the environment). - - """ - def value(command): - if command: - # sys.stderr.write("Found "+command+"\n") - app_set(command_id, command) - return command - else: - return app.config.get(command_id) - - # ---- Check whether environment exists - # print("Looking for "+command_id+"\n") - command = value(os.environ.get(command_id)) - if command is None or command == "": - # ---- Check whether setting exists in app - command = value(app.config.get(command_id)) - if command is None: - command = value(guess) - if command is None or command == "": - # print command - 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 False - - -def get_setting_int(id): - v = get_setting(id) - if isinstance(v, str): - return int(v) - if v is None: - 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 - if valid_path(try_gn): - return try_gn - 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)" - - -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(the_dir): - if not valid_path(the_dir): - raise FileNotFoundError(f"ERROR: can not find directory '{the_dir}'") - return the_dir - - -def assert_writable_dir(dir): - try: - fn = os.path.join(dir, "test.txt") - fh = open(fn, 'w') - fh.write("I am writing this text to the file\n") - fh.close() - os.remove(fn) - except IOError: - raise Exception('Unable to write test.txt to directory ' + dir) - return dir - - -def assert_file(fn): - if not valid_file(fn): - raise FileNotFoundError(f"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. - - This function throws an error when the file is not found. - """ - base = get_setting("GENENETWORK_FILES") - if subdir: - base = base + "/" + subdir - if valid_path(base): - lookfor = base + "/" + name - if valid_file(lookfor): - return lookfor - else: - 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) - - -def locate_ignore_error(name, subdir=None): - """ - Locate a static flat file in the GENENETWORK_FILES environment. - - This function does not throw an error when the file is not found - but returns None. - """ - base = get_setting("GENENETWORK_FILES") - if subdir: - base = base + "/" + subdir - if valid_path(base): - lookfor = base + "/" + name - if valid_file(lookfor): - return lookfor - 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 - - print(("Set global log level to " + BLUE + LOG_LEVEL + ENDC), - file=sys.stderr) - log_level = getattr(logging, LOG_LEVEL.upper()) - logging.basicConfig(level=log_level) - - logger.info(BLUE + "Mr. Mojo Risin 2" + ENDC) - keylist = list(app.config.keys()) - print("runserver.py: ****** Webserver configuration - k,v pairs from app.config ******", - file=sys.stderr) - keylist.sort() - for k in keylist: - try: - print(("%s: %s%s%s%s" % (k, BLUE, BOLD, get_setting(k), ENDC)), - file=sys.stderr) - except: - print(("%s: %s%s%s%s" % (k, GREEN, BOLD, app.config[k], ENDC)), - file=sys.stderr) - -def gn_version_repo_info(root_dir): - """retrieve the branch name and abbreviated commit hash.""" - try: - from git import Repo - repo = Repo(root_dir) - return f"{repo.head.ref.name}-{repo.head.commit.hexsha[0:9]}" - except: - return "" - -def gn_version(): - """Compute and return the version of the application.""" - hostname = socket.gethostname() - basedir = Path(__file__).absolute().parent.parent.parent - with open(Path(basedir, "etc", "VERSION"), encoding="utf8") as version_file: - version_contents = version_file.read().strip() - base_version = f"{hostname}:{basedir.name}:{version_contents}" - repo_info = gn_version_repo_info(basedir) - return f"{base_version}-{repo_info}" if bool(repo_info) else base_version - -# Cached values -GN_VERSION = 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') -AUTH_SERVER_URL = get_setting('AUTH_SERVER_URL') -GN_PROXY_URL = get_setting('GN_PROXY_URL') -GN3_LOCAL_URL = get_setting('GN3_LOCAL_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') -REDIS_URL = get_setting('REDIS_URL') -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') -# assert_dir(JS_GN_PATH) - -GITHUB_CLIENT_ID = get_setting('GITHUB_CLIENT_ID') -GITHUB_CLIENT_SECRET = get_setting('GITHUB_CLIENT_SECRET') -GITHUB_AUTH_URL = "" -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_API_URL = get_setting('GITHUB_API_URL') - -ORCID_CLIENT_ID = get_setting('ORCID_CLIENT_ID') -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_TOKEN_URL = get_setting('ORCID_TOKEN_URL') - - -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()) -assert(GEMMA_COMMAND is not None) -PLINK_COMMAND = app_set("PLINK_COMMAND", plink_command()) -GEMMA_WRAPPER_COMMAND = gemma_wrapper_command() -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') - -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")) -assert_dir(JS_TWITTER_POST_FETCHER_PATH) -assert_file(JS_TWITTER_POST_FETCHER_PATH + "/js/twitterFetcher_min.js") - -JS_CYTOSCAPE_PATH = get_setting("JS_CYTOSCAPE_PATH", js_path("cytoscape")) -assert_dir(JS_CYTOSCAPE_PATH) -assert_file(JS_CYTOSCAPE_PATH + '/cytoscape.min.js') - -# assert_file(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData") - -AUTH_SERVER_URL = get_setting("AUTH_SERVER_URL") -OAUTH2_CLIENT_ID = get_setting('OAUTH2_CLIENT_ID') -OAUTH2_CLIENT_SECRET = get_setting('OAUTH2_CLIENT_SECRET') diff --git a/wqflask/utility/type_checking.py b/wqflask/utility/type_checking.py deleted file mode 100644 index 5e98f4ae..00000000 --- a/wqflask/utility/type_checking.py +++ /dev/null @@ -1,47 +0,0 @@ -# Type checking functions - -def is_float(value): - try: - float(value) - return True - except: - return False - - -def is_int(value): - try: - int(value) - return True - except: - return False - - -def is_str(value): - if value is None: - return False - try: - str(value) - return True - 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 and not vars_obj[name] == "": - return str(vars_obj[name]) - return default diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py deleted file mode 100644 index 0cb71567..00000000 --- a/wqflask/utility/webqtlUtil.py +++ /dev/null @@ -1,118 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by GeneNetwork Core Team 2010/10/20 - -import string -import time -import re -import math -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'] -} - -######################################### -# Accessory Functions -######################################### - - -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) - - - Determine if the elements in a list are all null - - ''' - for item in lst: - if item is not None: - 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""" - returnList = line.split('","') - returnList[-1] = returnList[-1][:-2] - returnList[0] = returnList[0][1:] - return returnList - - -def cmpEigenValue(A, B): - try: - if A[0] > B[0]: - return -1 - elif A[0] == B[0]: - return 0 - else: - return 1 - 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(',')] - if userName in AuthorizedUsersList: - access_to_confidential_phenotype_trait = 1 - return access_to_confidential_phenotype_trait |