diff options
Diffstat (limited to 'gn3/utility')
| -rw-r--r-- | gn3/utility/__init__.py | 0 | ||||
| -rw-r--r-- | gn3/utility/bunch.py | 16 | ||||
| -rw-r--r-- | gn3/utility/chunks.py | 32 | ||||
| -rw-r--r-- | gn3/utility/corr_result_helpers.py | 45 | ||||
| -rw-r--r-- | gn3/utility/db_tools.py | 19 | ||||
| -rw-r--r-- | gn3/utility/get_group_samplelists.py | 47 | ||||
| -rw-r--r-- | gn3/utility/helper_functions.py | 24 | ||||
| -rw-r--r-- | gn3/utility/hmac.py | 50 | ||||
| -rw-r--r-- | gn3/utility/logger.py | 163 | ||||
| -rw-r--r-- | gn3/utility/species.py | 71 | ||||
| -rw-r--r-- | gn3/utility/tools.py | 37 | ||||
| -rw-r--r-- | gn3/utility/webqtlUtil.py | 66 |
12 files changed, 0 insertions, 570 deletions
diff --git a/gn3/utility/__init__.py b/gn3/utility/__init__.py deleted file mode 100644 index e69de29..0000000 --- a/gn3/utility/__init__.py +++ /dev/null diff --git a/gn3/utility/bunch.py b/gn3/utility/bunch.py deleted file mode 100644 index c1fd907..0000000 --- a/gn3/utility/bunch.py +++ /dev/null @@ -1,16 +0,0 @@ -"""module contains Bunch class a dictionary like with object notation """ - -from pprint import pformat as pf - - -class Bunch: - """Like a dictionary but using object notation""" - - def __init__(self, **kw): - self.__dict__ = kw - - def __repr__(self): - return pf(self.__dict__) - - def __str__(self): - return self.__class__.__name__ diff --git a/gn3/utility/chunks.py b/gn3/utility/chunks.py deleted file mode 100644 index fa27a39..0000000 --- a/gn3/utility/chunks.py +++ /dev/null @@ -1,32 +0,0 @@ -"""module for chunks functions""" - -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/gn3/utility/corr_result_helpers.py b/gn3/utility/corr_result_helpers.py deleted file mode 100644 index a68308e..0000000 --- a/gn3/utility/corr_result_helpers.py +++ /dev/null @@ -1,45 +0,0 @@ -"""module contains helper function for corr results""" - -#pylint:disable=C0103 -#above disable snake_case for variable tod refactor -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) - - """ - a_new = [] - b_new = [] - for a, b in zip(a_values, b_values): - if (a and b is not 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): - """function to normalize values with 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/gn3/utility/db_tools.py b/gn3/utility/db_tools.py deleted file mode 100644 index 446acda..0000000 --- a/gn3/utility/db_tools.py +++ /dev/null @@ -1,19 +0,0 @@ -"""module for db_tools""" -from MySQLdb import escape_string as escape_ - - -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_): - """escape function""" - return escape_(string_).decode('utf8') diff --git a/gn3/utility/get_group_samplelists.py b/gn3/utility/get_group_samplelists.py deleted file mode 100644 index 8fb322a..0000000 --- a/gn3/utility/get_group_samplelists.py +++ /dev/null @@ -1,47 +0,0 @@ - -"""module for group samplelist""" -import os - -#todo close the files after opening -def get_samplelist(file_type, geno_file): - """get samplelist function""" - if file_type == "geno": - return get_samplelist_from_geno(geno_file) - elif file_type == "plink": - return get_samplelist_from_plink(geno_file) - -def get_samplelist_from_geno(genofilename): - if os.path.isfile(genofilename + '.gz'): - genofilename += '.gz' - genofile = gzip.open(genofilename) - else: - genofile = open(genofilename) - - for line in genofile: - line = line.strip() - if not line: - continue - if line.startswith(("#", "@")): - continue - break - - headers = line.split("\t") - - if headers[3] == "Mb": - samplelist = headers[4:] - else: - samplelist = headers[3:] - return samplelist - - - -def get_samplelist_from_plink(genofilename): - """get samplelist from plink""" - genofile = open(genofilename) - - samplelist = [] - for line in genofile: - line = line.split(" ") - samplelist.append(line[1]) - - return samplelist diff --git a/gn3/utility/helper_functions.py b/gn3/utility/helper_functions.py deleted file mode 100644 index f5a8b80..0000000 --- a/gn3/utility/helper_functions.py +++ /dev/null @@ -1,24 +0,0 @@ -"""module contains general helper functions """ -from gn3.base.data_set import create_dataset -from gn3.base.trait import create_trait -from gn3.base.species import TheSpecies - - -def get_species_dataset_trait(self, start_vars): - """function to get species dataset and trait""" - if "temp_trait" in list(start_vars.keys()): - if start_vars['temp_trait'] == "True": - self.dataset = create_dataset( - dataset_name="Temp", dataset_type="Temp", group_name=start_vars['group']) - - else: - self.dataset = create_dataset(start_vars['dataset']) - - else: - self.dataset = 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) diff --git a/gn3/utility/hmac.py b/gn3/utility/hmac.py deleted file mode 100644 index eb39e59..0000000 --- a/gn3/utility/hmac.py +++ /dev/null @@ -1,50 +0,0 @@ -"""module for hmac """ - -# pylint: disable-all -import hmac -import hashlib - -# xtodo work on this file - -# from main import app - - -def hmac_creation(stringy): - """Helper function to create the actual hmac""" - - # secret = app.config['SECRET_HMAC_CODE'] - # put in config - secret = "my secret" - 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 - - - -# todo -# app.jinja_env.globals.update(url_for_hmac=url_for_hmac, -# data_hmac=data_hmac) diff --git a/gn3/utility/logger.py b/gn3/utility/logger.py deleted file mode 100644 index 4245a02..0000000 --- a/gn3/utility/logger.py +++ /dev/null @@ -1,163 +0,0 @@ -""" -# GeneNetwork logger -# -# The standard python logging module is very good. This logger adds a -# few facilities on top of that. Main one being that it picks up -# settings for log levels (global and by module) and (potentially) -# offers some fine grained log levels for the standard levels. -# -# All behaviour is defined here. Global settings (defined in -# default_settings.py). -# -# To use logging and settings put this at the top of a module: -# -# import utility.logger -# logger = utility.logger.getLogger(__name__ ) -# -# To override global behaviour set the LOG_LEVEL in default_settings.py -# or use an environment variable, e.g. -# -# env LOG_LEVEL=INFO ./bin/genenetwork2 -# -# To override log level for a module replace that with, for example, -# -# import logging -# import utility.logger -# logger = utility.logger.getLogger(__name__,level=logging.DEBUG) -# -# We'll add more overrides soon. -""" -# todo incomplete file - -# pylint: disable-all -import logging -import datetime -from inspect import isfunction -from inspect import stack - -from pprint import pformat as pf - - -# from utility.tools import LOG_LEVEL, LOG_LEVEL_DEBUG, LOG_SQL - -LOG_SQL = True - - -class GNLogger: - """A logger class with some additional functionality, such as - multiple parameter logging, SQL logging, timing, colors, and lazy - functions. - - """ - - def __init__(self, name): - self.logger = logging.getLogger(name) - - def setLevel(self, value): - """Set the undelying log level""" - self.logger.setLevel(value) - - def debug(self, *args): - """Call logging.debug for multiple args. Use (lazy) debugf and -level=num to filter on LOG_LEVEL_DEBUG. - - """ - self.collect(self.logger.debug, *args) - - def debug20(self, *args): - """Call logging.debug for multiple args. Use level=num to filter on -LOG_LEVEL_DEBUG (NYI). - - """ - if level <= LOG_LEVEL_DEBUG: - if self.logger.getEffectiveLevel() < 20: - self.collect(self.logger.debug, *args) - - def info(self, *args): - """Call logging.info for multiple args""" - self.collect(self.logger.info, *args) - - def warning(self, *args): - """Call logging.warning for multiple args""" - self.collect(self.logger.warning, *args) - # self.logger.warning(self.collect(*args)) - - def error(self, *args): - """Call logging.error for multiple args""" - now = datetime.datetime.utcnow() - time_str = now.strftime('%H:%M:%S UTC %Y%m%d') - l = [time_str]+list(args) - self.collect(self.logger.error, *l) - - def infof(self, *args): - """Call logging.info for multiple args lazily""" - # only evaluate function when logging - if self.logger.getEffectiveLevel() < 30: - self.collectf(self.logger.debug, *args) - - def debugf(self, level=0, *args): - """Call logging.debug for multiple args lazily and handle - LOG_LEVEL_DEBUG correctly - - """ - # only evaluate function when logging - if level <= LOG_LEVEL_DEBUG: - if self.logger.getEffectiveLevel() < 20: - self.collectf(self.logger.debug, *args) - - def sql(self, sqlcommand, fun=None): - """Log SQL command, optionally invoking a timed fun""" - if LOG_SQL: - caller = stack()[1][3] - if caller in ['fetchone', 'fetch1', 'fetchall']: - caller = stack()[2][3] - self.info(caller, sqlcommand) - if fun: - result = fun(sqlcommand) - if LOG_SQL: - self.info(result) - return result - - def collect(self, fun, *args): - """Collect arguments and use fun to output""" - out = "."+stack()[2][3] - for a in args: - if len(out) > 1: - out += ": " - if isinstance(a, str): - out = out + a - else: - out = out + pf(a, width=160) - fun(out) - - def collectf(self, fun, *args): - """Collect arguments and use fun to output one by one""" - out = "."+stack()[2][3] - for a in args: - if len(out) > 1: - out += ": " - if isfunction(a): - out += a() - else: - if isinstance(a, str): - out = out + a - else: - out = out + pf(a, width=160) - fun(out) - -# Get the module logger. You can override log levels at the -# module level - - -def getLogger(name, level=None): - """method to get logger""" - gnlogger = GNLogger(name) - _logger = gnlogger.logger - - # if level: - # logger.setLevel(level) - # else: - # logger.setLevel(LOG_LEVEL) - - # logger.info("Log level of "+name+" set to "+logging.getLevelName(logger.getEffectiveLevel())) - return gnlogger diff --git a/gn3/utility/species.py b/gn3/utility/species.py deleted file mode 100644 index 0140d41..0000000 --- a/gn3/utility/species.py +++ /dev/null @@ -1,71 +0,0 @@ -"""module contains species and chromosomes classes""" -import collections - -from flask import g - - -from gn3.utility.logger import getLogger -logger = getLogger(__name__) - - # pylint: disable=too-few-public-methods - # intentionally disabled check for few public methods - -class TheSpecies: - """class for Species""" - - def __init__(self, dataset=None, species_name=None): - if species_name is not None: - self.name = species_name - self.chromosomes = Chromosomes(species=self.name) - else: - self.dataset = dataset - self.chromosomes = Chromosomes(dataset=self.dataset) - - - -class IndChromosome: - """class for IndChromosome""" - - def __init__(self, name, length): - self.name = name - self.length = length - - @property - def mb_length(self): - """Chromosome length in megabases""" - return self.length / 1000000 - - - - -class Chromosomes: - """class for Chromosomes""" - - def __init__(self, dataset=None, species=None): - self.chromosomes = collections.OrderedDict() - if species is not None: - query = """ - Select - Chr_Length.Name, Chr_Length.OrderId, Length from Chr_Length, Species - where - Chr_Length.SpeciesId = Species.SpeciesId AND - Species.Name = '%s' - Order by OrderId - """ % species.capitalize() - else: - self.dataset = dataset - - query = """ - Select - Chr_Length.Name, Chr_Length.OrderId, Length from Chr_Length, InbredSet - where - Chr_Length.SpeciesId = InbredSet.SpeciesId AND - InbredSet.Name = '%s' - Order by OrderId - """ % self.dataset.group.name - logger.sql(query) - results = g.db.execute(query).fetchall() - - for item in results: - self.chromosomes[item.OrderId] = IndChromosome( - item.Name, item.Length) diff --git a/gn3/utility/tools.py b/gn3/utility/tools.py deleted file mode 100644 index 85df9f6..0000000 --- a/gn3/utility/tools.py +++ /dev/null @@ -1,37 +0,0 @@ -"""module contains general tools forgenenetwork""" - -import os - -from default_settings import GENENETWORK_FILES - - -def valid_file(file_name): - """check if file is valid""" - if os.path.isfile(file_name): - return file_name - return None - - -def valid_path(dir_name): - """check if path is valid""" - if os.path.isdir(dir_name): - return dir_name - return None - - -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 = GENENETWORK_FILES - if subdir: - base = base+"/"+subdir - if valid_path(base): - lookfor = base + "/" + name - if valid_file(lookfor): - return lookfor - - return None diff --git a/gn3/utility/webqtlUtil.py b/gn3/utility/webqtlUtil.py deleted file mode 100644 index 1c76410..0000000 --- a/gn3/utility/webqtlUtil.py +++ /dev/null @@ -1,66 +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 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'] -} - - -def has_access_to_confidentail_phenotype_trait(privilege, username, authorized_users): - """function to access to confidential phenotype Traits further implementation needed""" - access_to_confidential_phenotype_trait = 0 - - results = (privilege, username, authorized_users) - return access_to_confidential_phenotype_trait |