# 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)
from dataclasses import dataclass
from dataclasses import field
from dataclasses import InitVar
from typing import Optional, Dict, List
from db.call import fetchall, fetchone, fetch1
from utility.logger import getLogger
from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists, GN2_BASE_URL
from db.gn_server import menu_main
from pprint import pformat as pf
from utility.db_tools import escape
from utility.db_tools import mescape
from utility.db_tools import create_in_clause
from maintenance import get_group_samplelists
from utility.tools import locate, locate_ignore_error, flat_files
from utility import gen_geno_ob
from utility import chunks
from utility.benchmark import Bench
from utility import webqtlUtil
from db import webqtlDatabaseFunction
from base import species
from base import webqtlConfig
from flask import Flask, g
from base.webqtlConfig import TMPDIR
from urllib.parse import urlparse
from utility.tools import SQL_URI
import os
import math
import string
import collections
import codecs
import json
import requests
import gzip
import pickle as pickle
import itertools
import hashlib
import datetime
from redis import Redis
r = Redis()
logger = getLogger(__name__)
# Used by create_database to instantiate objects
# Each subclass will add to this
DS_NAME_MAP = {}
def create_dataset(dataset_name, dataset_type=None,
get_samplelist=True, group_name=None):
if dataset_name == "Temp":
dataset_type = "Temp"
if not dataset_type:
dataset_type = Dataset_Getter(dataset_name)
dataset_ob = DS_NAME_MAP[dataset_type]
dataset_class = globals()[dataset_ob]
if dataset_type == "Temp":
return dataset_class(dataset_name, get_samplelist, group_name)
else:
return dataset_class(dataset_name, get_samplelist)
@dataclass
class DatasetType:
"""Create a dictionary of samples where the value is set to Geno,
Publish or ProbeSet. E.g.
{'AD-cases-controls-MyersGeno': 'Geno',
'AD-cases-controls-MyersPublish': 'Publish',
'AKXDGeno': 'Geno',
'AXBXAGeno': 'Geno',
'AXBXAPublish': 'Publish',
'Aging-Brain-UCIPublish': 'Publish',
'All Phenotypes': 'Publish',
'B139_K_1206_M': 'ProbeSet',
'B139_K_1206_R': 'ProbeSet' ...
}
"""
redis_instance: InitVar[Redis]
datasets: Optional[Dict] = field(init=False, default_factory=dict)
data: Optional[Dict] = field(init=False)
def __post_init__(self, redis_instance):
self.redis_instance = redis_instance
data = redis_instance.get("dataset_structure")
if data:
self.datasets = json.loads(data)
else:
# ZS: I don't think this should ever run unless Redis is
# emptied
try:
data = json.loads(requests.get(
GN2_BASE_URL + "/api/v_pre1/gen_dropdown",
timeout=5).content)
for _species in data['datasets']:
for group in data['datasets'][_species]:
for dataset_type in data['datasets'][_species][group]:
for dataset in data['datasets'][_species][group][dataset_type]:
short_dataset_name = dataset[1]
if dataset_type == "Phenotypes":
new_type = "Publish"
elif dataset_type == "Genotypes":
new_type = "Geno"
else:
new_type = "ProbeSet"
self.datasets[short_dataset_name] = new_type
except Exception: # Do nothing
pass
self.redis_instance.set("dataset_structure",
json.dumps(self.datasets))
self.data = data
def set_dataset_key(self, t, name):
"""If name is not in the object's dataset dictionary, set it, and
update dataset_structure in Redis
args:
t: Type of dataset structure which can be: 'mrna_expr', 'pheno',
'other_pheno', 'geno'
name: The name of the key to inserted in the datasets dictionary
"""
sql_query_mapping = {
'mrna_expr': ("SELECT ProbeSetFreeze.Id FROM "
"ProbeSetFreeze WHERE "
"ProbeSetFreeze.Name = \"%s\" "),
'pheno': ("SELECT InfoFiles.GN_AccesionId "
"FROM InfoFiles, PublishFreeze, InbredSet "
"WHERE InbredSet.Name = '%s' AND "
"PublishFreeze.InbredSetId = InbredSet.Id AND "
"InfoFiles.InfoPageName = PublishFreeze.Name"),
'other_pheno': ("SELECT PublishFreeze.Name "
"FROM PublishFreeze, InbredSet "
"WHERE InbredSet.Name = '%s' AND "
"PublishFreeze.InbredSetId = InbredSet.Id"),
'geno': ("SELECT GenoFreeze.Id FROM GenoFreeze WHERE "
"GenoFreeze.Name = \"%s\" ")
}
dataset_name_mapping = {
"mrna_expr": "ProbeSet",
"pheno": "Publish",
"other_pheno": "Publish",
"geno": "Geno",
}
group_name = name
if t in ['pheno', 'other_pheno']:
group_name = name.replace("Publish", "")
results = g.db.execute(sql_query_mapping[t] % group_name).fetchone()
if results:
self.datasets[name] = dataset_name_mapping[t]
self.redis_instance.set(
"dataset_structure", json.dumps(self.datasets))
return True
return None
def __call__(self, name):
if name not in self.datasets:
for t in ["mrna_expr", "pheno", "other_pheno", "geno"]:
# This has side-effects, with the end result being a
# truth-y value
if(self.set_dataset_key(t, name)):
break
# Return None if name has not been set
return self.datasets.get(name, None)
# Do the intensive work at startup one time only
Dataset_Getter = DatasetType(r)
def create_datasets_list():
if USE_REDIS:
key = "all_datasets"
result = r.get(key)
if result:
logger.debug("Redis cache hit")
datasets = pickle.loads(result)
if result is None:
datasets = list()
with Bench("Creating DataSets object"):
type_dict = {'Publish': 'PublishFreeze',
'ProbeSet': 'ProbeSetFreeze',
'Geno': 'GenoFreeze'}
for dataset_type in type_dict:
query = "SELECT Name FROM {}".format(type_dict[dataset_type])
for result in fetchall(query):
# The query at the beginning of this function isn't
# necessary here, but still would rather just reuse
# it logger.debug("type: {}\tname:
# {}".format(dataset_type, result.Name))
dataset = create_dataset(result.Name, dataset_type)
datasets.append(dataset)
if USE_REDIS:
r.set(key, pickle.dumps(datasets, pickle.HIGHEST_PROTOCOL))
r.expire(key, 60 * 60)
return datasets
class Markers:
"""Todo: Build in cacheing so it saves us reading the same file more than once"""
def __init__(self, name):
json_data_fh = open(locate(name + ".json", 'genotype/json'))
markers = []
with open("%s/%s_snps.txt" % (flat_files('genotype/bimbam'), name), 'r') as bimbam_fh:
if len(bimbam_fh.readline().split(", ")) > 2:
delimiter = ", "
elif len(bimbam_fh.readline().split(",")) > 2:
delimiter = ","
elif len(bimbam_fh.readline().split("\t")) > 2:
delimiter = "\t"
else:
delimiter = " "
for line in bimbam_fh:
marker = {}
marker['name'] = line.split(delimiter)[0].rstrip()
marker['Mb'] = float(line.split(delimiter)[
1].rstrip()) / 1000000
marker['chr'] = line.split(delimiter)[2].rstrip()
markers.append(marker)
for marker in markers:
if (marker['chr'] != "X") and (marker['chr'] != "Y") and (marker['chr'] != "M"):
marker['chr'] = int(marker['chr'])
marker['Mb'] = float(marker['Mb'])
self.markers = markers
def add_pvalues(self, p_values):
logger.debug("length of self.markers:", len(self.markers))
logger.debug("length of p_values:", len(p_values))
if isinstance(p_values, list):
# THIS IS only needed for the case when we are limiting the number of p-values calculated
# if len(self.markers) > len(p_values):
# self.markers = self.markers[:len(p_values)]
for marker, p_value in zip(self.markers, p_values):
if not p_value:
continue
marker['p_value'] = float(p_value)
if math.isnan(marker['p_value']) or marker['p_value'] <= 0:
marker['lod_score'] = 0
marker['lrs_value'] = 0
else:
marker['lod_score'] = -math.log10(marker['p_value'])
# Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values
marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61
elif isinstance(p_values, dict):
filtered_markers = []
for marker in self.markers:
if marker['name'] in p_values:
marker['p_value'] = p_values[marker['name']]
if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
marker['lod_score'] = 0
marker['lrs_value'] = 0
else:
marker['lod_score'] = -math.log10(marker['p_value'])
# Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values
marker['lrs_value'] = - \
math.log10(marker['p_value']) * 4.61
filtered_markers.append(marker)
self.markers = filtered_markers
class HumanMarkers(Markers):
def __init__(self, name, specified_markers=[]):
marker_data_fh = open(flat_files('mapping') + '/' + name + '.bim')
self.markers = []
for line in marker_data_fh:
splat = line.strip().split()
if len(specified_markers) > 0:
if splat[1] in specified_markers:
marker = {}
marker['chr'] = int(splat[0])
marker['name'] = splat[1]
marker['Mb'] = float(splat[3]) / 1000000
else:
continue
else:
marker = {}
marker['chr'] = int(splat[0])
marker['name'] = splat[1]
marker['Mb'] = float(splat[3]) / 1000000
self.markers.append(marker)
def add_pvalues(self, p_values):
super(HumanMarkers, self).add_pvalues(p_values)
class DatasetGroup:
"""
Each group has multiple datasets; each species has multiple groups.
For example, Mouse has multiple groups (BXD, BXA, etc), and each group
has multiple datasets associated with it.
"""
def __init__(self, dataset, name=None):
"""This sets self.group and self.group_id"""
if name == None:
self.name, self.id, self.genetic_type, self.code = fetchone(
dataset.query_for_group)
else:
self.name, self.id, self.genetic_type, self.code = fetchone(
"SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType, InbredSet.InbredSetCode FROM InbredSet where Name='%s'" % name)
if self.name == 'BXD300':
self.name = "BXD"
self.f1list = None
self.parlist = None
self.get_f1_parent_strains()
self.mapping_id, self.mapping_names = self.get_mapping_methods()
self.species = webqtlDatabaseFunction.retrieve_species(self.name)
self.incparentsf1 = False
self.allsamples = None
self._datasets = None
self.genofile = None
def get_mapping_methods(self):
mapping_id = g.db.execute(
"select MappingMethodId from InbredSet where Name= '%s'" % self.name).fetchone()[0]
if mapping_id == "1":
mapping_names = ["GEMMA", "QTLReaper", "R/qtl"]
elif mapping_id == "2":
mapping_names = ["GEMMA"]
elif mapping_id == "3":
mapping_names = ["R/qtl"]
elif mapping_id == "4":
mapping_names = ["GEMMA", "PLINK"]
else:
mapping_names = []
return mapping_id, mapping_names
def get_markers(self):
def check_plink_gemma():
if flat_file_exists("mapping"):
MAPPING_PATH = flat_files("mapping") + "/"
if os.path.isfile(MAPPING_PATH + self.name + ".bed"):
return True
return False
if check_plink_gemma():
marker_class = HumanMarkers
else:
marker_class = Markers
if self.genofile:
self.markers = marker_class(self.genofile[:-5])
else:
self.markers = marker_class(self.name)
def get_f1_parent_strains(self):
try:
# NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py;
f1, f12, maternal, paternal = webqtlUtil.ParInfo[self.name]
except KeyError:
f1 = f12 = maternal = paternal = None
if f1 and f12:
self.f1list = [f1, f12]
if maternal and paternal:
self.parlist = [maternal, paternal]
def get_study_samplelists(self):
study_sample_file = locate_ignore_error(
self.name + ".json", 'study_sample_lists')
try:
f = open(study_sample_file)
except:
return []
study_samples = json.load(f)
return study_samples
def get_genofiles(self):
jsonfile = "%s/%s.json" % (webqtlConfig.GENODIR, self.name)
try:
f = open(jsonfile)
except:
return None
jsondata = json.load(f)
return jsondata['genofile']
def get_samplelist(self):
result = None
key = "samplelist:v3:" + self.name
if USE_REDIS:
result = r.get(key)
if result is not None:
self.samplelist = json.loads(result)
else:
genotype_fn = locate_ignore_error(self.name + ".geno", 'genotype')
if genotype_fn:
self.samplelist = get_group_samplelists.get_samplelist(
"geno", genotype_fn)
else:
self.samplelist = None
if USE_REDIS:
r.set(key, json.dumps(self.samplelist))
r.expire(key, 60 * 5)
def all_samples_ordered(self):
result = []
lists = (self.parlist, self.f1list, self.samplelist)
[result.extend(l) for l in lists if l]
return result
def read_genotype_file(self, use_reaper=False):
'''Read genotype from .geno file instead of database'''
# genotype_1 is Dataset Object without parents and f1
# genotype_2 is Dataset Object with parents and f1 (not for intercross)
# reaper barfs on unicode filenames, so here we ensure it's a string
if self.genofile:
if "RData" in self.genofile: # ZS: This is a temporary fix; I need to change the way the JSON files that point to multiple genotype files are structured to point to other file types like RData
full_filename = str(
locate(self.genofile.split(".")[0] + ".geno", 'genotype'))
else:
full_filename = str(locate(self.genofile, 'genotype'))
else:
full_filename = str(locate(self.name + '.geno', 'genotype'))
genotype_1 = gen_geno_ob.genotype(full_filename)
if genotype_1.type == "group" and self.parlist:
genotype_2 = genotype_1.add(
Mat=self.parlist[0], Pat=self.parlist[1]) # , F1=_f1)
else:
genotype_2 = genotype_1
# determine default genotype object
if self.incparentsf1 and genotype_1.type != "intercross":
genotype = genotype_2
else:
self.incparentsf1 = 0
genotype = genotype_1
self.samplelist = list(genotype.prgy)
return genotype
def datasets(group_name, this_group=None):
key = "group_dataset_menu:v2:" + group_name
dataset_menu = []
the_results = fetchall('''
(SELECT '#PublishFreeze',PublishFreeze.FullName,PublishFreeze.Name
FROM PublishFreeze,InbredSet
WHERE PublishFreeze.InbredSetId = InbredSet.Id
and InbredSet.Name = '%s'
ORDER BY PublishFreeze.Id ASC)
UNION
(SELECT '#GenoFreeze',GenoFreeze.FullName,GenoFreeze.Name
FROM GenoFreeze, InbredSet
WHERE GenoFreeze.InbredSetId = InbredSet.Id
and InbredSet.Name = '%s')
UNION
(SELECT Tissue.Name, ProbeSetFreeze.FullName,ProbeSetFreeze.Name
FROM ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue
WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id
and ProbeFreeze.TissueId = Tissue.Id
and ProbeFreeze.InbredSetId = InbredSet.Id
and InbredSet.Name like %s
ORDER BY Tissue.Name, ProbeSetFreeze.OrderList DESC)
''' % (group_name,
group_name,
"'" + group_name + "'"))
sorted_results = sorted(the_results, key=lambda kv: kv[0])
# ZS: This is kind of awkward, but need to ensure Phenotypes show up before Genotypes in dropdown
pheno_inserted = False
geno_inserted = False
for dataset_item in sorted_results:
tissue_name = dataset_item[0]
dataset = dataset_item[1]
dataset_short = dataset_item[2]
if tissue_name in ['#PublishFreeze', '#GenoFreeze']:
if tissue_name == '#PublishFreeze' and (dataset_short == group_name + 'Publish'):
dataset_menu.insert(
0, dict(tissue=None, datasets=[(dataset, dataset_short)]))
pheno_inserted = True
elif pheno_inserted and tissue_name == '#GenoFreeze':
dataset_menu.insert(
1, dict(tissue=None, datasets=[(dataset, dataset_short)]))
geno_inserted = True
else:
dataset_menu.append(
dict(tissue=None, datasets=[(dataset, dataset_short)]))
else:
tissue_already_exists = False
for i, tissue_dict in enumerate(dataset_menu):
if tissue_dict['tissue'] == tissue_name:
tissue_already_exists = True
break
if tissue_already_exists:
dataset_menu[i]['datasets'].append((dataset, dataset_short))
else:
dataset_menu.append(dict(tissue=tissue_name,
datasets=[(dataset, dataset_short)]))
if USE_REDIS:
r.set(key, pickle.dumps(dataset_menu, pickle.HIGHEST_PROTOCOL))
r.expire(key, 60 * 5)
if this_group != None:
this_group._datasets = dataset_menu
return this_group._datasets
else:
return dataset_menu
class DataSet:
"""
DataSet class defines a dataset in webqtl, can be either Microarray,
Published phenotype, genotype, or user input dataset(temp)
"""
def __init__(self, name, get_samplelist=True, group_name=None):
assert name, "Need a name"
self.name = name
self.id = None
self.shortname = None
self.fullname = None
self.type = None
self.data_scale = None # ZS: For example log2
self.accession_id = None
self.setup()
if self.type == "Temp": # Need to supply group name as input if temp trait
# sets self.group and self.group_id and gets genotype
self.group = DatasetGroup(self, name=group_name)
else:
self.check_confidentiality()
self.retrieve_other_names()
# sets self.group and self.group_id and gets genotype
self.group = DatasetGroup(self)
self.accession_id = self.get_accession_id()
if get_samplelist == True:
self.group.get_samplelist()
self.species = species.TheSpecies(self)
def as_dict(self):
return {
'name': self.name,
'shortname': self.shortname,
'fullname': self.fullname,
'type': self.type,
'data_scale': self.data_scale,
'group': self.group.name,
'accession_id': self.accession_id
}
def get_accession_id(self):
if self.type == "Publish":
results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where
InbredSet.Name = %s and
PublishFreeze.InbredSetId = InbredSet.Id and
InfoFiles.InfoPageName = PublishFreeze.Name and
PublishFreeze.public > 0 and
PublishFreeze.confidentiality < 1 order by
PublishFreeze.CreateTime desc""", (self.group.name)).fetchone()
elif self.type == "Geno":
results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, GenoFreeze, InbredSet where
InbredSet.Name = %s and
GenoFreeze.InbredSetId = InbredSet.Id and
InfoFiles.InfoPageName = GenoFreeze.ShortName and
GenoFreeze.public > 0 and
GenoFreeze.confidentiality < 1 order by
GenoFreeze.CreateTime desc""", (self.group.name)).fetchone()
else:
results = None
if results != None:
return str(results[0])
else:
return "None"
def retrieve_other_names(self):
"""This method fetches the the dataset names in search_result.
If the data set name parameter is not found in the 'Name' field of
the data set table, check if it is actually the FullName or
ShortName instead.
This is not meant to retrieve the data set info if no name at
all is passed.
"""
try:
if self.type == "ProbeSet":
query_args = tuple(escape(x) for x in (
self.name,
self.name,
self.name))
self.id, self.name, self.fullname, self.shortname, self.data_scale, self.tissue = fetch1("""
SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, ProbeSetFreeze.DataScale, Tissue.Name
FROM ProbeSetFreeze, ProbeFreeze, Tissue
WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id
AND ProbeFreeze.TissueId = Tissue.Id
AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFreeze.ShortName = '%s')
""" % (query_args), "/dataset/" + self.name + ".json",
lambda r: (r["id"], r["name"], r["full_name"],
r["short_name"], r["data_scale"], r["tissue"])
)
else:
query_args = tuple(escape(x) for x in (
(self.type + "Freeze"),
self.name,
self.name,
self.name))
self.tissue = "N/A"
self.id, self.name, self.fullname, self.shortname = fetchone("""
SELECT Id, Name, FullName, ShortName
FROM %s
WHERE (Name = '%s' OR FullName = '%s' OR ShortName = '%s')
""" % (query_args))
except TypeError:
logger.debug(
"Dataset {} is not yet available in GeneNetwork.".format(self.name))
pass
def chunk_dataset(self, dataset, n):
results = {}
query = """
SELECT ProbeSetXRef.DataId,ProbeSet.Name
FROM ProbeSet, ProbeSetXRef, ProbeSetFreeze
WHERE ProbeSetFreeze.Name = '{}' AND
ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
ProbeSetXRef.ProbeSetId = ProbeSet.Id
""".format(self.name)
# should cache this
traits_name_dict = dict(g.db.execute(query).fetchall())
for i in range(0, len(dataset), n):
matrix = list(dataset[i:i + n])
trait_name = traits_name_dict[matrix[0][0]]
my_values = [value for (trait_name, strain, value) in matrix]
results[trait_name] = my_values
return results
def get_probeset_data(self, sample_list=None, trait_ids=None):
# improvement of get trait data--->>>
if sample_list:
self.samplelist = sample_list
else:
self.samplelist = self.group.samplelist
if self.group.parlist != None and self.group.f1list != None:
if (self.group.parlist + self.group.f1list) in self.samplelist:
self.samplelist += self.group.parlist + self.group.f1list
query = """
SELECT Strain.Name, Strain.Id FROM Strain, Species
WHERE Strain.Name IN {}
and Strain.SpeciesId=Species.Id
and Species.name = '{}'
""".format(create_in_clause(self.samplelist), *mescape(self.group.species))
results = dict(g.db.execute(query).fetchall())
sample_ids = [results[item] for item in self.samplelist]
sorted_samplelist = [strain_name for strain_name, strain_id in sorted(
results.items(), key=lambda item: item[1])]
query = """SELECT * from ProbeSetData
where StrainID in {}
and id in (SELECT ProbeSetXRef.DataId
FROM (ProbeSet, ProbeSetXRef, ProbeSetFreeze)
WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id
and ProbeSetFreeze.Name = '{}'
and ProbeSet.Id = ProbeSetXRef.ProbeSetId)""".format(create_in_clause(sample_ids), self.name)
query_results = list(g.db.execute(query).fetchall())
data_results = self.chunk_dataset(query_results, len(sample_ids))
self.samplelist = sorted_samplelist
self.trait_data = data_results
def get_trait_data(self, sample_list=None):
if sample_list:
self.samplelist = sample_list
else:
self.samplelist = self.group.samplelist
if self.group.parlist != None and self.group.f1list != None:
if (self.group.parlist + self.group.f1list) in self.samplelist:
self.samplelist += self.group.parlist + self.group.f1list
query = """
SELECT Strain.Name, Strain.Id FROM Strain, Species
WHERE Strain.Name IN {}
and Strain.SpeciesId=Species.Id
and Species.name = '{}'
""".format(create_in_clause(self.samplelist), *mescape(self.group.species))
results = dict(g.db.execute(query).fetchall())
sample_ids = [results.get(item)
for item in self.samplelist if item is not None]
# MySQL limits the number of tables that can be used in a join to 61,
# so we break the sample ids into smaller chunks
# Postgres doesn't have that limit, so we can get rid of this after we transition
chunk_size = 50
number_chunks = int(math.ceil(len(sample_ids) / chunk_size))
cached_results = fetch_cached_results(self.name, self.type, self.samplelist)
if cached_results is None:
trait_sample_data = []
for sample_ids_step in chunks.divide_into_chunks(sample_ids, number_chunks):
if self.type == "Publish":
dataset_type = "Phenotype"
else:
dataset_type = self.type
temp = ['T%s.value' % item for item in sample_ids_step]
if self.type == "Publish":
query = "SELECT {}XRef.Id,".format(escape(self.type))
else:
query = "SELECT {}.Name,".format(escape(dataset_type))
data_start_pos = 1
query += ', '.join(temp)
query += ' FROM ({}, {}XRef, {}Freeze) '.format(*mescape(dataset_type,
self.type,
self.type))
for item in sample_ids_step:
query += """
left join {}Data as T{} on T{}.Id = {}XRef.DataId
and T{}.StrainId={}\n
""".format(*mescape(self.type, item, item, self.type, item, item))
if self.type == "Publish":
query += """
WHERE {}XRef.InbredSetId = {}Freeze.InbredSetId
and {}Freeze.Name = '{}'
and {}.Id = {}XRef.{}Id
order by {}.Id
""".format(*mescape(self.type, self.type, self.type, self.name,
dataset_type, self.type, dataset_type, dataset_type))
else:
query += """
WHERE {}XRef.{}FreezeId = {}Freeze.Id
and {}Freeze.Name = '{}'
and {}.Id = {}XRef.{}Id
order by {}.Id
""".format(*mescape(self.type, self.type, self.type, self.type,
self.name, dataset_type, self.type, self.type, dataset_type))
results = g.db.execute(query).fetchall()
trait_sample_data.append([list(result) for result in results])
trait_count = len(trait_sample_data[0])
self.trait_data = collections.defaultdict(list)
data_start_pos = 1
for trait_counter in range(trait_count):
trait_name = trait_sample_data[0][trait_counter][0]
for chunk_counter in range(int(number_chunks)):
self.trait_data[trait_name] += (
trait_sample_data[chunk_counter][trait_counter][data_start_pos:])
cache_dataset_results(
self.name, self.type, self.samplelist, self.trait_data)
else:
self.trait_data = cached_results
class PhenotypeDataSet(DataSet):
DS_NAME_MAP['Publish'] = 'PhenotypeDataSet'
def setup(self):
# Fields in the database table
self.search_fields = ['Phenotype.Post_publication_description',
'Phenotype.Pre_publication_description',
'Phenotype.Pre_publication_abbreviation',
'Phenotype.Post_publication_abbreviation',
'PublishXRef.mean',
'Phenotype.Lab_code',
'Publication.PubMed_ID',
'Publication.Abstract',
'Publication.Title',
'Publication.Authors',
'PublishXRef.Id']
# Figure out what display_fields is
self.display_fields = ['name', 'group_code',
'pubmed_id',
'pre_publication_description',
'post_publication_description',
'original_description',
'pre_publication_abbreviation',
'post_publication_abbreviation',
'mean',
'lab_code',
'submitter', 'owner',
'authorized_users',
'authors', 'title',
'abstract', 'journal',
'volume', 'pages',
'month', 'year',
'sequence', 'units', 'comments']
# Fields displayed in the search results table header
self.header_fields = ['Index',
'Record',
'Description',
'Authors',
'Year',
'Max LRS',
'Max LRS Location',
'Additive Effect']
self.type = 'Publish'
self.query_for_group = '''
SELECT
InbredSet.Name, InbredSet.Id, InbredSet.GeneticType, InbredSet.InbredSetCode
FROM
InbredSet, PublishFreeze
WHERE
PublishFreeze.InbredSetId = InbredSet.Id AND
PublishFreeze.Name = "%s"
''' % escape(self.name)
def check_confidentiality(self):
# (Urgently?) Need to write this
pass
def get_trait_info(self, trait_list, species=''):
for this_trait in trait_list:
if not this_trait.haveinfo:
this_trait.retrieve_info(get_qtl_info=True)
description = this_trait.post_publication_description
# If the dataset is confidential and the user has access to confidential
# phenotype traits, then display the pre-publication description instead
# of the post-publication description
if this_trait.confidential:
this_trait.description_display = ""
continue # for now, because no authorization features
if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(
privilege=self.privilege,
userName=self.userName,
authorized_users=this_trait.authorized_users):
description = this_trait.pre_publication_description
if len(description) > 0:
this_trait.description_display = description.strip()
else:
this_trait.description_display = ""
if not this_trait.year.isdigit():
this_trait.pubmed_text = "N/A"
else:
this_trait.pubmed_text = this_trait.year
if this_trait.pubmed_id:
this_trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % this_trait.pubmed_id
# LRS and its location
this_trait.LRS_score_repr = "N/A"
this_trait.LRS_location_repr = "N/A"
if this_trait.lrs:
query = """
select Geno.Chr, Geno.Mb from Geno, Species
where Species.Name = '%s' and
Geno.Name = '%s' and
Geno.SpeciesId = Species.Id
""" % (species, this_trait.locus)
result = g.db.execute(query).fetchone()
if result:
if result[0] and result[1]:
LRS_Chr = result[0]
LRS_Mb = result[1]
this_trait.LRS_score_repr = LRS_score_repr = '%3.1f' % this_trait.lrs
this_trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (
LRS_Chr, float(LRS_Mb))
def retrieve_sample_data(self, trait):
query = """
SELECT
Strain.Name, PublishData.value, PublishSE.error, NStrain.count, Strain.Name2
FROM
(PublishData, Strain, PublishXRef, PublishFreeze)
left join PublishSE on
(PublishSE.DataId = PublishData.Id AND PublishSE.StrainId = PublishData.StrainId)
left join NStrain on
(NStrain.DataId = PublishData.Id AND
NStrain.StrainId = PublishData.StrainId)
WHERE
PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
PublishData.Id = PublishXRef.DataId AND PublishXRef.Id = %s AND
PublishFreeze.Id = %s AND PublishData.StrainId = Strain.Id
Order BY
Strain.Name
"""
results = g.db.execute(query, (trait, self.id)).fetchall()
return results
class GenotypeDataSet(DataSet):
DS_NAME_MAP['Geno'] = 'GenotypeDataSet'
def setup(self):
# Fields in the database table
self.search_fields = ['Name',
'Chr']
# Find out what display_fields is
self.display_fields = ['name',
'chr',
'mb',
'source2',
'sequence']
# Fields displayed in the search results table header
self.header_fields = ['Index',
'ID',
'Location']
# Todo: Obsolete or rename this field
self.type = 'Geno'
self.query_for_group = '''
SELECT
InbredSet.Name, InbredSet.Id, InbredSet.GeneticType, InbredSet.InbredSetCode
FROM
InbredSet, GenoFreeze
WHERE
GenoFreeze.InbredSetId = InbredSet.Id AND
GenoFreeze.Name = "%s"
''' % escape(self.name)
def check_confidentiality(self):
return geno_mrna_confidentiality(self)
def get_trait_info(self, trait_list, species=None):
for this_trait in trait_list:
if not this_trait.haveinfo:
this_trait.retrieveInfo()
if this_trait.chr and this_trait.mb:
this_trait.location_repr = 'Chr%s: %.6f' % (
this_trait.chr, float(this_trait.mb))
def retrieve_sample_data(self, trait):
query = """
SELECT
Strain.Name, GenoData.value, GenoSE.error, "N/A", Strain.Name2
FROM
(GenoData, GenoFreeze, Strain, Geno, GenoXRef)
left join GenoSE on
(GenoSE.DataId = GenoData.Id AND GenoSE.StrainId = GenoData.StrainId)
WHERE
Geno.SpeciesId = %s AND Geno.Name = %s AND GenoXRef.GenoId = Geno.Id AND
GenoXRef.GenoFreezeId = GenoFreeze.Id AND
GenoFreeze.Name = %s AND
GenoXRef.DataId = GenoData.Id AND
GenoData.StrainId = Strain.Id
Order BY
Strain.Name
"""
results = g.db.execute(query,
(webqtlDatabaseFunction.retrieve_species_id(self.group.name),
trait, self.name)).fetchall()
return results
class MrnaAssayDataSet(DataSet):
'''
An mRNA Assay is a quantitative assessment (assay) associated with an mRNA trait
This used to be called ProbeSet, but that term only refers specifically to the Affymetrix
platform and is far too specific.
'''
DS_NAME_MAP['ProbeSet'] = 'MrnaAssayDataSet'
def setup(self):
# Fields in the database table
self.search_fields = ['Name',
'Description',
'Probe_Target_Description',
'Symbol',
'Alias',
'GenbankId',
'UniGeneId',
'RefSeq_TranscriptId']
# Find out what display_fields is
self.display_fields = ['name', 'symbol',
'description', 'probe_target_description',
'chr', 'mb',
'alias', 'geneid',
'genbankid', 'unigeneid',
'omim', 'refseq_transcriptid',
'blatseq', 'targetseq',
'chipid', 'comments',
'strand_probe', 'strand_gene',
'proteinid', 'uniprotid',
'probe_set_target_region',
'probe_set_specificity',
'probe_set_blat_score',
'probe_set_blat_mb_start',
'probe_set_blat_mb_end',
'probe_set_strand',
'probe_set_note_by_rw',
'flag']
# Fields displayed in the search results table header
self.header_fields = ['Index',
'Record',
'Symbol',
'Description',
'Location',
'Mean',
'Max LRS',
'Max LRS Location',
'Additive Effect']
# Todo: Obsolete or rename this field
self.type = 'ProbeSet'
self.query_for_group = '''
SELECT
InbredSet.Name, InbredSet.Id, InbredSet.GeneticType, InbredSet.InbredSetCode
FROM
InbredSet, ProbeSetFreeze, ProbeFreeze
WHERE
ProbeFreeze.InbredSetId = InbredSet.Id AND
ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND
ProbeSetFreeze.Name = "%s"
''' % escape(self.name)
def check_confidentiality(self):
return geno_mrna_confidentiality(self)
def get_trait_info(self, trait_list=None, species=''):
# Note: setting trait_list to [] is probably not a great idea.
if not trait_list:
trait_list = []
for this_trait in trait_list:
if not this_trait.haveinfo:
this_trait.retrieveInfo(QTL=1)
if not this_trait.symbol:
this_trait.symbol = "N/A"
# XZ, 12/08/2008: description
# XZ, 06/05/2009: Rob asked to add probe target description
description_string = str(
str(this_trait.description).strip(codecs.BOM_UTF8), 'utf-8')
target_string = str(
str(this_trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
if len(description_string) > 1 and description_string != 'None':
description_display = description_string
else:
description_display = this_trait.symbol
if (len(description_display) > 1 and description_display != 'N/A'
and len(target_string) > 1 and target_string != 'None'):
description_display = description_display + '; ' + target_string.strip()
# Save it for the jinja2 template
this_trait.description_display = description_display
if this_trait.chr and this_trait.mb:
this_trait.location_repr = 'Chr%s: %.6f' % (
this_trait.chr, float(this_trait.mb))
# Get mean expression value
query = (
"""select ProbeSetXRef.mean from ProbeSetXRef, ProbeSet
where ProbeSetXRef.ProbeSetFreezeId = %s and
ProbeSet.Id = ProbeSetXRef.ProbeSetId and
ProbeSet.Name = '%s'
""" % (escape(str(this_trait.dataset.id)),
escape(this_trait.name)))
result = g.db.execute(query).fetchone()
mean = result[0] if result else 0
if mean:
this_trait.mean = "%2.3f" % mean
# LRS and its location
this_trait.LRS_score_repr = 'N/A'
this_trait.LRS_location_repr = 'N/A'
# Max LRS and its Locus location
if this_trait.lrs and this_trait.locus:
query = """
select Geno.Chr, Geno.Mb from Geno, Species
where Species.Name = '{}' and
Geno.Name = '{}' and
Geno.SpeciesId = Species.Id
""".format(species, this_trait.locus)
result = g.db.execute(query).fetchone()
if result:
lrs_chr, lrs_mb = result
this_trait.LRS_score_repr = '%3.1f' % this_trait.lrs
this_trait.LRS_location_repr = 'Chr%s: %.6f' % (
lrs_chr, float(lrs_mb))
return trait_list
def retrieve_sample_data(self, trait):
query = """
SELECT
Strain.Name, ProbeSetData.value, ProbeSetSE.error, NStrain.count, Strain.Name2
FROM
(ProbeSetData, ProbeSetFreeze,
Strain, ProbeSet, ProbeSetXRef)
left join ProbeSetSE on
(ProbeSetSE.DataId = ProbeSetData.Id AND ProbeSetSE.StrainId = ProbeSetData.StrainId)
left join NStrain on
(NStrain.DataId = ProbeSetData.Id AND
NStrain.StrainId = ProbeSetData.StrainId)
WHERE
ProbeSet.Name = '%s' AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
ProbeSetFreeze.Name = '%s' AND
ProbeSetXRef.DataId = ProbeSetData.Id AND
ProbeSetData.StrainId = Strain.Id
Order BY
Strain.Name
""" % (escape(trait), escape(self.name))
results = g.db.execute(query).fetchall()
return results
def retrieve_genes(self, column_name):
query = """
select ProbeSet.Name, ProbeSet.%s
from ProbeSet,ProbeSetXRef
where ProbeSetXRef.ProbeSetFreezeId = %s and
ProbeSetXRef.ProbeSetId=ProbeSet.Id;
""" % (column_name, escape(str(self.id)))
results = g.db.execute(query).fetchall()
return dict(results)
class TempDataSet(DataSet):
'''Temporary user-generated data set'''
DS_NAME_MAP['Temp'] = 'TempDataSet'
def setup(self):
self.search_fields = ['name',
'description']
self.display_fields = ['name',
'description']
self.header_fields = ['Name',
'Description']
self.type = 'Temp'
# Need to double check later how these are used
self.id = 1
self.fullname = 'Temporary Storage'
self.shortname = 'Temp'
def geno_mrna_confidentiality(ob):
dataset_table = ob.type + "Freeze"
query = '''SELECT Id, Name, FullName, confidentiality,
AuthorisedUsers FROM %s WHERE Name = "%s"''' % (dataset_table, ob.name)
result = g.db.execute(query)
(dataset_id,
name,
full_name,
confidential,
authorized_users) = result.fetchall()[0]
if confidential:
return True
result = g.db.execute(query)
(dataset_id,
name,
full_name,
confidential,
authorized_users) = result.fetchall()[0]
if confidential:
return True
def parse_db_url():
parsed_db = urlparse(SQL_URI)
return (parsed_db.hostname, parsed_db.username,
parsed_db.password, parsed_db.path[1:])
def query_table_timestamp(dataset_type: str):
"""function to query the update timestamp of a given dataset_type"""
# computation data and actions
fetch_db_name = parse_db_url()
query_update_time = f"""
SELECT UPDATE_TIME FROM information_schema.tables
WHERE TABLE_SCHEMA = '{fetch_db_name[-1]}'
AND TABLE_NAME = '{dataset_type}Data'
"""
date_time_obj = g.db.execute(query_update_time).fetchone()[0]
return date_time_obj.strftime("%Y-%m-%d %H:%M:%S")
def generate_hash_file(dataset_name: str, dataset_type: str, dataset_timestamp: str, samplelist: str):
"""given the trait_name generate a unique name for this"""
string_unicode = f"{dataset_name}{dataset_timestamp}{samplelist}".encode()
md5hash = hashlib.md5(string_unicode)
return md5hash.hexdigest()
def cache_dataset_results(dataset_name: str, dataset_type: str, samplelist: List, query_results: List):
"""function to cache dataset query results to file
input dataset_name and type query_results(already processed in default dict format)
"""
# data computations actions
# store the file path on redis
table_timestamp = query_table_timestamp(dataset_type)
samplelist_as_str = ",".join(samplelist)
file_name = generate_hash_file(dataset_name, dataset_type, table_timestamp, samplelist_as_str)
file_path = os.path.join(TMPDIR, f"{file_name}.json")
with open(file_path, "w") as file_handler:
json.dump(query_results, file_handler)
def fetch_cached_results(dataset_name: str, dataset_type: str, samplelist: List):
"""function to fetch the cached results"""
table_timestamp = query_table_timestamp(dataset_type)
samplelist_as_str = ",".join(samplelist)
file_name = generate_hash_file(dataset_name, dataset_type, table_timestamp, samplelist_as_str)
file_path = os.path.join(TMPDIR, f"{file_name}.json")
try:
with open(file_path, "r") as file_handler:
return json.load(file_handler)
except FileNotFoundError:
pass
