diff options
Diffstat (limited to 'wqflask/base')
| -rw-r--r-- | wqflask/base/data_set.py | 156 | ||||
| -rw-r--r-- | wqflask/base/mrna_assay_tissue_data.py | 4 | ||||
| -rw-r--r-- | wqflask/base/webqtlCaseData.py | 3 |
3 files changed, 65 insertions, 98 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index a7811a30..f66bf186 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -21,10 +21,7 @@ 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 @@ -33,7 +30,6 @@ 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 @@ -42,6 +38,7 @@ from flask import Flask, g from base.webqtlConfig import TMPDIR from urllib.parse import urlparse from utility.tools import SQL_URI +from wqflask.database import database_connection import os import math import string @@ -60,8 +57,6 @@ 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 = {} @@ -200,26 +195,23 @@ def create_datasets_list(): 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) - + type_dict = {'Publish': 'PublishFreeze', + 'ProbeSet': 'ProbeSetFreeze', + 'Geno': 'GenoFreeze'} + + for dataset_type in type_dict: + with database_connection() as conn, conn.cursor() as cursor: + cursor.execute("SELECT Name FROM %s", + (type_dict[dataset_type],)) + results = cursor.fetchall(query) + if results: + for result in results: + datasets.append( + create_dataset(result.Name, dataset_type)) if USE_REDIS: r.set(key, pickle.dumps(datasets, pickle.HIGHEST_PROTOCOL)) r.expire(key, 60 * 60) @@ -259,9 +251,6 @@ class Markers: 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): @@ -332,12 +321,16 @@ class DatasetGroup: 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) + query = """SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType, + InbredSet.InbredSetCode FROM InbredSet where Name=%s + """ + if not name: + query, name = dataset.query_for_group, dataset.name + with database_connection() as conn, conn.cursor() as cursor: + cursor.execute(query, (name,)) + results = cursor.fetchone() + if results: + self.name, self.id, self.genetic_type, self.code = results if self.name == 'BXD300': self.name = "BXD" @@ -633,39 +626,33 @@ class DataSet: """ try: + query = "" + _vars = None + query_args = (self.name, self.name, self.name) 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"]) - ) + query = ( + "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)") else: - query_args = tuple(escape(x) for x in ( - (self.type + "Freeze"), - self.name, - self.name, - self.name)) - + query = ( + "SELECT Id, Name, FullName, ShortName " + f"FROM {self.type}Freeze " + "WHERE (Name = %s OR FullName = %s OR ShortName = %s)") 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)) - + with database_connection() as conn, conn.cursor() as cursor: + cursor.execute(query, query_args) + _vars = cursor.fetchone() + if self.type == "ProbeSet": + (self.id, self.name, self.fullname, self.shortname, + self.data_scale, self.tissue) = _vars + else: + self.id, self.name, self.fullname, self.shortname = _vars except TypeError: - logger.debug( - "Dataset {} is not yet available in GeneNetwork.".format(self.name)) pass def chunk_dataset(self, dataset, n): @@ -863,16 +850,8 @@ class PhenotypeDataSet(DataSet): '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) + 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""" def check_confidentiality(self): # (Urgently?) Need to write this @@ -979,16 +958,10 @@ class GenotypeDataSet(DataSet): # 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) + 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""" def check_confidentiality(self): return geno_mrna_confidentiality(self) @@ -1022,6 +995,14 @@ class GenotypeDataSet(DataSet): results = g.db.execute(query, (webqtlDatabaseFunction.retrieve_species_id(self.group.name), trait, self.name)).fetchall() + + if self.group.name in webqtlUtil.ParInfo: + f1_1, f1_2, ref, nonref = webqtlUtil.ParInfo[self.group.name] + results.append([f1_1, 0, None, "N/A", f1_1]) + results.append([f1_2, 0, None, "N/A", f1_2]) + results.append([ref, -1, None, "N/A", ref]) + results.append([nonref, 1, None, "N/A", nonref]) + return results @@ -1079,17 +1060,10 @@ class MrnaAssayDataSet(DataSet): # 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) + 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""" def check_confidentiality(self): return geno_mrna_confidentiality(self) diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py index 8f8e2b0a..d7e747aa 100644 --- a/wqflask/base/mrna_assay_tissue_data.py +++ b/wqflask/base/mrna_assay_tissue_data.py @@ -9,10 +9,6 @@ from utility.db_tools import escape from gn3.db_utils import database_connector -from utility.logger import getLogger -logger = getLogger(__name__) - - class MrnaAssayTissueData: def __init__(self, gene_symbols=None): diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py index 25b6cb8a..dd6fad04 100644 --- a/wqflask/base/webqtlCaseData.py +++ b/wqflask/base/webqtlCaseData.py @@ -21,9 +21,6 @@ # Created by GeneNetwork Core Team 2010/08/10 -from utility.logger import getLogger -logger = getLogger(__name__) - import utility.tools utility.tools.show_settings() |