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-rw-r--r--wqflask/base/data_set.py180
-rw-r--r--wqflask/base/mrna_assay_tissue_data.py4
-rw-r--r--wqflask/base/trait.py28
-rw-r--r--wqflask/base/webqtlCaseData.py3
4 files changed, 95 insertions, 120 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 72906515..2f4c1154 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"
@@ -483,28 +476,28 @@ class DatasetGroup:
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
+ the_results = g.db.execute('''
+ (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
+ 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
+ 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)
+ ORDER BY Tissue.Name, ProbeSetFreeze.OrderList DESC)
''' % (group_name,
- group_name,
- "'" + group_name + "'"))
+ group_name,
+ "'" + group_name + "'")).fetchall()
sorted_results = sorted(the_results, key=lambda kv: kv[0])
@@ -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)
@@ -1087,17 +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/trait.py b/wqflask/base/trait.py
index 11b28c5c..b02c6033 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -300,10 +300,16 @@ def jsonable(trait, dataset=None):
dataset_type=trait.dataset.type,
group_name=trait.dataset.group.name)
+ trait_symbol = "N/A"
+ if trait.symbol:
+ trait_symbol = trait.symbol
+
if dataset.type == "ProbeSet":
return dict(name=trait.name,
- view=trait.view,
- symbol=trait.symbol,
+ display_name=trait.display_name,
+ hmac=hmac.data_hmac('{}:{}'.format(trait.display_name, dataset.name)),
+ view=str(trait.view),
+ symbol=trait_symbol,
dataset=dataset.name,
dataset_name=dataset.shortname,
description=trait.description_display,
@@ -316,7 +322,10 @@ def jsonable(trait, dataset=None):
elif dataset.type == "Publish":
if trait.pubmed_id:
return dict(name=trait.name,
- view=trait.view,
+ display_name=trait.display_name,
+ hmac=hmac.data_hmac('{}:{}'.format(trait.display_name, dataset.name)),
+ view=str(trait.view),
+ symbol=trait_symbol,
dataset=dataset.name,
dataset_name=dataset.shortname,
description=trait.description_display,
@@ -332,7 +341,10 @@ def jsonable(trait, dataset=None):
)
else:
return dict(name=trait.name,
- view=trait.view,
+ display_name=trait.display_name,
+ hmac=hmac.data_hmac('{}:{}'.format(trait.display_name, dataset.name)),
+ view=str(trait.view),
+ symbol=trait_symbol,
dataset=dataset.name,
dataset_name=dataset.shortname,
description=trait.description_display,
@@ -346,14 +358,18 @@ def jsonable(trait, dataset=None):
)
elif dataset.type == "Geno":
return dict(name=trait.name,
- view=trait.view,
+ display_name=trait.display_name,
+ hmac=hmac.data_hmac('{}:{}'.format(trait.display_name, dataset.name)),
+ view=str(trait.view),
dataset=dataset.name,
dataset_name=dataset.shortname,
location=trait.location_repr
)
elif dataset.name == "Temp":
return dict(name=trait.name,
- view=trait.view,
+ display_name=trait.display_name,
+ hmac=hmac.data_hmac('{}:{}'.format(trait.display_name, dataset.name)),
+ view=str(trait.view),
dataset="Temp",
dataset_name="Temp")
else:
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()
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-26 12:03:58 +0000