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"Base Dataset class ..."
import math
import collections
from redis import Redis
from gn2.base import species
from gn2.utility import chunks
from gn2.utility.tools import get_setting
from gn3.monads import MonadicDict, query_sql
from pymonad.maybe import Maybe, Nothing
from .datasetgroup import DatasetGroup
from gn2.wqflask.database import database_connection
from gn2.utility.db_tools import escape, mescape, create_in_clause
from .utils import fetch_cached_results, cache_dataset_results
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, redis_conn=Redis()):
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 = Nothing
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(redis_conn)
self.species = species.TheSpecies(dataset=self)
def as_monadic_dict(self):
_result = MonadicDict({
'name': self.name,
'shortname': self.shortname,
'fullname': self.fullname,
'type': self.type,
'data_scale': self.data_scale,
'group': self.group.name
})
_result["accession_id"] = self.accession_id
return _result
def get_accession_id(self) -> Maybe[str]:
"""Get the accession_id of this dataset depending on the
dataset type."""
__query = ""
with database_connection(get_setting("SQL_URI")) as conn:
if self.type == "Publish":
__query = (
"SELECT InfoFiles.GN_AccesionId AS accession_id FROM "
"InfoFiles, PublishFreeze, InbredSet "
"WHERE InbredSet.Name = "
f"'{conn.escape_string(self.group.name).decode()}' "
"AND PublishFreeze.InbredSetId = InbredSet.Id "
"AND InfoFiles.InfoPageName = PublishFreeze.Name "
"AND PublishFreeze.public > 0 AND "
"PublishFreeze.confidentiality < 1 "
"ORDER BY PublishFreeze.CreateTime DESC"
)
elif self.type == "Geno":
__query = (
"SELECT InfoFiles.GN_AccesionId AS accession_id FROM "
"InfoFiles, GenoFreeze, InbredSet WHERE InbredSet.Name = "
f"'{conn.escape_string(self.group.name).decode()}' AND "
"GenoFreeze.InbredSetId = InbredSet.Id "
"AND InfoFiles.InfoPageName = GenoFreeze.ShortName "
"AND GenoFreeze.public > 0 AND "
"GenoFreeze.confidentiality < 1 "
"ORDER BY GenoFreeze.CreateTime DESC"
)
elif self.type == "ProbeSet":
__query = (
"SELECT InfoFiles.GN_AccesionId AS accession_id "
"FROM InfoFiles WHERE InfoFiles.InfoPageName = "
f"'{conn.escape_string(self.name).decode()}'"
)
else: # The Value passed is not present
raise LookupError
# Should there be an empty row, query_sql returns a None
# value instead of yielding a value; this block
# accomodates this non-intuitive edge-case
for result in query_sql(conn, __query) or ():
return result["accession_id"]
return Nothing
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.
"""
with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
try:
if self.type == "ProbeSet":
cursor.execute(
"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)",
(self.name,)*3)
(self.id, self.name, self.fullname, self.shortname,
self.data_scale, self.tissue) = cursor.fetchone()
else:
self.tissue = "N/A"
cursor.execute(
"SELECT Id, Name, FullName, ShortName "
f"FROM {self.type}Freeze "
"WHERE (Name = %s OR FullName = "
"%s OR ShortName = %s)",
(self.name,)*3)
(self.id, self.name, self.fullname,
self.shortname) = cursor.fetchone()
except TypeError:
pass
def chunk_dataset(self, dataset, n):
results = {}
traits_name_dict = ()
with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
cursor.execute(
"SELECT ProbeSetXRef.DataId,ProbeSet.Name "
"FROM ProbeSet, ProbeSetXRef, ProbeSetFreeze "
"WHERE ProbeSetFreeze.Name = %s AND "
"ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id "
"AND ProbeSetXRef.ProbeSetId = ProbeSet.Id",
(self.name,))
# should cache this
traits_name_dict = dict(cursor.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
with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
cursor.execute(
"SELECT Strain.Name, Strain.Id FROM "
"Strain, Species WHERE Strain.Name IN "
f"{create_in_clause(self.samplelist)} "
"AND Strain.SpeciesId=Species.Id AND "
"Species.name = %s", (self.group.species,)
)
results = dict(cursor.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])]
cursor.execute(
"SELECT * from ProbeSetData WHERE StrainID IN "
f"{create_in_clause(sample_ids)} AND id IN "
"(SELECT ProbeSetXRef.DataId FROM "
"(ProbeSet, ProbeSetXRef, ProbeSetFreeze) "
"WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id "
"AND ProbeSetFreeze.Name = %s AND "
"ProbeSet.Id = ProbeSetXRef.ProbeSetId)",
(self.name,)
)
query_results = list(cursor.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
with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
cursor.execute(
"SELECT Strain.Name, Strain.Id FROM Strain, Species "
f"WHERE Strain.Name IN {create_in_clause(self.samplelist)} "
"AND Strain.SpeciesId=Species.Id "
"AND Species.name = %s",
(self.group.species,)
)
results = dict(cursor.fetchall())
sample_ids = [
sample_id for sample_id in
(results.get(item) for item in self.samplelist
if item is not None)
if sample_id 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
if len(temp) > 0:
query = 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))
cursor.execute(query)
results = cursor.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
|
