aboutsummaryrefslogtreecommitdiff
path: root/wqflask/base/data_set/dataset.py
diff options
context:
space:
mode:
Diffstat (limited to 'wqflask/base/data_set/dataset.py')
-rw-r--r--wqflask/base/data_set/dataset.py292
1 files changed, 292 insertions, 0 deletions
diff --git a/wqflask/base/data_set/dataset.py b/wqflask/base/data_set/dataset.py
new file mode 100644
index 00000000..f035e028
--- /dev/null
+++ b/wqflask/base/data_set/dataset.py
@@ -0,0 +1,292 @@
+"Base Dataset class ..."
+
+import math
+import collections
+
+
+from redis import Redis
+
+
+from base import species
+from utility import chunks
+from .datasetgroup import DatasetGroup
+from wqflask.database import database_connection
+from 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 = 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(redis_conn)
+ 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):
+ results = None
+ with database_connection() as conn, conn.cursor() as cursor:
+ if self.type == "Publish":
+ cursor.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,)
+ )
+ results = cursor.fetchone()
+ elif self.type == "Geno":
+ cursor.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,)
+ )
+ results = cursor.fetchone()
+
+ if results:
+ return str(results[0])
+ 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.
+
+ """
+ with database_connection() 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() 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() 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() 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
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 14:27:12 +0000