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-rw-r--r--wqflask/base/data_set/dataset.py90
1 files changed, 50 insertions, 40 deletions
diff --git a/wqflask/base/data_set/dataset.py b/wqflask/base/data_set/dataset.py
index b6899278..dfe09921 100644
--- a/wqflask/base/data_set/dataset.py
+++ b/wqflask/base/data_set/dataset.py
@@ -2,13 +2,15 @@
import math
import collections
-
+import itertools
from redis import Redis
-
+from MySQLdb.cursors import DictCursor
from base import species
from utility import chunks
+from gn3.monads import MonadicDict, query_sql
+from pymonad.maybe import Maybe, Nothing
from .datasetgroup import DatasetGroup
from wqflask.database import database_connection
from utility.db_tools import escape, mescape, create_in_clause
@@ -30,7 +32,7 @@ class DataSet:
self.fullname = None
self.type = None
self.data_scale = None # ZS: For example log2
- self.accession_id = None
+ self.accession_id = Nothing
self.setup()
@@ -47,50 +49,58 @@ class DataSet:
self.group.get_samplelist(redis_conn)
self.species = species.TheSpecies(dataset=self)
- def as_dict(self):
- return {
+ 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,
- 'accession_id': self.accession_id
- }
-
- def get_accession_id(self):
- results = None
- with database_connection() as conn, conn.cursor() as cursor:
+ '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."""
+ __accession_id_dict = MonadicDict()
+ with database_connection() as conn:
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()
+ __accession_id_dict, = itertools.islice(
+ query_sql(conn,
+ ("SELECT InfoFiles.GN_AccesionId AS accession_id FROM "
+ "InfoFiles, PublishFreeze, InbredSet "
+ f"WHERE InbredSet.Name = '{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")
+ ), 1)
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()
-
- # Returns None by default if this is not executed
- if results:
- return str(results[0])
+ __accession_id_dict, = itertools.islice(
+ query_sql(conn,
+ ("SELECT InfoFiles.GN_AccesionId AS accession_id FROM "
+ "InfoFiles, GenoFreeze, InbredSet "
+ f"WHERE InbredSet.Name = '{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")
+ ), 1)
+ elif self.type == "ProbeSet":
+ __accession_id_dict, = itertools.islice(
+ query_sql(conn,
+ ("SELECT InfoFiles.GN_AccesionId AS accession_id "
+ f"FROM InfoFiles WHERE InfoFiles.InfoPageName = '{conn.escape_string(self.name).decode()}' "
+ f"AND InfoFiles.DB_Name = '{conn.escape_string(self.fullname).decode()}' "
+ f"OR InfoFiles.DB_Name = '{conn.escape_string(self.shortname).decode()}'")
+ ), 1)
+ else: # The Value passed is not present
+ raise LookupError
+ return __accession_id_dict["accession_id"]
def retrieve_other_names(self):
"""This method fetches the the dataset names in search_result.