aboutsummaryrefslogtreecommitdiff
path: root/gn3
diff options
context:
space:
mode:
authorMuriithi Frederick Muriuki2021-07-30 10:33:40 +0300
committerMuriithi Frederick Muriuki2021-07-30 10:33:40 +0300
commit238450af8aa3395b3ae5a636fada67206a863d85 (patch)
tree46ae9c5a26c290ae11443a327fbe498460ba698d /gn3
parentbeec957107298eef2b2a825ba0a744e4e95b0dcd (diff)
downloadgenenetwork3-238450af8aa3395b3ae5a636fada67206a863d85.tar.gz
Rework db functions to enable postprocessing
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Rework the database functions to return a dict of key-value pairs, which eases the postprocessing of the trait information. The postprocessing is mainly to try an maintain data compatibility with the code that is at the following locations: https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlDataset.py https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/Heatmap.py This was mainly a proof-of-concept, and the functions do not have testing added for them: there is therefore need to add testing for the new functions, and probably even rework them if they are found to be complicated.
Diffstat (limited to 'gn3')
-rw-r--r--gn3/db/traits.py87
1 files changed, 79 insertions, 8 deletions
diff --git a/gn3/db/traits.py b/gn3/db/traits.py
index 9742fa2..d8d2b62 100644
--- a/gn3/db/traits.py
+++ b/gn3/db/traits.py
@@ -1,5 +1,6 @@
"""This class contains functions relating to trait data manipulation"""
from typing import Any, Dict, Union
+from gn3.function_helpers import compose
def get_trait_csv_sample_data(conn: Any,
@@ -135,8 +136,7 @@ def retrieve_publish_trait_info(trait_data_source: Dict[str, Any], conn: Any):
"Phenotype.Id = PublishXRef.PhenotypeId AND "
"Publication.Id = PublishXRef.PublicationId AND "
"PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND "
- "PublishFreeze.Id =%(trait_dataset_id)s").format(
- columns = columns)
+ "PublishFreeze.Id =%(trait_dataset_id)s").format(columns=columns)
with conn.cursor() as cursor:
cursor.execute(
query,
@@ -144,7 +144,17 @@ def retrieve_publish_trait_info(trait_data_source: Dict[str, Any], conn: Any):
k:v for k, v in trait_data_source.items()
if k in ["trait_name", "trait_dataset_id"]
})
- return dict(zip((k.lower() for k in keys), cursor.fetchone()))
+ return dict(zip([k.lower() for k in keys], cursor.fetchone()))
+
+def set_confidential_field(trait_info):
+ """Post processing function for 'Publish' trait types.
+
+ It sets the value for the 'confidential' key."""
+ return {
+ **trait_info,
+ "confidential": 1 if (
+ trait_info.get("pre_publication_description", None)
+ and not trait_info.get("pubmed_id", None)) else 0}
def retrieve_probeset_trait_info(trait_data_source: Dict[str, Any], conn: Any):
"""Retrieve trait information for type `ProbeSet` traits.
@@ -168,7 +178,7 @@ def retrieve_probeset_trait_info(trait_data_source: Dict[str, Any], conn: Any):
"ProbeSetXRef.ProbeSetId = ProbeSet.Id AND "
"ProbeSetFreeze.Name = %(trait_dataset_name)s AND "
"ProbeSet.Name = %(trait_name)s").format(
- columns = ", ".join(["ProbeSet.{}".format(x) for x in keys]))
+ columns=", ".join(["ProbeSet.{}".format(x) for x in keys]))
with conn.cursor() as cursor:
cursor.execute(
query,
@@ -192,7 +202,7 @@ def retrieve_geno_trait_info(trait_data_source: Dict[str, Any], conn: Any):
"GenoXRef.GenoFreezeId = GenoFreeze.Id AND GenoXRef.GenoId = Geno.Id AND "
"GenoFreeze.Name = %(trait_dataset_name)s AND "
"Geno.Name = %(trait_name)s").format(
- columns = ", ".join(["Geno.{}".format(x) for x in keys]))
+ columns=", ".join(["Geno.{}".format(x) for x in keys]))
with conn.cursor() as cursor:
cursor.execute(
query,
@@ -209,7 +219,7 @@ def retrieve_temp_trait_info(trait_data_source: Dict[str, Any], conn: Any):
keys = ("name", "description")
query = (
"SELECT {columns} FROM Temp "
- "WHERE Name = %(trait_name)s").format(columns = ", ".join(keys))
+ "WHERE Name = %(trait_name)s").format(columns=", ".join(keys))
with conn.cursor() as cursor:
cursor.execute(
query,
@@ -219,9 +229,53 @@ def retrieve_temp_trait_info(trait_data_source: Dict[str, Any], conn: Any):
})
return dict(zip(keys, cursor.fetchone()))
+def set_haveinfo_field(trait_info):
+ """
+ Common postprocessing function for all trait types.
+
+ Sets the value for the 'haveinfo' field."""
+ return {**trait_info, "haveinfo": 1 if trait_info else 0}
+
+def set_homologene_id_field_probeset(trait_info, conn):
+ """
+ Postprocessing function for 'ProbeSet' traits.
+
+ Sets the value for the 'homologene' key.
+ """
+ query = (
+ "SELECT HomologeneId FROM Homologene, Species, InbredSet"
+ " WHERE Homologene.GeneId = %(geneid)s AND InbredSet.Name = %(riset)s"
+ " AND InbredSet.SpeciesId = Species.Id AND"
+ " Species.TaxonomyId = Homologene.TaxonomyId")
+ with conn.cursor() as cursor:
+ cursor.execute(
+ query,
+ {
+ k:v for k, v in trait_info.items()
+ if k in ["geneid", "riset"]
+ })
+ res = cursor.fetchone()
+ if res:
+ return {**trait_info, "homologeneid": res[0]}
+ return {**trait_info, "homologeneid": None}
+
+def set_homologene_id_field(trait_info, conn):
+ """
+ Common postprocessing function for all trait types.
+
+ Sets the value for the 'homologene' key."""
+ set_to_null = lambda ti: {**ti, "homologeneid": None}
+ functions_table = {
+ "Temp": set_to_null,
+ "Geno": set_to_null,
+ "Publish": set_to_null,
+ "ProbeSet": lambda ti: set_homologene_id_field_probeset(ti, conn)
+ }
+ return functions_table[trait_info["type"]](trait_info)
+
def retrieve_trait_info(
trait_type: str, trait_name: str, trait_dataset_id: int,
- trait_dataset_name: str, conn: Any, QTL = None):
+ trait_dataset_name: str, conn: Any, QTL=None):
"""Retrieves the trait information.
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L397-L456
@@ -234,7 +288,24 @@ def retrieve_trait_info(
"Geno": retrieve_geno_trait_info,
"Temp": retrieve_temp_trait_info
}
- return trait_info_function_table[trait_type](
+
+ common_post_processing_fn = compose(
+ lambda ti: set_homologene_id_field(ti, conn),
+ lambda ti: {"type": trait_type, **ti},
+ set_haveinfo_field)
+
+ trait_post_processing_functions_table = {
+ "Publish": compose(set_confidential_field, common_post_processing_fn),
+ "ProbeSet": compose(common_post_processing_fn),
+ "Geno": common_post_processing_fn,
+ "Temp": common_post_processing_fn
+ }
+
+ retrieve_info = compose(
+ trait_post_processing_functions_table[trait_type],
+ trait_info_function_table[trait_type])
+
+ return retrieve_info(
{
"trait_name": trait_name,
"trait_dataset_id": trait_dataset_id,