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-rw-r--r--gn3/db/datasets.py251
1 files changed, 251 insertions, 0 deletions
diff --git a/gn3/db/datasets.py b/gn3/db/datasets.py
new file mode 100644
index 0000000..3ad50f6
--- /dev/null
+++ b/gn3/db/datasets.py
@@ -0,0 +1,251 @@
+from typing import Any, Dict, Union
+
+def retrieve_probeset_trait_dataset_name(
+ threshold: int, name: str, connection: Any):
+ query = (
+ "SELECT Id, Name, FullName, ShortName, DataScale "
+ "FROM ProbeSetFreeze "
+ "WHERE "
+ "public > %(threshold)s "
+ "AND "
+ "(Name = %(name)s OR FullName = %(name)s OR ShortName = %(name)s)")
+ with connection.cursor() as cursor:
+ cursor.execute(
+ query,
+ {
+ "threshold": threshold,
+ "name": name
+ })
+ return dict(zip(
+ ["dataset_id", "dataset_name", "dataset_fullname",
+ "dataset_shortname", "dataset_datascale"],
+ cursor.fetchone))
+
+def retrieve_publish_trait_dataset_name(threshold: int, name: str, connection: Any):
+ query = (
+ "SELECT Id, Name, FullName, ShortName "
+ "FROM PublishFreeze "
+ "WHERE "
+ "public > %(threshold)s "
+ "AND "
+ "(Name = %(name)s OR FullName = %(name)s OR ShortName = %(name)s)")
+ with connection.cursor() as cursor:
+ cursor.execute(
+ query,
+ {
+ "threshold": threshold,
+ "name": name
+ })
+ return dict(zip(
+ ["dataset_id", "dataset_name", "dataset_fullname",
+ "dataset_shortname"],
+ cursor.fetchone))
+
+def retrieve_geno_trait_dataset_name(threshold: int, name: str, connection: Any):
+ query = (
+ "SELECT Id, Name, FullName, ShortName "
+ "FROM GenoFreeze "
+ "WHERE "
+ "public > %(threshold)s "
+ "AND "
+ "(Name = %(name)s OR FullName = %(name)s OR ShortName = %(name)s)")
+ with connection.cursor() as cursor:
+ cursor.execute(
+ query,
+ {
+ "threshold": threshold,
+ "name": name
+ })
+ return dict(zip(
+ ["dataset_id", "dataset_name", "dataset_fullname",
+ "dataset_shortname"],
+ cursor.fetchone))
+
+def retrieve_temp_trait_dataset_name(threshold: int, name: str, connection: Any):
+ query = (
+ "SELECT Id, Name, FullName, ShortName "
+ "FROM TempFreeze "
+ "WHERE "
+ "public > %(threshold)s "
+ "AND "
+ "(Name = %(name)s OR FullName = %(name)s OR ShortName = %(name)s)")
+ with connection.cursor() as cursor:
+ cursor.execute(
+ query,
+ {
+ "threshold": threshold,
+ "name": name
+ })
+ return dict(zip(
+ ["dataset_id", "dataset_name", "dataset_fullname",
+ "dataset_shortname"],
+ cursor.fetchone))
+
+def retrieve_dataset_name(
+ trait_type: str, threshold: int, trait_name: str, dataset_name: str,
+ conn: Any):
+ """
+ Retrieve the name of a trait given the trait's name
+
+ This is extracted from the `webqtlDataset.retrieveName` function as is
+ implemented at
+ https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlDataset.py#L140-L169
+ """
+ fn_map = {
+ "ProbeSet": retrieve_probeset_trait_dataset_name,
+ "Publish": retrieve_publish_trait_dataset_name,
+ "Geno": retrieve_geno_trait_dataset_name,
+ "Temp": retrieve_temp_trait_dataset_name}
+ if trait_type == "Temp":
+ return retrieve_temp_trait_dataset_name(threshold, trait_name, conn)
+ return fn_map[trait_type](threshold, dataset_name, conn)
+
+
+def retrieve_geno_riset_fields(name, conn):
+ """
+ Retrieve the RISet, and RISetID values for various Geno trait types.
+ """
+ query = (
+ "SELECT InbredSet.Name, InbredSet.Id "
+ "FROM InbredSet, GenoFreeze "
+ "WHERE GenoFreeze.InbredSetId = InbredSet.Id "
+ "AND GenoFreeze.Name = %(name)s")
+ with conn.cursor() as cursor:
+ cursor.execute(query, {"name": name})
+ return dict(zip(["riset", "risetid"], cursor.fetchone()))
+ return {}
+
+def retrieve_publish_riset_fields(name, conn):
+ """
+ Retrieve the RISet, and RISetID values for various Publish trait types.
+ """
+ query = (
+ "SELECT InbredSet.Name, InbredSet.Id "
+ "FROM InbredSet, PublishFreeze "
+ "WHERE PublishFreeze.InbredSetId = InbredSet.Id "
+ "AND PublishFreeze.Name = %(name)s")
+ with conn.cursor() as cursor:
+ cursor.execute(query, {"name": name})
+ return dict(zip(["riset", "risetid"], cursor.fetchone()))
+ return {}
+
+def retrieve_probeset_riset_fields(name, conn):
+ """
+ Retrieve the RISet, and RISetID values for various ProbeSet trait types.
+ """
+ query = (
+ "SELECT InbredSet.Name, InbredSet.Id "
+ "FROM InbredSet, ProbeSetFreeze, ProbeFreeze "
+ "WHERE ProbeFreeze.InbredSetId = InbredSet.Id "
+ "AND ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId "
+ "AND ProbeSetFreeze.Name = %(name)s")
+ with conn.cursor() as cursor:
+ cursor.execute(query, {"name": name})
+ return dict(zip(["riset", "risetid"], cursor.fetchone()))
+ return {}
+
+def retrieve_temp_riset_fields(name, conn):
+ query = (
+ "SELECT InbredSet.Name, InbredSet.Id "
+ "FROM InbredSet, Temp "
+ "WHERE Temp.InbredSetId = InbredSet.Id "
+ "AND Temp.Name = %(name)s")
+ with conn.cursor() as cursor:
+ cursor.execute(query, {"name": name})
+ return dict(zip(["riset", "risetid"], cursor.fetchone()))
+ return {}
+
+def retrieve_riset_fields(trait_type, trait_name, dataset_info, conn):
+ """
+ Retrieve the RISet, and RISetID values for various trait types.
+ """
+ riset_fns_map = {
+ "Geno": retrieve_geno_riset_fields,
+ "Publish": retrieve_publish_riset_fields,
+ "ProbeSet": retrieve_probeset_riset_fields
+ }
+
+ if trait_type == "Temp":
+ riset_info = retrieve_temp_riset_fields(trait_name, conn)
+ else:
+ riset_info = riset_fns_map[trait_type](dataset_info["dataset_name"], conn)
+
+ return {
+ **dataset_info,
+ **riset_info,
+ "riset": (
+ "BXD" if riset_info.get("riset") == "BXD300"
+ else riset_info.get("riset", ""))
+ }
+
+def retrieve_temp_trait_dataset():
+ return {
+ "searchfield": ["name", "description"],
+ "disfield": ["name", "description"],
+ "type": "Temp",
+ "dataset_id": 1,
+ "fullname": "Temporary Storage",
+ "shortname": "Temp"
+ }
+
+def retrieve_geno_trait_dataset():
+ return {
+ "searchfield": ["name","chr"],
+ "disfield": ["name","chr","mb", "source2", "sequence"],
+ "type": "Geno"
+ }
+
+def retrieve_publish_trait_dataset():
+ return {
+ "searchfield": [
+ "name", "post_publication_description", "abstract", "title",
+ "authors"],
+ "disfield": [
+ "name","pubmed_id", "pre_publication_description",
+ "post_publication_description", "original_description",
+ "pre_publication_abbreviation", "post_publication_abbreviation",
+ "lab_code", "submitter", "owner", "authorized_users",
+ "authors","title","abstract", "journal","volume","pages","month",
+ "year","sequence", "units", "comments"],
+ "type": "Publish"
+ }
+
+def retrieve_probeset_trait_dataset():
+ return {
+ "searchfield": [
+ "name", "description", "probe_target_description", "symbol",
+ "alias", "genbankid", "unigeneid", "omim", "refseq_transcriptid",
+ "probe_set_specificity", "probe_set_blat_score"],
+ "disfield": [
+ "name", "symbol", "description", "probe_target_description", "chr",
+ "mb", "alias", "geneid", "genbankid", "unigeneid", "omim",
+ "refseq_transcriptid", "blatseq", "targetseq", "chipid", "comments",
+ "strand_probe", "strand_gene", "probe_set_target_region",
+ "proteinid", "probe_set_specificity", "probe_set_blat_score",
+ "probe_set_blat_mb_start", "probe_set_blat_mb_end",
+ "probe_set_strand", "probe_set_note_by_rw", "flag"],
+ "type": "ProbeSet"
+ }
+
+def retrieve_trait_dataset(trait_type, trait, threshold, conn):
+ dataset_fns = {
+ "Temp": retrieve_temp_trait_dataset,
+ "Geno": retrieve_geno_trait_dataset,
+ "Publish": retrieve_publish_trait_dataset,
+ "ProbeSet": retrieve_probeset_trait_dataset
+ }
+ dataset_name_info = {
+ "dataset_id": None,
+ "dataset_name": trait["db"]["dataset_name"],
+ **retrieve_dataset_name(
+ trait_type, threshold, trait["trait_name"], trait["db"]["dataset_name"],
+ conn)
+ }
+ riset = retrieve_riset_fields(
+ trait_type, trait["trait_name"], dataset_name_info, conn)
+ return {
+ "display_name": dataset_name_info["dataset_name"],
+ **dataset_name_info,
+ **dataset_fns[trait_type](),
+ **riset
+ }
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 18:16:58 +0000