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-rw-r--r--gn3/db/datasets.py251
-rw-r--r--gn3/db/traits.py171
2 files changed, 324 insertions, 98 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
+ }
diff --git a/gn3/db/traits.py b/gn3/db/traits.py
index 9f89510..85cccfa 100644
--- a/gn3/db/traits.py
+++ b/gn3/db/traits.py
@@ -1,6 +1,7 @@
"""This class contains functions relating to trait data manipulation"""
from typing import Any, Dict, Union
from gn3.function_helpers import compose
+from gn3.db.datasets import retrieve_trait_dataset
def get_trait_csv_sample_data(conn: Any,
@@ -77,41 +78,6 @@ def update_sample_data(conn: Any,
return (updated_strains, updated_published_data,
updated_se_data, updated_n_strains)
-def retrieve_trait_dataset_name(
- trait_type: str, threshold: int, name: str, connection: 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
- """
- table_map = {
- "ProbeSet": "ProbeSetFreeze",
- "Publish": "PublishFreeze",
- "Geno": "GenoFreeze",
- "Temp": "TempFreeze"}
- columns = "Id, Name, FullName, ShortName{}".format(
- ", DataScale" if trait_type == "ProbeSet" else "")
- query = (
- "SELECT %(columns)s "
- "FROM %(table)s "
- "WHERE "
- "public > %(threshold)s "
- "AND "
- "(Name = %(name)s OR FullName = %(name)s OR ShortName = %(name)s)")
- with connection.cursor() as cursor:
- cursor.execute(
- query,
- {
- "table": table_map[trait_type],
- "columns": columns,
- "threshold": threshold,
- "name": name
- })
- return cursor.fetchone()
-
-
def retrieve_publish_trait_info(trait_data_source: Dict[str, Any], conn: Any):
"""Retrieve trait information for type `Publish` traits.
@@ -156,11 +122,11 @@ def retrieve_publish_trait_info(trait_data_source: Dict[str, Any], conn: Any):
})
return dict(zip([k.lower() for k in keys], cursor.fetchone()))
-def set_confidential_field(trait_info):
+def set_confidential_field(trait_type, trait_info):
"""Post processing function for 'Publish' trait types.
It sets the value for the 'confidential' key."""
- if trait_info["type"] == "Publish":
+ if trait_type == "Publish":
return {
**trait_info,
"confidential": 1 if (
@@ -271,7 +237,7 @@ def set_homologene_id_field_probeset(trait_info, conn):
return {**trait_info, "homologeneid": res[0]}
return {**trait_info, "homologeneid": None}
-def set_homologene_id_field(trait_info, conn):
+def set_homologene_id_field(trait_type, trait_info, conn):
"""
Common postprocessing function for all trait types.
@@ -283,84 +249,83 @@ def set_homologene_id_field(trait_info, conn):
"Publish": set_to_null,
"ProbeSet": lambda ti: set_homologene_id_field_probeset(ti, conn)
}
- return functions_table[trait_info["type"]](trait_info)
+ return functions_table[trait_type](trait_info)
-def set_geno_riset_fields(name, conn):
- """
- Retrieve the RISet, and RISetID values for various Geno trait types.
- """
+def load_publish_qtl_info(trait_info, conn):
query = (
- "SELECT InbredSet.Name, InbredSet.Id "
- "FROM InbredSet, GenoFreeze "
- "WHERE GenoFreeze.InbredSetId = InbredSet.Id "
- "AND GenoFreeze.Name = %(name)s")
+ "SELECT PublishXRef.Locus, PublishXRef.LRS, PublishXRef.additive "
+ "FROM PublishXRef, PublishFreeze "
+ "WHERE PublishXRef.Id = %(trait_name)s "
+ "AND PublishXRef.InbredSetId = PublishFreeze.InbredSetId "
+ "AND PublishFreeze.Id = %(dataset_id)s")
with conn.cursor() as cursor:
- return cursor.execute(query, {"name": name})
+ cursor.execute()
+ return dict(zip(["locus", "lrs", "additive"], cursor.fetchone()))
+ return {"locus": "", "lrs": "", "additive": ""}
-def set_publish_riset_fields(name, conn):
- """
- Retrieve the RISet, and RISetID values for various Publish trait types.
- """
+def load_probeset_qtl_info(trait_info, conn):
query = (
- "SELECT InbredSet.Name, InbredSet.Id "
- "FROM InbredSet, PublishFreeze "
- "WHERE PublishFreeze.InbredSetId = InbredSet.Id "
- "AND PublishFreeze.Name = %(name)s")
+ "SELECT ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, "
+ "ProbeSetXRef.mean, ProbeSetXRef.additive "
+ "FROM ProbeSetXRef, ProbeSet "
+ "WHERE ProbeSetXRef.ProbeSetId = ProbeSet.Id "
+ " AND ProbeSet.Name = %(trait_name)s "
+ "AND ProbeSetXRef.ProbeSetFreezeId = %(dataset_id)s")
with conn.cursor() as cursor:
- return cursor.execute(query, {"name": name})
+ cursor.execute()
+ return dict(zip(
+ ["locus", "lrs", "pvalue", "mean", "additive"], cursor.fetchone()))
+ return {"locus": "", "lrs": "", "pvalue": "", "mean": "", "additive": ""}
-def set_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:
- return cursor.execute(query, {"name": name})
-
-def set_riset_fields(trait_info, conn):
- """
- Retrieve the RISet, and RISetID values for various trait types.
- """
- riset_functions_map = {
- "Temp": lambda ti, con: (None, None),
- "Geno": set_geno_riset_fields,
- "Publish": set_publish_riset_fields,
- "ProbeSet": set_probeset_riset_fields
+def load_qtl_info(qtl, trait_type, trait_info, conn):
+ if not qtl:
+ return trait_info
+ qtl_info_functions = {
+ "Publish": load_publish_qtl_info,
+ "ProbeSet": load_probeset_qtl_info
}
- if not trait_info.get("haveinfo", None):
+ if trait_inf["name"] not in qtl_info_functions.keys():
return trait_info
- riset, riid = riset_functions_map[trait_info["type"]](
- trait_info["name"], conn)
- return {
- **trait_info, "risetid": riid,
- "riset": "BXD" if riset == "BXD300" else riset}
+ return qtl_info_functions[trait_type](trait_info, conn)
def build_trait_name(trait_fullname):
name_parts = trait_fullname.split("::")
assert len(name_parts) >= 2, "Name format error"
return {
- "trait_db": name_parts[0],
+ "db": {"dataset_name": name_parts[0]},
"trait_fullname": trait_fullname,
"trait_name": name_parts[1],
"cellid": name_parts[2] if len(name_parts) == 3 else ""
}
+def retrieve_probeset_sequence(trait, conn):
+ query = (
+ "SELECT ProbeSet.BlatSeq "
+ "FROM ProbeSet, ProbeSetFreeze, ProbeSetXRef "
+ "WHERE ProbeSet.Id=ProbeSetXRef.ProbeSetId "
+ "AND ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId "
+ "AND ProbeSet.Name = %(trait_name)s "
+ "AND ProbeSetFreeze.Name = %(dataset_name)s")
+ with conn.cursor() as cursor:
+ cursor.execute(
+ query,
+ {
+ "trait_name": trait["trait_name"],
+ "dataset_name": trait["db"]["dataset_name"]
+ })
+ seq = cursor.fetchone()
+ return {**trait, "sequence": seq[0] if seq else ""}
+
def retrieve_trait_info(
- trait_type: str, trait_full_name: str, trait_dataset_id: int,
- trait_dataset_name: str, conn: Any, qtl=None):
+ trait_type: str, threshold: int, trait_full_name: str, conn: Any,
+ qtl=None):
"""Retrieves the trait information.
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L397-L456
This function, or the dependent functions, might be incomplete as they are
currently."""
- # pylint: disable=[R0913]
trait = build_trait_name(trait_full_name)
trait_info_function_table = {
"Publish": retrieve_publish_trait_info,
@@ -370,15 +335,19 @@ def retrieve_trait_info(
}
common_post_processing_fn = compose(
- lambda ti: set_riset_fields(ti, conn),
- lambda ti: set_homologene_id_field(ti, conn),
- lambda ti: {"type": trait_type, **ti},
- lambda ti: {**ti, **trait},
+ lambda ti: load_qtl_info(qtl, trait_type, ti, conn),
+ lambda ti: set_homologene_id_field(trait_type, ti, conn),
+ lambda ti: {"trait_type": trait_type, **ti},
+ lambda ti: {**trait, **ti},
set_haveinfo_field)
trait_post_processing_functions_table = {
- "Publish": compose(set_confidential_field, common_post_processing_fn),
- "ProbeSet": compose(common_post_processing_fn),
+ "Publish": compose(
+ lambda ti: set_confidential_field(trait_type, ti),
+ common_post_processing_fn),
+ "ProbeSet": compose(
+ lambda ti: retrieve_probeset_sequence(ti, conn),
+ common_post_processing_fn),
"Geno": common_post_processing_fn,
"Temp": common_post_processing_fn
}
@@ -387,10 +356,16 @@ def retrieve_trait_info(
trait_post_processing_functions_table[trait_type],
trait_info_function_table[trait_type])
- return retrieve_info(
+ trait_dataset = retrieve_trait_dataset(trait_type, trait, threshold, conn)
+ trait_info = retrieve_info(
{
"trait_name": trait["trait_name"],
- "trait_dataset_id": trait_dataset_id,
- "trait_dataset_name":trait_dataset_name
+ "trait_dataset_id": trait_dataset["dataset_id"],
+ "trait_dataset_name": trait_dataset["dataset_name"]
},
conn)
+ return {
+ **trait_info,
+ "db": {**trait["db"], **trait_dataset},
+ "riset": trait_dataset["riset"]
+ }