Merge branch 'main' into Feature/Update-db-from-csv-data

1 files changed, 158 insertions, 1 deletions

diff --git a/gn3/db/traits.py b/gn3/db/traits.py
index a77e6a1..ae1939a 100644
--- a/gn3/db/traits.py
+++ b/gn3/db/traits.py
@@ -1,5 +1,5 @@
 """This class contains functions relating to trait data manipulation"""
-from typing import Any, Union
+from typing import Any, Dict, Union
 
 
 def get_trait_csv_sample_data(conn: Any,
@@ -75,3 +75,160 @@ def update_sample_data(conn: Any,
         updated_n_strains: int = cursor.rowcount
     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
+    """
+    columns = "Id, Name, FullName, ShortName{}".format(
+        ", DataScale" if trait_type == "ProbeSet" else "")
+    query = (
+        "SELECT {columns} "
+        "FROM {trait_type}Freeze "
+        "WHERE "
+        "public > %(threshold)s "
+        "AND "
+        "(Name = %(name)s OR FullName = %(name)s OR ShortName = %(name)s)").format(
+            columns=columns, trait_type=trait_type)
+    with connection.cursor() as cursor:
+        cursor.execute(query, {"threshold": threshold, "name": name})
+        return cursor.fetchone()
+
+PUBLISH_TRAIT_INFO_QUERY = (
+    "SELECT "
+    "PublishXRef.Id, Publication.PubMed_ID, "
+    "Phenotype.Pre_publication_description, "
+    "Phenotype.Post_publication_description, "
+    "Phenotype.Original_description, "
+    "Phenotype.Pre_publication_abbreviation, "
+    "Phenotype.Post_publication_abbreviation, "
+    "Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, "
+    "Phenotype.Authorized_Users, CAST(Publication.Authors AS BINARY), "
+    "Publication.Title, Publication.Abstract, Publication.Journal, "
+    "Publication.Volume, Publication.Pages, Publication.Month, "
+    "Publication.Year, PublishXRef.Sequence, Phenotype.Units, "
+    "PublishXRef.comments "
+    "FROM "
+    "PublishXRef, Publication, Phenotype, PublishFreeze "
+    "WHERE "
+    "PublishXRef.Id = %(trait_name)s AND "
+    "Phenotype.Id = PublishXRef.PhenotypeId AND "
+    "Publication.Id = PublishXRef.PublicationId AND "
+    "PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND "
+    "PublishFreeze.Id =%(trait_dataset_id)s")
+
+
+def retrieve_publish_trait_info(trait_data_source: Dict[str, Any], conn: Any):
+    """Retrieve trait information for type `Publish` traits.
+
+    https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L399-L421"""
+    with conn.cursor() as cursor:
+        cursor.execute(
+            PUBLISH_TRAIT_INFO_QUERY,
+            {
+                k:v for k, v in trait_data_source.items()
+                if k in ["trait_name", "trait_dataset_id"]
+            })
+        return cursor.fetchone()
+
+PROBESET_TRAIT_INFO_QUERY = (
+    "SELECT "
+    "ProbeSet.name, ProbeSet.symbol, ProbeSet.description, "
+    "ProbeSet.probe_target_description, ProbeSet.chr, ProbeSet.mb, "
+    "ProbeSet.alias, ProbeSet.geneid, ProbeSet.genbankid, ProbeSet.unigeneid, "
+    "ProbeSet.omim, ProbeSet.refseq_transcriptid, ProbeSet.blatseq, "
+    "ProbeSet.targetseq, ProbeSet.chipid, ProbeSet.comments, "
+    "ProbeSet.strand_probe, ProbeSet.strand_gene, "
+    "ProbeSet.probe_set_target_region, ProbeSet.proteinid, "
+    "ProbeSet.probe_set_specificity, ProbeSet.probe_set_blat_score, "
+    "ProbeSet.probe_set_blat_mb_start, ProbeSet.probe_set_blat_mb_end, "
+    "ProbeSet.probe_set_strand, ProbeSet.probe_set_note_by_rw, "
+    "ProbeSet.flag "
+    "FROM "
+    "ProbeSet, ProbeSetFreeze, ProbeSetXRef "
+    "WHERE "
+    "ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND "
+    "ProbeSetXRef.ProbeSetId = ProbeSet.Id AND "
+    "ProbeSetFreeze.Name = %(trait_dataset_name)s AND "
+    "ProbeSet.Name = %(trait_name)s")
+
+def retrieve_probeset_trait_info(trait_data_source: Dict[str, Any], conn: Any):
+    """Retrieve trait information for type `ProbeSet` traits.
+
+    https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L424-L435"""
+    with conn.cursor() as cursor:
+        cursor.execute(
+            PROBESET_TRAIT_INFO_QUERY,
+            {
+                k:v for k, v in trait_data_source.items()
+                if k in ["trait_name", "trait_dataset_name"]
+            })
+        return cursor.fetchone()
+
+GENO_TRAIT_INFO_QUERY = (
+    "SELECT "
+    "Geno.name, Geno.chr, Geno.mb, Geno.source2, Geno.sequence "
+    "FROM "
+    "Geno, GenoFreeze, GenoXRef "
+    "WHERE "
+    "GenoXRef.GenoFreezeId = GenoFreeze.Id AND GenoXRef.GenoId = Geno.Id AND "
+    "GenoFreeze.Name = %(trait_dataset_name)s AND Geno.Name = %(trait_name)s")
+
+def retrieve_geno_trait_info(trait_data_source: Dict[str, Any], conn: Any):
+    """Retrieve trait information for type `Geno` traits.
+
+    https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L438-L449"""
+    with conn.cursor() as cursor:
+        cursor.execute(
+            GENO_TRAIT_INFO_QUERY,
+            {
+                k:v for k, v in trait_data_source.items()
+                if k in ["trait_name", "trait_dataset_name"]
+            })
+        return cursor.fetchone()
+
+TEMP_TRAIT_INFO_QUERY = (
+    "SELECT name, description FROM Temp "
+    "WHERE Name = %(trait_name)s")
+
+def retrieve_temp_trait_info(trait_data_source: Dict[str, Any], conn: Any):
+    """Retrieve trait information for type `Temp` traits.
+
+    https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L450-452"""
+    with conn.cursor() as cursor:
+        cursor.execute(
+            TEMP_TRAIT_INFO_QUERY,
+            {
+                k:v for k, v in trait_data_source.items()
+                if k in ["trait_name"]
+            })
+        return cursor.fetchone()
+
+def retrieve_trait_info(
+        trait_type: str, trait_name: str, trait_dataset_id: int,
+        trait_dataset_name: str, conn: Any):
+    """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."""
+    trait_info_function_table = {
+        "Publish": retrieve_publish_trait_info,
+        "ProbeSet": retrieve_probeset_trait_info,
+        "Geno": retrieve_geno_trait_info,
+        "Temp": retrieve_temp_trait_info
+    }
+    return trait_info_function_table[trait_type](
+        {
+            "trait_name": trait_name,
+            "trait_dataset_id": trait_dataset_id,
+            "trait_dataset_name":trait_dataset_name
+        },
+        conn)