1 files changed, 77 insertions, 0 deletions
diff --git a/gn3/db/probesets.py b/gn3/db/probesets.py
new file mode 100644
index 0000000..19c6896
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+++ b/gn3/db/probesets.py
@@ -0,0 +1,77 @@
+"""Functions and utilities to handle ProbeSets from the database."""
+from typing import Optional
+from dataclasses import dataclass
+
+from MySQLdb.cursors import DictCursor
+
+from gn3.db_utils import Connection as DBConnection
+
+from .query_tools import mapping_to_query_columns
+
+@dataclass(frozen=True)
+class Probeset: # pylint: disable=[too-many-instance-attributes]
+    """Data Type that represents a Probeset"""
+    id_: Optional[int] = None
+    name: Optional[str] = None
+    symbol: Optional[str] = None
+    description: Optional[str] = None
+    probe_target_description: Optional[str] = None
+    chr_: Optional[str] = None
+    mb: Optional[float] = None  # pylint: disable=C0103
+    alias: Optional[str] = None
+    geneid: Optional[str] = None
+    homologeneid: Optional[str] = None
+    unigeneid: Optional[str] = None
+    omim: Optional[str] = None
+    refseq_transcriptid: Optional[str] = None
+    blatseq: Optional[str] = None
+    targetseq: Optional[str] = None
+    strand_probe: Optional[str] = None
+    probe_set_target_region: Optional[str] = None
+    probe_set_specificity: Optional[float] = None
+    probe_set_blat_score: Optional[float] = None
+    probe_set_blat_mb_start: Optional[float] = None
+    probe_set_blat_mb_end: Optional[float] = None
+    probe_set_strand: Optional[str] = None
+    probe_set_note_by_rw: Optional[str] = None
+    flag: Optional[str] = None
+
+
+# Mapping from the Phenotype dataclass to the actual column names in the
+# database
+probeset_mapping = {
+    "id_": "Id",
+    "name": "Name",
+    "symbol": "symbol",
+    "description": "description",
+    "probe_target_description": "Probe_Target_Description",
+    "chr_": "Chr",
+    "mb": "Mb",
+    "alias": "alias",
+    "geneid": "GeneId",
+    "homologeneid": "HomoloGeneID",
+    "unigeneid": "UniGeneId",
+    "omim": "OMIM",
+    "refseq_transcriptid": "RefSeq_TranscriptId",
+    "blatseq": "BlatSeq",
+    "targetseq": "TargetSeq",
+    "strand_probe": "Strand_Probe",
+    "probe_set_target_region": "Probe_set_target_region",
+    "probe_set_specificity": "Probe_set_specificity",
+    "probe_set_blat_score": "Probe_set_BLAT_score",
+    "probe_set_blat_mb_start": "Probe_set_Blat_Mb_start",
+    "probe_set_blat_mb_end": "Probe_set_Blat_Mb_end",
+    "probe_set_strand": "Probe_set_strand",
+    "probe_set_note_by_rw": "Probe_set_Note_by_RW",
+    "flag": "flag"
+}
+
+def fetch_probeset_metadata_by_name(conn: DBConnection, name: str) -> dict:
+    """Fetch a ProbeSet's metadata by its `name`."""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cols = ", ".join(mapping_to_query_columns(probeset_mapping))
+        cursor.execute((f"SELECT Id as id, {cols} "
+                        "FROM ProbeSet "
+                        "WHERE Name = %(name)s"),
+                       {"name": name})
+        return cursor.fetchone()