From cf8d133b110d87aed5cb6695711616625a6669fd Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 18 Jan 2024 05:52:52 +0300
Subject: Create new ProbeSet study.

---
 qc_app/db/datasets.py  | 38 +++++++++++++++++++++++++++++++++++++-
 qc_app/db/platforms.py | 25 +++++++++++++++++++++++++
 qc_app/db/tissues.py   | 22 ++++++++++++++++++++++
 3 files changed, 84 insertions(+), 1 deletion(-)
 create mode 100644 qc_app/db/platforms.py
 create mode 100644 qc_app/db/tissues.py

(limited to 'qc_app/db')

diff --git a/qc_app/db/datasets.py b/qc_app/db/datasets.py
index 086c103..5f6a2d5 100644
--- a/qc_app/db/datasets.py
+++ b/qc_app/db/datasets.py
@@ -1,4 +1,6 @@
 """Functions for accessing the database relating to datasets."""
+from datetime import date
+
 import MySQLdb as mdb
 from MySQLdb.cursors import DictCursor
 
@@ -43,9 +45,43 @@ def probeset_datasets_by_study(conn: mdb.Connection,
                        (studyid,))
         return tuple(dict(row) for row in cursor.fetchall())
 
-def probe_study_by_id(conn: mdb.Connection, studyid: int) -> dict:
+def probeset_study_by_id(conn: mdb.Connection, studyid: int) -> dict:
     """Retrieve ProbeSet study by ID"""
     with conn.cursor(cursorclass=DictCursor) as cursor:
         cursor.execute("SELECT * FROM ProbeFreeze WHERE Id=%s",
                        (studyid,))
         return dict(cursor.fetchone())
+
+def probeset_create_study(conn: mdb.Connection,#pylint: disable=[too-many-arguments]
+                          populationid: int,
+                          platformid: int,
+                          tissueid: int,
+                          studyname: str,
+                          studyfullname: str = "",
+                          studyshortname: str = ""):
+    """Create a new ProbeSet study."""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        studydata = {
+            "platid": platformid,
+            "tissueid": tissueid,
+            "name": studyname,
+            "fname": studyfullname or studyname,
+            "sname": studyshortname,
+            "today": date.today().isoformat(),
+            "popid": populationid
+        }
+        cursor.execute(
+            """
+            INSERT INTO ProbeFreeze(
+              ChipId, TissueId, Name, FullName, ShortName, CreateTime,
+              InbredSetId
+            ) VALUES (
+              %(platid)s, %(tissueid)s, %(name)s, %(fname)s, %(sname)s,
+              %(today)s, %(popid)s
+            )
+            """,
+            studydata)
+        studyid = cursor.lastrowid
+        cursor.execute("UPDATE ProbeFreeze SET ProbeFreezeId=%s",
+                       (studyid,))
+        return {**studydata, "studyid": studyid}
diff --git a/qc_app/db/platforms.py b/qc_app/db/platforms.py
new file mode 100644
index 0000000..cb527a7
--- /dev/null
+++ b/qc_app/db/platforms.py
@@ -0,0 +1,25 @@
+"""Handle db interactions for platforms."""
+from typing import Optional
+
+import MySQLdb as mdb
+from MySQLdb.cursors import DictCursor
+
+def platforms_by_species(
+        conn: mdb.Connection, speciesid: int) -> tuple[dict, ...]:
+    """Retrieve platforms by the species"""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute("SELECT * FROM GeneChip WHERE SpeciesId=%s "
+                       "ORDER BY GeneChipName ASC",
+                       (speciesid,))
+        return tuple(dict(row) for row in cursor.fetchall())
+
+def platform_by_id(conn: mdb.Connection, platformid: int) -> Optional[dict]:
+    """Retrieve a platform by its ID"""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute("SELECT * FROM GeneChip WHERE Id=%s",
+                       (platformid,))
+        result = cursor.fetchone()
+        if bool(result):
+            return dict(result)
+
+    return None
diff --git a/qc_app/db/tissues.py b/qc_app/db/tissues.py
new file mode 100644
index 0000000..ebf24fd
--- /dev/null
+++ b/qc_app/db/tissues.py
@@ -0,0 +1,22 @@
+"""Handle db interactions for tissue."""
+from typing import Optional
+
+import MySQLdb as mdb
+from MySQLdb.cursors import DictCursor
+
+def all_tissues(conn: mdb.Connection) -> tuple[dict, ...]:
+    """All available tissue."""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute("SELECT * FROM Tissue ORDER BY TissueName")
+        return tuple(dict(row) for row in cursor.fetchall())
+
+def tissue_by_id(conn: mdb.Connection, tissueid: int) -> Optional[dict]:
+    """Retrieve a tissue by its ID"""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute("SELECT * FROM Tissue WHERE Id=%s",
+                       (tissueid,))
+        result = cursor.fetchone()
+        if bool(result):
+            return dict(result)
+
+    return None
-- 
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