Rename module: qc_app --> uploader

1 files changed, 133 insertions, 0 deletions

diff --git a/uploader/db/datasets.py b/uploader/db/datasets.py
new file mode 100644
index 0000000..767ec41
--- /dev/null
+++ b/uploader/db/datasets.py
@@ -0,0 +1,133 @@
+"""Functions for accessing the database relating to datasets."""
+from datetime import date
+from typing import Optional
+
+import MySQLdb as mdb
+from MySQLdb.cursors import DictCursor
+
+def geno_datasets_by_species_and_population(
+        conn: mdb.Connection,
+        speciesid: int,
+        populationid: int) -> tuple[dict, ...]:
+    """Retrieve all genotypes datasets by species and population"""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute(
+            "SELECT gf.* FROM InbredSet AS iset INNER JOIN GenoFreeze AS gf "
+            "ON iset.InbredSetId=gf.InbredSetId "
+            "WHERE iset.SpeciesId=%(sid)s AND iset.InbredSetId=%(pid)s",
+            {"sid": speciesid, "pid": populationid})
+        return tuple(dict(row) for row in cursor.fetchall())
+
+def geno_dataset_by_id(conn: mdb.Connection, dataset_id) -> Optional[dict]:
+    """Retrieve genotype dataset by ID"""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute("SELECT * FROM GenoFreeze WHERE Id=%s", (dataset_id,))
+        _dataset = cursor.fetchone()
+        return dict(_dataset) if bool(_dataset) else None
+
+def probeset_studies_by_species_and_population(
+        conn: mdb.Connection,
+        speciesid: int,
+        populationid: int) -> tuple[dict, ...]:
+    """Retrieve all probesets"""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute(
+            "SELECT pf.* FROM InbredSet AS iset INNER JOIN ProbeFreeze AS pf "
+            "ON iset.InbredSetId=pf.InbredSetId "
+            "WHERE iset.SpeciesId=%(sid)s AND iset.InbredSetId=%(pid)s",
+            {"sid": speciesid, "pid": populationid})
+        return tuple(dict(row) for row in cursor.fetchall())
+
+def probeset_datasets_by_study(conn: mdb.Connection,
+                               studyid: int) -> tuple[dict, ...]:
+    """Retrieve all probeset databases by study."""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute("SELECT * FROM ProbeSetFreeze WHERE ProbeFreezeId=%s",
+                       (studyid,))
+        return tuple(dict(row) for row in cursor.fetchall())
+
+def probeset_study_by_id(conn: mdb.Connection, studyid) -> Optional[dict]:
+    """Retrieve ProbeSet study by ID"""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute("SELECT * FROM ProbeFreeze WHERE Id=%s", (studyid,))
+        _study = cursor.fetchone()
+        return dict(_study) if bool(_study) else None
+
+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 WHERE Id=%s",
+                       (studyid, studyid))
+        return {**studydata, "studyid": studyid}
+
+def probeset_create_dataset(conn: mdb.Connection,#pylint: disable=[too-many-arguments]
+                            studyid: int,
+                            averageid: int,
+                            datasetname: str,
+                            datasetfullname: str,
+                            datasetshortname: str="",
+                            public: bool = True,
+                            datascale="log2") -> dict:
+    """Create a new ProbeSet dataset."""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        dataset = {
+            "studyid": studyid,
+            "averageid": averageid,
+            "name2": datasetname,
+            "fname": datasetfullname,
+            "name": datasetshortname,
+            "sname": datasetshortname,
+            "today": date.today().isoformat(),
+            "public": 2 if public else 0,
+            "authorisedusers": "williamslab",
+            "datascale": datascale
+        }
+        cursor.execute(
+            """
+            INSERT INTO ProbeSetFreeze(
+              ProbeFreezeId, AvgId, Name, Name2, FullName, ShortName,
+              CreateTime, public, AuthorisedUsers, DataScale)
+            VALUES(
+              %(studyid)s, %(averageid)s, %(name)s, %(name2)s, %(fname)s,
+              %(sname)s, %(today)s, %(public)s, %(authorisedusers)s,
+              %(datascale)s)
+            """,
+            dataset)
+        return {**dataset, "datasetid": cursor.lastrowid}
+
+def probeset_dataset_by_id(conn: mdb.Connection, datasetid) -> Optional[dict]:
+    """Fetch a ProbeSet dataset by its ID"""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute("SELECT * FROM ProbeSetFreeze WHERE Id=%s", (datasetid,))
+        result = cursor.fetchone()
+        if bool(result):
+            return dict(result)
+
+    return None