Rename module: qc_app --> uploader

1 files changed, 0 insertions, 133 deletions

diff --git a/qc_app/db/datasets.py b/qc_app/db/datasets.py
deleted file mode 100644
index 767ec41..0000000
--- a/qc_app/db/datasets.py
+++ /dev/null
@@ -1,133 +0,0 @@
-"""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