Rename module: qc_app --> uploader

7 files changed, 315 insertions, 0 deletions

diff --git a/uploader/db/__init__.py b/uploader/db/__init__.py
new file mode 100644
index 0000000..36e93e8
--- /dev/null
+++ b/uploader/db/__init__.py
@@ -0,0 +1,8 @@
+"""Database functions"""
+from .species import species, species_by_id
+from .populations import (
+    save_population,
+    population_by_id,
+    populations_by_species,
+    population_by_species_and_id)
+from .datasets import geno_datasets_by_species_and_population
diff --git a/uploader/db/averaging.py b/uploader/db/averaging.py
new file mode 100644
index 0000000..62bbe67
--- /dev/null
+++ b/uploader/db/averaging.py
@@ -0,0 +1,23 @@
+"""Functions for db interactions for averaging methods"""
+from typing import Optional
+
+import MySQLdb as mdb
+from MySQLdb.cursors import DictCursor
+
+def averaging_methods(conn: mdb.Connection) -> tuple[dict, ...]:
+    """Fetch all available averaging methods"""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute("SELECT * FROM AvgMethod")
+        return tuple(dict(row) for row in cursor.fetchall())
+
+def averaging_method_by_id(
+        conn: mdb.Connection, averageid: int) -> Optional[dict]:
+    """Fetch the averaging method by its ID"""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute("SELECT * FROM AvgMethod WHERE Id=%s",
+                       (averageid,))
+        result = cursor.fetchone()
+        if bool(result):
+            return dict(result)
+
+    return None
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
diff --git a/uploader/db/platforms.py b/uploader/db/platforms.py
new file mode 100644
index 0000000..cb527a7
--- /dev/null
+++ b/uploader/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/uploader/db/populations.py b/uploader/db/populations.py
new file mode 100644
index 0000000..4485e52
--- /dev/null
+++ b/uploader/db/populations.py
@@ -0,0 +1,54 @@
+"""Functions for accessing the database relating to species populations."""
+import MySQLdb as mdb
+from MySQLdb.cursors import DictCursor
+
+def population_by_id(conn: mdb.Connection, population_id) -> dict:
+    """Get the grouping/population by id."""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute("SELECT * FROM InbredSet WHERE InbredSetId=%s",
+                       (population_id,))
+        return cursor.fetchone()
+
+def population_by_species_and_id(
+        conn: mdb.Connection, species_id, population_id) -> dict:
+    """Retrieve a population by its identifier and species."""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute("SELECT * FROM InbredSet WHERE SpeciesId=%s AND Id=%s",
+                       (species_id, population_id))
+        return cursor.fetchone()
+
+def populations_by_species(conn: mdb.Connection, speciesid) -> tuple:
+    "Retrieve group (InbredSet) information from the database."
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        query = "SELECT * FROM InbredSet WHERE SpeciesId=%s"
+        cursor.execute(query, (speciesid,))
+        return tuple(cursor.fetchall())
+
+    return tuple()
+
+def save_population(conn: mdb.Connection, population_details: dict) -> dict:
+    """Save the population details to the db."""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute(
+            "INSERT INTO InbredSet("
+            "InbredSetId, InbredSetName, Name, SpeciesId, FullName, "
+            "MenuOrderId, Description"
+            ") "
+            "VALUES ("
+            "%(InbredSetId)s, %(InbredSetName)s, %(Name)s, %(SpeciesId)s, "
+            "%(FullName)s, %(MenuOrderId)s, %(Description)s"
+            ")",
+            {
+                "MenuOrderId": 0,
+                "InbredSetId": 0,
+                **population_details
+            })
+        new_id = cursor.lastrowid
+        cursor.execute("UPDATE InbredSet SET InbredSetId=%s WHERE Id=%s",
+                       (new_id, new_id))
+        return {
+            **population_details,
+            "Id": new_id,
+            "InbredSetId": new_id,
+            "population_id": new_id
+        }
diff --git a/uploader/db/species.py b/uploader/db/species.py
new file mode 100644
index 0000000..653e59b
--- /dev/null
+++ b/uploader/db/species.py
@@ -0,0 +1,22 @@
+"""Database functions for species."""
+import MySQLdb as mdb
+from MySQLdb.cursors import DictCursor
+
+def species(conn: mdb.Connection) -> tuple:
+    "Retrieve the species from the database."
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute(
+            "SELECT SpeciesId, SpeciesName, LOWER(Name) AS Name, MenuName, "
+            "FullName FROM Species")
+        return tuple(cursor.fetchall())
+
+    return tuple()
+
+def species_by_id(conn: mdb.Connection, speciesid) -> dict:
+    "Retrieve the species from the database by id."
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute(
+            "SELECT SpeciesId, SpeciesName, LOWER(Name) AS Name, MenuName, "
+            "FullName FROM Species WHERE SpeciesId=%s",
+            (speciesid,))
+        return cursor.fetchone()
diff --git a/uploader/db/tissues.py b/uploader/db/tissues.py
new file mode 100644
index 0000000..9fe7bab
--- /dev/null
+++ b/uploader/db/tissues.py
@@ -0,0 +1,50 @@
+"""Handle db interactions for tissue."""
+from typing import Union, 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) -> 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
+
+
+def create_new_tissue(
+        conn: mdb.Connection,
+        name: str,
+        shortname: str,
+        birnlexid: Optional[str] = None,
+        birnlexname: Optional[str] = None
+) -> dict[str, Union[int, str, None]]:
+    """Add a new tissue, organ or biological material to the database."""
+    with conn.cursor() as cursor:
+        cursor.execute(
+            "INSERT INTO "
+            "Tissue(TissueName, Name, Short_Name, BIRN_lex_ID, BIRN_lex_Name) "
+            "VALUES (%s, %s, %s, %s, %s)",
+            (name, name, shortname, birnlexid, birnlexname))
+        tissueid = cursor.lastrowid
+        cursor.execute("UPDATE Tissue SET TissueId=%s WHERE Id=%s",
+                       (tissueid, tissueid))
+        return {
+            "Id": tissueid,
+            "TissueId": tissueid,
+            "TissueName": name,
+            "Name": name,
+            "Short_Name": shortname,
+            "BIRN_lex_ID": birnlexid,
+            "BIRN_lex_Name": birnlexname
+        }