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-rw-r--r--uploader/db/__init__.py8
-rw-r--r--uploader/db/averaging.py23
-rw-r--r--uploader/db/datasets.py133
-rw-r--r--uploader/db/platforms.py25
-rw-r--r--uploader/db/populations.py54
-rw-r--r--uploader/db/species.py22
-rw-r--r--uploader/db/tissues.py50
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
+ }