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 ++++++
.../rqtl2/create-probe-study-success.html | 53 +++++++++++++++
.../templates/rqtl2/select-probeset-study-id.html | 79 ++++++++++++++++++++--
qc_app/upload/rqtl2.py | 75 ++++++++++++++++----
6 files changed, 272 insertions(+), 20 deletions(-)
create mode 100644 qc_app/db/platforms.py
create mode 100644 qc_app/db/tissues.py
create mode 100644 qc_app/templates/rqtl2/create-probe-study-success.html
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
diff --git a/qc_app/templates/rqtl2/create-probe-study-success.html b/qc_app/templates/rqtl2/create-probe-study-success.html
new file mode 100644
index 0000000..1b85d0c
--- /dev/null
+++ b/qc_app/templates/rqtl2/create-probe-study-success.html
@@ -0,0 +1,53 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+Create ProbeSet Study
+
+
+
You successfully created the ProbeSet study with the following
+ information.
+
+ - ID
+ - {{study.id}}
+
+ - Name
+ - {{study.name}}
+
+ - Full Name
+ - {{study.fname}}
+
+ - Short Name
+ - {{study.sname}}
+
+ - Created On
+ - {{study.today}}
+
+
+
This page gives you the ability to do that.
+{{flash_all_messages()}}
+
{%endblock%}
diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
index 3411f98..0d80776 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -19,6 +19,9 @@ from r_qtl.errors import InvalidFormat
from qc_app.files import save_file, fullpath
from qc_app.dbinsert import species as all_species
from qc_app.db_utils import with_db_connection, database_connection
+
+from qc_app.db.tissues import all_tissues, tissue_by_id
+from qc_app.db.platforms import platform_by_id, platforms_by_species
from qc_app.db import (
species_by_id,
save_population,
@@ -28,6 +31,8 @@ from qc_app.db.datasets import (
geno_dataset_by_id,
geno_datasets_by_species_and_population,
+ probeset_study_by_id,
+ probeset_create_study,
probeset_datasets_by_study,
probeset_studies_by_species_and_population)
@@ -311,16 +316,58 @@ def select_probeset_study(species_id: int, population_id: int):
return error
summary_page = redirect(url_for("upload.rqtl2.select_dataset_info",
- species=species_by_id(conn, species_id),
- population=population_by_species_and_id(
- conn, species_id, population_id)),
+ species_id=species_id,
+ population_id=population_id),
code=307)
- if not bool(probe_study_by_id(conn, int(request.form["probe-study-id"]))):
+ if not bool(probeset_study_by_id(conn, int(request.form["probe-study-id"]))):
flash("Invalid study selected!", "alert-error alert-rqtl2")
return summary_page
return summary_page
+@rqtl2.route(("/upload/species//population/"
+ "/rqtl2-bundle/create-probeset-study"),
+ methods=["POST"])
+def create_probeset_study(species_id: int, population_id: int):
+ """Create a new probeset study."""
+ with database_connection(app.config["SQL_URI"]) as conn:
+ error = check_errors(
+ conn, "species", "population", "rqtl2_bundle_file", "geno-dataset")
+ if bool(error):
+ return error
+
+ form = request.form
+ select_study_page = redirect(
+ url_for("upload.rqtl2.select_probeset_study",
+ species_id=species_id,
+ population_id=population_id),
+ code=307)
+
+ if not (bool(form.get("platformid")) and
+ bool(platform_by_id(conn, int(form["platformid"])))):
+ flash("Invalid platform selected.", "alert-error alert-rqtl2")
+ return select_study_page
+
+ if not (bool(form.get("tissueid")) and
+ bool(tissue_by_id(conn, int(form["tissueid"])))):
+ flash("Invalid tissue selected.", "alert-error alert-rqtl2")
+ return select_study_page
+
+ study = probeset_create_study(
+ conn, population_id, int(form["platformid"]), int(form["tissueid"]),
+ form["studyname"], form.get("studyfullname") or "",
+ form.get("studyshortname") or "")
+ return render_template(
+ "rqtl2/create-probe-study-success.html",
+ species=species_by_id(conn, species_id),
+ population=population_by_species_and_id(
+ conn, species_id, population_id),
+ rqtl2_bundle_file=request.form["rqtl2_bundle_file"],
+ geno_dataset=geno_dataset_by_id(
+ conn,
+ int(request.form["geno-dataset-id"])),
+ study=study)
+
@rqtl2.route(("/upload/species//population/"
"/rqtl2-bundle/dataset-info"),
methods=["POST"])
@@ -359,17 +406,19 @@ def select_dataset_info(species_id: int, population_id: int):
rqtl2_bundle_file=thefile.name,
geno_dataset=geno_dataset,
studies=probeset_studies_by_species_and_population(
- conn, species_id, population_id))
+ conn, species_id, population_id),
+ platforms=platforms_by_species(conn, species_id),
+ tissues=all_tissues(conn))
if "pheno" in cdata and not bool(form.get("probe-dataset-id")):
- return render_template(
- "rqtl2/select-probeset-dataset.html",
- species=species,
- population=population,
- rqtl2_bundle_file=thefile.name,
- geno_dataset=geno_dataset,
- datasets=probeset_datasets_by_study(
- conn, int(form["probe-study-id"])))
+ return render_template(
+ "rqtl2/select-probeset-dataset.html",
+ species=species,
+ population=population,
+ rqtl2_bundle_file=thefile.name,
+ geno_dataset=geno_dataset,
+ datasets=probeset_datasets_by_study(
+ conn, int(form["probe-study-id"])))
return render_template("rqtl2/summary-info.html",
species=species,
--
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