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}}
+
+

+
+ +
+ Create ProbeSet study + + + + + + + +
+ +
+
+ +{%endblock%} diff --git a/qc_app/templates/rqtl2/select-probeset-study-id.html b/qc_app/templates/rqtl2/select-probeset-study-id.html index bb31fde..34aa54e 100644 --- a/qc_app/templates/rqtl2/select-probeset-study-id.html +++ b/qc_app/templates/rqtl2/select-probeset-study-id.html @@ -1,5 +1,5 @@ {%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} +{%from "flash_messages.html" import flash_messages, flash_all_messages%} {%block title%}Upload R/qtl2 Bundle{%endblock%} @@ -12,9 +12,13 @@

This page gives you the ability to do that.

+{{flash_all_messages()}} +
- Select from existing ProbeSet datasets + action="{{url_for('upload.rqtl2.select_probeset_study', + species_id=species.SpeciesId, population_id=population.Id)}}" + id="frm:select-probeset-study"> + Select from existing ProbeSet studies OR

- Create new ProbeSet dataset - Under construction + action="{{url_for('upload.rqtl2.create_probeset_study', + species_id=species.SpeciesId, population_id=population.Id)}}" + id="frm:create-probeset-study"> + Create new ProbeSet study + + + + + + +
+ + +
+ +
+ + +
+ +
+ + +
+ +
+ + +
+ +
+ + +
+ +
+ +
{%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, -- cgit v1.2.3