From 3e028bf0e9f8239b552bcd4b2d6133bb7965abd9 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 25 Sep 2024 12:09:46 -0500 Subject: Create new genotype datasets. --- uploader/genotypes/models.py | 33 +++++++++- uploader/genotypes/views.py | 34 ++++++++++ uploader/templates/genotypes/create-dataset.html | 82 ++++++++++++++++++++++++ uploader/templates/genotypes/list-genotypes.html | 4 +- 4 files changed, 151 insertions(+), 2 deletions(-) create mode 100644 uploader/templates/genotypes/create-dataset.html (limited to 'uploader') diff --git a/uploader/genotypes/models.py b/uploader/genotypes/models.py index db8cc3e..44c98b1 100644 --- a/uploader/genotypes/models.py +++ b/uploader/genotypes/models.py @@ -1,8 +1,9 @@ """Functions for handling genotypes.""" from typing import Optional +from datetime import datetime import MySQLdb as mdb -from MySQLdb.cursors import DictCursor +from MySQLdb.cursors import Cursor, DictCursor from uploader.db_utils import debug_query @@ -68,3 +69,33 @@ def genotype_dataset( if bool(result): return dict(result) return None + + +def save_new_dataset( + cursor: Cursor, + population_id: int, + name: str, + fullname: str, + shortname: str +) -> dict: + """Save a new genotype dataset into the database.""" + params = { + "InbredSetId": population_id, + "Name": name, + "FullName": fullname, + "ShortName": shortname, + "CreateTime": datetime.now().date().isoformat(), + "public": 2, + "confidentiality": 0, + "AuthorisedUsers": None + } + cursor.execute( + "INSERT INTO GenoFreeze(" + "Name, FullName, ShortName, CreateTime, public, InbredSetId, " + "confidentiality, AuthorisedUsers" + ") VALUES (" + "%(Name)s, %(FullName)s, %(ShortName)s, %(CreateTime)s, %(public)s, " + "%(InbredSetId)s, %(confidentiality)s, %(AuthorisedUsers)s" + ")", + params) + return {**params, "Id": cursor.lastrowid} diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py index 41cd21e..f79caba 100644 --- a/uploader/genotypes/views.py +++ b/uploader/genotypes/views.py @@ -1,4 +1,5 @@ """Views for the genotypes.""" +from MySQLdb.cursors import DictCursor from flask import (flash, request, url_for, @@ -18,6 +19,7 @@ from uploader.population.models import (populations_by_species, from .models import (genotype_markers, genotype_dataset, + save_new_dataset, genotype_markers_count, genocode_by_population) @@ -148,3 +150,35 @@ def view_dataset(species_id: int, population_id: int, dataset_id: int): population=population, dataset=dataset, activelink="view-dataset") + + +@genotypesbp.route( + "//populations//genotypes/datasets/" + "create", + methods=["GET", "POST"]) +@require_login +@with_population(species_redirect_uri="species.populations.genotypes.index", + redirect_uri="species.populations.genotypes.select_population") +def create_dataset(species: dict, population: dict, **kwargs):# pylint: disable=[unused-argument] + """Create a genotype dataset.""" + with (database_connection(app.config["SQL_URI"]) as conn, + conn.cursor(cursorclass=DictCursor) as cursor): + if request.method == "GET": + return render_template("genotypes/create-dataset.html", + species=species, + population=population, + activelink="create-dataset") + + form = request.form + _new_dataset = save_new_dataset( + cursor, + population["Id"], + form["geno-dataset-name"], + form["geno-dataset-fullname"], + form["geno-dataset-shortname"]) + + flash("Successfully created genotype dataset." + "alert-success") + return redirect(url_for("species.populations.genotypes.list_genotypes", + species_id=species["SpeciesId"], + population_id=population["Id"])) diff --git a/uploader/templates/genotypes/create-dataset.html b/uploader/templates/genotypes/create-dataset.html new file mode 100644 index 0000000..10331c1 --- /dev/null +++ b/uploader/templates/genotypes/create-dataset.html @@ -0,0 +1,82 @@ +{%extends "genotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Genotypes — Create Dataset{%endblock%} + +{%block pagetitle%}Genotypes — Create Dataset{%endblock%} + +{%block lvl4_breadcrumbs%} +
  • + Create Dataset +
    • +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +
    +
    + Create a new Genotype Dataset + +
    + + + +

    This is a short representative, but constrained name for the genotype + dataset.
    + The field will only accept letters ('A-Za-z'), numbers (0-9), hyphens + and underscores. Any other character will cause the name to be + rejected.

     +
    + +
    + + + +

    This is a longer, more descriptive name for your dataset.

     +
    + +
    + + + +

    A short name for your dataset. If you leave this field blank, the + short name will be set to the same value as the + "Name" field above.

     +
    + +
    + +
    +
    +
    +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} diff --git a/uploader/templates/genotypes/list-genotypes.html b/uploader/templates/genotypes/list-genotypes.html index cecb5a3..e4c39eb 100644 --- a/uploader/templates/genotypes/list-genotypes.html +++ b/uploader/templates/genotypes/list-genotypes.html @@ -123,7 +123,9 @@ There is no genotype dataset defined for this population.

    - create new genotype dataset

    -- cgit v1.2.3