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-rw-r--r--uploader/genotypes/models.py33
-rw-r--r--uploader/genotypes/views.py34
-rw-r--r--uploader/templates/genotypes/create-dataset.html82
-rw-r--r--uploader/templates/genotypes/list-genotypes.html4
4 files changed, 151 insertions, 2 deletions
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(
+ "/<int:species_id>/populations/<int:population_id>/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%}
+<li {%if activelink=="create-dataset"%}
+ class="breadcrumb-item active"
+ {%else%}
+ class="breadcrumb-item"
+ {%endif%}>
+ <a href="{{url_for('species.populations.genotypes.create_dataset',
+ species_id=species.SpeciesId,
+ population_id=population.Id)}}">Create Dataset</a>
+</li>
+{%endblock%}
+
+{%block contents%}
+{{flash_all_messages()}}
+
+<div class="row">
+ <form id="frm-geno-create-dataset"
+ method="POST"
+ action="{{url_for('species.populations.genotypes.create_dataset',
+ species_id=species.SpeciesId,
+ population_id=population.Id)}}">
+ <legend>Create a new Genotype Dataset</legend>
+
+ <div class="form-group">
+ <label for="txt-geno-dataset-name" class="form-label">Name</label>
+ <input type="text"
+ id="txt-geno-dataset-name"
+ name="geno-dataset-name"
+ required="required"
+ class="form-control" />
+ <small class="form-text text-muted">
+ <p>This is a short representative, but constrained name for the genotype
+ dataset.<br />
+ 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.</p></small>
+ </div>
+
+ <div class="form-group">
+ <label for="txt-geno-dataset-fullname" class="form-label">Full Name</label>
+ <input type="text"
+ id="txt-geno-dataset-fullname"
+ name="geno-dataset-fullname"
+ required="required"
+ class="form-control" />
+ <small class="form-text text-muted">
+ <p>This is a longer, more descriptive name for your dataset.</p></small>
+ </div>
+
+ <div class="form-group">
+ <label for="txt-geno-dataset-shortname"
+ class="form-label">Short Name</label>
+ <input type="text"
+ id="txt-geno-dataset-shortname"
+ name="geno-dataset-shortname"
+ class="form-control" />
+ <small class="form-text text-muted">
+ <p>A short name for your dataset. If you leave this field blank, the
+ short name will be set to the same value as the
+ "<strong>Name</strong>" field above.</p></small>
+ </div>
+
+ <div class="form-group">
+ <input type="submit"
+ class="btn btn-primary"
+ value="create dataset" />
+ </div>
+ </form>
+</div>
+{%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.
</p>
<p>
- <a href="#create-new-genotype-dataset"
+ <a href="{{url_for('species.populations.genotypes.create_dataset',
+ species_id=species.SpeciesId,
+ population_id=population.Id)}}"
title="Create a new genotype dataset for the '{{population.FullName}}' population for the '{{species.FullName}}' species."
class="btn btn-primary">
create new genotype dataset</a></p>