From 4c0186d281ff77b28fa1abe1f84da0e8cb72dea1 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 7 Oct 2024 13:32:01 -0500
Subject: Create new phenotype dataset (PublishFreeze).

Provide the UI and code to create a new phenotype dataset.
---
 uploader/phenotypes/models.py | 28 ++++++++++++++++++++++
 uploader/phenotypes/views.py  | 54 +++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 82 insertions(+)

(limited to 'uploader/phenotypes')

diff --git a/uploader/phenotypes/models.py b/uploader/phenotypes/models.py
index be970ac..9324601 100644
--- a/uploader/phenotypes/models.py
+++ b/uploader/phenotypes/models.py
@@ -1,6 +1,7 @@
 """Database and utility functions for phenotypes."""
 from typing import Optional
 from functools import reduce
+from datetime import datetime
 
 import MySQLdb as mdb
 from MySQLdb.cursors import Cursor, DictCursor
@@ -202,3 +203,30 @@ def phenotypes_data(conn: mdb.Connection,
         cursor.execute(_query, (population_id, dataset_id))
         debug_query(cursor)
         return tuple(dict(row) for row in cursor.fetchall())
+
+
+def save_new_dataset(cursor: Cursor,
+                     population_id: int,
+                     dataset_name: str,
+                     dataset_fullname: str,
+                     dataset_shortname: str) -> dict:
+    """Create a new phenotype dataset."""
+    params = {
+        "population_id": population_id,
+        "dataset_name": dataset_name,
+        "dataset_fullname": dataset_fullname,
+        "dataset_shortname": dataset_shortname,
+        "created": datetime.now().date().isoformat(),
+        "public": 2,
+        "confidentiality": 0,
+        "users": None
+    }
+    cursor.execute(
+        "INSERT INTO PublishFreeze(Name, FullName, ShortName, CreateTime, "
+        "public, InbredSetId, confidentiality, AuthorisedUsers) "
+        "VALUES(%(dataset_name)s, %(dataset_fullname)s, %(dataset_shortname)s, "
+        "%(created)s, %(public)s, %(population_id)s, %(confidentiality)s, "
+        "%(users)s)",
+        params)
+    debug_query(cursor)
+    return {**params, "Id": cursor.lastrowid}
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py
index 47fbd51..c7bc965 100644
--- a/uploader/phenotypes/views.py
+++ b/uploader/phenotypes/views.py
@@ -1,6 +1,7 @@
 """Views handling ('classical') phenotypes."""
 from functools import wraps
 
+from MySQLdb.cursors import DictCursor
 from flask import (flash,
                    request,
                    url_for,
@@ -18,10 +19,14 @@ from uploader.request_checks import with_species, with_population
 from uploader.datautils import safe_int, order_by_family, enumerate_sequence
 from uploader.population.models import (populations_by_species,
                                         population_by_species_and_id)
+from uploader.input_validation import (encode_errors,
+                                       decode_errors,
+                                       is_valid_representative_name)
 
 from .models import (dataset_by_id,
                      phenotype_by_id,
                      phenotypes_count,
+                     save_new_dataset,
                      dataset_phenotypes,
                      datasets_by_population)
 
@@ -222,3 +227,52 @@ def view_phenotype(# pylint: disable=[unused-argument]
             make_either_error_handler(
                 "There was an error fetching the roles and privileges."),
             lambda resp: resp)
+
+
+@phenotypesbp.route(
+    "<int:species_id>/populations/<int:population_id>/phenotypes/datasets/create",
+    methods=["GET", "POST"])
+@require_login
+@with_population(
+    species_redirect_uri="species.populations.phenotypes.index",
+    redirect_uri="species.populations.phenotypes.select_population")
+def create_dataset(species: dict, population: dict, **kwargs):
+    """Create a new phenotype dataset."""
+    with (database_connection(app.config["SQL_URI"]) as conn,
+          conn.cursor(cursorclass=DictCursor) as cursor):
+        if request.method == "GET":
+            return render_template("phenotypes/create-dataset.html",
+                                   activelink="create-dataset",
+                                   species=species,
+                                   population=population,
+                                   **decode_errors(
+                                       request.args.get("error_values", "")))
+
+        form = request.form
+        _errors = tuple()
+        if not is_valid_representative_name(
+                (form.get("dataset-name") or "").strip()):
+            _errors = _errors + (("dataset-name", "Invalid dataset name."),)
+
+        if not bool((form.get("dataset-fullname") or "").strip()):
+            _errors = _errors + (("dataset-fullname",
+                                  "You must provide a value for 'Full Name'."),)
+
+        if bool(_errors) > 0:
+            return redirect(url_for(
+                "species.populations.phenotypes.create_dataset",
+                species_id=species["SpeciesId"],
+                population_id=population["Id"],
+                error_values=encode_errors(_errors, form)))
+
+        dataset_shortname = (
+            form["dataset-shortname"] or form["dataset-name"]).strip()
+        pheno_dataset = save_new_dataset(
+            cursor,
+            population["Id"],
+            form["dataset-name"].strip(),
+            form["dataset-fullname"].strip(),
+            dataset_shortname)
+        return redirect(url_for("species.populations.phenotypes.list_datasets",
+                                species_id=species["SpeciesId"],
+                                population_id=population["Id"]))
-- 
cgit v1.2.3