From 2e12c23648be1b6827f1717ca143359d29043a39 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 6 Jul 2022 10:19:49 +0300
Subject: Implement UI for dataset selection
As part of updating the database with the new data, there is a need to
select the appropriate dataset that the data belongs to, and this
commit provides the UI to assist the user do that.
---
qc_app/__init__.py | 2 +
qc_app/dbinsert.py | 63 +++++++++++++++++++++
qc_app/parse.py | 3 +-
qc_app/static/css/styles.css | 19 +++++++
qc_app/static/js/dbinsert.js | 105 +++++++++++++++++++++++++++++++++++
qc_app/templates/dbupdate_error.html | 12 ++++
qc_app/templates/parse_results.html | 7 +++
qc_app/templates/select_dataset.html | 75 +++++++++++++++++++++++++
8 files changed, 285 insertions(+), 1 deletion(-)
create mode 100644 qc_app/dbinsert.py
create mode 100644 qc_app/static/js/dbinsert.js
create mode 100644 qc_app/templates/dbupdate_error.html
create mode 100644 qc_app/templates/select_dataset.html
(limited to 'qc_app')
diff --git a/qc_app/__init__.py b/qc_app/__init__.py
index 08b56c9..6b760b9 100644
--- a/qc_app/__init__.py
+++ b/qc_app/__init__.py
@@ -6,6 +6,7 @@ from flask import Flask
from .entry import entrybp
from .parse import parsebp
+from .dbinsert import dbinsertbp
def instance_path():
"""Retrieve the `instance_path`. Raise an exception if not defined."""
@@ -27,4 +28,5 @@ def create_app(instance_dir):
# setup blueprints
app.register_blueprint(entrybp, url_prefix="/")
app.register_blueprint(parsebp, url_prefix="/parse")
+ app.register_blueprint(dbinsertbp, url_prefix="/dbinsert")
return app
diff --git a/qc_app/dbinsert.py b/qc_app/dbinsert.py
new file mode 100644
index 0000000..0733e5f
--- /dev/null
+++ b/qc_app/dbinsert.py
@@ -0,0 +1,63 @@
+"Handle inserting data into the database"
+import os
+import json
+from functools import reduce
+
+import requests
+from redis import Redis
+from flask import request, Blueprint, render_template, current_app as app
+
+from . import jobs
+
+dbinsertbp = Blueprint("dbinsert", __name__)
+
+def render_error(error_msg):
+ "Render the generic error page"
+ return render_template("dbupdate_error.html", error_message=error_msg), 400
+
+def make_menu_items_grouper(grouping_fn=lambda item: item):
+ "Build function to be used to group menu items."
+ def __grouper__(acc, row):
+ grouping = grouping_fn(row[2])
+ row_values = (row[0].strip(), row[1].strip())
+ if acc.get(grouping) is None:
+ return {**acc, grouping: (row_values,)}
+ return {**acc, grouping: (acc[grouping] + (row_values,))}
+ return __grouper__
+
+@dbinsertbp.route("/select-dataset", methods=["POST"])
+def select_dataset():
+ "Select the dataset to add the file contents against"
+ job_id = request.form["job_id"]
+ with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
+ job = jobs.job(rconn, job_id)
+ if job:
+ filename = job["filename"]
+ filepath = f"{app.config['UPLOAD_FOLDER']}/{filename}"
+ if os.path.exists(filepath):
+ req = requests.get(
+ "https://genenetwork.org/api3/api/menu/generate/json")
+ menu_contents = req.json()
+ default_species = "mouse"
+ mouse_groups = reduce(
+ make_menu_items_grouper(
+ lambda item: item.strip()[7:].strip()),
+ menu_contents["groups"][default_species], {})
+ default_group = "BXD"
+ group_types = reduce(
+ make_menu_items_grouper(),
+ menu_contents["types"][default_species][default_group], {})
+ default_type = group_types[tuple(group_types)[0]][0][0]
+ datasets = menu_contents[
+ "datasets"][default_species][default_group][
+ default_type]
+
+ return render_template(
+ "select_dataset.html", job_id=job_id, job_name=filename,
+ species=menu_contents["species"],
+ default_species=default_species, groups=mouse_groups,
+ types=group_types, datasets=datasets,
+ menu_contents=json.dumps(menu_contents))
+ return render_error(f"File '{filename}' no longer exists.")
+ return render_error(f"Job '{job_id}' no longer exists.")
+ return render_error("Unknown error")
diff --git a/qc_app/parse.py b/qc_app/parse.py
index 5d75c37..2a33fd0 100644
--- a/qc_app/parse.py
+++ b/qc_app/parse.py
@@ -104,7 +104,8 @@ def results(job_id: str):
"parse_results.html",
errors=errors,
job_name = f"Parsing '{filename}'",
- user_aborted = job.get("user_aborted"))
+ user_aborted = job.get("user_aborted"),
+ job_id=job["job_id"])
return render_template("no_such_job.html", job_id=job_id)
diff --git a/qc_app/static/css/styles.css b/qc_app/static/css/styles.css
index 9e5a4ec..4d0fa8c 100644
--- a/qc_app/static/css/styles.css
+++ b/qc_app/static/css/styles.css
@@ -101,3 +101,22 @@ table {
border: 2px solid;
border-radius: 1em;
}
+
+form {
+ width: 30%;
+}
+
+fieldset {
+ border-style: none;
+ display: grid;
+ grid-template-columns: 5em 1fr;
+ column-gap: 5px;
+}
+
+label {
+ grid-column: 1 / 2;
+}
+
+input,select,button {
+ grid-column: 2 / 3;
+}
diff --git a/qc_app/static/js/dbinsert.js b/qc_app/static/js/dbinsert.js
new file mode 100644
index 0000000..3c0be54
--- /dev/null
+++ b/qc_app/static/js/dbinsert.js
@@ -0,0 +1,105 @@
+function remove_children(element) {
+ Array.from(element.children).forEach(child => {
+ element.removeChild(child);
+ });
+}
+
+function trigger_change_event(element) {
+ evt = new Event("change");
+ element.dispatchEvent(evt);
+}
+
+function setup_groups(group_data) {
+ elt = document.getElementById("group");
+ remove_children(elt);
+ the_groups = group_data.reduce(
+ function(acc, row) {
+ grouping = row[2].slice(7).trim();
+ if(acc[grouping] === undefined) {
+ acc[grouping] = [];
+ }
+ acc[grouping].push([row[0], row[1]]);
+ return acc;
+ },
+ {});
+ for(grouping in the_groups) {
+ optgrp = document.createElement("optgroup");
+ optgrp.setAttribute("label", grouping);
+ the_groups[grouping].forEach(group => {
+ opt = document.createElement("option");
+ opt.setAttribute("value", group[0]);
+ opt.appendChild(document.createTextNode(group[1]));
+ optgrp.appendChild(opt);
+ });
+ elt.appendChild(optgrp);
+ }
+ trigger_change_event(elt);
+}
+
+function setup_types(type_data) {
+ elt = document.getElementById("type");
+ remove_children(elt);
+ the_types = type_data.reduce(function(acc, row) {
+ grp = row[2];
+ if(acc[grp] === undefined) {
+ acc[grp] = [];
+ }
+ acc[grp].push([row[0], row[1]]);
+ return acc;
+ }, {});
+ for(type_group in the_types) {
+ optgrp = document.createElement("optgroup");
+ optgrp.setAttribute("label", type_group);
+ the_types[type_group].forEach(type => {
+ opt = document.createElement("option");
+ opt.setAttribute("value", type[0]);
+ opt.appendChild(document.createTextNode(type[1]));
+ optgrp.appendChild(opt);
+ });
+ elt.appendChild(optgrp);
+ }
+ trigger_change_event(elt);
+}
+
+function setup_datasets(dataset_data) {
+ console.info("DATASET DATA:", dataset_data);
+ elt = document.getElementById("dataset");
+ remove_children(elt);
+ dataset_data.forEach(dataset => {
+ opt = document.createElement("option");
+ opt.setAttribute("value", dataset[0]);
+ opt.appendChild(document.createTextNode(
+ "[" + dataset[1] + "] " + dataset[2]));
+ elt.appendChild(opt);
+ });
+ trigger_change_event(elt);
+}
+
+function menu_contents() {
+ return JSON.parse(
+ document.getElementsByTagName("form")[0].getAttribute(
+ "data-menu-content"));
+}
+
+function update_menu(event) {
+ menu = menu_contents();
+
+ species_elt = document.getElementById("species");
+ group_elt = document.getElementById("group");
+ type_elt = document.getElementById("type");
+ dataset_elt = document.getElementById("dataset");
+
+ if(event.target == species_elt) {
+ setup_groups(menu["groups"][species_elt.value]);
+ }
+
+ if(event.target == group_elt) {
+ setup_types(menu["types"][species_elt.value][group_elt.value]);
+ }
+
+ if(event.target == type_elt) {
+ setup_datasets(
+ menu["datasets"][species_elt.value][group_elt.value][type_elt.value]
+ );
+ }
+}
diff --git a/qc_app/templates/dbupdate_error.html b/qc_app/templates/dbupdate_error.html
new file mode 100644
index 0000000..83e34fe
--- /dev/null
+++ b/qc_app/templates/dbupdate_error.html
@@ -0,0 +1,12 @@
+{%extends "base.html"%}
+
+{%block title%}DB Update Error{%endblock%}
+
+{%block contents%}
+database update error
+
+
+ Database Update Error: {{error_message}}
+
+
+{%endblock%}
diff --git a/qc_app/templates/parse_results.html b/qc_app/templates/parse_results.html
index 358c5e8..1a224e8 100644
--- a/qc_app/templates/parse_results.html
+++ b/qc_app/templates/parse_results.html
@@ -12,4 +12,11 @@
{{errors_display(errors, "No errors found in the file", "We found the following errors")}}
+{%if errors | length == 0 %}
+
+{%endif%}
+
{%endblock%}
diff --git a/qc_app/templates/select_dataset.html b/qc_app/templates/select_dataset.html
new file mode 100644
index 0000000..5fefccc
--- /dev/null
+++ b/qc_app/templates/select_dataset.html
@@ -0,0 +1,75 @@
+{%extends "base.html"%}
+
+{%block title%}Select Dataset{%endblock%}
+
+{%block contents%}
+{{job_name}}: select dataset
+
+
+
+{%endblock%}
+
+{%block javascript%}
+
+
+{%endblock%}
--
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