")
+ cell = $('');
+ cell.append(
+ $(''));
+ cell.append(" ");
+ cell.append("No genotype datasets remaining.");
+ row.append(cell);
+ $(table_id + " tbody").append(row);
+ }
+ table_data.forEach(function(dataset) {
+ row = $("")
+ row.append(checkbox_function(dataset));
+ row.append(table_cell(dataset.InbredSetName));
+ row.append(table_cell(dataset.dataset_name));
+ row.append(table_cell(dataset.dataset_fullname));
+ row.append(table_cell(dataset.dataset_shortname));
+ $(table_id + " tbody").append(row);
+ });
+}
+
+function in_array(dataset, datasets) {
+ found = datasets.filter(function(dst) {
+ return (dst.SpeciesId == dataset.SpeciesId &&
+ dst.InbredSetId == dataset.InbredSetId &&
+ dst.GenoFreezeId == dataset.GenoFreezeId);
+ });
+ return found.length > 0;
+}
+
+function remove_from_table_data(dataset, table_data_source) {
+ let table_id = table_data_source.table_id.selector;
+ let data_attr_name = table_data_source.data_attribute_name;
+ without_dataset = JSON.parse($(table_id).attr(data_attr_name)).filter(
+ function(dst) {
+ return !(dst.SpeciesId == dataset.SpeciesId &&
+ dst.InbredSetId == dataset.InbredSetId &&
+ dst.GenoFreezeId == dataset.GenoFreezeId);
+ });
+ $(table_id).attr(data_attr_name, JSON.stringify(without_dataset));
+}
+
+function add_to_table_data(dataset, table_data_source) {
+ let table_id = table_data_source.table_id.selector;
+ let data_attr_name = table_data_source.data_attribute_name;
+ table_data = JSON.parse($(table_id).attr(data_attr_name));
+ if(!in_array(dataset, table_data)) {
+ table_data.push(dataset);
+ }
+ $(table_id).attr(data_attr_name, JSON.stringify(Array.from(table_data)));
+}
+
+function toggle_link_button() {
+ num_groups = $("#frm-link-genotypes select option").length - 1;
+ num_selected = JSON.parse(
+ $("#tbl-link-genotypes").attr("data-selected-datasets")).length;
+ if(num_groups > 0 && num_selected > 0) {
+ $("#frm-link-genotypes input[type='submit']").prop("disabled", false);
+ } else {
+ $("#frm-link-genotypes input[type='submit']").prop("disabled", true);
+ }
+}
+
+class InvalidCSSIDSelector extends Error {
+ constructor(message) {
+ super(message);
+ this.name = "InvalidCSSIDSelector";
+ }
+}
+
+class InvalidDataAttributeName extends Error {
+ constructor(message) {
+ super(message);
+ this.name = "InvalidDataAttributeName";
+ }
+}
+
+/**
+ * CSSIDSelector: A CSS ID Selector
+ * @param {String} A CSS selector of the form '#...'
+ */
+class CSSIDSelector {
+ constructor(selector) {
+ if(!selector.startsWith("#")) {
+ throw new InvalidCSSIDSelector(
+ "Expected the CSS selector to begin with a `#` character.");
+ }
+ let id_str = selector.slice(1, selector.length);
+ if(document.getElementById(id_str) == null) {
+ throw new InvalidCSSIDSelector(
+ "Element with ID '" + id_str + "' does not exist.");
+ }
+ this.selector = selector;
+ }
+}
+
+/**
+ * TableDataSource: A type to represent a table's data source
+ * @param {String} A CSS selector for an ID
+ * @param {String} A `data-*` attribute name
+ */
+class TableDataSource {
+ constructor(table_id, data_attribute_name) {
+ this.table_id = new CSSIDSelector(table_id);
+ let data = document.querySelector(
+ table_id).getAttribute(data_attribute_name);
+ if(data == null) {
+ throw new InvalidDataAttributeName(
+ "data-* attribute '" + data_attribute_name + "' does not exist " +
+ "for table with ID '" + table_id.slice(1, table_id.length) +
+ "'.");
+ } else {
+ this.data_attribute_name = data_attribute_name;
+ }
+ }
+}
+
+/**
+ * Switch the dataset from search table to selection table and vice versa
+ * @param {Object} A genotype dataset
+ * @param {TableDataSource} The table to switch the dataset from
+ * @param {TableDataSource} The table to switch the dataset to
+ */
+function select_deselect_dataset(dataset, source, destination) {
+ dest_selector = destination.table_id.selector
+ dest_data = JSON.parse(
+ $(dest_selector).attr(destination.data_attribute_name));
+ add_to_table_data(dataset, destination); // Add to destination table
+ remove_from_table_data(dataset, source); // Remove from source table
+ /***** BEGIN: Re-render tables *****/
+ // The `render_table` could be modified to use the checkbox creator function
+ // from the `TableDataSource` object, once that is modified to have that.
+ render_table(
+ "#tbl-link-genotypes", "data-selected-datasets", link_checkbox);
+ render_table("#tbl-genotypes", "data-datasets", search_checkbox);
+ toggle_link_button();
+ /***** END: Re-render tables *****/
+}
+
+$(document).ready(function() {
+ let search_table = new TableDataSource("#tbl-genotypes", "data-datasets");
+ let link_table = new TableDataSource(
+ "#tbl-link-genotypes", "data-selected-datasets");
+
+ $("#frm-search-traits").submit(function(event) {
+ event.preventDefault();
+ return false;
+ });
+
+ /* $("#txt-query").keyup(debounced_search()); */
+
+ $("#tbl-genotypes").on("change", ".checkbox-search", function(event) {
+ if(this.checked) {
+ select_deselect_dataset(
+ JSON.parse(this.value), search_table, link_table);
+ }
+ });
+
+ $("#tbl-link-genotypes").on("change", ".checkbox-selected", function(event) {
+ if(!this.checked) {
+ select_deselect_dataset(
+ JSON.parse(this.value), link_table, search_table);
+ }
+ });
+});
diff --git a/wqflask/wqflask/templates/oauth2/data-list-genotype.html b/wqflask/wqflask/templates/oauth2/data-list-genotype.html
index 3ef810ec..3b7cfc1f 100644
--- a/wqflask/wqflask/templates/oauth2/data-list-genotype.html
+++ b/wqflask/wqflask/templates/oauth2/data-list-genotype.html
@@ -54,7 +54,7 @@
{%for dataset in selected_datasets%}
-
@@ -151,102 +151,6 @@
{%endblock%}
{%block js%}
-
+
{%endblock%}
--
cgit v1.2.3
From 1383ab160b302601211b28db3e6a9ad97e53f8e3 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Sat, 8 Apr 2023 08:07:58 +0300
Subject: oauth2: Link the Genotype datasets.
---
wqflask/wqflask/oauth2/client.py | 9 ++++++--
wqflask/wqflask/oauth2/data.py | 26 ++++++++++++++++++++++
.../templates/oauth2/data-list-genotype.html | 5 ++++-
3 files changed, 37 insertions(+), 3 deletions(-)
diff --git a/wqflask/wqflask/oauth2/client.py b/wqflask/wqflask/oauth2/client.py
index 999bbfc8..0cecd965 100644
--- a/wqflask/wqflask/oauth2/client.py
+++ b/wqflask/wqflask/oauth2/client.py
@@ -1,4 +1,5 @@
"""Common oauth2 client utilities."""
+from typing import Optional
from urllib.parse import urljoin
from flask import session, current_app as app
@@ -29,13 +30,17 @@ def oauth2_get(uri_path: str, data: dict = {}) -> Either:
return Left(resp)
-def oauth2_post(uri_path: str, data: dict) -> Either:
+def oauth2_post(
+ uri_path: str, data: Optional[dict] = None, json: Optional[dict] = None,
+ **kwargs) -> Either:
token = session.get("oauth2_token")
config = app.config
client = OAuth2Session(
config["OAUTH2_CLIENT_ID"], config["OAUTH2_CLIENT_SECRET"],
token=token, scope=SCOPE)
- resp = client.post(urljoin(config["GN_SERVER_URL"], uri_path), data=data)
+ resp = client.post(
+ urljoin(config["GN_SERVER_URL"], uri_path), data=data, json=json,
+ **kwargs)
if resp.status_code == 200:
return Right(resp.json())
diff --git a/wqflask/wqflask/oauth2/data.py b/wqflask/wqflask/oauth2/data.py
index 1dcacb7e..e1b33b56 100644
--- a/wqflask/wqflask/oauth2/data.py
+++ b/wqflask/wqflask/oauth2/data.py
@@ -1,4 +1,5 @@
"""Handle linking data to groups."""
+import json
from urllib.parse import urljoin
from flask import (
@@ -154,3 +155,28 @@ def link_data():
except AssertionError as aserr:
flash("You must provide all the expected data.", "alert-danger")
return redirect(url_for("oauth2.data.list_data"))
+
+@data.route("/link/genotype", methods=["POST"])
+def link_genotype_data():
+ """Link genotype data to a group."""
+ form = request.form
+ link_source_url = redirect(url_for("oauth2.data.list_data"))
+ if bool(form.get("species_name")):
+ link_source_url = redirect(url_for(
+ "oauth2.data.list_data_by_species_and_dataset",
+ species_name=form["species_name"], dataset_type="genotype"))
+
+ def __link_error__(err):
+ flash(f"{err['error']}: {err['error_description']}", "alert-danger")
+ return link_source_url
+
+ def __link_success__(success):
+ flash(success["description"], "alert-success")
+ return link_source_url
+
+ return oauth2_post("oauth2/data/link/genotype", json={
+ "species_name": form.get("species_name"),
+ "group_id": form.get("group_id"),
+ "selected_datasets": tuple(json.loads(dataset) for dataset
+ in form.getlist("selected_datasets"))
+ }).either(lambda err: __link_error__(process_error(err)), __link_success__)
diff --git a/wqflask/wqflask/templates/oauth2/data-list-genotype.html b/wqflask/wqflask/templates/oauth2/data-list-genotype.html
index 3b7cfc1f..54479251 100644
--- a/wqflask/wqflask/templates/oauth2/data-list-genotype.html
+++ b/wqflask/wqflask/templates/oauth2/data-list-genotype.html
@@ -23,9 +23,12 @@