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-rw-r--r--wqflask/wqflask/oauth2/client.py5
-rw-r--r--wqflask/wqflask/oauth2/data.py47
-rw-r--r--wqflask/wqflask/oauth2/request_utils.py5
-rw-r--r--wqflask/wqflask/static/new/javascript/auth/search_genotypes.js50
-rw-r--r--wqflask/wqflask/templates/oauth2/data-list-genotype.html13
5 files changed, 103 insertions, 17 deletions
diff --git a/wqflask/wqflask/oauth2/client.py b/wqflask/wqflask/oauth2/client.py
index 0cecd965..1d3e07ae 100644
--- a/wqflask/wqflask/oauth2/client.py
+++ b/wqflask/wqflask/oauth2/client.py
@@ -16,7 +16,7 @@ def oauth2_client():
scope=SCOPE, token_endpoint_auth_method="client_secret_post",
token=session.get("oauth2_token"))
-def oauth2_get(uri_path: str, data: dict = {}) -> Either:
+def oauth2_get(uri_path: str, data: dict = {}, **kwargs) -> Either:
token = session.get("oauth2_token")
config = app.config
client = OAuth2Session(
@@ -24,7 +24,8 @@ def oauth2_get(uri_path: str, data: dict = {}) -> Either:
token=token, scope=SCOPE)
resp = client.get(
urljoin(config["GN_SERVER_URL"], uri_path),
- data=data)
+ data=data,
+ **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 e1b33b56..03fde15f 100644
--- a/wqflask/wqflask/oauth2/data.py
+++ b/wqflask/wqflask/oauth2/data.py
@@ -3,8 +3,8 @@ import json
from urllib.parse import urljoin
from flask import (
- flash, request, url_for, redirect, Response, Blueprint, render_template,
- current_app as app)
+ flash, request, jsonify, url_for, redirect, Response, Blueprint,
+ render_template, current_app as app)
from .request_utils import process_error
from .client import oauth2_get, oauth2_post
@@ -22,18 +22,29 @@ def __render_template__(templatepath, **kwargs):
def __search_mrna__(query, template, **kwargs):
return __render_template__(template, **kwargs)
+def __selected_datasets__():
+ if bool(request.json):
+ return request.json.get(
+ "selected",
+ request.args.get("selected",
+ request.form.get("selected", [])))
+ return request.args.get("selected",
+ request.form.get("selected", []))
+
def __search_genotypes__(query, template, **kwargs):
species_name = kwargs["species_name"]
+ search_uri = urljoin(app.config["GN_SERVER_URL"], "oauth2/data/search")
datasets = oauth2_get(
"oauth2/data/search",
- data = {
+ json = {
"query": query,
"dataset_type": "genotype",
- "species_name": species_name
+ "species_name": species_name,
+ "selected": __selected_datasets__()
}).either(
lambda err: {"datasets_error": process_error(err)},
lambda datasets: {"datasets": datasets})
- return __render_template__(template, **datasets, **kwargs)
+ return __render_template__(template, search_uri=search_uri, **datasets, **kwargs)
def __search_phenotypes__(query, template, **kwargs):
per_page = int(request.args.get("per_page", 500))
@@ -55,6 +66,28 @@ def __search_phenotypes__(query, template, **kwargs):
search_endpoint=urljoin(app.config["GN_SERVER_URL"], "search/"),
**kwargs)
+@data.route("/genotype/search", methods=["POST"])
+def json_search_genotypes() -> Response:
+ def __handle_error__(err):
+ error = process_error(err)
+ print(f"THE ERROR: {error}")
+ return jsonify(error), error["status_code"]
+
+ print(f"===============================================")
+ print(request.json)
+ print(f"===============================================")
+
+ return oauth2_get(
+ "oauth2/data/search",
+ json = {
+ "query": request.json["query"],
+ "dataset_type": "genotype",
+ "species_name": request.json["species_name"],
+ "selected": __selected_datasets__()
+ }).either(
+ __handle_error__,
+ lambda datasets: jsonify(datasets))
+
@data.route("/<string:species_name>/<string:dataset_type>/list",
methods=["GET", "POST"])
def list_data_by_species_and_dataset(
@@ -177,6 +210,6 @@ def link_genotype_data():
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"))
+ "selected": tuple(json.loads(dataset) for dataset
+ in form.getlist("selected"))
}).either(lambda err: __link_error__(process_error(err)), __link_success__)
diff --git a/wqflask/wqflask/oauth2/request_utils.py b/wqflask/wqflask/oauth2/request_utils.py
index ed523614..eefae900 100644
--- a/wqflask/wqflask/oauth2/request_utils.py
+++ b/wqflask/wqflask/oauth2/request_utils.py
@@ -23,9 +23,10 @@ def process_error(error: Response,
return {
"error": "NotFoundError",
"error_message": message,
- "error_description": message
+ "error_description": message,
+ "status_code": error.status_code
}
- return error.json()
+ return {**error.json(), "status_code": error.status_code}
def request_error(response):
app.logger.error(f"{response}: {response.url} [{response.status_code}]")
diff --git a/wqflask/wqflask/static/new/javascript/auth/search_genotypes.js b/wqflask/wqflask/static/new/javascript/auth/search_genotypes.js
index 39999e76..8d821f44 100644
--- a/wqflask/wqflask/static/new/javascript/auth/search_genotypes.js
+++ b/wqflask/wqflask/static/new/javascript/auth/search_genotypes.js
@@ -15,7 +15,7 @@ function link_checkbox(dataset) {
return __build_checkbox__(
dataset,
'<input type="checkbox" class="checkbox checkbox-selected" ' +
- 'name="selected_datasets" checked="checked">');
+ 'name="selected" checked="checked">');
}
function search_checkbox(dataset) {
@@ -179,6 +179,52 @@ function select_deselect_dataset(dataset, source, destination) {
/***** END: Re-render tables *****/
}
+function debounce(func, delay=500) {
+ var timeout;
+ return function search(event) {
+ clearTimeout(timeout);
+ timeout = setTimeout(func, delay);
+ };
+}
+
+function search_genotypes() {
+ query = document.getElementById("txt-query").value;
+ selected = JSON.parse(document.getElementById(
+ "tbl-link-genotypes").getAttribute("data-selected-datasets"));
+ species_name = document.getElementById("txt-species-name").value
+ search_endpoint = "/oauth2/data/genotype/search"
+ $.ajax(
+ search_endpoint,
+ {
+ "method": "POST",
+ "contentType": "application/json; charset=utf-8",
+ "dataType": "json",
+ "data": JSON.stringify({
+ "query": query,
+ "selected": selected,
+ "dataset_type": "genotype",
+ "species_name": species_name}),
+ "error": function(jqXHR, textStatus, errorThrown) {
+ data = jqXHR.responseJSON
+ elt = document.getElementById("search-error").setAttribute(
+ "style", "display: block;");
+ document.getElementById("search-error-text").innerHTML = (
+ data.error + " (" + data.status_code + "): " +
+ data.error_description);
+ document.getElementById("tbl-genotypes").setAttribute(
+ "data-datasets", JSON.stringify([]));
+ render_table("#tbl-genotypes", "data-datasets", search_checkbox);
+ },
+ "success": function(data, textStatus, jqXHR) {
+ document.getElementById("search-error").setAttribute(
+ "style", "display: none;");
+ document.getElementById("tbl-genotypes").setAttribute(
+ "data-datasets", JSON.stringify(data));
+ render_table("#tbl-genotypes", "data-datasets", search_checkbox);
+ }
+ });
+}
+
$(document).ready(function() {
let search_table = new TableDataSource("#tbl-genotypes", "data-datasets");
let link_table = new TableDataSource(
@@ -189,7 +235,7 @@ $(document).ready(function() {
return false;
});
- /* $("#txt-query").keyup(debounced_search()); */
+ $("#txt-query").keyup(debounce(search_genotypes));
$("#tbl-genotypes").on("change", ".checkbox-search", function(event) {
if(this.checked) {
diff --git a/wqflask/wqflask/templates/oauth2/data-list-genotype.html b/wqflask/wqflask/templates/oauth2/data-list-genotype.html
index 54479251..47c21079 100644
--- a/wqflask/wqflask/templates/oauth2/data-list-genotype.html
+++ b/wqflask/wqflask/templates/oauth2/data-list-genotype.html
@@ -58,7 +58,7 @@
<tr>
<td>
<input type="checkbox" class="checkbox checkbox-selected"
- name="selected_datasets"
+ name="selected"
value='{{dataset | tojson}}' />
</td>
<td>{{dataset.dataset_name}}</td>
@@ -91,12 +91,12 @@
<div class="row">
<span id="search-messages" class="alert-danger" style="display:none"></span>
- <form id="frm-search-traits"
- action="#"
+ <form id="frm-search"
+ action="{{search_uri}}"
method="POST">
<legend>Search: Genotype</legend>
<input type="hidden" value="{{species_name}}" name="species"
- id="txt-species" />
+ id="txt-species-name" />
<input type="hidden" value="{{dataset_type}}" name="dataset_type"
id="txt-dataset-type" />
<input type="hidden" value="{{per_page}}" name="per_page"
@@ -111,6 +111,11 @@
</div>
<div class="row">
+ <div id="search-error" class="text-danger" style="display: none;">
+ <span class="glyphicon glyphicon-exclamation-sign"></span>
+ &nbsp
+ <span id="search-error-text"></span>
+ </div>
<table id="tbl-genotypes"
class="table-hover table-striped cell-border dataTable no-footer"
data-datasets='{{datasets | list | tojson}}'>
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-21 15:25:18 +0000