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-rw-r--r--wqflask/wqflask/__init__.py3
-rw-r--r--wqflask/wqflask/jupyter_notebooks.py21
-rw-r--r--wqflask/wqflask/static/new/css/jupyter_notebooks.css16
-rw-r--r--wqflask/wqflask/templates/base.html2
-rw-r--r--wqflask/wqflask/templates/display_files.html119
-rw-r--r--wqflask/wqflask/templates/jupyter_notebooks.html28
6 files changed, 188 insertions, 1 deletions
diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py
index 7d46fbad..fbf1c9f5 100644
--- a/wqflask/wqflask/__init__.py
+++ b/wqflask/wqflask/__init__.py
@@ -23,6 +23,8 @@ from wqflask.api.markdown import facilities_blueprint
from wqflask.api.markdown import blogs_blueprint
from wqflask.api.markdown import news_blueprint
+from wqflask.jupyter_notebooks import jupyter_notebooks
+
app = Flask(__name__)
@@ -60,6 +62,7 @@ app.register_blueprint(environments_blueprint, url_prefix="/environments")
app.register_blueprint(facilities_blueprint, url_prefix="/facilities")
app.register_blueprint(blogs_blueprint, url_prefix="/blogs")
app.register_blueprint(news_blueprint, url_prefix="/news")
+app.register_blueprint(jupyter_notebooks, url_prefix="/jupyter_notebooks")
app.register_blueprint(resource_management, url_prefix="/resource-management")
diff --git a/wqflask/wqflask/jupyter_notebooks.py b/wqflask/wqflask/jupyter_notebooks.py
new file mode 100644
index 00000000..dbea04dd
--- /dev/null
+++ b/wqflask/wqflask/jupyter_notebooks.py
@@ -0,0 +1,21 @@
+from flask import Blueprint, render_template
+
+jupyter_notebooks = Blueprint('jupyter_notebooks', __name__)
+
+@jupyter_notebooks.route("/launcher", methods=("GET",))
+def launcher():
+ links = (
+ {
+ "main_url": "http://notebook.genenetwork.org/51091/tree?",
+ "notebook_name": "COVID-19 in mybinder.org federation",
+ "src_link_url": "https://github.com/jgarte/covid19_in_binder"},
+ {
+ "main_url": "http://notebook.genenetwork.org/35639/tree?",
+ "notebook_name": "Simple requirements.txt based example",
+ "src_link_url": "https://github.com/jgarte/requirements"},
+ {
+ "main_url": "http://notebook.genenetwork.org/40733/tree?",
+ "notebook_name": "Guile Jupyter Notebook Querying GeneNetwork API",
+ "src_link_url": "https://github.com/jgarte/guile-notebook-genenetwork-api"})
+
+ return render_template("jupyter_notebooks.html", links=links)
diff --git a/wqflask/wqflask/static/new/css/jupyter_notebooks.css b/wqflask/wqflask/static/new/css/jupyter_notebooks.css
new file mode 100644
index 00000000..db972a17
--- /dev/null
+++ b/wqflask/wqflask/static/new/css/jupyter_notebooks.css
@@ -0,0 +1,16 @@
+.jupyter-links {
+ padding: 1.5em;
+}
+
+.jupyter-links:nth-of-type(2n) {
+ background: #EEEEEE;
+}
+
+.jupyter-links .main-link {
+ font-size: larger;
+ display: block;
+}
+
+.jupyter-links .src-link {
+ font-size: smaller;
+}
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 4a6674c6..6e922f24 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -87,7 +87,7 @@
<li><a href="https://systems-genetics.org/">Systems Genetics PheWAS</a></li>
<li><a href="http://ucscbrowser.genenetwork.org/">Genome Browser</a></li>
<li><a href="http://power.genenetwork.org">BXD Power Calculator</a></li>
- <li><a href="http://notebook.genenetwork.org/">Jupyter Notebook Launcher</a></li>
+ <li><a href="{{url_for('jupyter_notebooks.launcher')}}">Jupyter Notebook Launcher</a></li>
<li><a href="http://datafiles.genenetwork.org">Interplanetary File System</a></li>
</ul>
</li>
diff --git a/wqflask/wqflask/templates/display_files.html b/wqflask/wqflask/templates/display_files.html
new file mode 100644
index 00000000..d5295fb4
--- /dev/null
+++ b/wqflask/wqflask/templates/display_files.html
@@ -0,0 +1,119 @@
+{% extends "base.html" %}
+{% block title %}Trait Submission{% endblock %}
+{% block content %}
+<!-- Start of body -->
+{% with messages = get_flashed_messages(with_categories=true) %}
+{% if messages %}
+{% for category, message in messages %}
+<div class="container-fluid bg-{{ category }}">
+ <p>{{ message }}</p>
+</div>
+{% endfor %}
+{% endif %}
+{% endwith %}
+
+
+<div class="container">
+
+ {% if waiting %}
+ <div class="row">
+ Files for approval:
+ <div class="table-responsive">
+ <table class="table m-0">
+ <thead>
+ <th scope="col">Resource Id</</th>
+ <th scope="col">Author</th>
+ <th scope="col">TimeStamp</th>
+ <th scope="col"></th>
+ <th scope="col"></th>
+ </thead>
+ <tbody>
+ {% for data in waiting %}
+ <tr>
+ {% set file_url = url_for('metadata_edit.show_diff', name=data.get('file_name')) %}
+ <td><a href="{{ file_url }}" target="_blank">{{ data.get("resource_id") }}</a></td>
+ <td>{{ data.get("author")}}</td>
+ <td>{{ data.get("time_stamp")}}</td>
+ {% if data.get("roles").get("admin") > AdminRole.EDIT_ACCESS %}
+ {% set reject_url = url_for('metadata_edit.reject_data', resource_id=data.get('resource_id'), file_name=data.get('file_name')) %}
+ {% set approve_url = url_for('metadata_edit.approve_data', resource_id=data.get('resource_id'), file_name=data.get('file_name')) %}
+ <td>
+ <button type="button"
+ class="btn btn-secondary btn-sm">
+ <a href="{{ reject_url }}">Reject</a>
+ </button>
+ </td>
+ <td>
+ <button type="button"
+ class="btn btn-warning btn-sm">
+ <a href="{{ approve_url }}">Approve</a>
+ </button>
+ </td>
+ {% endif %}
+ </tr>
+ {% endfor %}
+ </tbody>
+ </table>
+ </div>
+ </div>
+ {% endif %}
+
+ {% if rejected %}
+ <div class="row">
+ Rejected Files:
+ <div class="table-responsive">
+ <table class="table m-0">
+ <thead>
+ <th scope="col">Resource Id</</th>
+ <th scope="col">Author</th>
+ <th scope="col">TimeStamp</th>
+ </thead>
+ <tbody>
+ {% for data in rejected %}
+ <tr>
+ {% set file_url = url_for('metadata_edit.show_diff', name=data.get('file_name')) %}
+ <td><a href="{{ file_url }}" target="_blank">{{ data.get("resource_id") }}</a></td>
+ <td>{{ data.get("author")}}</td>
+ <td>{{ data.get("time_stamp")}}</td>
+ </tr>
+ {% endfor %}
+ </tbody>
+ </table>
+ </div>
+ </div>
+ {% endif %}
+
+ {% if approved %}
+ <div class="row">
+ Approved Data:
+ <div class="table-responsive">
+ <table class="table m-0">
+ <thead>
+ <th scope="col">Resource Id</</th>
+ <th scope="col">Author</th>
+ <th scope="col">TimeStamp</th>
+ </thead>
+ <tbody>
+ {% for data in approved %}
+ <tr>
+ {% set file_url = url_for('metadata_edit.show_diff', name=data.get('file_name')) %}
+ <td><a href="{{ file_url }}" target="_blank">{{ data.get("resource_id") }}</a></td>
+ <td>{{ data.get("author")}}</td>
+ <td>{{ data.get("time_stamp")}}</td>
+ </tr>
+ {% endfor %}
+ </tbody>
+ </table>
+ </div>
+ </div>
+ {% endif %}
+</div>
+
+{%endblock%}
+
+{% block js %}
+<script>
+ gn_server_url = "{{ gn_server_url }}";
+
+</script>
+{% endblock %}
diff --git a/wqflask/wqflask/templates/jupyter_notebooks.html b/wqflask/wqflask/templates/jupyter_notebooks.html
new file mode 100644
index 00000000..afc95a15
--- /dev/null
+++ b/wqflask/wqflask/templates/jupyter_notebooks.html
@@ -0,0 +1,28 @@
+{%extends "base.html"%}
+
+{%block title%}
+Jupyter Notebooks
+{%endblock%}
+
+{%block css%}
+<link rel="stylesheet" type="text/css" href="/static/new/css/jupyter_notebooks.css" />
+{%endblock%}
+
+{%block content%}
+
+<div class="container">
+ <h1>Current Notebooks</h1>
+
+ {%for item in links:%}
+ <div class="jupyter-links">
+ <a href="{{item.get('main_url')}}"
+ title="Access running notebook for '{{item.get('notebook_name')}}' on GeneNetwork"
+ class="main-link">{{item.get("notebook_name")}}</a>
+ <a href="{{item.get('src_link_url')}}"
+ title="Link to the notebook repository for {{item.get('notebook_name', '_')}}"
+ class="src-link">View Source</a>
+ </div>
+ {%endfor%}
+</div>
+
+{%endblock%}