Reporting Dummy Pull Request

.gitignore

@@ -16,3 +16,4 @@ docs/source/images/*_dag.png
 /docs/source/config.yaml
 /workflows/mapping/fastq_screen_config.txt
 /workflows/mapping/Snakefile.log
+.DS_Store

Makefile

@@ -7,9 +7,14 @@ tests:
 	source activate lcdb-workflows-$(USER)-env && python -m unittest discover -s 'lcdb' -p "*_test.py"
 	source activate lcdb-workflows-$(USER)-env && python lcdb/interface.py
 
+report-test:
+	source activate lcdb-workflows-$(USER)-env && python -m unittest lcdb/test/reporting_test.py
+	source activate lcdb-workflows-$(USER)-env && python lcdb/reporting.py 
+
 workflowtest: $(workflow)
 	test/run_test.py . --build-env --clean --workflow=$(workflow)
 
-osx-dev:
+dev:
+	# pyinotify can be installed with: conda install -c conda-forge pyinotify
 	clear
-	fswatch -o -0 -r lcdb | xargs -0 -n 1 bash -c "clear && make tests"
+	python -m pyinotify -e IN_MODIFY -r lcdb/ -c "clear && make report-test"

lcdb/reporting.py

@@ -0,0 +1,75 @@
+#!/usr/bin/env python
+""" Reporting System """
+
+import os
+import sys
+import base64
+from textwrap import dedent
+
+import markdown
+import jinja2
+
+TEMPLATES_DIR = os.path.join(os.path.dirname(__file__), 'templates')
+loader = jinja2.FileSystemLoader(TEMPLATES_DIR)
+ENV = jinja2.Environment(loader=loader)
+
+def report(string, **kwargs):
+    """ Build a report """
+    md = markdown.Markdown(output_format='html5')
+    tp = ENV.get_template('base.html')
+    return tp.render(content=md.convert(dedent(string).format(**kwargs)))
+
+
+class Report(object):
+    """ Basic report class """
+    pass
+
+
+class Section(object):
+    """ Basic section class """
+    pass
+
+
+class Image(object):
+    """ Image class """
+
+    def __init__(self, png, name='', caption=''):
+        with open(png, 'rb') as fh:
+            uri = base64.b64encode(fh.read()).decode('utf-8').replace('\n', '')
+            self.image = 'data:image/png;base64,{uri}'.format(uri=uri)
+            self.image_html = '<a href={0}><img src="{0}"/></a>'.format(self.image)
+
+            self.name = name
+            self.caption = caption
+
+    def __repr__(self):
+        return self.image
+
+    def __str__(self):
+        return self.image
+
+
+class JinjaPanel(object):
+    """ Image panel class """
+
+    def __init__(self):
+        self.tp = ENV.get_template('panel.html')
+        self.panel = ''
+
+    def add_row(self, images, caption=''):
+        self.panel += self.tp.render(caption=caption, images=images)
+
+    def __repr__(self):
+        return self.panel
+
+    def __str__(self):
+        return self.panel
+
+
+if __name__ == '__main__':
+    import doctest
+    from textwrap import dedent
+    from unittest import TestCase
+
+    def assertRaises(*args, **kwargs):
+        return TestCase.assertRaises(None, *args, **kwargs)

lcdb/static/css/dashboard.css

@@ -0,0 +1,105 @@
+/*
+ * Base structure
+ */
+
+/* Move down content because we have a fixed navbar that is 50px tall */
+body {
+  padding-top: 50px;
+}
+
+
+/*
+ * Global add-ons
+ */
+
+.sub-header {
+  padding-bottom: 10px;
+  border-bottom: 1px solid #eee;
+}
+
+/*
+ * Top navigation
+ * Hide default border to remove 1px line.
+ */
+.navbar-fixed-top {
+  border: 0;
+}
+
+/*
+ * Sidebar
+ */
+
+/* Hide for mobile, show later */
+.sidebar {
+  display: none;
+}
+@media (min-width: 768px) {
+  .sidebar {
+    position: fixed;
+    top: 51px;
+    bottom: 0;
+    left: 0;
+    z-index: 1000;
+    display: block;
+    padding: 20px;
+    overflow-x: hidden;
+    overflow-y: auto; /* Scrollable contents if viewport is shorter than content. */
+    background-color: #f5f5f5;
+    border-right: 1px solid #eee;
+  }
+}
+
+/* Sidebar navigation */
+.nav-sidebar {
+  margin-right: -21px; /* 20px padding + 1px border */
+  margin-bottom: 20px;
+  margin-left: -20px;
+}
+.nav-sidebar > li > a {
+  padding-right: 20px;
+  padding-left: 20px;
+}
+.nav-sidebar > .active > a,
+.nav-sidebar > .active > a:hover,
+.nav-sidebar > .active > a:focus {
+  color: #fff;
+  background-color: #428bca;
+}
+
+
+/*
+ * Main content
+ */
+
+.main {
+  padding: 20px;
+}
+@media (min-width: 768px) {
+  .main {
+    padding-right: 40px;
+    padding-left: 40px;
+  }
+}
+.main .page-header {
+  margin-top: 0;
+}
+
+
+/*
+ * Placeholder dashboard ideas
+ */
+
+.placeholders {
+  margin-bottom: 30px;
+  text-align: center;
+}
+.placeholders h4 {
+  margin-bottom: 0;
+}
+.placeholder {
+  margin-bottom: 20px;
+}
+.placeholder img {
+  display: inline-block;
+  border-radius: 50%;
+}

lcdb/templates/base.html

@@ -0,0 +1,40 @@
+<!DOCTYPE html>
+<html lang="en">
+    <head>
+        <meta charset="utf-8">
+        <meta http-equiv="X-UA-Compatible" content="IE=edge">
+        <meta name="viewport" content="width=device-width, initial-scale=1">
+        <!-- The above 3 meta tags *must* come first in the head; any other head content must come *after* these tags -->
+        <title>{% block title %}{% endblock %}</title>
+
+        <!-- Bootstrap -->
+        <link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet">
+        <link href="static/css/dashboard.css" rel="stylesheet">
+
+        <!-- Bokeh CSS -->
+        <link rel="stylesheet" href="static/css/bokeh-0.11.1.min.css" type="text/css" />
+
+        <!-- jQuery (necessary for Bootstrap's JavaScript plugins) -->
+        <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.11.3/jquery.min.js"></script>
+        <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.jst">
+        <script src="static/js/bokeh-0.11.1.min.js"></script>
+
+        <!-- Bokeh Scripts go here -->
+        {% block bokeh %}{% endblock %}
+
+    </head>
+    <body>
+        {%block navbar %}{% endblock %}
+        <div class="container-fluid">
+            <div id="content">
+                {% block content %}{% endblock %}
+                {{ content }}
+            </div>
+            <div id="footer">
+                {% block footer %}
+                &copy; Copyright 2016 by LCDB
+                {% endblock %}
+            </div>
+        </div>
+    </body>
+</html>

lcdb/templates/panel.html

@@ -0,0 +1,10 @@
+<div class="row">
+    <div class="legend">{{ caption }}</div>
+{% for image in images %}
+        <div class="col-sm-3 thumbnail figure">
+            <div class="legend">{{ image.name }}</div>
+            <a href="{{ image.image }}"><img src="{{ image.image }}" /></a>
+            <div class="legend">{{ image.caption }}</div>
+        </div>
+{% endfor %}
+</div>