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update bcs and others
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@danielecook
danielecook committed Feb 26, 2016
1 parent 116c72a commit aa4146c
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Showing 9 changed files with 109 additions and 99 deletions.
34 changes: 16 additions & 18 deletions cendr/cegwas.py
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Original file line number Diff line number Diff line change
@@ -1,17 +1,20 @@
from cendr import app
from models import trait, report
from flask import render_template
from flask import render_template, request, Markup, url_for
import markdown
from datetime import datetime
import os
from collections import OrderedDict
import dateutil
from werkzeug.contrib.atom import AtomFeed
from urlparse import urljoin

def make_external(url):
return urljoin(request.url_root, url)


def render_markdown(filename, directory="static/content/markdown/"):
with open(directory + filename) as f:
def render_markdown(filename, directory="cendr/static/content/markdown/"):
with open(directory + filename + ".md") as f:
return Markup(markdown.markdown(f.read()))


Expand All @@ -26,8 +29,7 @@ def format_datetime(value):
@app.route('/')
def main():
page_title = "Caenorhabditis elegans Natural Diversity Resource"
files = [x for x in os.listdir(
"cendr/static/content/news/") if x.startswith(".") is False]
files = [x for x in os.listdir("cendr/static/content/news/") if x.startswith(".") is False]
files.reverse()
# latest mappings
latest_mappings = list(report.filter(report.release == 0).join(trait).order_by(
Expand All @@ -36,34 +38,30 @@ def main():


@app.route("/news/")
def news():
title = "Andersen Lab News"
files = os.listdir("static/content/news/")
files.reverse()
bcs = OrderedDict([("News", "")])
return render_template('news.html', **locals())


@app.route("/news/<filename>/")
def news_item(filename):
def news_item(filename = ""):
files = os.listdir("cendr/static/content/news/")
files.reverse()
if not filename:
filename = files[0].strip(".md")
title = filename[11:].strip(".md").replace("-", " ")
bcs = OrderedDict([("news", None), (title, None)])
return render_template('news_item.html', **locals())


@app.route('/feed.atom')
def feed():
feed = AtomFeed('CNDR News',
feed_url=request.url, url=request.url_root)
files = os.listdir("static/content/news/")
files = os.listdir("cendr/static/content/news/")
files.reverse()
for filename in files:
filename[11:]
title = filename[11:].strip(".md").replace("-", " ")
content = render_markdown(filename, "static/content/news/")
content = render_markdown(filename.strip(".md"), "cendr/static/content/news/")
date_published = datetime.strptime(filename[:10], "%Y-%m-%d")
feed.add(title, unicode(content),
content_type='html',
author="CNDR News",
author="CeNDR News",
url=make_external(
url_for("news_item", filename=filename.strip(".md"))),
updated=date_published,
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71 changes: 32 additions & 39 deletions cendr/templates/_includes/footer.html
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Expand Up @@ -3,46 +3,39 @@
<br />
<br />
<footer>
<div class="row">
<div class="col-md-12">


<div class="panel panel-default">
<div class="panel-body text-center">


</div>





</div>



</div>
</div>
<div class="row">

<div class="col-sm-12">
<div class="text-center">
<a href="http://www.northwestern.edu/"><img src="/static/img/logos/NU.jpg" /></a>
<div class="row">
<div class="col-md-12">
<div class="panel panel-default">
<div class="panel-body text-center">
<a href="{{ url_for("strain_submission_page") }}" class='btn btn-xs'>Submit Strains</a>
</div>
</div>
</div>
</div>
<br /><br />
</div>

<div class="row">
<div class="col-sm-12">
<div class="text-center">
<a href="http://www.northwestern.edu/"><img src="/static/img/logos/NU.jpg" /></a>
</div>
<br />
<br />
</div>
</footer>
</div><!--Closes Container -->

</div>
<!--Closes Container -->
<script>
(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
})(window,document,'script','//www.google-analytics.com/analytics.js','ga');

ga('create', 'UA-24677584-4', 'auto');
ga('send', 'pageview');

(function(i, s, o, g, r, a, m) {
i['GoogleAnalyticsObject'] = r;
i[r] = i[r] || function() {
(i[r].q = i[r].q || []).push(arguments)
}, i[r].l = 1 * new Date();
a = s.createElement(o),
m = s.getElementsByTagName(o)[0];
a.async = 1;
a.src = g;
m.parentNode.insertBefore(a, m)
})(window, document, 'script', '//www.google-analytics.com/analytics.js', 'ga');

ga('create', 'UA-24677584-4', 'auto');
ga('send', 'pageview');
</script>

11 changes: 10 additions & 1 deletion cendr/templates/data.html
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Expand Up @@ -74,7 +74,16 @@ <h4>Variant Data</h4>
{% for isotype, strains in strain_listing|groupby('isotype') %}
<tr>
<td><a href="{{ url_for('isotype_page', isotype_name=isotype) }}">{{ isotype }}</a></td>
<td>{{ strains|join(" ") }}</td>
<td>{% for s in strains %}
{% if s.sequenced == 1 %}
<strong>
{{ s }}
</strong>
{% else %}
{{ s }}
{% endif %}
{% endfor %}
</td>
<td>
{% if strains[0].bam_file %}
<a href="{{ strains[0].bam_file }}">{{ isotype }}.bam</a>
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4 changes: 2 additions & 2 deletions cendr/templates/home.html
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Expand Up @@ -24,7 +24,7 @@
</div>
</div>
</div>

</div>
<div class="row">
<div class="col-md-4 col-sm-4">
<div class="thumbnail img-responsive" style="border: 1px solid black; padding: 0; border-radius: 5px; min-height: 425px" >
Expand Down Expand Up @@ -78,7 +78,7 @@
<div>
<h4>News &amp; Updates <a href = "{{ url_for('feed') }}" type="button" style="background-color: #FFA500; border: 1px solid black; color: black;" class="btn btn-primary btn-xs">RSS</a>

<a href = "{{ url_for('news') }}" type="button" class="btn btn-primary btn-xs">Archive</a>
<a href = "{{ url_for('news_item') }}" type="button" class="btn btn-primary btn-xs">Archive</a>
</h4>
{% for f in files %}

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22 changes: 0 additions & 22 deletions cendr/templates/news.html
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This file was deleted.

21 changes: 16 additions & 5 deletions cendr/templates/news_item.html
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Expand Up @@ -3,10 +3,21 @@

{% block content %}
<div class="row">
<div class="col-md-12">
<h4>News &amp; Updates</h4>
{{ filename }}
{{ render_markdown(filename + ".md", directory = "static/content/news/") }}
<div class="col-md-8">
{{ render_markdown(filename + ".md", directory = "cendr/static/content/news/") }}
</div>
<div class = 'col-md-4'>

</div>
<ul class="list-group">
{% for f in files %}
<a class="list-group-item {% if f.strip(".md") == filename %}active{% endif %}" href="{{ url_for('news_item', filename = f.strip('.md')) }}">
<small class="pull-right">{{ f[:10] }}</small><strong>{{ f[11:].strip(".md").replace("-", " ") }}</strong>
</a>

</li>

{% endfor %}
</ul>

</div>
{% endblock %}
17 changes: 16 additions & 1 deletion cendr/templates/statistics.html
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Expand Up @@ -25,7 +25,22 @@
{% block content %}
<div class="row">
<div class="col-md-6">


<div class="panel panel-default">
<div class="panel-heading">
<h3 class="panel-title">Summary</h3>
</div>

<ul class='list-group'>
<li class='list-group-item'><strong>Reports Submitted</strong> <div class='pull-right'>{{ n_reports }}</div></li>
<li class='list-group-item'><strong>Traits Submitted</strong><div class='pull-right'>{{ n_traits }}</div></li>
<li class='list-group-item'><strong>Significant Mappings</strong><div class='pull-right'>{{ n_significant_mappings}}</div></li>
<li class='list-group-item'><strong>Strains</strong><div class='pull-right'>{{ n_distinct_strains }}</div></li>
<li class='list-group-item'><strong>Isotypes</strong><div class='pull-right'>{{ n_distinct_isotypes }}</div></li>
</ul>

</div>

</div>
<div class="col-md-6" style="text-align: center;">
<div class="timeline_strain_growth" style="height:250px;"></div>
Expand Down
20 changes: 13 additions & 7 deletions cendr/views/about_us.py
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Original file line number Diff line number Diff line change
@@ -1,9 +1,8 @@
from cendr import app
from flask import render_template
from flask import Markup
from flask import render_template, url_for, Markup
import markdown
import yaml
from cendr.models import strain, report
from cendr.models import strain, report, mapping, trait
from collections import OrderedDict

@app.context_processor
Expand All @@ -18,15 +17,15 @@ def render_markdown(filename, directory="cendr/static/content/markdown/"):
def about():
# About us Page - directs to other pages.
title = "About"
bcs = OrderedDict([("about", "/about/")])
bcs = OrderedDict([("about", None)])
return render_template('about.html', **locals())


@app.route('/about/panel/')
def panel():
# Scientific Panel Page
title = "Scientific Advisory Panel"
bcs = OrderedDict([("about", "/about/"), ("panel", "")])
bcs = OrderedDict([("about", url_for("about")), ("panel", "")])
panel_data = yaml.load(open("cendr/static/content/data/advisory-panel.yaml", 'r'))
return render_template('panel.html', **locals())

Expand All @@ -35,15 +34,22 @@ def panel():
def staff():
# Staff Page
title = "Staff"
bcs = OrderedDict([("about", "/about/"), ("staff", "")])
bcs = OrderedDict([("about", url_for("about") ), ("staff", "")])
staff_data = yaml.load(open("cendr/static/content/data/staff.yaml", 'r'))
return render_template('staff.html', **locals())


@app.route('/about/statistics/')
def statistics():
title = "Site Statistics"
bcs = OrderedDict([("about", "/about/"), ("statistics", None)])
bcs = OrderedDict([("about", url_for("about")), ("statistics", None)])

# Number of reports
n_reports = report.select().count()
n_traits = trait.select().count()
n_significant_mappings = mapping.select().count()
n_distinct_strains = strain.select(strain.strain).distinct().count()
n_distinct_isotypes = strain.select(strain.isotype).filter(strain.isotype != None).distinct().count()

# Collection dates
collection_dates = list(strain.select().filter(
Expand Down
8 changes: 4 additions & 4 deletions cendr/views/strains.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
from cendr import app
from cendr import json_serial
from flask import render_template, request
from flask import render_template, request, url_for
from cendr.models import strain
from collections import OrderedDict
import json
Expand All @@ -21,7 +21,7 @@
@app.route('/strain/global-strain-map/')
def map_page():
title = "Global Strain Map"
bcs = OrderedDict([("strain", "/strain/"), ("global-strain-map", None)])
bcs = OrderedDict([("strain", url_for("strain_listing_page")), ("global-strain-map", "")])
strain_list_dicts = []
strain_listing = list(strain.select().filter(strain.isotype.is_null() == False).filter(
strain.latitude.is_null() == False).execute())
Expand Down Expand Up @@ -60,7 +60,7 @@ def strain_listing_page():

@app.route('/strain/submit/')
def strain_submission_page():
bcs = OrderedDict([("strain", "submission")])
bcs = OrderedDict([("strain", url_for("strain_listing_page")), ("Strain Submission", "")])
title = "Strain Submission"
return render_template('strain_submission.html', **locals())

Expand All @@ -72,7 +72,7 @@ def strain_submission_page():
@app.route("/strain/protocols/")
def protocols():
title = "Protocols"
bcs = OrderedDict([("strain", "/strain/"), ("protocols", "")])
bcs = OrderedDict([("strain", url_for("strain_listing_page")), ("protocols", "")])
protocols = yaml.load(open("cendr/static/content/data/protocols.yaml", 'r'))
return render_template('protocols.html', **locals())

Expand Down

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