Initial experimental time series.

Goutte
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Showing 6 changed files with 463 additions and 0 deletions Show diff stats
CHANGELOG.md
config.yml
res/dummy.nc
web/run.py
web/view/home.html.jinja2
web/view/layout.html.jinja2
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+## 0.0.0
+
+- Initial website skeleton
+- Initial data bridge between netCDF and CSV
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+# WARNING : IF YOU BREAK THIS FILE YOU'LL BREAK THE WEBSITE. Tread carefully.
+# Remember, you can test the website locally, see the README.
+
+
+# The HTML metadata in the page header.
+# Don't put double quotes (") in any of these fields.
+meta:
+    title: Space Weather
+    keywords:
+        - science
+        - cdpp
+        - europlanet
+        - space
+        - weather
+    # Will be shown by search engines below the title of the page.
+    description: Space weather predictions around solar celestial bodies.
+
+
+# A list of authors that will appear in the HTML metadata and possibly in the
+# authorship page as well. The order does not matter, it will be shuffled.
+authors:
+    - name: Antoine Goutenoir
+      role: Software Ninja
+      mail: antoine.goutenoir@irap.omp.eu
+    - name: Myriam Bouchemit
+      role: Server Maintenance
+      mail: myriam.bouchemit@irap.omp.eu
+    - name: Mikel Indurain
+      role: Simulation Software
+      mail: mindurain@irap.omp.eu
+    - name: Nicolas André
+      role: Project Lead
+      mail: nicolas.andre@irap.omp.eu
+    - name: Vincent Genot
+      role: Project Coordinator
+      mail: vincent.genot@irap.omp.eu
+
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+import random
+import datetime
+import StringIO
+
+from os import listdir, environ
+from os.path import isfile, join, abspath, dirname
+
+import csv
+from pprint import pprint
+from csv import writer as csv_writer
+from yaml import load as yaml_load
+from flask import Flask
+from flask import redirect, url_for, send_from_directory
+from flask import request
+from jinja2 import Environment, FileSystemLoader
+from netCDF4 import Dataset
+
+# from model.Config import Config
+# from model.News import NewsCollection, News
+
+
+# PATH RELATIVITY #############################################################
+
+THIS_DIRECTORY = dirname(abspath(__file__))
+
+
+def get_path(relative_path):
+    return abspath(join(THIS_DIRECTORY, relative_path))
+
+
+# COLLECT GLOBAL INFORMATION FROM SOURCES #####################################
+
+# VERSION
+with open(get_path('../VERSION'), 'r') as version_file:
+    version = version_file.read().strip()
+
+# CONFIG
+with open(get_path('../config.yml'), 'r') as config_file:
+    config = yaml_load(config_file.read())
+
+
+# SETUP FLASK ENGINE ##########################################################
+
+app = Flask(__name__, root_path=THIS_DIRECTORY)
+app.debug = environ.get('DEBUG') == 'true'
+
+
+# SETUP JINJA2 TEMPLATE ENGINE ################################################
+
+def static_global(filename):
+    return url_for('static', filename=filename)
+
+
+def shuffle_filter(seq):
+    """
+    This shuffles the sequence it is applied to.
+    'tis a failure of jinja2 to not provide a shuffle filter by default.
+    """
+    try:
+        result = list(seq)
+        random.shuffle(result)
+        return result
+    except:
+        return seq
+
+
+def markdown_filter(value, nl2br=False, p=True):
+    """
+    nl2br: set to True to replace line breaks with <br> tags
+    p: set to False to remove the enclosing <p></p> tags
+    """
+    from markdown import markdown
+    from markdown.extensions.nl2br import Nl2BrExtension
+    from markdown.extensions.abbr import AbbrExtension
+    extensions = [AbbrExtension()]
+    if nl2br is True:
+        extensions.append(Nl2BrExtension())
+    markdowned = markdown(value, output_format='html5', extensions=extensions)
+    if p is False:
+        markdowned = markdowned.replace(r"<p>", "").replace(r"</p>", "")
+    return markdowned
+
+
+tpl_engine = Environment(loader=FileSystemLoader([get_path('view')]),
+                         trim_blocks=True,
+                         lstrip_blocks=True)
+
+tpl_engine.globals.update(
+    url_for=url_for,
+    static=static_global,
+)
+
+tpl_engine.filters['markdown'] = markdown_filter
+tpl_engine.filters['md'] = markdown_filter
+tpl_engine.filters['shuffle'] = shuffle_filter
+
+tpl_global_vars = {
+    'request': request,
+    'version': version,
+    'config': config,
+    'now': datetime.datetime.now(),
+}
+
+
+# HELPERS #####################################################################
+
+def render_view(view, context=None):
+    """
+    A simple helper to render [view] template with [context] vars.
+    It automatically adds the global template vars defined above, too.
+    It returns a string, usually the HTML contents to display.
+    """
+    context = {} if context is None else context
+    return tpl_engine.get_template(view).render(
+        dict(tpl_global_vars.items() + context.items())
+    )
+
+
+# def render_page(page, title="My Page", context=None):
+#     """
+#     A simple helper to render the md_page.html template with [context] vars &
+#     the additional contents of `page/[page].md` in the `md_page` variable.
+#     It automagically adds the global template vars defined above, too.
+#     It returns a string, usually the HTML contents to display.
+#     """
+#     if context is None:
+#         context = {}
+#     context['title'] = title
+#     context['md_page'] = ''
+#     with file(get_path('page/%s.md' % page)) as f:
+#         context['md_page'] = f.read()
+#     return tpl_engine.get_template('md_page.html').render(
+#         dict(tpl_global_vars.items() + context.items())
+#     )
+
+
+# ROUTING #####################################################################
+
+@app.route("/")
+@app.route("/home.html")
+@app.route("/index.html")
+def home():
+    return render_view('home.html.jinja2', {})
+
+
+@app.route("/inspect")
+def analyze_cdf():
+    cdf_to_inspect = get_path("../res/dummy.nc")
+
+    si = StringIO.StringIO()
+    cw = csv.DictWriter(si, fieldnames=['Name', 'Shape', 'Length'])
+    cw.writeheader()
+
+    # Time, StartTime, StopTime, V, B, N, T, Delta_angle, P_dyn, QualityFlag
+    cdf_handle = Dataset(cdf_to_inspect, "r", format="NETCDF4")
+    for variable in cdf_handle.variables:
+        v = cdf_handle.variables[variable]
+        cw.writerow({
+            'Name': variable,
+            'Shape': v.shape,
+            'Length': v.size,
+        })
+    cdf_handle.close()
+
+    return si.getvalue()
+
+
+@app.route("/test.csv")
+def get_csv():
+    si = StringIO.StringIO()
+    cw = csv_writer(si)
+
+    # Time, StartTime, StopTime, V, B, N, T, Delta_angle, P_dyn, QualityFlag
+    cdf_handle = Dataset(get_path("../res/dummy.nc"), "r", format="NETCDF4")
+    # YYYY DOY HH MM SS .ms
+    times = cdf_handle.variables['Time']
+    data_v = cdf_handle.variables['V']
+    data_b = cdf_handle.variables['B']
+    data_p = cdf_handle.variables['P_dyn']
+    cw.writerow(('time', 'vrad', 'vtan', 'magn', 'pdyn'))
+    for time, datum_v, datum_b, datum_p in zip(times, data_v, data_b, data_p):
+        # Day Of Year starts at 0, but for our datetime parser it starts at 1
+        doy = '{:03d}'.format(int(''.join(time[4:7])) + 1)
+        d = datetime.datetime.strptime(
+            "%s%s%s" % (''.join(time[0:4]), doy, ''.join(time[7:])),
+            "%Y%j%H%M%S%f"
+        )
+        cw.writerow((
+            d.strftime("%Y-%m-%dT%H:%M:%S+00:00"),
+            datum_v[0], datum_v[1],
+            datum_b, datum_p
+        ))
+    cdf_handle.close()
+
+    return si.getvalue()
+
+# MAIN ########################################################################
+
+if __name__ == "__main__":
+    # Debug mode on, as the production server does not use this.
+    extra_files = [get_path('../config.yml')]
+    app.run(debug=True, extra_files=extra_files)
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+{% extends 'layout.html.jinja2' %}
+{% set menu_section = 'home' %}
+{% block title %}Home{% endblock %}
+
+{% block content %}
+
+<h2>Overview</h2>
+
+
+
+<p>
+TODO
+</p>
+
+<section id="time_series"></section>
+
+{% endblock %}
+
+
+{% block styles %}
+  <style>
+    path.line {
+      fill: none;
+      stroke: steelblue;
+      stroke-width: 1px;
+    }
+  </style>
+{% endblock %}
+
+
+{% block scripts_footer %}
+<script type="application/javascript" src="{{ static('js/d3.min.js') }}"></script>
+<script type="application/javascript">
+
+var swApp = (function (window, d3, $) {
+
+  var $time_series = $("#time_series");
+
+  // fixme
+  var plotTimeSeries = function(data, options) {
+    console.log("Init time series with data", data, options);
+
+    var xScale, yScale, xAxis, yAxis;
+    var line;
+    var svg, plotWrapper, path;
+    var width, height;
+    var margin = {
+      top: 30,
+      right: 20,
+      bottom: 30,
+      left: 60
+    };
+
+    // INIT SCALES
+    xScale = d3.scaleTime().domain(d3.extent(data, function (d) {
+      return d.x;
+    }));
+    yScale = d3.scaleLinear().domain(d3.extent(data, function (d) {
+      return d.y;
+    }));
+
+    // INIT AXISES
+    xAxis = d3.axisBottom()
+        .ticks(7, ",f")
+        .tickFormat(d3.timeFormat("%Y-%m-%d"));
+    yAxis = d3.axisLeft()
+        .ticks(15);
+
+    // INIT LINE
+    line = d3.line()
+        .x(function (d) { return xScale(d.x) })
+        .y(function (d) { return yScale(d.y) });
+
+    // INIT SVG
+    svg = d3.select('#time_series').append('svg');
+
+    plotWrapper = svg.append('g');
+
+    path = plotWrapper.append('path')
+        .datum(data)
+        .classed('line', true);
+
+    plotWrapper.append('g')
+        .classed('x axis', true);
+    plotWrapper.append('g')
+        .classed('y axis', true);
+
+    width = $time_series.width() - margin.left - margin.right;
+    height = .618 * width;
+
+    xScale.range([0, width]);
+    yScale.range([height, 0]);
+
+    svg.attr('width', width + margin.right + margin.left)
+        .attr('height', height + margin.top + margin.bottom);
+
+    plotWrapper.attr('transform', 'translate(' + margin.left + ',' + margin.top + ')');
+
+    path.attr('d', line);
+
+    xAxis.scale(xScale);
+    yAxis.scale(yScale);
+
+    // if (window.innerWidth < 800) { xAxis.ticks(3); }
+
+    svg.select('.x.axis')
+        .attr('transform', 'translate(0,' + height + ')')
+        .call(xAxis);
+
+    svg.select('.y.axis')
+        .call(yAxis);
+
+
+  };
+
+  return {
+    plotTimeSeries: plotTimeSeries
+  };
+})(window, d3, jQuery);
+
+
+jQuery().ready(function($){
+  d3.csv("{{ url_for('get_csv') }}", function(csv){
+    var timeFormat = d3.timeParse('%Y-%m-%dT%H:%M:%S%Z');
+    var data = {'pdyn': [], 'magn': []};
+    csv.forEach(function (d) {
+      data['pdyn'].push({x: timeFormat(d['time']), y: parseFloat(d['pdyn'])});
+      data['magn'].push({x: timeFormat(d['time']), y: parseFloat(d['magn'])});
+    });
+    swApp.plotTimeSeries(data['pdyn'], {});
+    swApp.plotTimeSeries(data['magn'], {});
+  });
+});
+</script>
+
+{% endblock %}
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+<!DOCTYPE HTML>
+<html>
+  <head>
+    <meta charset="utf-8">
+
+    <title>{% block title %}Welcome{% endblock %} &mdash; {{ config.meta.title }}</title>
+
+    <meta name="description" content="{{ config.meta.description }}">
+    <meta name="keywords"    content="{{ config.meta.keywords | join(', ') }}">
+{% for author in config.authors | shuffle %}
+    <meta name="author"      content="{{ author.name }} <{{ author.mail }}>">
+{% endfor %}
+
+    <meta name="viewport" content="width=device-width, initial-scale=1">
+
+    <link rel="shortcut icon" href="{{ static('img/favicon.ico') }}">
+
+    <link rel="stylesheet" type="text/css" href="{{ static('css/main.css') }}">
+{% block styles %}{% endblock %}
+
+{#    <script type="text/javascript">#}
+{#      // Good javascript is no javascript -- hurray! \o/#}
+{#    </script>#}
+{% block scripts_header %}{% endblock %}
+  </head>
+
+  <body>
+
+    <div id="page-container" class="container">
+
+      <header>
+        <div class="header">
+          <img class="logo" src="{{ static('img/logo/logo_cnrs.png') }}" alt="CNRS" id="logo-cnrs" />
+          <h1 class="hidden">Space Weather <small>v{{ version }}</small></h1>
+          <span id="version-number">v{{ version }}</span>
+        </div>
+      </header>
+
+      <div class="">
+
+        <nav id="menu" role="navigation">
+          <ul>
+            <li class="home{% if menu_section == 'home' %} active{% endif %}">
+              <a href="index.html"></a>
+            </li>
+            <li{% if menu_section == 'authors' %} class="active"{% endif %}>
+              <a href="authors.html">Authors</a>
+            </li>
+          </ul>
+        </nav>
+
+        <div id="content">
+{% block content %}
+          <p>Please override the "content" block in the page template.</p>
+{% endblock %}
+        </div>
+
+      </div>
+
+      <footer>
+        <a href="http://www.irap.omp.eu/">IRAP</a> OMP &copy 2017
+      </footer>
+    </div>
+
+    <script type="application/javascript">
+      // fixme: GOOGLE ANALYTICS
+      /*
+      (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-56037907-1', 'auto');
+      ga('send', 'pageview');
+      */
+    </script>
+
+    <script type="application/javascript" src="{{ static('js/jquery.min.js') }}"></script>
+    <script type="application/javascript">
+      jQuery().ready(function($){ $(".nojs").hide(); });
+    </script>
+{% block scripts_footer %}{% endblock %}
+
+  </body>
+</html>
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