fixing a mess

geomagio/imfjson/IMFJSONWriter.py

@@ -48,7 +48,7 @@ class IMFJSONWriter(object):
         formatted_timeseries = json.dumps(
             file_dict, ensure_ascii=True, separators=(",", ":")
         ).encode("utf8")
-        out.write(str(formatted_timeseries))
+        out.write(formatted_timeseries)
 
     def _format_data(self, timeseries, channels, stats):
         """Format all data lines.

geomagio/webservice/app.py

@@ -3,6 +3,7 @@ from __future__ import absolute_import, unicode_literals
 import os
 import flask
 
+from . import data
 from . import database
 from . import login
 from . import session
@@ -17,6 +18,7 @@ def create_app():
     database.init_app(app)
     login.init_app(app)
     session.init_app(app)
+    data.init_app(app)
 
     # add default route
     @app.route("/")

geomagio/webservice/data.py

+from datetime import datetime
+from flask import Blueprint, Flask, jsonify, render_template, request, Response
+from obspy import UTCDateTime
+
+from geomagio.edge import EdgeFactory
+from geomagio.iaga2002 import IAGA2002Writer
+from geomagio.imfjson import IMFJSONWriter
+
+blueprint = Blueprint('data', __name__)
+
+
+def init_app(app: Flask):
+    global blueprint
+
+    app.register_blueprint(blueprint)
+
+
+@blueprint.route('/data', methods=['GET'])
+def get_data():
+    query_params = request.args
+
+    url = request.url
+
+    if not query_params:
+
+        return render_template('usage.html')
+
+    query = parse_query(query_params)
+
+    timeseries = get_timeseries(query)
+
+    return format_timeseries(timeseries, query)
+
+
+def parse_query(query):
+    """Parse request arguments into a set of parameters
+
+    Parameters
+    ----------
+    query: Immutable Dict
+        request.args object
+
+    Returns
+    -------
+    params: dictionary
+        query parameters dictionary
+
+    Raises
+    ------
+    WebServiceException
+        if any parameters are not supported.
+    """
+    params = {}
+
+    # Get end time
+    if not query.get('endtime'):
+        now = datetime.now()
+        today = UTCDateTime(
+                    now.year,
+                    now.month,
+                    now.day,
+                    0)
+        end_time = today
+        params['End Time'] = end_time
+    else:
+        params['End Time'] = UTCDateTime(query.get('endtime'))
+
+    # Get start time
+    if not query.get('starttime'):
+        start_time = UTCDateTime(params['End Time']) - (24 * 60 * 60 - 1)
+        params['Start Time'] = UTCDateTime(start_time)
+    else:
+        params['Start Time'] = UTCDateTime(query.get('starttime'))
+
+    # Get sampling period
+    params['Sampling Period'] = query.get('sampling_period')
+
+    if params['Sampling Period'] == '1':
+        params['Sampling Period'] = 'second'
+
+    if params['Sampling Period'] == '60':
+        params['Sampling Period'] = 'minute'
+
+    # Get format
+    if query.get('format'):
+        params['Format'] = query.get('format')
+    else:
+        params['Format'] = 'iaga2002'
+
+    # Get observatory
+    params['Observatory'] = query.get('observatory')
+
+    # Get channels
+    channels = query.get('channels').split(',')
+    params['Channels'] = channels
+
+    # Get data type
+    params['Type'] = query.get('type')
+
+    validate_parameters(params)
+
+    return params
+
+
+def validate_parameters(params):
+    """Verify that parameters are valid.
+
+    Parameters
+    ----------
+    params: dict
+        dictionary of parsed query parameters
+
+    Raises
+    ------
+    WebServiceException
+        if any parameters are not supported.
+    """
+    valid_data_types = ['variation', 'adjusted',
+        'quasi-definitive', 'definitive']
+    valid_formats = ['iaga2002', 'json']
+    valid_sampling_periods = ['second', 'minute']
+
+    if len(params['Channels']) > 4 and params['Format'] == 'iaga2002':
+        raise WebServiceException(
+            'No more than four elements allowed for Iaga2002 format.')
+
+    if params['Start Time'] > params['End Time']:
+        raise WebServiceException('Start time must be before end time.')
+
+    if params['Type'] not in valid_data_types:
+        raise WebServiceException('Bad data type: ' + params['Type'] +
+        '. Valid values are: ' + ', '.join(valid_data_types) + '.')
+
+    if params['Sampling Period'] not in valid_sampling_periods:
+        raise WebServiceException('Bad sampling_period value: ' + params['Sampling Period'] +
+        '. Valid values are: 1, 60.')
+
+    if params['Format'] not in valid_formats:
+        raise WebServiceException('Bad format value: ' + params['Format'] +
+        '. Valid values are: ' + ', '.join(valid_formats))
+
+
+def get_timeseries(query):
+    """
+    Parameters
+    ----------
+    query: dict
+        dictionary of parsed query parameters
+
+    Returns
+    -------
+    obspy.core.Stream
+        timeseries object with requested data
+    """
+    factory = EdgeFactory()
+
+    timeseries = factory.get_timeseries(
+            query['Start Time'], query['End Time'], query['Observatory'], query['Channels'],
+            query['Type'], query['Sampling Period'])
+
+    return timeseries
+
+
+def format_timeseries(timeseries, query):
+    """Formats timeseries into JSON or IAGA data
+
+    Parameters
+    ----------
+    obspy.core.Stream
+        timeseries object with requested data
+
+    query: dict
+        dictionary of parsed query parameters
+
+    Returns
+    -------
+    unicode
+        IAGA2002 or JSON formatted string.
+    """
+    if query['Format'] == 'json':
+        json_output = IMFJSONWriter.format(timeseries, query['Channels'])
+
+        return json_output
+
+    else:
+        iaga_output = IAGA2002Writer.format(timeseries, query['Channels'])
+
+        iaga_output = Response(iaga_output, mimetype="text / plain")
+
+        return iaga_output
+
+
+class WebServiceException(Exception):
+    """Base class for exceptions thrown by web services."""
+    pass

geomagio/webservice/metadata.py

@@ -41,8 +41,13 @@ class Metadata(db.Model):
         comment = 'automatic adjusted matrix',
         priority = 1,
         value = {
+<<<<<<< HEAD
+            'parameters' => {'x': 1, 'y': 2, 'z': 3}
+            'matrix' => [ ... ]
+=======
             'parameters': {'x': 1, 'y': 2, 'z': 3}
             'matrix': [ ... ]
+>>>>>>> master
         }
     )
     ```

geomagio/webservice/static/usage.css

+p {
+  font-weight: bold;
+}
+
+/* Import your custom theme */
+.hazdev-site-header {
+  background-color: #1b3c43;
+  height: 100px;
+  position: relative;
+}
+/* position usgs logo over background. */
+.hazdev-site-header > .hazdev-site-logo {
+  /* bottom padding of 0 + overflow: hidden + image height 140% = hide "science for a changing world" on small screens. */
+  display: block;
+  height: 30px;
+  left: 0;
+  overflow: hidden;
+  padding: 14px 14px 0;
+  position: absolute;
+  top: 0;
+}
+.hazdev-site-header > .hazdev-site-logo > img {
+  height: 140%;
+  border: none;
+}
+hazdev-template-cooperator {
+  display: none;
+  height: 100%;
+  left: 136px;
+  overflow: hidden;
+  padding-left: 1em;
+  position: absolute;
+}
+/* visually hide navigation jumplink. */
+.hazdev-jumplink-navigation {
+  display: block;
+  left: -9999px;
+  position: absolute;
+  top: 0;
+}
+@media screen and (min-width: 768px) {
+  /* make banner larger on large screens. */
+  /* also adjust size of usgs logo */
+  /*width: 157px;
+	*/
+  .hazdev-site-header {
+    background-color: #1b3c43;
+    background-position: 186px 0;
+    background-repeat: no-repeat;
+    background-size: auto 100%;
+    height: 90px;
+    /* 1.5 line-height on 1em text, with 0.25em padding top/bottom */
+    margin-bottom: 1em;
+  }
+  .hazdev-site-header > .hazdev-site-logo {
+    height: 100%;
+    padding: 0;
+  }
+  .hazdev-site-header > .hazdev-site-logo > img {
+    height: 100%;
+    padding: 1em;
+  }
+  hazdev-template-cooperator {
+    background-image: none;
+    display: block;
+    left: 186px;
+    padding-left: 0;
+  }
+}
+@media print {
+  /** Only show USGS logo when printing, requires background colors... */
+  [role='banner'] {
+    background-color: #fff;
+    height: 0;
+    margin: 0;
+    padding: 0;
+    visibility: hidden;
+    width: 100%;
+  }
+  [role='banner']:after {
+    color: #333;
+    content: 'U.S. Geological Survey - National Geomagnetism Program';
+    display: block;
+    visibility: visible;
+  }
+  [role='main'] {
+    padding: 1em 0 0 !important;
+  }
+}
+
+.site-commonnav {
+  display: block;
+  font-size: 0.88em;
+  margin: 4em 0 0;
+  padding: 2em 1em;
+  position: relative;
+}
+.site-commonnav > .hazdev-site-logo {
+  display: block;
+  height: 56px;
+  margin-bottom: 2em;
+  width: 152px;
+}
+.site-commonnav > .hazdev-site-logo > img {
+  height: 100%;
+  border: none;
+}
+.interior-nav,
+.common-nav,
+.social-nav,
+.space-between {
+  margin: 1em 0 0;
+}
+.interior-nav > a,
+.common-nav > a,
+.social-nav > a,
+.space-between > a {
+  color: #fff;
+  display: inline-block;
+  margin: 0.5em 1em 0.5em 0;
+}
+.interior-nav > a:hover,
+.common-nav > a:hover,
+.social-nav > a:hover,
+.space-between > a:hover,
+.interior-nav > a:visited,
+.common-nav > a:visited,
+.social-nav > a:visited,
+.space-between > a:visited,
+.interior-nav > a:active,
+.common-nav > a:active,
+.social-nav > a:active,
+.space-between > a:active {
+  color: #fff;
+}
+@media print {
+  .site-commonnav {
+    display: none;
+  }
+}
+.space-between {
+  border-top: 1px solid #eee;
+}
+@media screen and (min-width: 1000px) {
+  .space-between {
+    display: flex;
+    justify-content: space-between;
+  }
+}

geomagio/webservice/static/usgs-logo.svg

+<?xml version="1.0" encoding="utf-8"?>
+<!-- Generator: Adobe Illustrator 16.0.0, SVG Export Plug-In . SVG Version: 6.00 Build 0)  -->
+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
+<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
+	 width="2353.326px" height="869.157px" viewBox="40.233 28.698 2353.326 869.157"
+	 enable-background="new 40.233 28.698 2353.326 869.157" xml:space="preserve">
+<g>
+	<g>
+		<path fill="#FFFFFF" d="M1135.755,38.678v425.73c0,89.8-50.726,184.595-203.721,184.595c-138.031,0-204.552-71.51-204.552-184.595
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+		<path fill="#FFFFFF" d="M1339.936,649.003c-155.496,0-184.599-91.467-177.949-195.406h125.556
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+	<g>
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+	</g>
+	<path fill="#FFFFFF" d="M203.474,239.716l2.103,2.02c58.821,49.265,122.312,44.486,170.67,12.332
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+		L278.565,332.388z"/>
+	<path fill="#FFFFFF" d="M622.658,396.804c-22.844,15.398-46.074,31.052-55.317,37.243c-20.657,13.84-68.479,48.14-148.067,10.101
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+</g>
+</svg>

geomagio/webservice/templates/_template.html

@@ -10,8 +10,8 @@
   </head>
   <body>
     <nav>
-      {% if current_user.is_authenticated %}
-      Logged in as {{ current_user.email }}
+      {% if current_user.is_authenticated %} Logged in as {{ current_user.email
+      }}
       <a href="{{ url_for('login.logout') }}">Log Out</a>
       {% else %}
       <a href="{{ url_for('login.login') }}">Log In</a>

geomagio/webservice/templates/hello.html

-{% extends '_template.html' %}
-
-{% block header %}
+{% extends '_template.html' %} {% block header %}
 <h1>{% block title %}Hello{% endblock %}</h1>
-{% endblock %}
-
-
-{% block content %}
+{% endblock %} {% block content %}
 <p>This is the page when logged in</p>
-{{ current_user.to_dict() | tojson }}
-
-{% endblock %}
+{{ current_user.to_dict() | tojson }} {% endblock %}

geomagio/webservice/templates/usage.html

+{% extends '_template.html' %} {% block header %}
+<link rel="stylesheet" type="text/css" href="{{ url_for('static', filename='usage.css') }}"/>
+
+{% endblock %} {% block content %}
+<header role="banner" class="hazdev-site-header">
+  <a
+    class="hazdev-site-logo"
+    href="https://www.usgs.gov/"
+    title="U.S. Geological Survey"
+  >
+    <img src="/static/usgs-logo.svg" alt="U.S. Geological Survey logo" />
+  </a>
+  <a class="hazdev-jumplink-navigation" href="#site-sectionnav">
+    Jump to Navigation
+  </a>
+  <ng-content></ng-content>
+</header>
+
+
+  <div class="views-field views-field-field-intro">        <div class="field-content lead pane-border"><p><strong>Example Requests</strong><br /></p><dl><dt>BOU observatory data for current UTC day in IAGA2002 format</dt>
+<dd><a href="http://geomag.usgs.gov/ws/edge/?id=BOU">http://geomag.usgs.gov/ws/edge/?id=BOU</a></dd>
+<dt>BOU observatory data for current UTC day in JSON format</dt>
+<dd><a href="http://geomag.usgs.gov/ws/edge/?id=BOU&amp;format=json">http://geomag.usgs.gov/ws/edge/?id=BOU&amp;format=json</a></dd>
+<dt>BOU electric field data for current UTC day in IAGA2002 format</dt>
+<dd><a href="http://geomag.usgs.gov/ws/edge/?id=BOU&amp;elements=E-N,E-E">http://geomag.usgs.gov/ws/edge/?id=BOU&amp;elements=E-N,E-E</a></dd>
+</dl><p><a href="/natural-hazards/geomagnetism/science/more-examples">See more examples</a></p>
+</div>  </div>
+  <div class="views-field views-field-field-science-tab-intro">        <div class="field-content"></div>  </div>
+  <div class="views-field views-field-field-science-object-body">        <div class="field-content"><div class="tex2jax"><p><strong>Request Limits</strong></p>
+<p>To ensure availability for users, the web service restricts the amount of data that can be retrieved in one request. The amount of data requested is computed as follows, where an interval is the number of seconds between start time and end time:</p>
+<p>samples = count(elements) * interval / sampling_period</p>
+<p><strong>Limits by the output format</strong></p>
+<p><strong>json</strong></p>
+<ul><li>172800 samples = 4 elements * 12 hours * 3600 samples/hour.</li>
+</ul><p><strong>iaga2002</strong></p>
+<ul><li>345600 samples = 4 elements * 24 hours * 3600 samples/hour.</li>
+<li>NOTE: while the json format supports fewer total samples per request, users may request fewer elements to retrieve longer intervals.</li>
+</ul><p><strong>Parameters</strong></p>
+<p><strong>id</strong></p>
+<ul><li>Observatory code. Required.</li>
+<li>Valid values: BDT, BOU, TST, BRW, BRT, BSL, CMO, CMT, DED, DHT, FRD, FRN, GUA, HON, NEW, SHU, SIT, SJG, TUC,  USGS, BLC, BRD, CBB, EUA, FCC, IQA, MEA, OTT, RES, SNK, STJ, VIC, YKC, HAD, HER, KAK</li>
+</ul><p><strong>starttime</strong></p>
+<ul><li>Time of first requested data.</li>
+<li>Default: start of current UTC day</li>
+<li>Format: ISO8601 (YYYY-MM-DDTHH:MM:SSZ)</li>
+<li>Example: 2018-08-06T22:10:14Z</li>
+</ul><p><strong>endtime</strong></p>
+<ul><li>Time of last requested data.</li>
+<li>Default: starttime + 24 hours</li>
+<li>Format: ISO8601 (YYYY-MM-DDTHH:MM:SSZ)</li>
+<li>Example: 2018-08-06T22:10:14Z</li>
+</ul><p><strong>elements</strong></p>
+<ul><li>Comma separated list of requested elements.</li>
+<li>Default: X,Y,Z,F</li>
+<li>Valid values: D, DIST, DST, E, E-E, E-N, F, G, H, SQ, SV, UK1, UK2, UK3, UK4, X, Y, Z</li>
+</ul><p><strong>sampling_period</strong></p>
+<ul><li>Interval in seconds between values.</li>
+<li>Default: 60</li>
+<li>Valid values: 1, 60, 3600</li>
+</ul><p><strong>type</strong></p>
+<ul><li>Type of data.</li>
+<li>Default: variation Valid values: variation, adjusted, quasi-definitive,definitive</li>
+<li>NOTE: the USGS web service also supports specific EDGE location codes. For example: R0 is "internet variation",R1 is "satellite variation".</li>
+</ul><p><strong>format</strong></p>
+<ul><li>Output format.</li>
+<li>Default: iaga2002</li>
+<li>Valid values: iaga2002, json.</li>
+</ul></div></div>  </div>
+
+
+<footer class="site-commonnav">
+  <a class="hazdev-site-logo" href="/" title="U.S. Geological Survey">
+    <img src="/static/usgs-logo.svg" alt="U.S. Geological Survey logo" />
+  </a>
+  <div class="interior-nav">
+    <a href="https://www.doi.gov/">
+      U.S. Department of the Interior
+    </a>
+    <a href="https://www.usgs.gov/">
+      U.S. Geological Survey
+    </a>
+  </div>
+  <div class="space-between">
+    <div class="common-nav">
+      <a href="https://www.doi.gov/privacy">
+        DOI Privacy Policy
+      </a>
+      <a href="https://www.usgs.gov/policies-and-notices">
+        Legal
+      </a>
+       <a href="https://www.usgs.gov/sitemap">
+        Site Map
+      </a>
+      <a href="https://answers.usgs.gov/">
+        Contact USGS
+      </a>
+    </div>
+
+  </div>
+</footer></body>
+</html>
+{% endblock %}
\ No newline at end of file

migrations/alembic.ini

+# A generic, single database configuration.
+
+[alembic]
+# template used to generate migration files
+# file_template = %%(rev)s_%%(slug)s
+
+# set to 'true' to run the environment during
+# the 'revision' command, regardless of autogenerate
+# revision_environment = false
+
+
+# Logging configuration
+[loggers]
+keys = root,sqlalchemy,alembic
+
+[handlers]
+keys = console
+
+[formatters]
+keys = generic
+
+[logger_root]
+level = WARN
+handlers = console
+qualname =
+
+[logger_sqlalchemy]
+level = WARN
+handlers =
+qualname = sqlalchemy.engine
+
+[logger_alembic]
+level = INFO
+handlers =
+qualname = alembic
+
+[handler_console]
+class = StreamHandler
+args = (sys.stderr,)
+level = NOTSET
+formatter = generic
+
+[formatter_generic]
+format = %(levelname)-5.5s [%(name)s] %(message)s
+datefmt = %H:%M:%S

migrations/env.py

+from __future__ import with_statement
+
+import logging
+from logging.config import fileConfig
+
+from sqlalchemy import engine_from_config
+from sqlalchemy import pool
+
+from alembic import context
+
+# this is the Alembic Config object, which provides
+# access to the values within the .ini file in use.
+config = context.config
+
+# Interpret the config file for Python logging.
+# This line sets up loggers basically.
+fileConfig(config.config_file_name)
+logger = logging.getLogger('alembic.env')
+
+# add your model's MetaData object here
+# for 'autogenerate' support
+# from myapp import mymodel
+# target_metadata = mymodel.Base.metadata
+from flask import current_app
+config.set_main_option(
+    'sqlalchemy.url', current_app.config.get(
+        'SQLALCHEMY_DATABASE_URI').replace('%', '%%'))
+target_metadata = current_app.extensions['migrate'].db.metadata
+
+# other values from the config, defined by the needs of env.py,
+# can be acquired:
+# my_important_option = config.get_main_option("my_important_option")
+# ... etc.
+
+
+def run_migrations_offline():
+    """Run migrations in 'offline' mode.
+
+    This configures the context with just a URL
+    and not an Engine, though an Engine is acceptable
+    here as well.  By skipping the Engine creation
+    we don't even need a DBAPI to be available.
+
+    Calls to context.execute() here emit the given string to the
+    script output.
+
+    """
+    url = config.get_main_option("sqlalchemy.url")
+    context.configure(
+        url=url, target_metadata=target_metadata, literal_binds=True
+    )
+
+    with context.begin_transaction():
+        context.run_migrations()
+
+
+def run_migrations_online():
+    """Run migrations in 'online' mode.
+
+    In this scenario we need to create an Engine
+    and associate a connection with the context.
+
+    """
+
+    # this callback is used to prevent an auto-migration from being generated
+    # when there are no changes to the schema
+    # reference: http://alembic.zzzcomputing.com/en/latest/cookbook.html
+    def process_revision_directives(context, revision, directives):
+        if getattr(config.cmd_opts, 'autogenerate', False):
+            script = directives[0]
+            if script.upgrade_ops.is_empty():
+                directives[:] = []
+                logger.info('No changes in schema detected.')
+
+    connectable = engine_from_config(
+        config.get_section(config.config_ini_section),
+        prefix='sqlalchemy.',
+        poolclass=pool.NullPool,
+    )
+
+    with connectable.connect() as connection:
+        context.configure(
+            connection=connection,
+            target_metadata=target_metadata,
+            process_revision_directives=process_revision_directives,
+            **current_app.extensions['migrate'].configure_args
+        )
+
+        with context.begin_transaction():
+            context.run_migrations()
+
+
+if context.is_offline_mode():
+    run_migrations_offline()
+else:
+    run_migrations_online()