Initial commit

README.md

+# pollenviz
+The purpose of the application is store and visualise sensor data. 
+
+## PLEASE NOTE
+This branch (master) is under development and will frequently change.  
+Please use the v1.0 tag to install pollenviz.  
+
+## Features
+* Simple data import with csv files via gui or api
+* GUI for editing data
+* View and compare data
+
+
+## Requirements
+The following is required to install and run the application:
+* Postgres 9.5+ (https://www.postgresql.org/download/)
+* Postgis extension (https://postgis.net/install/)
+* Python 3 (https://www.python.org/downloads/)
+* Yarn/NPM
+* WSGI complient server
+* See requirements.txt for external python libraries used
+
+## Configuration
+Add a file in the web folder called config.ini.   
+Look at config.example.ini to see what needs to be inside.
+
+## Database
+Setup postgres database with the postgis extension.  
+Import the schema.sql file from the db_scripts folder.  
+
+## Running the app
+Install all required python libraries with:  
+```powershell
+pip install -r requirements.txt
+```   
+
+Navigate to the web/client folder and build the gui with the command: 
+```powershell
+yarn install
+yarn build
+```  
+
+Run the python server with the the following command:  
+**Linux**
+```powershell
+export FLASK_APP=web
+flask run
+```  
+
+**Windows**
+```powershell
+$env:FLASK_APP = "web" 
+flask run
+```  
+See https://flask.palletsprojects.com/en/1.1.x/quickstart/ for more information.
+
+
+## Development
+Make sure you have all javascript packages installed by running `yarn` in the web/client folder.  
+Run `yarn build` once so the python server has the required files.  
+Start the web server as described in "running the app"  
+Start the client side server by running the command `yarn serve`
+
+## Linux web server
+
+On the webserver we have to start with a configuration for apache2. Write a custom configuration file, /etc/apache2/sites-available/pollenviz.conf.
+
+The ServerName settings in pollenviz.conf has to be registered as a CNAME, pointing to the A-record for the webserver, in the DNS-servers.
+
+Make ssl-certs for https://someurl.com, and put the key and crt file into /etc/apache2/ssl.
+
+Make a DocumentRoot directory under /var/www/html, call it pollenviz. Give it sufficient permissions for apache2 to be able to read it.
+
+Copy all of the files in the web folder to there.
+
+Make a pollenviz.wsgi file, to start the application. Here we source the virtual environment and starts the application.
+
+Next is to make a virtual environment for python, and then installing all the modules from requirement.txt from that. psycopg2 is dependent on libpq-dev and python-dev. 
+
+
+## IIS  
+Please follow this article to install the application on IIS:
+http://netdot.co/2015/03/09/flask-on-iis/
+
+Make sure the Python folder has IIS_IUSRS rights.  
+Install all dependencies from requirements.txt globally or with virtualenv.  
+To do this globally run the following line in the python script folder:  
+```pip install -r requirements.txt```    
+It is highly recommended that you set up your server with **https**  
+
+
+## Importing data
+Importing data is done by uploading sensors and observations as csv files. See csv_examples.  
+Use [Curl](https://curl.haxx.se/), [Postman](https://chrome.google.com/webstore/detail/postman/fhbjgbiflinjbdggehcddcbncdddomop) or similar tools for this.   
+Set Content-Type to "multipart/form-data" and use the form name "csv".  
+Example uploading networks with curl  
+```
+curl -X POST -u usr:psw --form "csv=@path/to/sensors.csv" https://someurl.com/imports/sensors
+```
+If you upload a content with id's that exists, it will be updated.  
+  
+There are dependencies between the csv files, so the import order is important.  
+Start with sensors and observations
+
+### Security  
+This application uses basic authentication.  
+The default user:password combination is admin:admin  
+It is recommended to change the default password immediately.   
+You can do this with the user management module on pollenviz web site.
+

app.py

+from  web import create_app
+app = create_app()
+
+if __name__ == "__main__":
+    app.run(debug=False)
\ No newline at end of file

db_scripts/schema.sql

+/*
+Source Database       : pollenviz
+Source Schema         : public
+
+Date: 2019-12-16 22:47:00
+*/
+
+CREATE EXTENSION IF NOT EXISTS postgis WITH SCHEMA public;
+COMMENT ON EXTENSION postgis IS 'PostGIS geometry, geography, and raster spatial types and functions';
+
+CREATE TABLE public.parameters (
+    id integer NOT NULL,
+    label character varying(100) NOT NULL,
+    notation character varying(100) NOT NULL
+);
+ALTER TABLE public.parameters OWNER TO postgres;
+
+CREATE TABLE public.units (
+    id integer NOT NULL,
+    label character varying(100) NOT NULL,
+    notation character varying(100) NOT NULL
+);
+ALTER TABLE public.units OWNER TO postgres;
+
+CREATE TABLE public.timesteps (
+    id integer NOT NULL,
+    label character varying(100) NOT NULL,
+    notation character varying(100) NOT NULL
+);
+ALTER TABLE public.timesteps OWNER TO postgres;
+
+CREATE TABLE public.sensors
+(
+    id integer NOT NULL,
+    name character varying(100) NOT NULL,
+    parameter integer NOT NULL,
+    unit integer NOT NULL,
+    timestep integer NOT NULL,
+    from_time timestamp without time zone,
+    to_time timestamp without time zone,
+    geom geometry NOT NULL,
+    comment character varying(500),
+    CONSTRAINT sensors_pkey PRIMARY KEY (id)
+)
+WITH (
+    OIDS = FALSE
+)
+TABLESPACE pg_default;
+
+ALTER TABLE public.sensors OWNER TO postgres;
+
+
+CREATE TABLE public.observations
+(
+    id bigint NOT NULL DEFAULT nextval('observations_id_seq'::regclass),
+    sensor_id integer NOT NULL,
+    value numeric(255,5) NOT NULL,
+    from_time timestamp without time zone NOT NULL,
+    to_time timestamp without time zone NOT NULL
+    
+)
+WITH (
+    OIDS = FALSE
+)
+TABLESPACE pg_default;
+
+ALTER TABLE public.observations OWNER to postgres;
+
+ALTER TABLE ONLY public.observations ADD CONSTRAINT observations_pkey PRIMARY KEY (id);
+
+ALTER TABLE ONLY public.observations
+    ADD CONSTRAINT observations_sensors_id_fkey FOREIGN KEY (sensor_id) REFERENCES public.sensors(id) ON UPDATE CASCADE ON DELETE CASCADE;
+
+ALTER TABLE public.observations
+    ADD CONSTRAINT sensor_id_from_to UNIQUE (sensor_id, from_time, to_time);
+
+CREATE SEQUENCE public.observations_id_seq
+    START WITH 1
+    INCREMENT BY 1
+    NO MINVALUE
+    NO MAXVALUE
+    CACHE 1;
+
+ALTER TABLE public.observations_id_seq OWNER TO postgres;
+
+ALTER SEQUENCE public.observations_id_seq OWNED BY public.observations.id;
+
+CREATE TABLE public.users (
+    username character varying(255) NOT NULL,
+    password character varying(255) NOT NULL,
+    created timestamp without time zone,
+    createdby character varying(255)
+);
+ALTER TABLE public.users OWNER TO postgres;
+
+REVOKE ALL ON SCHEMA public FROM PUBLIC;
+REVOKE ALL ON SCHEMA public FROM postgres;
+GRANT ALL ON SCHEMA public TO postgres;
+GRANT ALL ON SCHEMA public TO PUBLIC;
+
+
+
+
+CREATE FUNCTION public.pollenviz_update_time()
+    RETURNS trigger
+    LANGUAGE 'plpgsql'
+    COST 100
+    VOLATILE NOT LEAKPROOF
+AS $BODY$  
+DECLARE
+  fromtime timestamp without time zone;
+  totime timestamp without time zone; 
+ 
+BEGIN
+	SELECT from_time, to_time
+    INTO  fromtime, totime
+    FROM sensors 
+	WHERE id = NEW.sensor_id;
+	
+	-- UPDATE FROMTIME IN THE SENSORS TABLE
+	IF fromtime IS NULL OR NEW.from_time < fromtime THEN
+	 	UPDATE sensors SET from_time = NEW.from_time WHERE id = NEW.sensor_id;
+	END IF;
+
+	-- UPDATE TOTIME IN THE SENSORS TABLE
+	IF totime IS NULL OR NEW.to_time > totime THEN
+	 	UPDATE sensors SET to_time = NEW.to_time WHERE id = NEW.sensor_id;
+	END IF;
+	
+	RETURN NEW;
+END;
+$BODY$;
+
+ALTER FUNCTION public.pollenviz_update_time()
+    OWNER TO postgres;
+
+CREATE TRIGGER pollenviz_update_time_trigger
+    AFTER INSERT
+    ON public.observations
+    FOR EACH ROW
+    EXECUTE PROCEDURE public.pollenviz_update_time();
+
+
+
+INSERT INTO public.users VALUES ('admin', 'pbkdf2:sha256:150000$JAxTlbED$0fb0aa01ce950de3204185af3d4c61001d9b077895067b050b2ecd78d6835cd8', NULL, NULL);
+
+
+INSERT INTO public.parameters VALUES (1, 'Temperature', 'Temp');
+INSERT INTO public.parameters VALUES (2, 'Relative Humidity', 'RH');
+INSERT INTO public.units VALUES (3, 'Percentage', '%');
+
+INSERT INTO public.units VALUES (4, 'birch', 'cnt/m3');
+INSERT INTO public.units VALUES (5, 'hazel', 'cnt/m3');
+INSERT INTO public.units VALUES (6, 'ash', 'cnt/m3');
+
+
+INSERT INTO public.timesteps VALUES (1, 'Second', 's');
+INSERT INTO public.timesteps VALUES (2, 'Minute', 'm');
+INSERT INTO public.timesteps VALUES (3, 'Hour', 'h');
+INSERT INTO public.timesteps VALUES (4, 'Variable', 'variable');
+INSERT INTO public.timesteps VALUES (5, 'Instantaneous', 'instantaneous');

node_modules/.bin/cdl

+../cardinal/bin/cdl.js
\ No newline at end of file

node_modules/.bin/esparse

+../esprima/bin/esparse.js
\ No newline at end of file

node_modules/.bin/esvalidate

+../esprima/bin/esvalidate.js
\ No newline at end of file

node_modules/.bin/geojson-rewind

+../@mapbox/geojson-rewind/geojson-rewind
\ No newline at end of file

node_modules/.bin/pbf

+../pbf/bin/pbf
\ No newline at end of file

node_modules/.bin/sharkdown

+../sharkdown/sharkdown
\ No newline at end of file

node_modules/.yarn-integrity

+{
+  "systemParams": "darwin-x64-64",
+  "modulesFolders": [],
+  "flags": [],
+  "linkedModules": [],
+  "topLevelPatterns": [],
+  "lockfileEntries": {},
+  "files": [],
+  "artifacts": {}
+}
\ No newline at end of file

node_modules/@mapbox/geojson-area/.travis.yml

+language: node_js

node_modules/@mapbox/geojson-area/CHANGELOG.md

+<a name="0.2.2"></a>
+## [0.2.2](https://github.com/mapbox/geojson-area/compare/v0.2.1...v0.2.2) (2016-12-19)
+
+
+### Bug Fixes
+
+* **algorithm:** Avoid accidental global i, fixes use strict ([1646944](https://github.com/mapbox/geojson-area/commit/1646944))
+
+
+

node_modules/@mapbox/geojson-area/LICENSE

+Copyright 2005-2013 OpenLayers Contributors. All rights reserved. See
+authors.txt for full list.
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+
+ 1. Redistributions of source code must retain the above copyright notice, this
+list of conditions and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright notice,
+this list of conditions and the following disclaimer in the documentation and/or
+other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY OPENLAYERS CONTRIBUTORS ``AS IS'' AND ANY EXPRESS
+OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT
+SHALL COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+The views and conclusions contained in the software and documentation are those
+of the authors and should not be interpreted as representing official policies,
+either expressed or implied, of OpenLayers Contributors.

node_modules/@mapbox/geojson-area/README.md

+[![Build Status](https://travis-ci.org/mapbox/geojson-area.png)](https://travis-ci.org/mapbox/geojson-area)
+
+# geojson-area
+
+Calculate the area inside of any [GeoJSON](http://geojson.org/) geometry.
+
+## usage
+
+    npm install @mapbox/geojson-area
+
+## example
+
+```js
+var geojsonArea = require('@mapbox/geojson-area');
+
+var area = geojsonArea.geometry(obj);
+```
+
+## api
+
+### `geojsonArea.geometry(obj)`
+
+Given a Geometry object, return contained
+area as square meters. Invalid input will return `null`.
+
+Adapted from [OpenLayers](http://openlayers.org/)

node_modules/@mapbox/geojson-area/index.js

+var wgs84 = require('wgs84');
+
+module.exports.geometry = geometry;
+module.exports.ring = ringArea;
+
+function geometry(_) {
+    var area = 0, i;
+    switch (_.type) {
+        case 'Polygon':
+            return polygonArea(_.coordinates);
+        case 'MultiPolygon':
+            for (i = 0; i < _.coordinates.length; i++) {
+                area += polygonArea(_.coordinates[i]);
+            }
+            return area;
+        case 'Point':
+        case 'MultiPoint':
+        case 'LineString':
+        case 'MultiLineString':
+            return 0;
+        case 'GeometryCollection':
+            for (i = 0; i < _.geometries.length; i++) {
+                area += geometry(_.geometries[i]);
+            }
+            return area;
+    }
+}
+
+function polygonArea(coords) {
+    var area = 0;
+    if (coords && coords.length > 0) {
+        area += Math.abs(ringArea(coords[0]));
+        for (var i = 1; i < coords.length; i++) {
+            area -= Math.abs(ringArea(coords[i]));
+        }
+    }
+    return area;
+}
+
+/**
+ * Calculate the approximate area of the polygon were it projected onto
+ *     the earth.  Note that this area will be positive if ring is oriented
+ *     clockwise, otherwise it will be negative.
+ *
+ * Reference:
+ * Robert. G. Chamberlain and William H. Duquette, "Some Algorithms for
+ *     Polygons on a Sphere", JPL Publication 07-03, Jet Propulsion
+ *     Laboratory, Pasadena, CA, June 2007 http://trs-new.jpl.nasa.gov/dspace/handle/2014/40409
+ *
+ * Returns:
+ * {float} The approximate signed geodesic area of the polygon in square
+ *     meters.
+ */
+
+function ringArea(coords) {
+    var p1, p2, p3, lowerIndex, middleIndex, upperIndex, i,
+    area = 0,
+    coordsLength = coords.length;
+
+    if (coordsLength > 2) {
+        for (i = 0; i < coordsLength; i++) {
+            if (i === coordsLength - 2) {// i = N-2
+                lowerIndex = coordsLength - 2;
+                middleIndex = coordsLength -1;
+                upperIndex = 0;
+            } else if (i === coordsLength - 1) {// i = N-1
+                lowerIndex = coordsLength - 1;
+                middleIndex = 0;
+                upperIndex = 1;
+            } else { // i = 0 to N-3
+                lowerIndex = i;
+                middleIndex = i+1;
+                upperIndex = i+2;
+            }
+            p1 = coords[lowerIndex];
+            p2 = coords[middleIndex];
+            p3 = coords[upperIndex];
+            area += ( rad(p3[0]) - rad(p1[0]) ) * Math.sin( rad(p2[1]));
+        }
+
+        area = area * wgs84.RADIUS * wgs84.RADIUS / 2;
+    }
+
+    return area;
+}
+
+function rad(_) {
+    return _ * Math.PI / 180;
+}
\ No newline at end of file

node_modules/@mapbox/geojson-area/package.json

+{
+  "_from": "@mapbox/geojson-area@0.2.2",
+  "_id": "@mapbox/geojson-area@0.2.2",
+  "_inBundle": false,
+  "_integrity": "sha1-GNeBSqNr8j+7zDefjiaiKSfevxA=",
+  "_location": "/@mapbox/geojson-area",
+  "_phantomChildren": {},
+  "_requested": {
+    "type": "version",
+    "registry": true,
+    "raw": "@mapbox/geojson-area@0.2.2",
+    "name": "@mapbox/geojson-area",
+    "escapedName": "@mapbox%2fgeojson-area",
+    "scope": "@mapbox",
+    "rawSpec": "0.2.2",
+    "saveSpec": null,
+    "fetchSpec": "0.2.2"
+  },
+  "_requiredBy": [
+    "/@mapbox/geojson-rewind"
+  ],
+  "_resolved": "https://registry.npmjs.org/@mapbox/geojson-area/-/geojson-area-0.2.2.tgz",
+  "_shasum": "18d7814aa36bf23fbbcc379f8e26a22927debf10",
+  "_spec": "@mapbox/geojson-area@0.2.2",
+  "_where": "/Users/runeodegard/code/firefly/node_modules/@mapbox/geojson-rewind",
+  "author": {
+    "name": "Tom MacWright"
+  },
+  "bugs": {
+    "url": "https://github.com/mapbox/geojson-area/issues"
+  },
+  "bundleDependencies": false,
+  "config": {
+    "commitizen": {
+      "path": "./node_modules/cz-conventional-changelog"
+    }
+  },
+  "dependencies": {
+    "wgs84": "0.0.0"
+  },
+  "deprecated": false,
+  "description": "calculate the physical area of a geojson geometry",
+  "devDependencies": {
+    "cz-conventional-changelog": "^1.2.0",
+    "tape": "^3.0.3"
+  },
+  "directories": {
+    "test": "test"
+  },
+  "homepage": "https://github.com/mapbox/geojson-area#readme",
+  "keywords": [
+    "geojson",
+    "area",
+    "geodesy"
+  ],
+  "license": "BSD-2-Clause",
+  "main": "index.js",
+  "name": "@mapbox/geojson-area",
+  "repository": {
+    "type": "git",
+    "url": "git+ssh://git@github.com/mapbox/geojson-area.git"
+  },
+  "scripts": {
+    "test": "tape test/basic.js"
+  },
+  "version": "0.2.2"
+}

node_modules/@mapbox/geojson-area/test/all.json

+{
+  "type": "Polygon",
+  "coordinates": [[
+      [-180, -90],
+      [-180, 90],
+      [180, 90],
+      [180, -90],
+      [-180, -90]
+    ]
+  ]
+}

node_modules/@mapbox/geojson-area/test/basic.js

+var gjArea = require('../'),
+    test = require('tape'),
+    ill = require('./illinois.json'),
+    all = require('./all.json');
+
+test('geojson area', function(t) {
+    t.test('computes the area of illinois', function(t) {
+        t.equal(gjArea.geometry(ill), 145978332359.36746);
+        t.end();
+    });
+    // http://www.wolframalpha.com/input/?i=surface+area+of+earth
+    t.test('computes the area of the world', function(t) {
+        t.equal(gjArea.geometry(all), 511207893395811.06);
+        t.end();
+    });
+    t.test('point has zero area', function(t) {
+        t.equal(gjArea.geometry({ type: 'Point', coordinates: [0,0] }), 0);
+        t.end();
+    });
+    t.test('linestring has zero area', function(t) {
+        t.equal(gjArea.geometry({ type: 'LineString', coordinates: [[0,0],[1,1]] }), 0);
+        t.end();
+    });
+    t.test('geometrycollection is the sum', function(t) {
+        t.equal(gjArea.geometry({ type: 'GeometryCollection', geometries: [all, ill] }), 511353871728170.44);
+        t.end();
+    });
+    t.end();
+});

node_modules/@mapbox/geojson-area/test/illinois.json

+{
+  "type": "MultiPolygon",
+  "coordinates": [[
+    [
+      [
+        -88.071564,
+        37.51099
+      ],
+      [
+        -88.087883,
+        37.476273
+      ],
+      [
+        -88.311707,
+        37.442852
+      ],
+      [
+        -88.359177,
+        37.409309
+      ],
+      [
+        -88.419853,
+        37.420292
+      ],
+      [
+        -88.467644,
+        37.400757
+      ],
+      [
+        -88.511322,