Merge lp:~zack-krejci/healthscapes/trunk into lp:healthscapes/trunk

[Zack]

[lp:~zack-krejci/healthscapes/trunk]

13. By <email address hidden> on 2011-02-09

Geoserver url is now dynamic

14. By <email address hidden> on 2011-02-12

Added Lit Tool, Wiki, NPR API

15. By <email address hidden> on 2011-02-12

Fixed geoserver url

=== modified file 'controllers/gis.py'
--- controllers/gis.py	2011-02-04 20:12:08 +0000
+++ controllers/gis.py	2011-02-12 21:37:13 +0000
@@ -1983,6 +1983,7 @@
 
 def hs():
     output=geoexplorer()
+    output.update ({'geoserver': deployment_settings.geoserver})
     output.update ({'tool_list': load_tools (), 'tool_saved_results': load_results (), 'tool_saved_analyses': load_analyses ()})
     return(output)
 

=== added file 'controllers/lit.py'
--- controllers/lit.py	1970-01-01 00:00:00 +0000
+++ controllers/lit.py	2011-02-12 21:37:13 +0000
@@ -0,0 +1,40 @@
+import simplejson as json
+
+def kw():
+    from BeautifulSoup import BeautifulStoneSoup 
+    from urllib2 import urlopen
+
+    tmp_create_lit ()
+    disease = request.vars.get ('d')
+    result = db.executesql ('''
+    SELECT keyword.kw, counts.count 
+    FROM (SELECT keycount.kw_id, keycount.count 
+          FROM (SELECT id 
+                FROM disease 
+                WHERE d = 'malaria') AS diseases
+          INNER JOIN keycount
+          ON keycount.d_id = diseases.id) AS counts
+    INNER JOIN keyword
+    ON keyword.id = counts.kw_id;
+    ''')
+    rList = []
+    capabilities = urlopen (deployment_settings.geoserver.url + '/wms?SERVICE=WMS&REQUEST=GetCapabilities').read ()
+    soup = BeautifulStoneSoup (capabilities)
+    keywords = soup.findAll (name = 'keyword')
+    for r in result:
+        words = []
+        for k in keywords:
+            if k.text == r[0]:
+                words.append (k)
+        mapList = []
+        for w in words:
+            layer = w.parent.parent
+            id = layer.find ('name').text
+            name = layer.find ('title').text
+            mapList.append ({'id': id, 'name': name})
+        d = dict (kw = r[0], count = r[1], numMaps = len (words), maps = mapList)
+        rList.append (d)
+    return json.dumps (rList)
+    
+def map():
+    pass

=== added file 'controllers/sources.py'
--- controllers/sources.py	1970-01-01 00:00:00 +0000
+++ controllers/sources.py	2011-02-12 21:37:13 +0000
@@ -0,0 +1,27 @@
+import simplejson as json
+
+def index():
+    return {}
+
+def wiki():
+    from urllib2 import urlopen, Request
+    from re import sub
+    
+    disease = request.vars.get ('disease')
+
+    r = Request ('http://en.wikipedia.org/w/index.php?action=render&title=%s' % (disease,), headers = {'User-Agent': 'Healthscapes'})
+    result = urlopen (r)
+    html = result.read ()
+    return sub ('(<table class\=\"infobox[^>]*style=")', '\\1float: left; margin-right: 10px;', html)
+
+
+def npr():
+    from urllib2 import urlopen
+
+    disease = request.vars.get ('disease')
+
+    result = urlopen ('http://api.npr.org/query?apiKey=' + deployment_settings.npr_key +'&fields=title,teaser&output=JSON&searchTerm=%s' % (disease,))
+
+    return result.read ()
+
+

=== modified file 'controllers/tool.py'
--- controllers/tool.py	2011-02-04 20:12:08 +0000
+++ controllers/tool.py	2011-02-12 21:37:13 +0000
@@ -85,7 +85,7 @@
         return json.dumps ({'err': 'Bad filename'})
     mod = get_tool (tool_ob['id'])
     pairs = []
-    for ob in mod.cargs:
+    for ob in mod['args']:
         key = ob[0]
         pairs.append ((key, request.vars.get (key)))
     val = json.dumps (dict (pairs))

=== added file 'models/lit.py'
--- models/lit.py	1970-01-01 00:00:00 +0000
+++ models/lit.py	2011-02-12 21:37:13 +0000
@@ -0,0 +1,25 @@
+db.define_table('keyword',
+    Field('kw'),
+)
+
+db.define_table('disease',
+    Field('d'),
+)
+
+db.define_table('keycount',
+    Field('kw_id', db.keyword),
+    Field('d_id', db.disease),
+    Field('count','integer'),
+)
+
+def tmp_create_lit ():
+    db.keyword.truncate ()
+    db.disease.truncate ()
+    db.keycount.truncate ()
+    m_key = db.keyword.insert (kw ='malaria')
+    p_key = db.keyword.insert (kw = 'precipitation')
+    s_key = db.keyword.insert (kw = 'spearfish')
+    m = db.disease.insert (d = 'malaria')
+    db.keycount.insert (kw_id = m_key, d_id = m, count = 100)
+    db.keycount.insert (kw_id = p_key, d_id = m, count = 67)
+    db.keycount.insert (kw_id = s_key, d_id = m, count = 42)

=== modified file 'modules/geo/func.py'
--- modules/geo/func.py	2011-01-24 22:39:23 +0000
+++ modules/geo/func.py	2011-02-12 21:37:13 +0000
@@ -16,14 +16,17 @@
     else:
         return arg
 
-def makeCount (src):
+'''def makeCount (src):
     def COUNT (*args):
         count = 0
         for a in args:
             if a == src:
                 count += 1
         return count
-    return COUNT
+    return COUNT'''
+
+def COUNT (*args):
+    return len (args)
 
 def MIN (*args):
     return min (args)
@@ -42,7 +45,8 @@
     elif name == 'NONZERO':
         return NONZERO
     elif name == 'COUNT':
-        return makeCount (*args)
+        #return makeCount (*args)
+        return COUNT
     elif name == 'MIN':
         return MIN
     elif name == 'MAX':

=== modified file 'static/scripts/hs/hs_base.js'
--- static/scripts/hs/hs_base.js	2011-02-04 20:12:08 +0000
+++ static/scripts/hs/hs_base.js	2011-02-12 21:37:13 +0000
@@ -1,6 +1,9 @@
 var hs = {
-    geoserver: function (mapname) {
-	return 'http://zk.healthscapes.org/geoserver/wfs?request=DescribeFeatureType&typename=hsd:' + mapname + '&version=1.1.0';
+    geoserver: {
+	url: geoserver_url,
+	describe: function (mapname) {
+	    return hs.geoserver.url + '/wfs?request=DescribeFeatureType&typename=hsd:' + mapname + '&version=1.1.0';
+	}
     },
     application: 'healthscapes',
     /*SelectBox: Ext.extend (Ext.Panel, {

=== modified file 'static/scripts/hs/panels/tool_panel.js'
--- static/scripts/hs/panels/tool_panel.js	2011-02-04 20:55:45 +0000
+++ static/scripts/hs/panels/tool_panel.js	2011-02-12 21:37:13 +0000
@@ -369,6 +369,7 @@
 		var method = 'mean'
 		var groups = [];
 		var thisWindow = this;
+		var aggPanel;
 		
 		this.getValue = function () {
 		    return aggPanel.json ();
@@ -392,7 +393,7 @@
 		}
 		
 		var store = new GeoExt.data.AttributeStore ({
-		    url: hs.geoserver (mapname)
+		    url: hs.geoserver.describe (mapname)
 		});
 		store.load ();
 		
@@ -471,6 +472,7 @@
 		    groupCount ++;
 
 		    this.json = function () {
+			console.log (fieldType.getValue ());
 			var ob = {
 			    name: this.name,
 			    output: output.getValue (),
@@ -709,7 +711,7 @@
 		    }
 		    this.setValue (map_ob.name);
 		    store = new GeoExt.data.AttributeStore ({
-			url: hs.geoserver (map_ob.id)
+			url: hs.geoserver.describe (map_ob.id)
 		    });
 		    store.load ();
 		};
@@ -794,23 +796,33 @@
 	}),
 	Agg: Ext.extend (Ext.Button, {
 	    constructor: function (label, mapSource, config) {
+		var map;
 		var w;
 
 		this.getValue = function () {
 		    //if (preset)
 		        //return JSON.stringify (preset);
-		    if (w)
-			return w.getValue ();
+		    console.log ('val', w.getValue ());
+		    if (w) {
+			return JSON.stringify ({
+			    map: map,
+			    data: w.getValue (),
+			});
+		    }
 		    else
-			return {};
+			return '{}';
 		};
 
 		var thisValue = this;
 		
 		this.setField = function (ob) {
 		    var preset = JSON.parse (ob);
-		    w = new hs.tool.Agg.Window ('br_precip');
-		    w.setField (preset);
+		    map = preset.map;
+		    data = JSON.parse (preset.data);
+		    w = new hs.tool.Agg.Window (map.id);
+		    w.setField (data);
+		    w.show ();
+		    w.hide ();
 		};
 
 		if (!config) config = {}
@@ -818,11 +830,11 @@
 		    fieldLabel: label,
 		    text: 'Configure',
 		    handler: function (event) {
-			var mapname = mapSource.getValue ();
-			if (!mapname)
+			map = JSON.parse (mapSource.getValue ());
+			if (!map)
 			    return;
 			if (!w)
-			    w = new hs.tool.Agg.Window (mapname);
+			    w = new hs.tool.Agg.Window (map.id);
 			w.show ();
 		    },
 		});

=== modified file 'tool/aggregate.py'
--- tool/aggregate.py	2011-01-24 22:39:23 +0000
+++ tool/aggregate.py	2011-02-12 21:37:13 +0000
@@ -42,14 +42,16 @@
     keys = {}
     output = []
 
-    for inst in attr['agg']:
+    aggSource = attr['agg']['map']
+    dataSource = attr['agg']['data']
+    for inst in dataSource:
         dst = keygen (inst['name'])
         if inst['output']:
             output.append (dst)
         for poly in polygons:
             keys[(None, inst['name'])] = dst
             src = keymap (keys, inst['data'])
-            func = get (str (inst ['method']))
+            func = get (str (inst ['method']), attr['points'])
             if inst['dir'] == 'extern':
                 mode = enum.MANY_TO_ONE
             else:

=== modified file 'views/gis/hs.html'
--- views/gis/hs.html	2011-02-04 20:12:08 +0000
+++ views/gis/hs.html	2011-02-12 21:37:13 +0000
@@ -44,6 +44,9 @@
 {{pass}}
 
     <script language="javascript" type="text/javascript" src="/{{=request.application}}/static/scripts/edit_area/edit_area_full.js"></script>
+<script type="text/javascript">
+    var geoserver_url = '{{=geoserver.url}}';
+</script>
 <script type="text/javascript" src="/{{=request.application}}/static/scripts/hs/hs_base.js"></script>
 <script type="text/javascript" src="/{{=request.application}}/static/scripts/hs/panels/tool_panel.js"></script>
 <script type="text/javascript" src="/{{=request.application}}/static/scripts/hs/panels/side_panel.js"></script>
@@ -62,11 +65,29 @@
 	    filename: 'br_pop',
 	    type: 'db',
 	},
+
+
 	{
 	    name: 'Brazil Precipitation',
 	    filename: 'br_precip',
 	    type: 'db',
 	},
+
+	{
+	    name: 'Wher Wildlife Disease',
+	    filename: 'wher',
+	    type: 'db',
+	},
+
+	{
+	    name: 'US States',
+	    filename: 'us_states',
+	    type: 'db',
+	},
+
+
+
+
     ]);
 
     var tool_list = new hs.side.Tools ({{response.write (tool_list, escape = False)}});
@@ -110,19 +131,322 @@
         ],
     });
 
+
+    // Temp Disease Pages START 
+
+
+
+
+    
+    var nprPanel = new Ext.Panel ({
+	region: 'west',
+	title: 'NPR',
+	autoScroll: true,
+	width: 400,
+	padding: 10,
+	listeners: {
+            render: function () {
+		var element = this;
+		Ext.Ajax.request ({
+		    url: '/{{=request.application}}/sources/npr',
+		    method: 'GET',
+		    params: {
+			disease: 'Malaria',
+		    },
+		    success: function (data) {
+			var ob = JSON.parse (data.responseText);
+			console.log (ob);
+			var stories = ob.list.story;
+			console.log (stories);
+			for (var i = 0; i < stories.length; i ++) {
+			    var html = '<div><a href="' + stories[i].link[2]['$text'] + '">' + stories[i].title['$text']  + '</a><br />' + stories[i].teaser['$text'] + '</div>';
+			    element.add ({
+				border: false,
+				padding: 10,
+				html: html,
+			    });
+			}
+			element.doLayout ();
+		    },
+		    failure: function () {
+			console.log ('NPR API returned error');
+		    },
+		});
+            },
+	},
+    });
+
+
+    //http://api.npr.org/query?apiKey=MDA2OTc4ODY2MDEyOTc0NTMyMjFmZGNjZg001&searchTerm=malaria
+    
+    var wikiPanel = new Ext.Panel ({
+	title: 'Wikipedia',
+	region: 'center',
+	autoScroll: true,
+	padding: 10,
+	listeners: {
+            render: function () {
+		var element = this;
+		Ext.Ajax.request ({
+		    url: '/{{=request.application}}/sources/wiki',
+		    method: 'GET',
+		    params: {
+			disease: 'Malaria',
+		    },
+		    success: function (data) {
+			var ob = data.responseText;
+			element.add ({
+			    border: false,
+			    html: ob,
+			});
+			element.doLayout ();
+		    },
+		    failure: function () {
+			console.log ('Wiki API returned error');
+		    },
+		});
+            },
+	},
+    });
+
+    var LitPanel = Ext.extend (Ext.Panel, {
+	constructor: function (config) {
+	    var keywords;
+	    var maps;
+	    
+	    var store = new Ext.data.JsonStore ({
+
+	    });
+
+	    /*var keyword_root = new Ext.tree.AsyncTreeNode({
+		expanded: true,
+		children: childNodes,
+	    });*/
+
+	    var KeywordRecord = Ext.data.Record.create ([
+		'kw',
+		'count',
+		'numMaps',
+		'maps',
+	    ]);
+
+	    var keywordCols = new Ext.grid.ColumnModel ([
+		 {
+		     id: 'kw',
+		     header: 'Keyword',
+		     sortable: true,
+		     dataIndex: 'kw'
+		 },
+		 {
+		     id: 'count',
+		     header: 'Rank',
+		     sortable: true,
+		     dataIndex: 'count'
+		 },
+		 {
+		     id: 'numMaps',
+		     header: 'Maps',
+		     sortable: true,
+		     dataIndex: 'numMaps'
+		 },
+	    ]);
+
+	    var mapList = [];
+	    
+	    var populate = function () {
+		Ext.Ajax.request ({
+		    url: '/{{=request.application}}/lit/kw',
+		    method: 'GET',
+		    params: {
+			d: 'malaria',
+		    },
+		    success: function (data) {
+			mapList = [];
+			var ob = JSON.parse (data.responseText);
+			records = [];
+			store.removeAll ();
+			for (var i = 0; i < ob.length; i ++) {
+			    mapList.push (ob[i]['maps']);
+			    records.push (new KeywordRecord (ob[i]));
+			}
+			console.log (ob, mapList);
+			store.add (records);
+			keywords.reconfigure (store, keywordCols);
+		    },
+		    failure: function () {
+			console.log ('Lit call went wrong');
+		    },
+		});
+	    };
+
+	    populate ();
+
+	    var addMapNode = function (ob) {
+		root.appendChild ({
+		    text: ob.name,
+		    leaf: true,
+		    cls: 'file',
+		    id: ob.id,
+		});
+	    };
+
+	    var root = new Ext.tree.AsyncTreeNode({
+		expanded: true,
+		children: [],
+	    });
+	    
+	    maps = new Ext.tree.TreePanel ({
+		title: 'Maps',
+		rootVisible: false,
+		root: root,
+		expanded: true,
+		enableDrag: true,
+		columnWidth: .75,
+		dragConfig: {
+		    ddGroup: 'layers',
+		    dragAllowed: true,
+		    dropAllowed: false,
+		},
+	    });
+
+	    keywords = new Ext.grid.GridPanel ({
+		title: 'Keywords',
+		store: store,
+		columns: keywordCols,
+		columnWidth: .25,
+		autoHeight: true,
+		listeners: {
+		    celldblclick: function (el, rowIndex, colIndex, event) {
+			root.removeAll ();
+			var m = mapList[rowIndex];
+			for (var i = 0; i < m.length; i ++) {
+			    addMapNode (m[i]);
+			}
+			maps.doLayout ();
+		    }
+		},
+	    });
+
+	    if (!config)
+		config = {};
+
+	    Ext.apply (config, {
+		title: 'Automated',
+		layout: 'column',
+		hideBorders: true,
+		items: [
+		    keywords,
+		    maps,
+		],
+	    });
+
+	    LitPanel.superclass.constructor.call (this, config);
+	},
+    });
+
+    var litPanel = new LitPanel ();
+
+
+    var mainPanel = new Ext.Panel ({
+    title: 'Info',
+    layout: 'border',
+    region: 'center',
+    items: [
+        wikiPanel,
+        nprPanel,
+    ],
+    });
+    
+    var tabsPanel = new Ext.TabPanel ({    
+        region: 'center',
+        activeTab: 0,
+        items: [
+            mainPanel,
+            {
+		title: 'Tools',
+		html: 'A simple tab',
+            },{
+		title: 'Maps',
+		html: 'A simple tab'        
+            },{
+		title: 'Research',
+		html: 'A simple tab'  
+            },
+	    litPanel,
+        ]
+    });
+
+    //wrapDateLine: true,
+    //displayOutsideMaxExtent: true,
+
+    map = new OpenLayers.Map("Disease Map");
+    var base = new OpenLayers.Layer.OSM ();
+    var overlay = new OpenLayers.Layer.WMS (
+        "Brazil",
+        geoserver_url + '/wms',
+        {
+	    layers: "hsd:brazil",
+	    transparent: true,
+	    format: "image/png",
+	    projection: 'EPSG:9000913',
+	},
+	{
+	    isBaseLayer: false,
+	    displayOutsideMaxExtent: true,
+	}
+    );
+    map.addLayer (base);
+    map.addLayer (overlay);
+    //map.addLayer(overlay);
+    //map.zoomTo (7);
+    //map.setCenter (new OpenLayers.LonLat(13.41,52.52), 7);
+    
+    var mapPanel = new GeoExt.MapPanel({
+        height: 300,
+	region: 'north',
+        map: map,
+        title: 'Map',
+	listeners: {
+	    afterlayout: function () {
+		var center = new OpenLayers.LonLat (-55.0, -10.0);
+		var proj4326 = new OpenLayers.Projection('EPSG:4326');
+		var projection_current = new OpenLayers.Projection('EPSG:900913');
+		center.transform(proj4326, projection_current);
+		map.setCenter (center, 4);
+		
+		//map.zoomTo (7);
+	    },
+	},
+    });
+
+    var diseasePages = new Ext.Panel ({
+	title: 'Diseases',
+	region: 'center',
+	layout: 'border',
+	items: [
+	    mapPanel,
+            tabsPanel,
+	],
+    });
+
+
+
+
+    // Temp Disease Pages END
+
+
     var tabPanel = new Ext.TabPanel ({
         activeTab: 0,
 	layoutOnChange: true,
 	region: 'center',
 	items: [
 	    mapTab,
-            dataTab,
+            diseasePages,
             toolTab,
             createTab,
         ],
     });
     saved_analyses.setToolPanel (toolTab, tabPanel, 2);
-    
 
     var win = new Ext.Window({
         title: 'Healthscapes v0.3',
@@ -182,6 +506,10 @@
             },
             defaultSourceType: 'gx_wmssource',
             sources: {
+		local: {
+		    url: geoserver_url + '/wms',
+		    title: 'HS Geoserver',
+		},
 		{{if geoserver_url:}}
 		local: {
                     url: s3_gis_geoserver_url,
@@ -225,23 +553,31 @@
 		units: s3_gis_units,
 		maxResolution: s3_gis_maxResolution,
 		maxExtent: s3_gis_maxExtent,
-		layers: [{
-                    source: 'osm',
-                    name: 'cyclemap',
-                    group: 'background'
-		}, {
-                    source: 'osm',
-                    name: 'mapnik',
-                    group: 'background'
-		}, {
-                    source: 'ol',
-                    group: 'background',
-                    fixed: true,
-                    type: 'OpenLayers.Layer',
-                    args: [
-			'None', {visibility: false}
-                    ]
-		}],
+		layers: [
+		    {
+			source: 'osm',
+			name: 'cyclemap',
+			group: 'background'
+		    }, 
+		    {
+			source: 'osm',
+			name: 'mapnik',
+			group: 'background'
+		    }, 
+		    {
+			source: 'ol',
+			group: 'background',
+			fixed: true,
+			type: 'OpenLayers.Layer',
+			args: [
+			    'None', {visibility: false}
+			]
+		    },
+		    /*{
+                        source: 'local',
+			name: 'topp:states',
+		    },*/
+		],
 		center: [s3_gis_center.lon, s3_gis_center.lat],
 		zoom: s3_gis_zoom,
 		numZoomLevels: s3_gis_numZoomLevels
@@ -274,4 +610,4 @@
 	{{pass}}
     }, false);
 </script>
-    
\ No newline at end of file
+