Thursday, April 29, 2010

Some thoughts on NoSQL

So I have been playing with various database systems, many pertaining to the NoSQL category. Here are some thoughts:

  • Mongo is cool. I definitely like it. However, it differs from Cache in one important way: JSON objects are native to JavaScript. To everything else, they are just a text format (that Python can understand easily, true) not necessarily any more efficient than XML. Cache objects are more or less portable across languages and the impedance mismatch between the consumer and the database is definitely much less significant than in the case of Mongo;
  • Mongo is fast, and easy enough to understand for perhaps a dozen or two 'collections'. I am not sure how well it would support (or perform) with a 3000-table schema, which is not at all unlikely in an enterprise application. While the proliferation of tables is a perverse effect of relational normalization, the fact is that the relational model is easy to understand. Complex text representations of object hierarchies, which Mogo really allows for, might quickly spin out of control (assuming that the schema is kept under control by restricting access to the database through the front end, and object collections to not degenerate to the point of being simple bit buckets);
  • so Mongo might be best appropriate in an environment with a few deep entities with loose connections: e.g. 12-25 'tables' with million+ rows, especially for client apps that can read JSON (or derivatives: such as Python's collection objects) more or less natively.

More on this:

Twitter Python Mongo

...or how many buzzwords can you get in one title. Here is a shortish piece of code that pulls data from Twitter and inserts it into Mongo. Other than the shortness of the code (given what it accomplishes!), what is remarkable is the ease of use of the data that is passed around, with a minimum amount of marshalling: Twitter can return data in JSON which is the native Mongo format and Python can use with a minimum of tweaking (mostly to reduce the response from Twitter).

import urllib
import json
import string
from pymongo import Connection

def runQuery(query, pp, pages):
ret = []
for pg in range(1, pages+1):
print 'page...' + str(pg)
p = urllib.urlopen('' + query + '&rpp=' + str(pp) + '&page=' + str(pg))
s = json.load(p)
dic = json.dumps(s)
dic = string.replace(dic, 'null', '"none"')
dx = eval(dic)
listOfResults = dx['results']
for result in listOfResults:
ret.append( { 'id':result['id'], 'from_user':result['from_user'], 'created_at':result['created_at'], 'text': result['text'] } )
completeRet = {"results": ret}
return completeRet

c = Connection()
d = c.twitterdb
coll = d.postbucket
res = runQuery('Iran', 100, 15)
ptrData = res.get('results')
for item in ptrData:

A Twitter Python web service

Taking the code from the previous post: here is a Python web service that reads the Twitter feed for a given query and returns a subset of the results in JSON:

import urllib
import json
import string
import SimpleXMLRPCServer
from SimpleXMLRPCServer import SimpleXMLRPCServer
from SimpleXMLRPCServer import SimpleXMLRPCRequestHandler

def runQuery(query, pp, pages):
p = urllib.urlopen('' + query + '&rpp=' + str(pp) + '&page=' + str(pages))
s = json.load(p)
dic = json.dumps(s)
dic = string.replace(dic, 'null', '"none"')
dx = eval(dic)
listOfResults = dx['results']
ret = []
for result in listOfResults:
ret.append( { 'id':result['id'], 'from_user':result['from_user'], 'created_at':result['created_at'], 'text': result['text'] } )
completeRet = {"results": json.dumps(str(ret))}
return str(completeRet)

class RequestHandler(SimpleXMLRPCRequestHandler):

server=SimpleXMLRPCServer(("localhost", 8000), requestHandler=RequestHandler)
server.register_function(runQuery, 'qry')

More potential uses of this (including Google Apps, Mongo, or Processing) later. And here is how to use it (from Python):

>>> import xmlrpclib
>>> s = xmlrpclib.ServerProxy('http://localhost:8000')
>>> print s.qry('Bumrungrad', 10, 1)

Where the first numeric parameter is the number of records per page and the second, the number of page (max 100/15).

Wednesday, April 28, 2010

Twitter API

A bit of topical coding.... getting tweets regarding the situation in Bangkok:

>>> import urllib
>>> from xml.dom import minidom
>>> p=urllib.urlopen('')
>>> xml=minidom.parse(p)
>>> p.close()
>>> nodes=xml.getElementsByTagName('title')
>>> for node in nodes:
print node.firstChild.NodeValue

It's the first time I try the Twitter API, and it seems simple enough!

Tuesday, April 27, 2010

Mongo and Cache

Some similarities:

  • the system-generated row id: (_id for Mongo)
  • object references, and a kind of relationship definition in Mongo:

> x = {name:'Lab test'}
{ "name" : "Lab test" }
> pat = {name:'Amornrakot', test:[new DBRef('second', x._id)]}
"name" : "Amornrakot",
"test" : [
"$ref" : "second",
"$id" : ObjectId("4bd6d7c64e660000000f665a")
> pat.test[0].fetch()
{ "_id" : ObjectId("4bd6d7c64e660000000f665a"), "name" : "Lab test" }

The similarities aren't surprising perhaps; it is the differences that trouble me (in this case, Mongo's looseness - lack of structure); although SQLite was the first one to go down that path, by not enforcing strict data typing, and now Mongo doesn't even enforce schemas. A discussion on Mongo database design principles here.

For now I have a couple of other questions:

  • is there a reporting tool that binds to JSON/Mongo natively?
  • how do you update an existing JSON entry? just one tuple, not the entire record; some notes:
  • var p = db.coll.findOne();
  • p.member (notation supported, p is an object already and there is no need to eval() it; originally, say p{member:"y"} ) = "x" and now p is disconnected from the collection, but does update it in place

What is cool is that you can save JS objects (declared using the JS object notation):

function pobj(param){this.p1=param;}

var newObj = new pobj("test");;

db.coll.find(); returns { "_id" : ObjectId("4bd722a6eb29000000007ac4"), "p1" : "test" }. You can even 'serialize' objects' methods, and then call the method for the objects deserialized using findOne. All of this might be JS-specific candy, I am curious how this ports over to other language drivers.

So you can view Mongo as a (JS) object-oriented database, with nothing in the way of SQL facilities though; a tuple serialization mechanism; a key-value pair list; a 'document'/hierarchical database using JSON as the document format (as opposed to xDB's XML), all of which are correct.

Another question: when you have an embedded object, var ptrUser = {name : "Mr Iwata", address : { city : "Tokyo }}, how do you search by the inner object properties? db.coll.find({address:{ city : "criteria" }} does not seem to work.RTfM

Also, if you store objects with different structures in one collection, they can be inspected:

from pymongo import Connection
c = Connection()
d = c.clinical
coll = d.physician
for item in coll.find():
itmkeys = []
print item.get("_id")
for ky in item.iterkeys():
print itmkeys

Lots of interesting info at the Wikipedia JSON page.

Monday, April 26, 2010

Data visualization

Some resources:

Very basic Google Chart

  • create the URL
  • you can then pull it in Python:

>>> import urllib
>>> p=urlopen(',40,90,20&cht=p3')
>>> data =
>>> f = file('d:\\file.png', 'wb')
>>> f.write(data)
>>> f.close()

It's quite easy to build the URL based on the data in a Googledoc spreadsheet: (code modified from Google's own documentation)

from xml.etree import ElementTree
except ImportError:
from elementtree import ElementTree
import gdata.spreadsheet.service
import gdata.service
import atom.service
import gdata.spreadsheet
import atom
import string

def main():
gd_client = gdata.spreadsheet.service.SpreadsheetsService() = ''
gd_client.password = '________'
gd_client.source = 'SpreadSheet data source'

print 'List of spreadsheets'
feed = gd_client.GetSpreadsheetsFeed()

key = feed.entry[string.atoi('0')].id.text.rsplit('/', 1)[1]

print 'Worksheets for spreadsheet 0'
feed = gd_client.GetWorksheetsFeed(key)

key_w = feed.entry[string.atoi('0')].id.text.rsplit('/', 1)[1]

print 'Contents of worksheet'
feed = gd_client.GetListFeed(key, key_w)


def PrintFeed(feed):
for i, entry in enumerate(feed.entry):
if isinstance(feed, gdata.spreadsheet.SpreadsheetsCellsFeed):
print 'Cells Feed: %s %s\n' % (entry.title.text, entry.content.text)
elif isinstance(feed, gdata.spreadsheet.SpreadsheetsListFeed):
print 'List Feed: %s %s %s' % (i, entry.title.text, entry.content.text)
print ' Contents:'
for key in entry.custom:
print ' %s: %s' % (key, entry.custom[key].text)
print '\n',
print 'Other Feed: %s. %s\n' % (i, entry.title.text)

if __name__ == "__main__":

Friday, April 23, 2010

NHS Choices on GoogleApps

Here is the Google Apps version of the (Python) NHS Choices application I discussed in the previous posts.

I can't even begin to say how cool this is. 3 hours in Notepad (hence the crudeness) and we get the hospitals in the UK, from anywhere. This is really amazing.

The source code.

Sunday, April 11, 2010

Searching in Python

There is perhaps a more Pyhton-specific way of storing the data to be loaded into the Mongo database: a list of dictionaries. In this case, a dictionary is defined as {'name':__name__, 'service':__service__, 'web':__web__}.To add an element to the holding list (say, NHS): NHS.append({'name':'Wigan General', 'service':5, 'web':None}). Then, a function can be defined which will return the index of the list containing the element matching its parameter; i.e.:

>>> def idx(ky, val):

for item in NHS:

if item[ky] == val:

return NHS.index(item)


>>> print idx('name', 'Wigan General')
will yield Wigan's index in the list. I'm quite curious how fast this is with several thousand records! But Python's ability to easily make sense of a complex data structure is impressive.

Another way of searching, using list comprehensions:

>>> def idx2(ky, val):

lstIdx = [item[ky] == val for item in NHS]

return lstIdx.index(True)

It would also be interesting to know if the bytecode generated by Python is different between the two.

Saturday, April 10, 2010

Mongo, Python, and NHS Choices

Using Python, NHS open data (NHS Choices), and Mongo: for example, getting the name and the web sites of all the providers in the Wigan area (why Wigan? No idea, just that their football team seems to be pretty bad recently defeated Arsenal, and the name stuck with me).

Start the database: go to the bin subdirectory of the install directory, and type mongod –dbpath .\

I will connect to the database using the Python API (pymongo).

NHS choices offers several health data feeds:

  • News
  • Find Services
  • Live Well
  • Health A-Z (Conditions)
  • Common Health Questions

As mentioned, I will use the second; to access it, you need to get a password and a login (apply for one here).

The basic Python code to query for providers and extract their names and web addresses is this:

First, build a list of services, as per the NHS documentation (the service code and the location are two required parameters):

services = [[1, 'GPs'], [2,'Dentists'], etc]

Then, query the web service:

for x in range(0, len(services)):

endpoint='' + str(x)




nodes = xmldoc.getElementsByTagName("Service")

for node in nodes:

website = node.getElementsByTagName("Website")

name = node.getElementsByTagName("Name")

if website[0].firstChild <> None:


The response will have a 3-item dataset, the service type, the provider name, and the web site (if one exists).

Mongo is a bit different in that the 'server' does not create a database physically until something is written to that database, so from the console client (launch, in \bin\: mongo) you can connect to a database that does not exist yet (use NHS in this case will create the NHS database - in effect, it will create files named NHS in the current directory).

Creating the 'table' from the console client: NHS = { service : "service", name : "name", website : "website" };; will create a collection (similar to SQL namespaces) and save the NHS table into it. The mongo client uses JavaScript as language and JSON notation to define the tables.

To access this collection in Python:

>>> from pymongo import Connection

>>> connection = Connection()

>>> db=connection.NHS


>>> post={"service" : 1, "name" : "python", "website" : "mongo" }

>>> storage.insert(post)

Here is the full code in Python to populate the database:

import urllib

from xml.dom import minidom

from pymongo import Connection

print "Building list of services..."

services = [[1, 'GPs'], [2,'Dentists'], [3, 'Pharmacists'], [4, 'Opticians'], [5, 'Hospitals'], [7, 'Walk-in centres'],[9, 'Stop-smoking services'], [10, 'NHS trusts'], [11, 'Sexual health services'], [12,' DISABLED (Maternity units)'], [13, 'Sport and fitness services'], [15, 'Parenting & Childcare services'], [17, 'Alcohol services'], [19, 'Services for carers'], [20, 'Renal Services'], [21, 'Minor injuries units'], [22, 'Mental health services'], [23, 'Breast cancer screening'], [24, 'Support for independent living'], [26, 'Memory problems'], [27, 'Termination of pregnancy (abortion) clinics'], [28, 'Foot services'], [29, 'Diabetes clinics'], [30, 'Asthma clinics'], [31,' Midwifery teams'], [32, 'Community clinics']]

print "Connecting to the database..."

connection = Connection()

db = connection.NHS

storage =

print "Scanning the web service..."

for x in range(0, len(services)):

print '*** ' + services[x][1] + ' ***'

endpoint='' + str(x)




nodes = xmldoc.getElementsByTagName("Service")

for node in nodes:

website = node.getElementsByTagName("Website")

name = node.getElementsByTagName("Name")

namei = name[0].firstChild.nodeValue

if website[0].firstChild <> None:

websitei = ' ' + website[0].firstChild.nodeValue


websitei = 'none'

post = { "service" : x, "name" : namei, "website" : websitei }



To see the results from the Mongo client:


Will return all the hospitals inserted in the database (service for hospitals = 5); the response looks like this:


"_id" : ObjectId("4bc062dbc7ccc10428000032"),

"website" : "",

"name" : "Thomas Linacre Outpatient Centre",

"service" : 5


Next, it might be interesting to try this using Mongo's REST API, and perhaps to build a GoogleApp to do so.

Friday, April 09, 2010

Internet, 247

This is tiresome. I've complained about it before. Until there is a seamless Internet experience, where things work most of the time, I won't buy into the Internet platform. It's unreliable.


Yet another non-relational database. There definitely seems to be a trend in that direction, a market corner that the RDBMS's do not address convincingly. I would guess that for a general purpose system, which might have power users/report writers, a full-fledged database makes sense, but for a turnkey system where speed is important and there is no need to expose too much of the internals to the users, this type of offering is useful.

Saturday, April 03, 2010

More Cache-specific features

Using dates in Cache: (an alternative to this)

  • Class Person…. { DOB As %Date }
  • INSERT INTO Person(… DOB) VALUES(…, TO_DATE('12 Jan 1989')

Using queries in Cache:

Class HIS.Patient Extends %Persistent

Property Name As %String;

Property DOB As %Date;

Property Inpatient As %Boolean;

/// Class query
Query GetInpatients(Inpatient As %Boolean=1) As %SQLQuery(SELECTMODE="RUNTIME")
WHERE Inpatient = :Inpatient


Insert some data in SQL, then:

  • S rset=##class(%RecordSet).%New()
  • S rset.ClassName="HIS.Patient"
  • S rset.QueryName="GetInpatients"
  • Do rset.Execute(1)
  • W rset.Next()
  • If result is 1, w rset.Data("Name")

Cache Streams

Used to store large (>32k) amounts of data:

  • binary
  • character

Hence, streams are supersized binary (%Binary) or character (%String) types. The difference with other databases systems is that streams in Cache can be stored in external files or database global variables.

The following code:

Class CM.Patient Extends %Persistent

Property PatientName As %String;

Property PatientData As %FileCharacterStream(LOCATION = "D:/");


Executed in Terminal:

> DO %^CD

> S p = ##class(CM.Patient).%New()

> DO p.PatientData.Write("Test")

Will create a temporary file on drive D: where the "Test" string will be written to; when the Terminal session ends, the file will be deleted as the object is garbage-collected. In the order for the stream to persist, you have to %Save() the object.

SQL Server just recently started offering FILESTREAMs.

O'Reilly's take on the IOS

Interesting, the Internet Operating System.