1. Relational Databases: Object Relational Mappers - SQLObject BCHB524 2014 Lecture 22 11/14/2014BCHB524 - 2014 - Edwards

2. 11/14/2014BCHB524 - 2014 - Edwards2 Outline Object relational mappers Tables as classes, rows as instances Advantages & disadvantages Minimal SQLObject example Legacy databases Exercises

3. 11/14/2014BCHB524 - 2014 - Edwards3 Relational Databases Store information in a table Rows represent items Columns represent items' properties or attributes NameContinentRegionSurface AreaPopulationGNP BrazilSouth America 8547403170115000776739 IndonesiaAsiaSoutheast Asia190456921210700084982 IndiaAsiaSouthern and Central Asia32872631013662000447114 ChinaAsiaEastern Asia95729001277558000982268 PakistanAsiaSouthern and Central Asia79609515648300061289 United StatesNorth America 93635202783570008510700

4. 11/14/2014BCHB524 - 2014 - Edwards4... as Objects Objects have data members or attributes. Store objects in a list or iterable. Abstract away details of underlying RDBMS c1 = Country() c1.name = 'Brazil' c1.continent = 'South America' c1.region = 'South America' c1.surfaceArea = 8547403 c1.population = 170115000 c1.gnp = 776739 # initialize c2,..., c6 countryTable = [ c1, c2, c3, c4, c5, c6 ] for cnty in countryTable: if cnty.population > 100000000: print cnty.name, cnty.population

5. 11/14/2014BCHB524 - 2014 - Edwards5 Pros and Cons Pros: Learn one language Ease of development Simplified joins One set of data-types Easy storage of higher-level objects Can apply the power of python as necessary Abstract away RDBMS Distribute CPU load Cons: Execution speed Sometimes forced into poor strategies Optimal SQL construct may be impossible Tend not to take advantage of RDBMS quirks. Can be difficult to apply to legacy databases

6. 11/14/2014BCHB524 - 2014 - Edwards6 SQLObject Just one of many object-relational mappers Each tool makes different tradeoffs in Table/row/attribute abstraction How much SQL you need to know Overhead Ease of adapting to legacy databases SQLObject is almost completely devoid of SQL and is almost entirely "objecty". See http://sqlobject.org.

7. 11/14/2014BCHB524 - 2014 - Edwards7 Minimal SQLObject Example: Define the database model (model.py) from sqlobject import * import os.path dbfile = 'myworld.db3' # Magic formatting for database URI conn_str = os.path.abspath(dbfile) conn_str = 'sqlite:'+ conn_str sqlhub.processConnection = connectionForURI(conn_str) class Country(SQLObject): name = StringCol() continent = StringCol() region = StringCol() surfaceArea = FloatCol() population = IntCol() gnp = FloatCol()

8. 11/14/2014BCHB524 - 2014 - Edwards8 Minimal SQLObject Example: Populate the database from model import Country # Initialize the table Country.createTable() # Add some rows c = Country(name="Brazil", continent="South America", region="South America", surfaceArea=8547403, population=170115000, gnp=776739) c = Country(name="China", continent="Asia", region="Eastern Asia", surfaceArea=9572900, population=1277558000, gnp=982268) #... c = Country(name="United States", continent="North America", region="North America", surfaceArea=9363520, population=278357000, gnp=8510700) # Retrieve and print all countries for c in Country.select(): print c.id, c.name, c.continent, c.gnp

9. 11/14/2014BCHB524 - 2014 - Edwards9 Minimal SQLObject Example: Access/Change the database from model import Country # Change country #6 c = Country.get(6) c.name = 'United States of America' # Retrieve and print all countries for c in Country.select(): print c.id, c.name, c.continent, c.gnp

10. 11/14/2014BCHB524 - 2014 - Edwards10 Minimal SQLObject Example: Access the rows as objects from model import Country # Select countries with more than 500,000,000 in population for c in Country.select(Country.q.population >= 500000000): print "A:", c.id, c.name, c.population # Select countries that start with 'U' for c in Country.select(Country.q.name.startswith("U")): print "B:", c.id, c.name, c.population # Lookup by id, exactly 1 country with each id c = Country.get(5) print "C:", c.id, c.name, c.population # Get exception for bad id # c = Country.get(100) # Shortcut for select, countries with continent == 'Asia' for c in Country.selectBy(continent = 'Asia'): print "D:", c.id, c.name, c.population

11. 11/14/2014BCHB524 - 2014 - Edwards11 Legacy databases If the legacy database is well-structured, SQLObject can figure out (most of) the definitions If there is no id column... Need to tell SQLObject what to use for the ID. May need to specify the id at instantiation time. Have to fill in MultipleJoins and ForeignKeys yourself Need to declare which columns in two different tables should correspond. Enables SQLObject to make relationships explicit Enables SQLObject to turn joins into lists

12. 11/14/2014BCHB524 - 2014 - Edwards12 Legacy databases from sqlobject import * import os.path dbfile = 'taxa.db3' conn_str = os.path.abspath(dbfile) conn_str = 'sqlite:'+ conn_str sqlhub.processConnection = connectionForURI(conn_str) class Taxonomy(SQLObject): class sqlmeta: idName = "tax_id" fromDatabase = True names = MultipleJoin('Name', joinColumn="tax_id") class Name(SQLObject): class sqlmeta: fromDatabase = True taxa = ForeignKey('Taxonomy', dbName="tax_id")

13. 11/14/2014BCHB524 - 2014 - Edwards13 Legacy databases # Set up data-model from model import * # get homo sapiens hs1 = Taxonomy.get(9606) # select the Taxonomy object # with scientific name Homo sapiens hs2 = Taxonomy.selectBy(scientificName='Homo sapiens')[0] # get the name human try: hsname = Name.selectBy(name='human')[0] except IndexError: print "Can't find name 'human'" sys.exit(1) # get the Taxonomy object from the Name object # Uses the magic Foreign Key attribute hs3 = hsname.taxa # hs1, hs2, hs3 the same! print hs1 print hs2 print hs3

14. 11/14/2014BCHB524 - 2014 - Edwards14 Legacy databases # Set up data-model from model import * # get homo sapiens hs = Taxonomy.get(9606) # find rows in the Name table with taxa the same as hs # Use ForeignKey to create condition, equality test # between objects condition = (Name.q.taxa == hs) for n in Name.select(condition): print n # find rows in the Name table corresonding to hs # Easy shortcut, using MultipleJoin iterable for n in hs.names: print n.name, "|", n.nameClass # More general conditions condition = Name.q.name.startswith('Da') for n in Name.select(condition): print n.name, "|", n.nameClass

15. 11/14/2014BCHB524 - 2014 - Edwards15 Exercises Read through the SQLObject documentation Write a python program using SQLObject to lookup the scientific name for a user-supplied organism name.