1. Relational Databases: Object Relational Mappers – SQLObject II
BCHB524 Lecture 23
BCHB524 - Edwards

2. Relational Databases Store information in a table Rows represent items
Columns represent items' properties or attributes
Name
Continent
Region
Surface Area
Population
GNP
Brazil
South America
776739
Indonesia
Asia
Southeast Asia
84982
India
Southern and Central Asia
447114
China
Eastern Asia
982268
Pakistan
796095
61289
United States
North America
BCHB524 - Edwards

3. ... 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 =  c1.population =  c1.gnp =  # initialize c2, ..., c6 countryTable = [ c1, c2, c3, c4, c5, c6 ] for cnty in countryTable:     if cnty.population >  :         print cnty.name, cnty.population
BCHB524 - Edwards

4. Taxonomy Database, from scratch
Specify the model
Tables: Taxonomy and Name
Populate basic data-values in the Taxonomy table from “small_nodes.dmp”
Populate the Names table from “small_names.dmp”
Insert basic data-values
Insert relationship with Taxonomy table
Fix Taxonomy parent relationship
Fix Taxonomy derived information
Use in a program…
BCHB524 - Edwards

5. Taxonomy Database: model.py
from sqlobject import * import os.path, sys dbfile = 'small_taxa.db3' def init(new=False):     # Magic formatting for database URI     conn_str = os.path.abspath(dbfile)     conn_str = 'sqlite:'+ conn_str     # Connect to database     sqlhub.processConnection = connectionForURI(conn_str)     if new:         # Create new tables (remove old ones if they exist)         Taxonomy.dropTable(ifExists=True)         Name.dropTable(ifExists=True)         Taxonomy.createTable()         Name.createTable()
BCHB524 - Edwards

6. Taxonomy Database: model.py
# model.py continued…
class Taxonomy(SQLObject):     taxid = IntCol(alternateID=True)     scientific_name = StringCol()     rank = StringCol()     parent = ForeignKey("Taxonomy") class Name(SQLObject):     taxonomy = ForeignKey("Taxonomy")     name = StringCol()     name_class = StringCol()
BCHB524 - Edwards

7. Taxonomy Database structure
Name
Taxonomy 1 2 3 4 5 6 1 2 3 4 5
parent
taxonomy
taxonomy: 4
parent: 2
taxonomy: 4
parent: 2
taxonomy: 4
Foreign Key: id number of some other row
BCHB524 - Edwards

8. Populate Taxonomy table: load_taxa.py
import sys from model import * init(new=True) # Read in the taxonomy nodes, populate taxid and rank h = open(sys.argv[1]) for l in h:     l = l.strip('\t|\n')             sl = l.split('\t|\t')     taxid = int(sl[0])     rank = sl[2]     t = Taxonomy(taxid=taxid, rank=rank,                  scientific_name=None,                  parent=None) h.close()
import sys
from model import *
init(new=True)
# Read in the taxonomy nodes, populate taxid and rank
h = open(sys.argv[1])
for l in h:
l = l.strip('\t|\n')
sl = l.split('\t|\t')
taxid = int(sl[0])
rank = sl[2]
t = Taxonomy(taxid=taxid, rank=rank,
scientific_name=None,
parent=None)
h.close()
BCHB524 - Edwards

9. Populate Name table: load_names.py
import sys from model import * init() # Read in the names, populate name, class, and id of  # taxonomy row h = open(sys.argv[1]) for l in h:     l = l.strip('\t|\n')             sl = l.split('\t|\t')     taxid = int(sl[0])     name_class = sl[3]     name = sl[1]     t = Taxonomy.byTaxid(taxid)     n = Name(name=name, name_class=name_class, taxonomy=t) h.close()
import sys
from model import *
init()
# Read in the names, populate name, class, and id of taxonomy row
h = open(sys.argv[1])
for l in h:
l = l.strip('\t|\n')
sl = l.split('\t|\t')
taxid = int(sl[0])
name_class = sl[3]
name = sl[1]
t = Taxonomy.byTaxid(taxid)
n = Name(name=name, name_class=name_class, taxonomy=t)
h.close()
BCHB524 - Edwards

10. Fix up the Taxonomy table: fix_taxa.py
import sys from model import * init() # Read in the taxonomy nodes, get self and parent taxonomy objects, # and fix the parent field appropriately h = open(sys.argv[1]) for l in h:     l = l.strip('\t|\n')             sl = l.split('\t|\t')     taxid = int(sl[0])     parent_taxid = int(sl[1])     t = Taxonomy.byTaxid(taxid)     p = Taxonomy.byTaxid(parent_taxid)     t.parent = p h.close() # Find all scientific names and fix their taxonomy objects' scientific # name files appropriately for n in Name.select(Name.q.name_class == 'scientific name'):     n.taxonomy.scientific_name = n.name
import sys
from model import *
init()
# Read in the taxonomy nodes, get self and parent taxonomy objects,
# and fix the parent field appropriately
h = open(sys.argv[1])
for l in h:
l = l.strip('\t|\n')
sl = l.split('\t|\t')
taxid = int(sl[0])
parent_taxid = int(sl[1])
t = Taxonomy.byTaxid(taxid)
p = Taxonomy.byTaxid(parent_taxid)
t.parent = p
h.close()
# Find all scientific names and fix their taxonomy objects' scientific
# name files appropriately
for n in Name.select(Name.q.name_class == 'scientific name'):
n.taxonomy.scientific_name = n.name
BCHB524 - Edwards

11. Back to the Taxonomy example
Each taxonomy entry can have multiple names
Many names can point (ForeignKey) to a single taxonomy entry
name → taxonomy is easy...
taxonomy → list of names requires a select statement
from model import * init() hs = Taxonomy.byTaxid(9606) for n in Name.select(Name.q.taxonomy==hs):      print n.name
BCHB524 - Edwards

12. Taxonomy Database structure
Name
Taxonomy 1 2 3 4 5 6 1 2 3 4 5
parent
taxonomy
taxonomy: 4
parent: 2
taxonomy: 4
parent: 2
taxonomy: 4
Foreign Key: id number of some other row
BCHB524 - Edwards

13. Taxonomy table relationships
This relationship (one-to-many) is called a multiple join.
Related joins (many-to-many) too...
class Taxonomy(SQLObject):     # other data members     names = MultipleJoin("Name")     children = MultipleJoin("Taxonomy",joinColumn='parent_id')
from model import * init() hs = Taxonomy.byTaxid(9606) for n in hs.names:      print n.name for c in hs.children:      print c.scientific_name
BCHB524 - Edwards

14. SQLObject Exceptions What happens when the row isn't in the table?
from model import * try:    hs = Taxonomy.get(7921)    hs = Taxonomy.byTaxid(9606) except SQLObjectNotFound:    # if row id 7921 / Tax id 9606 is not in table... results = Taxonomy.selectBy(taxid=9606) if results.count() == 0:    # No rows satisfy the constraint!     try:    first_item = results[0] except IndexError:    # No first item in the results
BCHB524 - Edwards

15. Example Program import sys from model import * init()
try:     taxid = int(sys.argv[1]) except IndexError:     print >>sys.stderr, "Need a taxonomy id argument"     sys.exit(1) except ValueError:     print >>sys.stderr, "Taxonomy id should be an intenger"     sys.exit(1)      #Get taxonomy row try:     t = Taxonomy.byTaxid(taxid) except SQLObjectNotFound:     print >>sys.stderr, "Taxonomy id",taxid,"does not exist"     sys.exit(1) for n in t.names:     print "Organism",t.scientific_name,"has name",n.name for c in t.children:     print "Organism",t.scientific_name,"has child",c.scientific_name,c.taxid print "Organism",t.scientific_name,"has parent",t.parent.scientific_name,t.parent.taxid
BCHB524 - Edwards

16. Example Program # Continued...
# Iterate up through the taxonomy tree from t, to find its genus r = t g = None while r != r.parent:     if r.rank == 'genus':         g = r         break     r = r.parent if g == None:     print "Organism",t.scientific_name,"has no genus" else:     print "Organism",t.scientific_name,"has genus",g.scientific_name
BCHB524 - Edwards

17. Exercises
Write a python program using SQLObject to find the taxonomic lineage of a user-supplied organism name.
Make sure you use the small_taxa.db3 file from the course data-folder
Note that the supplied model.py files from Lectures 23 and 24 are different!
Lecture 23 uses taxa.db3, Lecture 24 uses small_taxa.db3
BCHB524 - Edwards

18. Homework 11 Due Monday, November 27th. Exercise from Lecture 22
BCHB524 - Edwards