1. Relational Databases: Object Relational Mappers – SQLObject II BCHB524 2013 Lecture 23 11/20/2013BCHB524 - 2013 - Edwards

2. 11/20/2013BCHB524 - 2013 - Edwards2 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

3. 11/20/2013BCHB524 - 2013 - Edwards3... 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

4. 11/20/2013BCHB524 - 2013 - Edwards4 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…

5. 11/20/2013BCHB524 - 2013 - Edwards5 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()

6. 11/20/2013BCHB524 - 2013 - Edwards6 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()

7. 11/20/2013BCHB524 - 2013 - Edwards7 Taxonomy Database structure TaxonomyName 123456123456 1234512345 taxonomy: 4 parent: 2 Foreign Key: id number of some other row taxonomy parent parent: 2 taxonomy: 4

8. 11/20/2013BCHB524 - 2013 - Edwards8 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()

9. 11/20/2013BCHB524 - 2013 - Edwards9 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()

10. 11/20/2013BCHB524 - 2013 - Edwards10 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

11. 11/20/2013BCHB524 - 2013 - Edwards11 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

12. 11/20/2013BCHB524 - 2013 - Edwards12 Taxonomy Database structure TaxonomyName 123456123456 1234512345 taxonomy: 4 parent: 2 Foreign Key: id number of some other row taxonomy parent parent: 2 taxonomy: 4

13. 11/20/2013BCHB524 - 2013 - Edwards13 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

14. 11/20/2013BCHB524 - 2013 - Edwards14 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

15. 11/20/2013BCHB524 - 2013 - Edwards15 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

16. 11/20/2013BCHB524 - 2013 - Edwards16 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

17. 11/20/2013BCHB524 - 2013 - Edwards17 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