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yap-6.3/packages/prosqlite/examples/uniprot.pl

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2015-09-21 23:05:36 +01:00
:- module( uniprot, [uniprot/0] ).
:- nl, nl, nl.
:- write( 'To get the example database used in this examples do:' ), nl.
:- write( 'wget http://stoics.org.uk/~nicos/sware/sqlite/uniprot.sqlite' ), nl.
:- nl, nl.
:- use_module( library(prosqlite) ).
/** <module> uniprot: A complete example for proSQLite.
Look at the sources for the difference predicate calls.
You need the test database from
http://stoics.org.uk/~nicos/sware/sqlite/uniprot.sqlite
The output should look like:
==
άμπελος;lib/db% swipl -f none
?- uniprot.
Running on :date(2012,10,17)
Using database at: uniprot.sqlite
table:secondary_accessions
table:identifier_mapping
secondary_accessions/secondary_accession
secondary_accessions/primary_accession
identifier_mapping/uniprot_accession
identifier_mapping/identifier_type
identifier_mapping/target_identifier
secondary_accessions:286525
identifier_mapping:3044651
secondary_accessions+286525
identifier_mapping+3044651
[A0A111,Q10706]-_G309
rows_for(_G309):[row(A0A111),row(Q10706)]
by_findall(P64943,[A0A111,Q10706])
Caution! Deleting db entries for-P64943
Affected rows:row(2)
now(P64943,[])
Not to worry! Adding back the db entries for-P64943
affected_two(row(1),row(1))
finally(P64943,[A0A111,Q10706])
v:0:1:0
vd:date(2012,10,17)
citation
Exploring file based databases via an Sqlite interface.
Canisius Sander, Nicos Angelopoulos and Lodewyk Wessels
In the ICLP Workshop on Logic-based methods in Programming Environments (WLPE'12),
p.2-9, 2012. Budapest, Hungary.
true.
?-
==
@version 0.1.2, 2013/11/1
@see latest version at http://stoics.org.uk/~nicos/sware/prosqlite/uniprot.pl
@see also http://stoics.org.uk/~nicos/sware/sqlite/uniprot.sqlite (184Mb)
*/
/** uniprot.
Test predicate for prosqlite. Tests all components.
You need the test database from
http://stoics.org.uk/~nicos/sware/sqlite/uniprot.sqlite
*/
uniprot :-
date( Date ),
write( 'Running on ':Date ), nl,
sqlite_connect('uniprot.sqlite',uniprot, as_predicates(true) ), % connect the database
nl,
show_tables,
show_columns,
show_counts,
findall_counts,
Id = 'P64943',
findall( A, secondary_accessions(A,Id), As ),
write( As-Id ), nl,
Q = 'Select secondary_accession From secondary_accessions Where primary_accession="~w"',
findall( Row, sqlite_format_query( uniprot, Q-'P64943', Row ), Rows ),
write(rows_for(Id):Rows), nl, nl,
findall( S, secondary_accessions(S,Id), SetBef ),
write( by_findall(Id,SetBef) ), nl,
write( 'Caution! Deleting db entries for'-Id ), nl,
sqlite_query( uniprot, 'Delete from secondary_accessions where primary_accession="P64943";', Aff ),
write( 'Affected rows':Aff ), nl,
findall( S, secondary_accessions(S,Id), SetAft ),
write( now(Id,SetAft) ), nl, nl,
write( 'Not to worry! Adding back the db entries for'-Id ), nl,
sqlite_query( uniprot, 'Insert into secondary_accessions (primary_accession,secondary_accession) Values ("P64943","A0A111");', Aff1 ),
sqlite_query( uniprot, 'Insert into secondary_accessions (secondary_accession,primary_accession) Values ("Q10706","P64943");', Aff2 ),
write( affected_two( Aff1, Aff2 ) ), nl,
findall( S, secondary_accessions(S,Id), SetFin ),
write( finally(Id,SetFin) ), nl, nl,
sqlite_version( Ver, VerDate ),
write( v:Ver ), nl,
write( vd:VerDate ), nl, nl,
sqlite_citation( AtmCite, _B ),
write( citation ), nl,
write( AtmCite ), nl.
show_tables :-
sqlite_current_table( uniprot, Table ),
write( table:Table ), nl,
fail.
show_tables :-
nl.
show_columns :-
sqlite_table_column( uniprot, Table, Col ),
write( Table/Col ), nl,
fail.
show_columns :-
nl.
show_counts :-
sqlite_current_table(uniprot, Table),
sqlite_table_count(uniprot, Table, Count),
write(Table:Count), nl,
fail.
show_counts :-
nl.
findall_counts :-
sqlite_current_table(uniprot, Table, arity(Arity) ),
length(List, Arity),
Pred =.. [Table|List],
findall(1, Pred, Ones),
length(Ones, Count),
write( Table+Count ), nl,
fail.
findall_counts :-
nl.