Mentions légales du service

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Commit 2bfda6d5 authored by Jérôme Euzenat's avatar Jérôme Euzenat
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- updated the database schema (for version 4.0)

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src/fr/inrialpes/exmo/align/service/CacheImpl.java
+ 53
− 33
View file @ 2bfda6d5
...@@ -70,12 +70,16 @@ public class CacheImpl { ...@@ -70,12 +70,16 @@ public class CacheImpl {
String port = null; String port = null;
int rights = 1; // writing rights in the database (default is 1) int rights = 1; // writing rights in the database (default is 1)
final int VERSION = 340; // Version of the API to be stored in the database final int VERSION = 400; // Version of the API to be stored in the database
/* 300: initial database format /* 300: initial database format
301: added alignment id as primary key 301: added alignment id as primary key
302: changed cached/stored/ouri tag forms 302: changed cached/stored/ouri tag forms
310: changed extension table with added URIs and method -> val 310: changed extension table with added URIs and method -> val
340: changed size of relation in cell table (5 -> 25) 340: changed size of relation in cell table (5 -> 25)
400: changed size of relation in cell table (5 -> 255 because of URIs)
changed all URI size to 255
changed level size to 25
added cell_id as keys?
*/ */
DBService service = null; DBService service = null;
...@@ -203,7 +207,7 @@ public class CacheImpl { ...@@ -203,7 +207,7 @@ public class CacheImpl {
* onto1 is the Ontology object * onto1 is the Ontology object
* uri1 is the URI object from which loading the ontologies * uri1 is the URI object from which loading the ontologies
* In the database we store: * In the database we store:
* owlontology1 the URI string of the ontology * ontology1 the URI string of the ontology
* file1 the URI string from which loading the ontologies * file1 the URI string from which loading the ontologies
* uri1 which should be the same as the last one... * uri1 which should be the same as the last one...
* Since alignments are indexed by the URI of the ontologies, we use * Since alignments are indexed by the URI of the ontologies, we use
...@@ -226,10 +230,10 @@ public class CacheImpl { ...@@ -226,10 +230,10 @@ public class CacheImpl {
// Either uri1 or file1 // Either uri1 or file1
result.setFile1( new URI( rs.getString("file1") ) ); result.setFile1( new URI( rs.getString("file1") ) );
result.setFile2( new URI( rs.getString("file2") ) ); result.setFile2( new URI( rs.getString("file2") ) );
result.getOntologyObject1().setURI( new URI(rs.getString("owlontology1")) ); result.getOntologyObject1().setURI( new URI(rs.getString("ontology1")) );
result.getOntologyObject2().setURI( new URI(rs.getString("owlontology2")) ); result.getOntologyObject2().setURI( new URI(rs.getString("ontology2")) );
result.setExtension( SVCNS, OURI1, rs.getString("owlontology1") ); result.setExtension( SVCNS, OURI1, rs.getString("ontology1") );
result.setExtension( SVCNS, OURI2, rs.getString("owlontology2") ); result.setExtension( SVCNS, OURI2, rs.getString("ontology2") );
result.setLevel(rs.getString("level")); result.setLevel(rs.getString("level"));
result.setType(rs.getString("type")); result.setType(rs.getString("type"));
} }
...@@ -388,27 +392,33 @@ public class CacheImpl { ...@@ -388,27 +392,33 @@ public class CacheImpl {
} }
/** /**
* returns the alignmants between two ontologies * returns the alignments between two ontologies
* if one of the ontologies is null, then return them all * if one of the ontologies is null, then return them all
*/ */
public Set<Alignment> getAlignments( URI uri1, URI uri2 ) { public Set<Alignment> getAlignments( URI uri1, URI uri2 ) {
Set<Alignment> result; Set<Alignment> result;
Set<Alignment> potential = new HashSet<Alignment>(); Set<Alignment> potential = new HashSet<Alignment>();
// Just does not work properly if there is a uri2 but no result
if ( uri2 != null ){ if ( uri2 != null ){
String uri2String = uri2.toString(); String uri2String = uri2.toString();
for( Alignment al : ontologyTable.get( uri2 ) ) { Set<Alignment> found = ontologyTable.get( uri2 );
if ( al.getExtension(SVCNS, OURI2).equals( uri2String ) ) { if ( found != null ) {
potential.add( al ); for( Alignment al : found ) {
if ( al.getExtension(SVCNS, OURI2).equals( uri2String ) ) {
potential.add( al );
}
} }
} }
} }
if ( uri1 != null ) { if ( uri1 != null ) {
if ( potential.isEmpty() ) potential = ontologyTable.get( uri1 ); if ( potential.isEmpty() ) {
Set<Alignment> found = ontologyTable.get( uri1 );
if ( found != null ) {
potential = found;
} else return potential;
}
result = new HashSet<Alignment>(); result = new HashSet<Alignment>();
String uri1String = uri1.toString();
for( Alignment al : potential ) { for( Alignment al : potential ) {
String uri1String = uri1.toString();
// This is not the best because URI are not resolved here... // This is not the best because URI are not resolved here...
if ( al.getExtension(SVCNS, OURI1).equals( uri1String ) ) { if ( al.getExtension(SVCNS, OURI1).equals( uri1String ) ) {
result.add( al ); result.add( al );
...@@ -526,11 +536,11 @@ public class CacheImpl { ...@@ -526,11 +536,11 @@ public class CacheImpl {
Alignment alignment = getAlignment( id ); Alignment alignment = getAlignment( id );
if ( alignment != null ) { if ( alignment != null ) {
Statement st = createStatement(); Statement st = createStatement();
String query = "DELETE FROM extension WHERE id=''"; String query = "DELETE FROM extension WHERE id='"+id+"'";
st.executeUpdate(query); st.executeUpdate(query);
query = "DELETE FROM alignment WHERE id=''"; query = "DELETE FROM alignment WHERE id='"+id+"'";
st.executeUpdate(query); st.executeUpdate(query);
query = "DELETE FROM cell WHERE id=''"; query = "DELETE FROM cell WHERE id='"+id+"'";
st.executeUpdate(query); st.executeUpdate(query);
alignment.setExtension( SVCNS, STORED, (String)null); alignment.setExtension( SVCNS, STORED, (String)null);
st.close(); st.close();
...@@ -569,7 +579,7 @@ public class CacheImpl { ...@@ -569,7 +579,7 @@ public class CacheImpl {
String level = alignment.getLevel(); String level = alignment.getLevel();
query = "INSERT INTO alignment " + query = "INSERT INTO alignment " +
"(id, owlontology1, owlontology2, type, level, file1, file2, uri1, uri2) " + "(id, ontology1, ontology2, type, level, file1, file2, uri1, uri2) " +
"VALUES ('" + quote(id) + "','" + quote(s_O1) + "','" + quote(s_O2) + "','" + quote(type) + "','" + quote(level) + "','" + quote(s_File1) + "','" + quote(s_File2) + "','" + quote(s_uri1) + "','" + quote(s_uri2) + "')"; "VALUES ('" + quote(id) + "','" + quote(s_O1) + "','" + quote(s_O2) + "','" + quote(type) + "','" + quote(level) + "','" + quote(s_File1) + "','" + quote(s_File2) + "','" + quote(s_uri1) + "','" + quote(s_uri2) + "')";
st.executeUpdate(query); st.executeUpdate(query);
for ( String[] ext : alignment.getExtensions() ) { for ( String[] ext : alignment.getExtensions() ) {
...@@ -668,26 +678,26 @@ public class CacheImpl { ...@@ -668,26 +678,26 @@ public class CacheImpl {
create table alignment ( create table alignment (
id varchar(100), id varchar(100),
owlontology1 varchar(250), ontology1 varchar(255),
owlontology2 varchar(250), ontology2 varchar(255),
type varchar(5), type varchar(5),
level varchar(1), level varchar(25),
file1 varchar(250), file1 varchar(255),
file2 varchar(250), file2 varchar(255),
uri1 varchar(250), uri1 varchar(255),
uri2 varchar(250), uri2 varchar(255),
primary key (id)); primary key (id));
# cell info # cell info
create table cell( create table cell(
id varchar(100), id varchar(100),
cell_id varchar(250), cell_id varchar(255),
uri1 varchar(250), uri1 varchar(255),
uri2 varchar(250), uri2 varchar(255),
semantics varchar(30), semantics varchar(30),
measure varchar(20), measure varchar(20),
relation varchar(5)); relation varchar(255));
# extension info # extension info
...@@ -702,8 +712,8 @@ public class CacheImpl { ...@@ -702,8 +712,8 @@ public class CacheImpl {
public void initDatabase() throws SQLException { public void initDatabase() throws SQLException {
Statement st = createStatement(); Statement st = createStatement();
// Create tables // Create tables
st.executeUpdate("CREATE TABLE alignment (id VARCHAR(100), owlontology1 VARCHAR(250), owlontology2 VARCHAR(250), type VARCHAR(5), level VARCHAR(1), file1 VARCHAR(250), file2 VARCHAR(250), uri1 VARCHAR(250), uri2 VARCHAR(250), primary key (id))"); st.executeUpdate("CREATE TABLE alignment (id VARCHAR(100), ontology1 VARCHAR(255), ontology2 VARCHAR(255), type VARCHAR(5), level VARCHAR(25), file1 VARCHAR(255), file2 VARCHAR(255), uri1 VARCHAR(255), uri2 VARCHAR(255), primary key (id))");
st.executeUpdate("CREATE TABLE cell(id VARCHAR(100), cell_id VARCHAR(250), uri1 VARCHAR(250), uri2 VARCHAR(250), semantics VARCHAR(30), measure VARCHAR(20), relation VARCHAR(10))"); st.executeUpdate("CREATE TABLE cell(id VARCHAR(100), cell_id VARCHAR(255), uri1 VARCHAR(255), uri2 VARCHAR(255), semantics VARCHAR(30), measure VARCHAR(20), relation VARCHAR(255))");
st.executeUpdate("CREATE TABLE extension(id VARCHAR(100), uri VARCHAR(200), tag VARCHAR(50), val VARCHAR(500))"); st.executeUpdate("CREATE TABLE extension(id VARCHAR(100), uri VARCHAR(200), tag VARCHAR(50), val VARCHAR(500))");
st.executeUpdate("CREATE TABLE server (host VARCHAR(50), port VARCHAR(5), edit BOOLEAN, version VARCHAR(5))"); st.executeUpdate("CREATE TABLE server (host VARCHAR(50), port VARCHAR(5), edit BOOLEAN, version VARCHAR(5))");
st.close(); st.close();
...@@ -787,9 +797,19 @@ public class CacheImpl { ...@@ -787,9 +797,19 @@ public class CacheImpl {
} }
} }
} }
if ( version < 340 ) { // Nothing to do with 340: subsumed by 400
if ( version < 400 ) {
// Change database // Change database
st.executeUpdate("ALTER TABLE cell CHANGE relation relation VARCHAR(25)"); st.executeUpdate("ALTER TABLE cell CHANGE relation relation VARCHAR(255)");
st.executeUpdate("ALTER TABLE cell CHANGE uri1 uri1 VARCHAR(255)");
st.executeUpdate("ALTER TABLE cell CHANGE uri2 uri2 VARCHAR(255)");
st.executeUpdate("ALTER TABLE alignment CHANGE level level VARCHAR(25)");
st.executeUpdate("ALTER TABLE alignment CHANGE uri1 uri1 VARCHAR(255)");
st.executeUpdate("ALTER TABLE alignment CHANGE uri2 uri2 VARCHAR(255)");
st.executeUpdate("ALTER TABLE alignment CHANGE file1 file1 VARCHAR(255)");
st.executeUpdate("ALTER TABLE alignment CHANGE file2 file2 VARCHAR(255)");
st.executeUpdate("ALTER TABLE alignment CHANGE owlontology1 ontology1 VARCHAR(255)");
st.executeUpdate("ALTER TABLE alignment CHANGE owlontology2 ontology2 VARCHAR(255)");
} }
// Change version // Change version
st.executeUpdate("UPDATE server SET version='"+VERSION+"' WHERE port='port'"); st.executeUpdate("UPDATE server SET version='"+VERSION+"' WHERE port='port'");
......
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