Author: osallou-guest
Date: 2011-08-19 07:01:03 +0000 (Fri, 19 Aug 2011)
New Revision: 7476
Added:
trunk/packages/biomaj/trunk/debian/biomaj-properties.install
trunk/packages/biomaj/trunk/debian/biomaj.install
trunk/packages/biomaj/trunk/debian/biomaj.links
trunk/packages/biomaj/trunk/debian/patches/removeSqlToolDependency
trunk/packages/biomaj/trunk/debian/watch
Modified:
trunk/packages/biomaj/trunk/debian/changelog
trunk/packages/biomaj/trunk/debian/control
trunk/packages/biomaj/trunk/debian/get-orig-source
trunk/packages/biomaj/trunk/debian/patches/series
trunk/packages/biomaj/trunk/debian/postinst
trunk/packages/biomaj/trunk/debian/rules
Log:
updates for upstream 1.2
Added: trunk/packages/biomaj/trunk/debian/biomaj-properties.install
===================================================================
--- trunk/packages/biomaj/trunk/debian/biomaj-properties.install
(rev 0)
+++ trunk/packages/biomaj/trunk/debian/biomaj-properties.install
2011-08-19 07:01:03 UTC (rev 7476)
@@ -0,0 +1 @@
+usr/share/biomaj/examples/db_properties
Added: trunk/packages/biomaj/trunk/debian/biomaj.install
===================================================================
--- trunk/packages/biomaj/trunk/debian/biomaj.install
(rev 0)
+++ trunk/packages/biomaj/trunk/debian/biomaj.install 2011-08-19 07:01:03 UTC
(rev 7476)
@@ -0,0 +1,10 @@
+usr/share/biomaj/sql
+usr/share/biomaj/bin
+usr/share/biomaj/conf
+usr/share/biomaj/workflows
+usr/share/biomaj/lib
+usr/share/doc/biomaj
+var/lib/biomaj
+var/log/biomaj
+etc/biomaj
+usr/bin
Added: trunk/packages/biomaj/trunk/debian/biomaj.links
===================================================================
--- trunk/packages/biomaj/trunk/debian/biomaj.links
(rev 0)
+++ trunk/packages/biomaj/trunk/debian/biomaj.links 2011-08-19 07:01:03 UTC
(rev 7476)
@@ -0,0 +1,2 @@
+etc/biomaj/general.conf usr/share/biomaj/general.conf
+etc/biomaj/unix_command_system.cfg
usr/share/biomaj/conf/process/unix_command_system.cfg
Modified: trunk/packages/biomaj/trunk/debian/changelog
===================================================================
--- trunk/packages/biomaj/trunk/debian/changelog 2011-08-18 23:49:14 UTC
(rev 7475)
+++ trunk/packages/biomaj/trunk/debian/changelog 2011-08-19 07:01:03 UTC
(rev 7476)
@@ -1,3 +1,11 @@
+biomaj (1.2.0-1) unstable; urgency=low
+
+ * New upstream release with new features and bug fixes.
+ * Change in database model, migration script ran at install
+ * New post processes added in default install (emboss)
+
+ -- Olivier Sallou <[email protected]> Thu, 18 Aug 2011 09:55:23 +0200
+
biomaj (1.1.0-3) unstable; urgency=low
* Change priority in debconf message for jdk home
Modified: trunk/packages/biomaj/trunk/debian/control
===================================================================
--- trunk/packages/biomaj/trunk/debian/control 2011-08-18 23:49:14 UTC (rev
7475)
+++ trunk/packages/biomaj/trunk/debian/control 2011-08-19 07:01:03 UTC (rev
7476)
@@ -9,19 +9,33 @@
Homepage: http://biomaj.genouest.org
Build-Depends: debhelper (>= 7.1)
Build-Depends-Indep: debconf, po-debconf,
openjdk-6-jdk|default-jdk|sun-java6-jdk, ant, libhsqldb-java, ant-contrib,
- liblog4j1.2-java, libcommons-net-java, libcommons-dbcp-java, libgnumail-java,
libcommons-pool-java,
- libgnujaf-java, libjgoodies-forms-java, liboro-java, libregexp-java,
libjfreechart-java,
+ liblog4j1.2-java, libcommons-net2-java, libcommons-dbcp-java,
libgnumail-java, libcommons-pool-java,
+ libgnujaf-java, libjgoodies-forms-java, liboro-java, libregexp-java,
libjcommon-java, libjsch-java, libjdom1-java, junit4, libsaxonb-java, junit4,
libjdepend-java,
- javahelper (>=0.25)
+ javahelper (>=0.25), libcommons-cli-java, libcommons-codec-java,
libcommons-httpclient-java, libcommons-logging-java,
+ libjets3t-java
Standards-Version: 3.9.1
Package: biomaj
Architecture: all
Depends: openjdk-6-jdk|default-jdk|sun-java6-jdk, ant, libmysql-java, debconf,
${misc:Depends}, ${java:Depends},
- libhsqldb-java,ant-contrib,liblog4j1.2-java,libcommons-net-java (>=
1.4),libcommons-dbcp-java (>= 1.2), libgnumail-java, libcommons-pool-java (>=
1.5), libgnujaf-java, libjgoodies-forms-java (>= 1.2),liboro-java (>=
2.0),libregexp-java (>= 1.4),libjfreechart-java (>= 1.0),libjcommon-java (>=
1.0),libjsch-java (>= 0.1.42),libjdom1-java (>= 1.1),junit4,libsaxonb-java (>=
0.9)
+ libhsqldb-java,ant-contrib,liblog4j1.2-java,libcommons-net2-java (>=
2.2),libcommons-dbcp-java (>= 1.2),
+ libgnumail-java, libcommons-pool-java (>= 1.5), libgnujaf-java,
libjgoodies-forms-java (>= 1.2),
+ liboro-java (>= 2.0),libregexp-java (>= 1.4),libjcommon-java (>=
1.0),libjsch-java (>= 0.1.42),
+ libjdom1-java (>= 1.1),junit4,libsaxonb-java (>= 0.9), libcommons-cli-java,
libcommons-codec-java,
+ libcommons-httpclient-java, libcommons-logging-java,libjets3t-java, perl
Suggests: mysql-community-server-5.0, ncbi-tools-bin, blast2
Description: Biological banks updater
BioMAJ downloads remote data banks, check their status and apply
transformation
workflows, with consistent state,to provide ready-to-use data to biologists
and
bioinformaticians. For example, it can transform original fasta files to
blast
indexes. It is very flexible and post-processes can be extended very easily.
+
+Package: biomaj-properties
+Architecture: all
+Depends: ${misc:Depends}
+Description: bank properties file examples
+ This package contains a set of bank properties that can be used
+ as examples for biomaj. It contains many existing banks descriptions
+ with or without workflows to transform data.
+ Some files may required additional programs for post processes (blast..)
Modified: trunk/packages/biomaj/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/biomaj/trunk/debian/get-orig-source 2011-08-18 23:49:14 UTC
(rev 7475)
+++ trunk/packages/biomaj/trunk/debian/get-orig-source 2011-08-19 07:01:03 UTC
(rev 7476)
@@ -1,12 +1,12 @@
#!/bin/bash -e
#biomaj version
-export BMAJVERSION="1.1.0"
+export BMAJVERSION="1.2.0"
-svn export svn://scm.gforge.inria.fr/svn/biomaj/tags/1.1.0/biomaj_deb
+svn export svn://scm.gforge.inria.fr/svn/biomaj/trunk/biomaj_deb
rmdir biomaj_deb/usr/share/biomaj/apache-tomcat-6.0.24
-svn export svn://scm.gforge.inria.fr/svn/biomaj/BioMAJ-$BMAJVERSION
+svn export svn://scm.gforge.inria.fr/svn/biomaj/biomaj_dev BioMAJ-$BMAJVERSION
chmod 755 BioMAJ-$BMAJVERSION/bin/*
cp -R BioMAJ-$BMAJVERSION/bin/* biomaj_deb/usr/share/biomaj/bin/
mkdir -p biomaj_deb/usr/share/doc/biomaj
@@ -15,11 +15,6 @@
cp -R BioMAJ-$BMAJVERSION/doc/UsersGuide_BioMAJ_EN.odt
biomaj_deb/usr/share/doc/biomaj/
cp -R BioMAJ-$BMAJVERSION/doc/UsersGuide_BioMAJ_FR.odt
biomaj_deb/usr/share/doc/biomaj/
-#cp BioMAJ-$BMAJVERSION/lib/commons-cli-2.0-SNAPSHOT.jar
biomaj_deb/usr/share/biomaj/lib/
-
-svn export http://svn.apache.org/repos/asf/commons/sandbox/cli2/trunk
biomaj_deb/usr/share/biomaj/lib/vendor/commons-cli2
-chmod 644
biomaj_deb/usr/share/biomaj/lib/vendor/commons-cli2/src/site/resources/images/1x1.gif
-
if [ -e biomaj_deb/usr/share/biomaj/lib/biomaj.jar ]
then
rm biomaj_deb/usr/share/biomaj/lib/biomaj.jar
@@ -27,6 +22,9 @@
echo "Copy files..."
cp -R BioMAJ-$BMAJVERSION/src/* biomaj_deb/usr/share/biomaj/src/
cp -R BioMAJ-$BMAJVERSION/sql/* biomaj_deb/usr/share/biomaj/sql/
+mkdir -p biomaj_deb/var/lib/biomaj/
+chmod 755 biomaj_deb/usr/share/biomaj/sql/migration/*.pl
+mv biomaj_deb/usr/share/biomaj/sql/migration biomaj_deb/var/lib/biomaj/
cp -R BioMAJ-$BMAJVERSION/workflows/* biomaj_deb/usr/share/biomaj/workflows/
cp -R BioMAJ-$BMAJVERSION/xslt/* biomaj_deb/usr/share/biomaj/xslt/
cp BioMAJ-$BMAJVERSION/*.* biomaj_deb/usr/share/biomaj/
@@ -38,15 +36,26 @@
echo "Delete unnecessary files"
-rm biomaj_deb/usr/share/biomaj/general.conf
+#rm -f biomaj_deb/usr/share/biomaj/general.conf
rm -rf biomaj_deb/usr/share/biomaj/xslt/css
rm -rf biomaj_deb/usr/share/biomaj/doc
echo "Update configuration"
+sed -i
's/$BIOMAJ_ROOT=$Bin\."\/\.\.\/\.\."/$BIOMAJ_ROOT="\/usr\/share\/biomaj"/'
biomaj_deb/var/lib/biomaj/migration/update.pl
cp -R BioMAJ-$BMAJVERSION/conf/* biomaj_deb/etc/biomaj/
+mkdir -p biomaj_deb/usr/share/biomaj/examples/db_properties
+mv biomaj_deb/etc/biomaj/db_properties/workflow_withprocess
biomaj_deb/usr/share/biomaj/examples/db_properties/
+mv biomaj_deb/etc/biomaj/db_properties/workflow_without_process
biomaj_deb/usr/share/biomaj/examples/db_properties/
sed 's/data.dir=/data.dir=\/var\/lib\/biomaj\//'
biomaj_deb/etc/biomaj/db_properties/global.properties >
biomaj_deb/etc/biomaj/db_properties/global.properties.tmp
mv biomaj_deb/etc/biomaj/db_properties/global.properties.tmp
biomaj_deb/etc/biomaj/db_properties/global.properties
+mkdir -p biomaj_deb/etc/biomaj/db_properties/admin
+# put banks
+mv biomaj_deb/etc/biomaj/db_properties/alu.properties
biomaj_deb/etc/biomaj/db_properties/admin/
+mv biomaj_deb/etc/biomaj/db_properties/sts.properties
biomaj_deb/etc/biomaj/db_properties/admin/
+
+
mv biomaj_deb/etc/biomaj/process/* biomaj_deb/usr/share/biomaj/conf/process/
+mv biomaj_deb/usr/share/biomaj/conf/process/unix_command_system.cfg
biomaj_deb/etc/biomaj/
rmdir biomaj_deb/etc/biomaj/process
echo "Updating file rights"
Added: trunk/packages/biomaj/trunk/debian/patches/removeSqlToolDependency
===================================================================
--- trunk/packages/biomaj/trunk/debian/patches/removeSqlToolDependency
(rev 0)
+++ trunk/packages/biomaj/trunk/debian/patches/removeSqlToolDependency
2011-08-19 07:01:03 UTC (rev 7476)
@@ -0,0 +1,351 @@
+Author: Olivier Sallou <[email protected]>
+Subject: remove usage of hsqld2
+Description: remote sqltool references, not used in debian packaging as
hsqldb2 is not packaged.
+Last-Update: 2011-08
+---
a/usr/share/biomaj/src/org/inria/biomaj/exe/migration/CoreMigrationFrom1_1To1_2.java
++++
b/usr/share/biomaj/src/org/inria/biomaj/exe/migration/CoreMigrationFrom1_1To1_2.java
+@@ -14,8 +14,8 @@
+ import java.util.List;
+ import java.util.UUID;
+
+-import org.hsqldb.cmdline.SqlFile;
+-import org.hsqldb.cmdline.SqlToolError;
++//import org.hsqldb.cmdline.SqlFile;
++//import org.hsqldb.cmdline.SqlToolError;
+ import org.inria.biomaj.singleton.BiomajInformation;
+ import org.inria.biomaj.sql.SQLConnection;
+ import org.inria.biomaj.sql.SQLConnectionFactory;
+@@ -210,19 +210,6 @@
+ }
+
+ private static void createNewHSQLTables(Statement stat) {
+- File file = new File(biomajRoot + "/sql/hsql-to_1.2.sql");
+- try {
+- SqlFile sqlFile = new SqlFile(file);
+- sqlFile.setConnection(stat.getConnection());
+-
+- sqlFile.execute();
+- } catch (IOException e) {
+- e.printStackTrace();
+- } catch (SQLException e) {
+- e.printStackTrace();
+- } catch (SqlToolError e) {
+- e.printStackTrace();
+- }
+ }
+
+ private static boolean createNewMySQLTables(SQLConnection connection,
Statement stat) {
+--- a/usr/share/biomaj/src/org/inria/biomaj/sql/HSQLDBConnection.java
++++ b/usr/share/biomaj/src/org/inria/biomaj/sql/HSQLDBConnection.java
+@@ -21,8 +21,6 @@
+ import java.util.UUID;
+
+ import org.apache.commons.dbcp.BasicDataSource;
+-import org.hsqldb.cmdline.SqlFile;
+-import org.hsqldb.cmdline.SqlToolError;
+ import org.inria.biomaj.singleton.BiomajLogger;
+ import org.inria.biomaj.utils.BiomajConst;
+ import org.inria.biomaj.utils.BiomajUtils;
+@@ -131,156 +129,7 @@
+ @Override
+ public boolean createDB(String adminLogin, String adminPasswd, String
adminMail) {
+
+- Statement statement = getStatement();
+- try {
+-
+- TreeSet<String> versions = new TreeSet<String>();
+- File[] filz = new File(dbPath).listFiles(new
FilenameFilter() {
+-
+- @Override
+- public boolean accept(File dir, String name) {
+- return name.startsWith("hsql-to");
+- }
+- });
+-
+- for (File fl : filz) {
+- versions.add(fl.getName()); // sort versions
+- }
+-
+- List<String> runFiles = new ArrayList<String>();
+- Collections.addAll(runFiles, new File(dbPath +
"/migration").list());
+-
+- if (!runFiles.contains("hsql.sql")) { // Run all
+- System.out.println("Run all sql scripts...");
+- /*
+- * Base file
+- */
+- File file = new File(dbPath + "/hsql.sql");
+- SqlFile sqlFile = new SqlFile(file);
+-
sqlFile.setConnection(statement.getConnection());
+-
+- sqlFile.execute();
+-
+- System.out.println("hsql.sql run.");
+- writeFileVersion("hsql.sql");
+-
+- /*
+- * New versions
+- */
+- for (String name : versions) {
+- File nf = new File(dbPath + "/" + name);
+- sqlFile = new SqlFile(nf);
+-
sqlFile.setConnection(statement.getConnection());
+- sqlFile.execute();
+-
+- System.out.println(name + " run.");
+- writeFileVersion(name);
+- }
+-
+- } else {
+- System.out.println("Run new sql scripts...");
+- /*
+- * New versions only
+- */
+- for (String name : versions) {
+- if (!runFiles.contains(name)) {
+- File file = new File(dbPath +
"/" + name);
+- SqlFile sqlFile = new
SqlFile(file);
+-
sqlFile.setConnection(statement.getConnection());
+-
+- sqlFile.execute();
+-
+- System.out.println(name + "
run.");
+- writeFileVersion(name);
+- }
+- }
+- }
+-
+- /*
+- * Insert admin records
+- */
+-
+- // Generates admin auth_key
+- String key = UUID.randomUUID().toString();
+- String hash = "";
+-
+- // Generates password hash
+- MessageDigest digest;
+- try {
+- digest = MessageDigest.getInstance("SHA1");
+- digest.update(passwd.getBytes());
+- byte[] hashedPasswd = digest.digest();
+- hash = BiomajUtils.getHexString(hashedPasswd);
+- } catch (NoSuchAlgorithmException e) {
+- e.printStackTrace();
+- }
+-
+- String testUser = "SELECT * FROM bw_user WHERE login='"
+ adminLogin + "'";
+- ResultSet rs = executeQuery(testUser, statement);
+- if (!rs.next()) {
+-
+- String insertUser = "INSERT INTO bw_user(login,
password, auth_type, auth_key, mail_address) " +
+- "VALUES('" + adminLogin + "','"
+ hash + "','local','" + key + "','" + adminMail + "')";
+- int userId =
executeUpdateAndGetGeneratedKey(insertUser, statement);
+-
+- String testGroup = "SELECT idgroup FROM
bw_group WHERE name='admin'";
+- rs = executeQuery(testGroup, statement);
+- int groupId;
+- if (rs.next()) {
+- System.out.println("Adding " +
adminLogin + " to current admin group");
+- groupId = rs.getInt(1);
+- } else {
+- String createGroup = "INSERT INTO
bw_group(name) VALUES('admin')";
+- groupId =
executeUpdateAndGetGeneratedKey(createGroup, statement);
+- }
+-
+- String userToGroup = "INSERT INTO
bw_user_has_group(ref_iduser, ref_idgroup) VALUES(" + userId + "," + groupId +
")";
+- executeUpdate(userToGroup, statement);
+-
+-
+- boolean updated = false;
+- try {
+- String testTable = "SELECT visibility
FROM bank";
+- statement.executeQuery(testTable);
+- updated = true; // No error, column
already added
+- } catch (SQLException e) {
+- updated = false;
+- }
+-
+- if (!updated) { // Not yet updated
+-
+- String hsql_addColumnToBank = "ALTER
TABLE bank ADD COLUMN ref_iduser INT DEFAULT " + userId;
+- executeUpdate(hsql_addColumnToBank,
statement);
+-
+- hsql_addColumnToBank = "ALTER TABLE
bank ADD COLUMN visibility BOOLEAN DEFAULT false";
+- executeUpdate(hsql_addColumnToBank,
statement);
+-
+- String hsql_addConstraint = "ALTER
TABLE bank ADD CONSTRAINT fk_bank_to_user FOREIGN KEY (ref_iduser) REFERENCES
bw_user(iduser)";
+- executeUpdate(hsql_addConstraint,
statement);
+- }
+-
+- } else {
+- System.err.println("User " + adminLogin + "
already exists");
+- }
+-
+-
+-
+- SQLConnectionFactory.closeConnection(statement);
+-// statement.executeBatch();
+- } catch (SQLException e) {
+- SQLConnectionFactory.closeConnection(statement);
+- e.printStackTrace();
+- return false;
+- } catch (IOException e) {
+- SQLConnectionFactory.closeConnection(statement);
+- e.printStackTrace();
+- return false;
+- } catch (SqlToolError e) {
+- SQLConnectionFactory.closeConnection(statement);
+- e.printStackTrace();
+- return false;
+- }
+- return true;
++ return false;
+ }
+
+ private void writeFileVersion(String name) throws IOException {
+--- a/usr/share/biomaj/src/org/inria/biomaj/sql/TestConnection.java
++++ b/usr/share/biomaj/src/org/inria/biomaj/sql/TestConnection.java
+@@ -16,8 +16,6 @@
+ import java.util.UUID;
+
+ import org.apache.commons.dbcp.BasicDataSource;
+-import org.hsqldb.cmdline.SqlFile;
+-import org.hsqldb.cmdline.SqlToolError;
+ import org.inria.biomaj.singleton.BiomajLogger;
+ import org.inria.biomaj.utils.BiomajUtils;
+
+@@ -61,132 +59,7 @@
+ @Override
+ public boolean createDB(String adminLogin, String adminPasswd, String
adminMail) {
+
+- Statement statement = getStatement();
+- try {
+-
+- TreeSet<String> versions = new TreeSet<String>();
+- File[] filz = new File(dbPath).listFiles(new
FilenameFilter() {
+-
+- @Override
+- public boolean accept(File dir, String name) {
+- return name.startsWith("hsql-to");
+- }
+- });
+-
+- for (File fl : filz) {
+- versions.add(fl.getName()); // sort versions
+- }
+-
+-
+- /*
+- * Base file
+- */
+- File file = new File(dbPath + "/hsql.sql");
+- SqlFile sqlFile = new SqlFile(file);
+- sqlFile.setConnection(statement.getConnection());
+-
+- sqlFile.execute();
+-
+- System.out.println("hsql.sql run.");
+-
+- /*
+- * New versions
+- */
+- for (String name : versions) {
+- File nf = new File(dbPath + "/" + name);
+- sqlFile = new SqlFile(nf);
+-
sqlFile.setConnection(statement.getConnection());
+- sqlFile.execute();
+-
+- System.out.println(name + " run.");
+- }
+-
+-
+-
+- /*
+- * Insert admin records
+- */
+-
+- // Generates admin auth_key
+- String key = UUID.randomUUID().toString();
+- String hash = "";
+-
+- // Generates password hash
+- MessageDigest digest;
+- try {
+- digest = MessageDigest.getInstance("SHA1");
+- digest.update(passwd.getBytes());
+- byte[] hashedPasswd = digest.digest();
+- hash = BiomajUtils.getHexString(hashedPasswd);
+- } catch (NoSuchAlgorithmException e) {
+- e.printStackTrace();
+- }
+-
+- String testUser = "SELECT * FROM bw_user WHERE login='"
+ adminLogin + "'";
+- ResultSet rs = executeQuery(testUser, statement);
+- if (!rs.next()) {
+-
+- String insertUser = "INSERT INTO bw_user(login,
password, auth_type, auth_key, mail_address) " +
+- "VALUES('" + adminLogin + "','"
+ hash + "','local','" + key + "','" + adminMail + "')";
+- int userId =
executeUpdateAndGetGeneratedKey(insertUser, statement);
+-
+- String testGroup = "SELECT idgroup FROM
bw_group WHERE name='admin'";
+- rs = executeQuery(testGroup, statement);
+- int groupId;
+- if (rs.next()) {
+- System.out.println("Adding " +
adminLogin + " to current admin group");
+- groupId = rs.getInt(1);
+- } else {
+- String createGroup = "INSERT INTO
bw_group(name) VALUES('admin')";
+- groupId =
executeUpdateAndGetGeneratedKey(createGroup, statement);
+- }
+-
+- String userToGroup = "INSERT INTO
bw_user_has_group(ref_iduser, ref_idgroup) VALUES(" + userId + "," + groupId +
")";
+- executeUpdate(userToGroup, statement);
+-
+- boolean updated = false;
+- try {
+- String testTable = "SELECT visibility
FROM bank";
+- statement.executeQuery(testTable);
+- updated = true; // No error, column
already added
+- } catch (SQLException e) {
+- updated = false;
+- }
+-
+- if (!updated) { // Not yet updated
+-
+- String hsql_addColumnToBank = "ALTER
TABLE bank ADD COLUMN ref_iduser INT DEFAULT " + userId;
+- executeUpdate(hsql_addColumnToBank,
statement);
+-
+- hsql_addColumnToBank = "ALTER TABLE
bank ADD COLUMN visibility BOOLEAN DEFAULT false";
+- executeUpdate(hsql_addColumnToBank,
statement);
+-
+- String hsql_addConstraint = "ALTER
TABLE bank ADD CONSTRAINT fk_bank_to_user FOREIGN KEY (ref_iduser) REFERENCES
bw_user(iduser)";
+- executeUpdate(hsql_addConstraint,
statement);
+- }
+-
+- } else {
+- System.err.println("User " + adminLogin + "
already exists");
+- }
+-
+-
+-
+- SQLConnectionFactory.closeConnection(statement);
+-// statement.executeBatch();
+- } catch (SQLException e) {
+- SQLConnectionFactory.closeConnection(statement);
+- e.printStackTrace();
+- return false;
+- } catch (IOException e) {
+- SQLConnectionFactory.closeConnection(statement);
+- e.printStackTrace();
+- return false;
+- } catch (SqlToolError e) {
+- SQLConnectionFactory.closeConnection(statement);
+- e.printStackTrace();
+- return false;
+- }
+- return true;
++ return false;
+ }
+
+ private Connection getConnection() {
Modified: trunk/packages/biomaj/trunk/debian/patches/series
===================================================================
--- trunk/packages/biomaj/trunk/debian/patches/series 2011-08-18 23:49:14 UTC
(rev 7475)
+++ trunk/packages/biomaj/trunk/debian/patches/series 2011-08-19 07:01:03 UTC
(rev 7476)
@@ -1 +1 @@
-fix623558_remove_pid
+removeSqlToolDependency
Modified: trunk/packages/biomaj/trunk/debian/postinst
===================================================================
--- trunk/packages/biomaj/trunk/debian/postinst 2011-08-18 23:49:14 UTC (rev
7475)
+++ trunk/packages/biomaj/trunk/debian/postinst 2011-08-19 07:01:03 UTC (rev
7476)
@@ -10,8 +10,6 @@
ant_home="/usr/share/ant"
biomaj_root="/usr/share/biomaj"
jdk_home=$(readlink -f /usr/bin/javac | sed "s:/bin/javac::")
- #db_get biomaj/jdk_home
- #jdk_home="$RET"
db_type="MySQL"
db_get biomaj/mysql_host
db_url="jdbc:mysql://$RET/biomaj_log"
@@ -24,15 +22,13 @@
cd $biomaj_root
- #javac -d $biomaj_root/bin $biomaj_root/bin/Configurator.java
-
java -cp $biomaj_root/bin Configurator java_home:=$jdk_home
ant_home:=$ant_home biomaj_root:=$biomaj_root use_ldap:=$use_ldap
ldap_host:=$ldap_host ldap_dn:=$ldap_dn opt_filter:=$opt_filter
db_type:=$db_type db_url:=$db_url db_login:=$db_login db_passwd:=$db_passwd
app_login:=$app_login app_passwd:=$app_passwd tomcat_port:=$tomcat_port
- if [ $db_type = "MySQL" ]; then
- echo "Installation Complete."
- echo "You now need to create the biomaj_log database on your MySQL
server."
- echo "The creation script is provided at
/usr/share/biomaj/sql/mysql.sql."
- fi
+ if [ ! -e /usr/share/biomaj/sql/migration ]; then
+ ln -s /var/lib/biomaj/migration /usr/share/biomaj/sql/migration
+ fi
+ # Database and scripts install and upgrades
+ perl /var/lib/biomaj/migration/update.pl -dbuser $db_login -dbpwd
$db_passwd -db mysql
;;
Modified: trunk/packages/biomaj/trunk/debian/rules
===================================================================
--- trunk/packages/biomaj/trunk/debian/rules 2011-08-18 23:49:14 UTC (rev
7475)
+++ trunk/packages/biomaj/trunk/debian/rules 2011-08-19 07:01:03 UTC (rev
7476)
@@ -10,36 +10,21 @@
export DH_OPTIONS
export ANT_HOME=/usr/share/ant
-#export JAVA_HOME=/usr/lib/jvm/java-6-openjdk/
JAVA_HOME=$(readlink -f /usr/bin/javac | sed "s:/bin/javac::")
%:
dh $@ --with javahelper
override_dh_auto_build:
- ant -f usr/share/biomaj/lib/vendor/commons-cli2.xml
- cp
usr/share/biomaj/lib/vendor/commons-cli2-build/dist/commons-cli-2.0-SNAPSHOT.jar
usr/share/biomaj/lib/
- ant -f usr/share/biomaj/lib/vendor/commons-cli2.xml clean
ant -f usr/share/biomaj/build.xml
javac -d usr/share/biomaj/bin usr/share/biomaj/bin/Configurator.java
override_dh_clean:
dh_clean
- if test -e usr/share/biomaj/lib/vendor/commons-cli2-build;then ant -f
usr/share/biomaj/lib/vendor/commons-cli2.xml clean;fi;
- rm -f usr/share/biomaj/lib/commons-cli-2.0-SNAPSHOT.jar
rm -rf usr/share/biomaj/build
rm -rf usr/share/biomaj/dist
rm -f usr/share/biomaj/lib/biomaj.jar
rm -f usr/share/biomaj/bin/*.class
-override_dh_install:
- # dh_install
- dh_install --exclude=usr/share/biomaj/lib/vendor
--exclude=usr/share/biomaj/build --exclude=usr/share/biomaj/dist
usr/share/biomaj
- dh_install usr/share/doc
- dh_install usr/bin/biomaj
- dh_install var/lib/biomaj
- dh_install var/log/biomaj
- dh_install etc/biomaj
-
get-orig-source:
. debian/get-orig-source
Added: trunk/packages/biomaj/trunk/debian/watch
===================================================================
--- trunk/packages/biomaj/trunk/debian/watch (rev 0)
+++ trunk/packages/biomaj/trunk/debian/watch 2011-08-19 07:01:03 UTC (rev
7476)
@@ -0,0 +1,2 @@
+version=3
+https://gforge.inria.fr/frs/?group_id=369
.*/biomaj_(\d[\d.-]+)\.orig.(?:tar(?:\.gz|\.bz2)?|tgz|zip)
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