From Beta 1 to Beta 2:

To update the differents Proline Databases, you need to get the appropriated version of ProlineAdmin. ProlineAdmin is released as an archive file, extract this archive in your preferred folder to install this application.

The configuration files didn't change. You can just copy theses files from your previous ProlineAdmin to the new one. Configuration files are locates under config folder. Note: default naming scheme of databases created by Proline can be modified by editing config/application-<dbtype>.conf file. (To see configuration description, see first install section.)

Update datastore by executing the following command:

> run_cmd.bat upgrade_dbs

or, on linux system

> run_cmd.sh upgrade_dbs

Wait until this operation is finish, it may be relatively long if lots of result files import with spectral matches have been done !

Download apropriated Proline WebCore and extract the resulting zip file to the location of your choice, use a different location than previous installation. Before running Jetty, you first need to modify ProlineWeb-Core configuration.

The configuration files, located at <your_folder>\ProlineWeb-Core-x.y.z\Proline\WEB-INF\classes, are different from previous version.

You can copy the datastore description from previous release back to the new application.conf file (see Setting up the Datastore).

You also need to configure the mount_points entry as explain here

Result identification files (Mascot dat or OMSSA) as well as mzDB files (for the XIC Quantitation process) are only browsed from Proline Server side.

Administrator must configure the target directory/ies in the entry mount_points in the application.conf file

Mascot dat or OMSSA path should be configured in result_files sub-entry, administrator can add one or more mappings as label = “<absolute/directory/path>”. mzDB files path should be set under mzdb_files sub-entry.

Label can be any valid string chosen by Administrator to help user identify mount_point. If multiple repositories are defined, labels must be different.

Configuration examples :

mount_points {

  result_files {
    mascot_data = "Z:/"
    omssa_data = "/local/omssa/data"
    ...
  }
  ...
  
  mzdb_files {
    mzd_path = "/local/data/mzdb"
  }

}

Run jetty-runner.bat (or jetty-runner.sh on linux system) to start the jetty server. You should now be able to access ProlineWeb-Core by typing http://localhost:8080/proline orhttp://<host>:8080/proline in your favorite browser. The following message must appear :

ProlineWeb-Core working !

Number of IVersion services : <X>
fr.proline.core.wsl.Version Module: ProlineWeb-Core Version: <XXX>
fr.proline.module.parser.omssa.Version Module: PM-OmssaParser Version: <YYY>
fr.proline.module.parser.mascot.Version Module: PM-MascotParser Version:<XYZ>
fr.proline.admin.Version Module: Proline-Admin Version: <ZYW>
fr.proline.util.ScalaVersion Module: ProFI-Commons-Scala Version: <YZX>
fr.proline.util.JavaVersion Module: ProFI-Commons-Java Version: <YXZ>
fr.proline.core.service.Version Module: Proline-OMP Version: <WYZ>

In previous version, there were a common logging between Proline Web and Prolibe Server but different passwords. We changed this behaviour, so after you upgrade your proline server, your password will be reset to 'proline'. You can change this from Proline Studio (Connection Managment page) or Proline Web

A new module is available in Proline Beta2. Even if this is a optionnal module it is recommended to install it, mostly if you want to view the proteins sequences in the user interfaces !

This module is distributed as an archive file and need to be extract in your preferred folder to install. However as this module will parse the mascot fasta files to extract sequence and description from it, it will be more efficient if installed on the same server as your Mascot Server. You should also be able to access to the database server from the server where Sequence Repository is installed.

Configuration files are located under the “<your_folder>/config”. pg_uds.properties define datastore description to access to the UDS database (for postgresql database):

javax.persistence.jdbc.driver=org.postgresql.Driver
javax.persistence.jdbc.url=jdbc:postgresql://<host>:<port>/<uds_db>
javax.persistence.jdbc.user=<user_proline>
javax.persistence.jdbc.password=<proline_user_password>

note :

• If you didn't change the default naming scheme of databases the <uds_db>= 'uds_db' so javax.persistence.jdbc.url=jdbc:postgresql:<host>:5432/uds_db * proline_user_password and user_proline are the same as specified in application.conf for Proline Admin or Proline WebCore ===== Upgrading Proline Studio ===== * Proline Studio application distribution is a zip file that must be unzip on each client PC. You should unzip it under a different folder than previous version ===== Upgrading and configuring Proline Web Desktop =====