From Beta 2 to Version 1_0:
or
From Version 1_0 to Version 1_1:

To update the different Proline Databases, you need to get the appropriate version of ProlineAdmin GUI. ProlineAdmin GUI is released as an archive file (in ProlineServer archive), extract this archive in your preferred folder to install this application. From this tool you can use the command line or the provided graphical tool.

The configuration files didn't change. You can just copy theses files from your previous ProlineAdmin to the new one. Configuration files are located 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 the datastore by executing the following command:

> run_cmd.bat upgrade_dbs

> chmod +x run_cmd.sh
> run_cmd.sh upgrade_dbs

Verbose mode is used in order to display as much information as needed. You can view all displayed information in proline_admin_log.txt, and especially search for any “ERROR” message.

Open the graphical interface by running start.bat (or start.sh on linux system). If you used the Windows installer, a shortcut “Proline Admin” is available in the Windows Start Menu, under the Proline folder.

If you don't have a valid configuration file, you can change it or edit it (see how to).

Click the button named Upgrade Proline databases.

Note: This functionnality will be disable if the configuration is invalid or if Proline is not set up (see how to configure and set up Proline, or using ProlineAdmin GUI)

Wait until this operation is finished!

Extract Proline WebCore zip file (packaged into ProlineServer archive) to the location of your choice, use a different location than previous installation. This could be also be done using installer.

Configuration files

Before running the server, you first need to modify ProlineWeb-Core configuration. Configuration files are located at <your_folder>\ProlineWeb-Core-x.y.z\Proline\WEB-INF\classes.

The configuration files didn't change. You can just copy theses files from your previous ProlineWeb-Core to the new one.

To use the XIC Quantitation process, you should also configure the mzDB files mount_points entry. See first installation documentation for more details.

Runner
You can upgrade the amount of memory used by the server in the jetty-runner.bat /jetty-runner.sh file. If the server is configured with large amount of memory, it is recommanded to increase this value. Change the value of -Xmx option: Xmx4g ⇒ -Xmx8g to upgrade from 4 GB (defaults) to 8GB.

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 or http://<hostname>: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>

This module is unchanged since Beta3.

Even if this is an optional module it is recommended to install it, mostly if you want to view the proteins sequences in the user interfaces! 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.

Extract archive file (packaged into ProlineServer archive) to the location of your choice, use a different location than previous installation.

Configuration files didn't change, you can copy them from previous version to new one. They are located under the “<your_folder>/config”.

Here is a description of these files, for new Sequence Reposiroty's user:

Datastore description

pg_uds.properties file 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

Protein description parsing rule

As this module is used to extract Protein Sequence, description from a fasta file for a specific protein accession, it is necessary to configure the rule used to parse the protein ACC, from fasta description line. This is similar to the rules specified in Mascot Server. To do this, retrieve-service.properties file should be edited. In this file it is necessary to escape (this means prefix with '\') some characters: '\' , ':' and '='

# Name of the UDS Db configuration file (Java properties format)
fr.proline.module.seq.udsDbConfigurationFile=pg_uds.properties

# Paths must exist (regular file or directory) and multiple paths must be separated by ';' character
fr.proline.module.seq.localFASTAPaths=Y\:\\sequence;D\:\\Temp\\Admin\\FASTAs

# Java Regex with capturing group for SEDbInstance release version string (CASE_INSENSITIVE)
fr.proline.module.seq.defaultReleaseRegex=_(?:D|(?:Decoy))_(.*)\\.fasta

# UniProt style SEDb (FASTA file name must contain this Java Regex CASE_INSENSITIVE) multiple Regex separated by ';' character
fr.proline.module.seq.uniProtSEDbNames=\\AUP_;ISA_D

# Java Regex with capturing group for SEDbIdentifier value (without double quote)
# UniProt EntryName ">\\w{2}\\|[^\\|]*\\|(\\S+)"
# UniProt UniqueIdentifier (primary accession number) ">\\w{2}\\|([^\\|]+)\\|"
# GENERIC Regex ">(\\S+)"
fr.proline.module.seq.uniProtSEDbIdentifierRegex=>\\w{2}\\|[^\\|]*\\|(\\S+)

_Note_:

• fr.proline.module.seq.localFASTAPaths: only one instance should be defined. For linux system, fr.proline.module.seq.localFASTAPaths=/local/data/fasta;/local/mascot/sequence
• fr.proline.module.seq.defaultReleaseRegex: Regular expression to extract release version (CASE_INSENSITIVE) from the fasta files.
• fr.proline.module.seq.uniProtSEDbNames: Regular expression to identify Uniprot like fasta. The entry of these files will be parse using specific rule (fr.proline.module.seq.uniProtSEDbIdentifierRegex) to extract protein accession.

For other fasta file the protein accession will be extract by using string before first blank.

• 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.