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--- setupguide:upgrade [2014/10/03 11:24]
132.168.72.225
+++ setupguide:upgrade [2016/07/07 10:03] (current)
132.168.72.225 [From graphical interface ProlineAdmin GUI]
@@ Line 5: / Line 5: @@
 ===== Updating the Datastore =====
-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.
+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. You can also use the provided graphical tool, ProlineAdmin GUI.
 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 [[setupguide:firstinstall|first install]] section.)
+==== Command line (ProlineAdmin) ====
 Update datastore by executing the following command:
@@ Line 22: / Line 24: @@
 </code>
-Wait until this operation is finish, it may be relatively long if lots of result files import with spectral matches have been done !
+==== From graphical interface ProlineAdmin GUI ====
+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.
-===== Installing & Running Proline WebCore =====
+If you don't have a valid configuration file, you can change it or edit it (see [[setupguide:setup_with_prolineadmin_gui|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 [[setupguide:start#installing_upgrading_the_proline_suite|configure and set up Proline]], or [[setupguide:setup_with_prolineadmin_gui#setup with prolineadmin gui|using ProlineAdmin GUI]])
+{{ :setupguide:upgrade_proline_databases.png?nolink&800 |}}
+==== ====
+Wait until this operation is finished, it may be relatively long if lots of result files with spectral matches have been imported !
+----
+===== Installing, upgrading & running Proline WebCore =====
 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.
@@ Line 35: / Line 53: @@
 You also need to configure the **''mount_points''** entry as explain here
-===== Setting up Mount-points  =====
+==== Setting up Mount-points  ====
-Result identification files (Mascot dat or OMSSA) as well as mzDB files (for the XIC Quantitation process)  are only browsed from Proline Server side.
+Result identification files (Mascot dat, OMSSA or X!Tandem) 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
+Administrator must configure the target directory(ies) in the entry ''mount_points'' in the ''application.conf'' file by editing the file manually or [[setupguide:setup_with_prolineadmin_gui#Configure the mount-points|using ProlineAdmin GUI]].
 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>"''.
@@ Line 53: / Line 72: @@
     mascot_data = "Z:/"
     omssa_data = "/local/omssa/data"
+    xtandem_data = "U:/"
     ...
   }
@@ Line 80: / Line 100: @@
 fr.proline.core.service.Version Module: Proline-OMP Version: <WYZ>
 </code>
+----
 ===== Account update =====
@@ Line 85: / Line 107: @@
 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 ([[how_to:studio:connectionmgmt|Connection Managment
  page]]) or Proline Web
+----
+===== Installing Sequence Reposiroty =====
+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 =====
+Configuration files are located under the "<your_folder>/config".
+**Datastore description **
+//pg_uds.properties// file define datastore description to access to the UDS database (for postgresql database):
+<code>
+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>
+</code>
+__note__ :
+  * If you didn't change the default naming scheme of databases the <uds_db>= 'uds_db' so <code>javax.persistence.jdbc.url=jdbc:postgresql://<host>:5432/uds_db</code>
+  * 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 '='
+<code>
+# 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+)
+</code>
+_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 theses files will be parse using specific rule (fr.proline.module.seq.uniProtSEDbIdentifierRegex) to extract protein accession.
+For other fasta file the protein accssion will be extract by using string before first blank.
+----
 ===== Upgrading Proline Studio =====
@@ Line 90: / Line 177: @@
   * 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
+----
-===== Installing and configuring Proline Web Desktop =====
-    * [[prolineconcepts:PWD| Install, Configure and launch the Desktop]]
+===== Upgrading and configuring Proline Web Desktop =====
+//TODO

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