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--- setupguide:upgrade [2014/10/03 14:56]
132.168.72.225
+++ setupguide:upgrade [2016/07/07 10:03] (current)
132.168.72.225 [From graphical interface ProlineAdmin GUI]
@@ Line 11: / Line 11: @@
 (To see configuration description, see [[setupguide:firstinstall|first install]] section.)
-==== Command line ====
+==== Command line (ProlineAdmin) ====
 Update datastore by executing the following command:
@@ Line 26: / Line 26: @@
 ==== From graphical interface ProlineAdmin GUI ====
-Once you have editted your configuration file, click the "Upgrade databases" button.
+Open the graphical interface by running ''start.bat'' (or ''start.sh'' on linux system).
-{{ :setupguide:upgrade_dbs.png?nolink&600 |}}
+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 [[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 import with spectral matches have been done !
+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 =====
@@ Line 45: / Line 55: @@
 ==== 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 61: / Line 72: @@
     mascot_data = "Z:/"
     omssa_data = "/local/omssa/data"
+    xtandem_data = "U:/"
     ...
   }
@@ Line 88: / Line 100: @@
 fr.proline.core.service.Version Module: Proline-OMP Version: <WYZ>
 </code>
+----
 ===== Account update =====
@@ Line 93: / 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 =====
@@ Line 103: / Line 119: @@
 ==== Configuration =====
-Configuration files are located under the "<your_folder>/config". //pg_uds.properties// define datastore description to access to the UDS database (for postgresql database):
+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>
@@ Line 117: / Line 137: @@
   * proline_user_password and user_proline are the same as specified in ''application.conf'' for Proline Admin or Proline WebCore
-As this module is used to extract Protein Sequence, description from a fasta file for specific protein ID, it is necessary to configure also the rule used to parse the protein ID from fasta description line. This is similar to the rules specified in Mascot Server.
+**Protein description parsing rule **
-To do this, //retrieve-service.properties// file should be edited. This file is used by the module, in order to read
+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 126: / 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
+----
 ===== Upgrading and configuring Proline Web Desktop =====
+//TODO

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