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--- how_to:spectrummatchfeeder [2011/03/08 15:34]
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+++ how_to:spectrummatchfeeder [2013/04/11 10:41] (current)
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@@ Line 1: / Line 1: @@
 ====== How-to populate MSI database with spectrum details ======
-Before [[how_to:exportpride|exporting a given UserContext to PRIDE XML file]], check if the MSI database need to be populated with spectrum details:
+Before [[how_to:exportpride|exporting a given UserContext to PRIDE XML file]], check if the MSI database need to be populated with spectrum details.
+:!: **Since hEIDI 1.11.1, this functionality is no more available from the hEIDI GUI, but has to be executed (outside from hEIDI, see bellow) [by your system administrator]. **
+===== Import spectrum using tool outside hEIDI [by your system administrator] =====
+To import spectrum detail for a specified context using ''Paloma'' tool, you need to have the context id. This property is accessible in Context property sheet. View in [[how_to:accessproperties|]] page.
+  * Download Paloma-<version>.zip and unzip to <Paloma-install> directory. (Download is available at the following FTP site : [[ftp://ftp.cea.fr/pub/edyp/heidi]])
+  * In command prompt (Run -> Cmd), go to <Paloma-install>/ and run : <code>java -Djava.library.path=./lib -Xms512m  -Xmx1024m  -classpath ./paloma-<version>.jar cea.edyp.palomae1.MainSpectrumFeeder [OPTIONS]</code>
+    * -Xmx option allow you to specify amount of memory to use for yhios process. Depending on your system (amount of memory and 32bits or 64bits), you can set more memory : -Xmx4000m for example
+    * OPTIONS are described if no parameter is specified in command line... Nevertheless, here they are : ''-u <user> -p <password> -url <dbURL> -m <root> [-d <driver>]  -cid <context_id>''  where
+      * <user> : user for DB connection
+      * <password> : password for DB connection
+      * <dbURL> : url to DB such as jdbc:postgresql:/ / <server_name>/<DB_Name>
+      * <root> : Path to mascot data files
+      * <driver> : Optional, default is Postgresql driver (org.postgresql.Driver)
+      * <context_id> : Context ID to get spectra for
+  * You can verify there were no error by opening paloma-<user>.log from <Paloma-install> directory. This file contains lots of information, for debug purpose.
+      * Search for any "ERROR " string to verify no error occurs.
+      * You can also see how many mascot dat file were parsed.
+       Look for entry such has
+           INFO SpectrumEntriesSearch - The selected context contains 2,686 species and 2,686 spectrum are needed
+           INFO SpectrumEntriesSearch - Paloma - SpectrumEntriesSearch - identify 44 dat files
+           INFO SpectrumEntriesSearch -  .... featuring 2686 peptides
+           INFO SpectrumMatchFeeder - Paloma - SpectrumMatchFeeder - will parse 44 dat files
+      * You will also see "44" entry like ''Parser dat file : XXXXX''. Each followed by ''Parser dat file DONE''
+===== Import spectrum using hEIDI =====
+:!: **Since hEIDI 1.11.1, this functionality is no more available. Should be reintegrated ... **
   * **After having [[how_to:createproject|created ]]or [[how_to:loadproject|opened an hEIDI project]], [[how_to:opensession|open your MSI session]]** but :!: **Don't forget to __activate__ your hEIDI project**.{{ :how_to:spectrummatchfeeder_menu.png|}}
+  * **Check, in Windows Explorer, you have mapped a drive to the Mascot data folder** (\\cp-mascot\data) and you are connected to that folder.
   * **Select a UserContext**. It has to be [[how_to:proteingrouping|grouped ]]and [[how_to:savetomsidb|saved to MSIdb]].
   * Select the menu **''MS Identifications->Database Update->Populate with spectra''**
   * A dialog will appear on the screen to indicate if spectrum details are missing for this UserContext
-  * Check Mascot data root path is correct
+  * **Check the Mascot data root path**. You can use ''\\cp-mascot\data'' or the corresponding Drive Letter you have set up in Windows Explorer, for example ''Y:''.
 {{:how_to:spectrummatchfeeder_dialog.png|}}
   * If spectrum details are missing, click on ''Ok, populate MSIdb with missing spectra'', else click on ''Do nothing & Close this window''
   * In case you have clicked ''Yes'', a message will appear when process is finished
 {{:how_to:spectrummatchfeeder_success.png|}}

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