====== How to export a UserContext into the PRIDE XML Format ======

**Warning:**
  * :!: **Exporting a UserContext to PRIDE XML format is only available for [[http://biodev.extra.cea.fr/docs/irma/doku.php?id=msidb|MSIdb]] version D.4 (or later versions).**  
  * :!: **In hEIDI versions v1.10.1, v1.11.0 and up to now (MSIdb E.1), the ''header'' of the generated PRIDE XML file is not totally achieved** (contact info, experiment & sample details, protocol steps, etc.). **The user will have to use PRIDE Converter to build another PRIDE XML file, from which he will only copy the meta-infos and paste them into the hEIDI generated PRIDE XML file.**

**Note:** 

  * Only visible typical proteins of each protein group will be exported

===== Main steps to export a UserContext to PRIDE XML format =====

  - **From a UserContext in hEIDI**, launch the PRIDE XML Export to create a first PRIDE XML file (see details below)
    - If necessary, a dialog will appear (see below), [[how_to:spectrummatchfeeder|import spectra into MSIdb]]. 
  - **From the PRIDE Converter wizard**, create a second PRIDE XML file (see **[[userguide:pride_converter|here]]**) 
  - **Copy the ''header'' from the second PRIDE XML file and paste it into the first PRIDE XML file** (see below)
  - Check your modified PRIDE XML file using **[[userguide:pride_inspector|PRIDE Inspector]]**

===== 1. Launch PRIDE XML Export from hEIDI =====

Follow these steps to generate a PRIDE XML file from a given context: {{ :how_to:prideexport_compo_1_new.png|}}

  * **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**.
  * **Check the ''runDescriptor.properties'' file** exists in your hEIDI project (see next section)
  * **Select the UserContext you want to export**. It has to be [[how_to:proteingrouping|grouped ]]and [[how_to:savetomsidb|saved to MSIdb]].
  * **Select ''MS Identifications > Context > Export > PRIDE XML''**  
  * **Enter a name for your PRIDE XML file and browse to the directory of your choice** (default is to use the name of the selected UserContext with the .xml extension in the hEIDI project directory).
  * **[WARNING]** A dialog may appear if spectra are missing 
    * Answer ''No'' to stop the PRIDE XML Export process (Ask the INFO Team to populate the MSIdb with missing spectra)          
  * If PRIDE XML Export ended successfully, **a dialog message is displayed at the end of the export process** {{ :how_to:prideexport_success.png |}}
  * A dialog appears to display the log file (see [[how_to:exportpridelog|]] for more details)

  * :!: **Open the resulting .xml Pride file out of hEIDI using any external text editor**. Opening the file in the hEIDI environment may cause memory issue if the file size is too big 

==== The ''runDescriptor.properties'' file ====

In the ''runDescriptor.properties'' file you provide meta information about your experiment (title, description, contact info), your sample(s), the instrument, the protocol steps, etc.\\
The PRIDE XML Export fonctionnality will then parse properties from the ''runDescriptor.properties'' file and create the appropriate //header// in the resulting XML file.

**:!: Warning :!:**

  * **This feature is in progress, so __we highky recommand to [[userguide:pride_converter|use the PRIDE Converter instead of using ''runDescriptor.properties'' file]]__, in order to easily create a full detailled header for your PRIDE XML file.** Nevertheless, if you want to learn more about using the ''runDescriptor.properties'' file, click **[[userguide:pride_export_properties|here]]** for more details about filling in this file)\\
\\
When you create a new hEIDI project, a default ''runDescriptor.properties'' file is created.\\

=== Warning about reusing old hEIDI Project ===

:!: If you use an //old// hEIDI project (created with hEIDI version lower than v1.10.1), check: 

  * A ''runDescriptor.properties'' file exists under **''<HEIDI_PROJECT_DIR>\heidi.project\''**. If it doesn't exist, simply create an empty text file, named ''runDescriptor.properties''
  
=== How to modify the ''runDescriptor.properties'' file in hEIDI === 

  * On the left side of the hEIDI interface, select the ''Files'' tab (or select in the main menu bar ''Window->Files'')
  * Expand the node corresponding to the hEIDI project you are working on. Finally, expand the ''heidi.project'' directory. 
  * Double-click on the ''runDescriptor.properties'' file to open it in the hEIDI editor view (you can also right-click on the ''runDescriptor.properties'' and select ''Open'', it will display the contents of this file in a tabular way)   
  * Change the contents of the file
  * Don't forget to save your changes by selecting ''File->Save'' in the main menu bar
{{:how_to:priderundescriptorfileexample.png|}}

===== 2. Use PRIDE Converter to create another XML file =====

See **[[userguide:pride_converter|here]]** to create a PRIDE XML file from a MASCOT DAT file. 

===== 3. Extract meta-info from PRIDE XML file (generated by PRIDE Converter) to update the PRIDE XML file generated by hEIDI =====

The purpose is to replace meta-information from the first PRIDE XML file (generated by hEIDI) with the more detailled meta-information of the second PRIDE XML file (generated by PRIDE Converter)

{{:how_to:prideconverter_header.png|}}

===== 4. Check your PRIDE XML file using PRIDE Inspector =====