Differences

This shows you the differences between two versions of the page.

--- how_to:exportpride [2011/03/08 12:31]
132.168.74.230
+++ how_to:exportpride [2013/01/28 08:05] (current)
132.168.72.131
@@ Line 3: / Line 3: @@
 **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 the current hEIDI version (v1.10.1 / 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.**
+  * :!: **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 typical proteins of each protein group will be exported
+  * 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 **PRIDE Inspector**
+  - 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.png|}}
+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 Context you want to export**. For a User Context, it has to be [[how_to:proteingrouping|grouped ]]and [[how_to:savetomsidb|saved to MSIdb]].
+  * **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).
-  * **[Optional]** A dialog may appear if spectra are missing
+  * **[WARNING]** A dialog may appear if spectra are missing
-    * Answer ''No'' if you want to stop the PRIDE XML Export process (you will then need to populate the MSIdb using the SpectrumMatchFeeder tool)
+    * Answer ''No'' to stop the PRIDE XML Export process (Ask the INFO Team to populate the MSIdb with missing spectra)
-    * Answer ''Yes'' if you want hEIDI to launch for you the tool to populate MSIdb with missing spectra
-      * **Check the Mascot data root path**. You can keep the default value (''\\cp-mascot\data'') or use the corresponding Drive Letter you have set up in Windows Explorer, for example ''Y:''. Check, in Windows Explorer, you have mapped a drive to the Mascot data folder (\\cp-mascot\data) and you are connected to that folder.
-      * **Click ''Ok, populate MSIdb with missing info''** to update database
-      * A dialog will appear when MSIdb is populated with missing spectra and **ask you to relaunch PRIDE XML Export**.
   * 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
+  * :!: **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 ====
@@ Line 69: / Line 65: @@
 ===== 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 (divided in 2 parts) 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)
+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 =====

hEIDI

User Tools

Site Tools

Differences

Page Tools