how_to:exportpride
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how_to:exportpride [2011/12/05 14:48] 132.168.73.124 |
how_to:exportpride [2013/01/28 08:05] (current) 132.168.72.131 |
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| **Warning:** | **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).** | * :!: **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, v1.11.1 & v1.12.0 (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:** | **Note:** | ||
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| ===== Main steps to export a UserContext to PRIDE XML format ===== | ===== Main steps to export a UserContext to PRIDE XML format ===== | ||
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| - | - :!: **__Ask the team info for importing spectra into MSIdb__** (while waiting the [[how_to:spectrummatchfeeder|populate MSIdb with spectrum feature]], coming soon !) | ||
| - **From a UserContext in hEIDI**, launch the PRIDE XML Export to create a first PRIDE XML file (see details below) | - **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]]**) | - **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) | - **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]]** | - Check your modified PRIDE XML file using **[[userguide:pride_inspector|PRIDE Inspector]]** | ||
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| ===== 1. Launch PRIDE XML Export from hEIDI ===== | ===== 1. Launch PRIDE XML Export from hEIDI ===== | ||
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| * Answer ''No'' to stop the PRIDE XML Export process (Ask the INFO Team to populate the MSIdb with missing spectra) | * 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 |}} | * 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 ==== | ==== The ''runDescriptor.properties'' file ==== | ||
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| ===== 4. Check your PRIDE XML file using PRIDE Inspector ===== | ===== 4. Check your PRIDE XML file using PRIDE Inspector ===== | ||
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how_to/exportpride.1323092929.txt.gz · Last modified: 2011/12/05 14:48 by 132.168.73.124
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