Base Upgrade Instrucations
--------------------------
cd /opt/xnat-production_build_area/NITRCSRC
cvs updat -d -r IR_5_1
cd feddata2/xnat
emacs build.properties (enter correct settings)
rm -rf deployments/ir
sh bin/setup.sh
#
# Check if there is a upgrade.sql file in ./deployments/ir/sql
# Run it if found.
#
cp /usr/share/tomcat5-producation/webapps/ir/conf/WEB-INF/conf/authentication.properties /usr/share/tomcat5-production
cp deployments/ir/target/ir.war /usr/share/tomcat5-producation/webapps/ir.war
cp /usr/share/tomcat5-producation/webapps/ir/conf/WEB-INF/conf/authentication.properties /usr/share/tomcat5-production
# check to see if tomcat needs a restart!

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[#????] Meta-data changes that don't have a FR/task
----------------------------------

Update the long titles and descriptions of the existing IR datasets as follows:

fcon_1000
Title: 1000 Functional Connectomes
Running Title: 1000 FC
Description: The 1000 Functional Connectomes Project.

adhd_200
Title: ADHD-200
Running Title: ADHD-200
Description: The ADHD-200 sample from the 1000 Functional Connectomes
project.

cs_schizbull08
Title: CANDI Share: Schizophrenia Bulletin 2008
Running Title: Schiz Bull 2008
Description: Version 1.1 of the CANDI Share Schizophrenia Bulletin 2008
data.

-----------------------------------
[#6658] Promotion part of Task 1034
-----------------------------------
Run the ADHD_200 data import.  This is documented in ~/NITRCSRC/feddata2/adhd_200/README

----------------------------------
[#6593] IR metadata tweaks
----------------------------------
Set the following environment variables:

    XNAT_URL (http://www.nitrc.org/ir for production)
    XNAT_USER
    XNAT_PASSWORD

Then cd to each directory in NITRCSRC/feddata2 before running each script (some scripts need configuration files in the containing directory):

    adhd_200/add_resting_tr: add resting TR to adhd_200
    fcon_1000_updates/fix_units: fix voxel dimension units in fcon_1000
    fcon_1000_updates/fix_diagnoses: set fcon_1000 diagnoses
    fcon_1000_updates/fix_tr: fix fcon_1000 TRs
    cs_schizbull2008/set_field_strength: set cs_schizbull08 field strength
    cs_schizbull2008/fix_ages: fix cs_schizbull08 ages
    cs_schizbull2008/add_params: set additional cs_schizbull08 parameters

----------------------------------
[#????] Add ADHD_200 custom link
----------------------------------
Add a custom link to the fcon_1000 project with the link title: ADHD-200 Downloads
The Link URL should be:  http://www.nitrc.org/account/login.php?feedback=A%20NITRC%20account%20is%20required%20to%20access%20this%20data.%20%20Please%20log%20in%20or%20register%20for%20an%20account%20if%20you%20do%20not%20have%20one.<br>%20%20If%20you%20are%20not%20a%20member%20of%20the%201000%20Functional%20Connectomes%20Project%20you%20will%20be%20prompted%20to%20request%20access%20to%20this%20data%20after%20completing%20your%20log%20in.&return_to=http%3A%2F%2Fwww.nitrc.org%2Fxnat%2Flogin_return.php%3Freturn_to%3Dhttp%3A%2F%2Fwww.nitrc.org%2Fir%2Fapp%2Ftemplate%2FXDATScreen_report_xnat_projectData.vm%2Fsearch_element%2Fxnat%3AprojectData%2Fsearch_field%2Fxnat%3AprojectData.ID%2Fsearch_value%2Fadhd_200

------------------------------
[#????] Update the sync script 
------------------------------

- update /opt/nitrc_import to the latest files from NITRCSRC/feddata2/nitrc_import
- Update nitrc_import_config.xml to the correct values:
<import_data>
<project nitrc_name='fcon_1000' ir_name='fcon_1000' visibility=public' />
<project nitrc_name='fcon_1000' ir_name='adhd_200' visibility='protected' />
<project nitrc_name='cs_schizbull2008' ir_name='cs_schizbull2008' visibility='public' />
</import_data>

