rherrick

# Get a session
http --auth admin:minda --session=admin xnat164.xnat.org/data/projects

# Create the reconstruction and resource folder
http --session=admin PUT xnat164.xnat.org/data/archive/projects/prj001/subjects/prj001_001/experiments/prj001_001_MR2/reconstructions/prj001_001_MR2_recon_001 xnat:reconstructedImageData/type==RECON_A
http --session=admin PUT xnat164.xnat.org/data/archive/projects/prj001/subjects/prj001_001/experiments/prj001_001_MR2/reconstructions/prj001_001_MR2_recon_001/resources/NIFTI format==NIFTI

# Upload NIFTI and JSON to the reconstruction resource
for SERIES in t1_mpr_1mm_p2_pos50_20061214091206_4 t1_mpr_1mm_p2_pos50_20061214091206_5 t2_spc_1mm_p2_20061214091206_6; do
    http --session=admin PUT xnat164.xnat.org/data/archive/projects/prj001/subjects/prj001_001/experiments/prj001_001_MR2/reconstructions/prj001_001_MR2_recon_001/resources/NIFTI/files/${SERIES}.nii.gz inbody==true < ${SERIES}.nii.gz

rherrick

-- Change 'xnat' to the database user that owns the XNAT tables.
-- You need to stop Tomcat before running this query.
SELECT drop_user_views('xnat');

rherrick

dpham@ipg-radiology:~$ xnatimport http://cnrmimages.ninds.nih.gov radiologics /data/cnrmimages/images/test Test
Setting work folder to /home/dpham/xnat/20160905191242.
radiologics is sending data for subject in /data/cnrmimages/images/test to project Test on the server http://cnrmimages.ninds.nih.gov
Enter host password for user 'radiologics':
Found session SUBJECT_02_MR03 in folder /data/cnrmimages/images/test/SUBJECT_02
Committing session to /data/prearchive/projects/Test/20160905_191248631/SUBJECT_02_MR03
Found session SUBJECT_02_MR02 in folder /data/cnrmimages/images/test/SUBJECT_02
Committing session to /data/prearchive/projects/Test/20160905_191259072/SUBJECT_02_MR02
Found session SUBJECT_02_MR01 in folder /data/cnrmimages/images/test/SUBJECT_02
Committing session to /data/prearchive/projects/Test/20160905_191310101/SUBJECT_02_MR01

rherrick

00000000: 7573 6572 6e61 6d65 4077 6f72 6b73 7461  username@worksta
00000010: 7469 6f6e 207e 2024 2073 7368 2073 6572  tion ~ $ ssh ser
00000020: 7665 720a 4c61 7374 206c 6f67 696e 3a20  ver.Last login: 
00000030: 5361 7420 5365 7020 2033 2031 343a 3034  Sat Sep  3 14:04
00000040: 3a30 3820 3230 3136 2066 726f 6d20 3130  :08 2016 from 10
00000050: 2e32 302e 3530 2e38 380a 0a1b 5d31 3333  .20.50.88...]133
00000060: 373b 5265 6d6f 7465 486f 7374 3d75 7365  7;RemoteHost=use
00000070: 726e 616d 6540 7365 7276 6572 2e68 6f73  rname@server.hos
00000080: 742e 6564 751b 5d31 3333 373b 4375 7272  t.edu.]1337;Curr
00000090: 656e 7444 6972 3d2f 686f 6d65 2f75 7365  entDir=/home/use

rherrick

	<DisplayField id="WORKSHOP_BIOSAMPLECOLLECTION_PROJECT_IDENTIFIER" header="WORKSHOP_BIOSAMPLECOLLECTION ID" visible="true" searchable="false" data-type="string" xsi:type="SubQueryField">
		<Content type="sql">workshop_biosamplecollection_project_id</Content>
		<HTML-Link>
			<SecureLink elementName="workshop:biosampleCollection">
				<securityMappingValue displayFieldId="PROJECTS" schemaElementMap="workshop:biosampleCollection/sharing/share/project"/>
				<securityMappingValue displayFieldId="PROJECT" schemaElementMap="workshop:biosampleCollection/project"/>
			</SecureLink>
			<Property name="HREF" value="@WEBAPPapp/action/DisplayItemAction/search_value/@Field1/search_element/workshop:biosampleCollection/search_field/workshop:biosampleCollection.ID/project/@Field2">
				<InsertValue id="Field1" field="EXPT_ID"/>
				<InsertValue id="Field2" field="@WHERE"/>

rherrick

# Shut down Tomcat if it's running.
[[ $(sudo service tomcat7 status) == *running* ]] && { echo Tomcat 7 is running, shutting it down.; sudo service tomcat7 stop; } || { echo Tomcat 7 is not running.; }

# Sleep for a couple seconds just to make sure it's done.
sleep 2

# Clear the database and recreate it.
psql -lqt | cut -d \| -f 1 | grep -qw xnatdev
[[ $? == 0 ]] && { echo Dropping existing database xnatdev...; dropdb xnatdev; } || { echo Database xnatdev does not exist.; }
echo Creating new empty database xnatdev.

rherrick

import requests


def get_nifti_resource_id(json):
    result_set = json['ResultSet']
    if result_set is None:
        return

    result = result_set['Result']
    if result is None:

rherrick

Feb 04, 2016 7:35:50 PM javax.jmdns.impl.constants.DNSRecordClass classForIndex
WARNING: Could not find record class for index: -1
Feb 04, 2016 7:35:50 PM javax.jmdns.impl.DNSIncoming$MessageInputStream readName
SEVERE: bad domain name: possible circular name detected. Bad offset: 0xffffffff at 0x2d
Feb 04, 2016 7:35:50 PM javax.jmdns.impl.constants.DNSRecordType typeForIndex
SEVERE: Could not find record type for index: -1
Feb 04, 2016 7:35:50 PM javax.jmdns.impl.DNSIncoming readQuestion
SEVERE: Could not find record type: dns[query,158.255.6.220:36002, length=47, id=0x0, questions=10990
questions:
    [DNSQuestion@1096711572 type: TYPE_IGNORE index 0, class: CLASS_UNKNOWN index 0, name: ]

rherrick

# /etc/exports: the access control list for filesystems which may be exported
#               to NFS clients.  See exports(5).
#
# Example for NFSv2 and NFSv3:
# /srv/homes       hostname1(rw,sync,no_subtree_check) hostname2(ro,sync,no_subtree_check)
#
# Example for NFSv4:
# /srv/nfs4        gss/krb5i(rw,sync,fsid=0,crossmnt,no_subtree_check)
# /srv/nfs4/homes  gss/krb5i(rw,sync,no_subtree_check)
#

rherrick

#!/bin/bash

# If you're on Ubuntu/Debian or a different version of Tomcat, you'll need to change this path.
cd /usr/share/tomcat6/webapps/xnat/WEB-INF/lib
wget -O standard-1.1.2.jar http://search.maven.org/remotecontent?filepath=taglibs/standard/1.1.2/standard-1.1.2.jar
wget -O jstl-1.2.jar http://search.maven.org/remotecontent?filepath=javax/servlet/jstl/1.2/jstl-1.2.jar