XNAT Extras Releases

ARC Queue Tools ARC Queue Tools

chcma@stage.nitrcce.org (Christian Haselgrove) — Thu, 08 Nov 2012 19:35:00 GMT

Command queueing tools by Dan Marcus.

Set ARC_TOOLS in each script to a directory where the queue and logs will be written. Then use:[code]arc-queue command arg ...[/code]
to queue a command, and:[quote][code]arc-qrunner[/code][/quote]
to run the commands in the queue.

Normally arc-queue is called from pipeline/bin/schedule or pipeline/bin/XnatPipelineLauncher (to catch the auto-run pipelines as well), and arc-qrunner is called by a cron job.

See the comments at the head of each file for more information.

Multi-version VM Version 1.6.0-0

chcma@stage.nitrcce.org (Christian Haselgrove) — Wed, 08 Aug 2012 18:15:00 GMT

XNAT Test VM

Version 1.6.0-0
August 8, 2012

Christian Haselgrove
christian.haselgrove@umassmed.edu

This virtual machine contains instances of several XNAT versions:

    1.5.0 (xnat150)
    1.5.1 (xnat151)
    1.5.2 (xnat152)
    1.5.3 (xnat153)
    1.5.4 (xnat154)
    1.6.0 (xnat160)

XNATs can be accessed at http://HOST:8080/VERSION, e.g.
http://localhost:8080/xnat154 for XNAT 1.5.4.

Accounts are root:rootpw and xnat:xnat.

DICOM server ports are:

    8150 for XNAT 1.5.0
    8151 for XNAT 1.5.1
    8152 for XNAT 1.5.2
    8153 for XNAT 1.5.3
    8154 for XNAT 1.5.4
    8160 for XNAT 1.6.0

Multi-version VM Version 1.0

chcma@stage.nitrcce.org (Christian Haselgrove) — Wed, 27 Jun 2012 22:01:00 GMT

XNAT Test VM

Version 1.0
June 27, 2012

Christian Haselgrove
christian.haselgrove@umassmed.edu

This virtual machine contains instances of several XNAT versions:

    1.5.0 (xnat150)
    1.5.1 (xnat151)
    1.5.2 (xnat152)
    1.5.3 (xnat153)
    1.5.4 (xnat154)
    1.6B1 (xnat16b1)

XNATs can be accessed at http://HOST:8080/VERSION, e.g.
http://localhost:8080/xnat154 for XNAT 1.5.4.

Accounts are root:rootpw and xnat:xnat.

xnat_extras xnat_sync 0.21-alpha

chcma@stage.nitrcce.org (Christian Haselgrove) — Wed, 21 Dec 2011 18:40:00 GMT

[b]Installation[/b]

Requirements:

[list][url=https://github.com/pyxnat/pyxnat]bleeding edge pyxnat[/url]
[url=http://pypi.python.org/pypi/python-dateutil]python-dateutil[/url]
[url=../download.php/4247/xnat_sync]xnat_sync[/url]
[/list]
[b]Running[/b]

Run xnat_sync with no options for usage.

"xnat_sync
init" will make the connection between an XNAT resource and the local
directory xnat_sync is run from. Use "init -c" to create the resource
on XNAT if it does not exist.

"xnat_sync pull" will pull new or
changed files from XNAT to the local directory. Use "pull -f" to force a
pull in the case of a conflict.

"xnat_sync push" will push new or changed files to XNAT. Use "push -f" to force a push in the case of a conflict.

"xnat_sync status" will give the synchronization status.

Define
the environment variables XNAT_USER and XNAT_PASSWORD for authenticated
use. If these are undefined, the connection will be unauthenticated.

If
xnat_sync is run with -s, xnat_sync will execute in "dry run" mode: the
actions that would be taken are reported, but no changes are made.

All commands must be run in the top-level directory of the local copy of the resource.

xnat_sync uses file modification times to keep track of what has been synchronized and what has changed.

[b]Examples[/b]

Copy remote scans to a local directory:[list]unset XNAT_USER
mkdir OAS1_0010_MR1-mpr-1
cd OAS1_0010_MR1-mpr-1
xnat_sync
init https://central.xnat.org
/data/projects/CENTRAL_OASIS_CS/subjects/OAS1_0010/experiments/OAS1_0010_MR1/scans/mpr-1/resources/2760
xnat_sync status
xnat_sync pull[/list]Synchronize a directory with a resource of your own:[list]export XNAT_USER=yourlogin
export XNAT_PASSWORD=yourpassword
cd /directory/with/data/for/xnat
xnat_sync
init -c http://your.server/xnat
/data/projects/EXISTING_PROJECT/subjects/EXISTING_SUBJECT/experiments/EXISTING_EXPERIMENT/resources/test
xnat_sync status
xnat_sync push

...modify, edit, delete...

xnat_sync status[/list]Please send comments to christian.haselgrove@umassmed.edu.

xnat_extras xnat_sync 0.2-alpha

chcma@stage.nitrcce.org (Christian Haselgrove) — Tue, 20 Dec 2011 14:41:00 GMT

[b]Installation[/b]

Requirements:

[list][url=https://github.com/pyxnat/pyxnat]bleeding edge pyxnat[/url]
[url=http://pypi.python.org/pypi/python-dateutil]python-dateutil[/url]
[url=../download.php/4246/xnat_sync]xnat_sync[/url]
[/list]
[b]Running[/b]

Run xnat_sync with no options for usage.

"xnat_sync
init" will make the connection between an XNAT resource and the local
directory xnat_sync is run from. Use "init -c" to create the resource
on XNAT if it does not exist.

"xnat_sync pull" will pull new or
changed files from XNAT to the local directory. Use "pull -f" to force a
pull in the case of a conflict.

"xnat_sync push" will push new or changed files to XNAT. Use "push -f" to force a push in the case of a conflict.

"xnat_sync status" will give the synchronization status.

Define
the environment variables XNAT_USER and XNAT_PASSWORD for authenticated
use. If these are undefined, the connection will be unauthenticated.

If
xnat_sync is run with -s, xnat_sync will execute in "dry run" mode: the
actions that would be taken are reported, but no changes are made.

All commands must be run in the top-level directory of the local copy of the resource.

xnat_sync uses file modification times to keep track of what has been synchronized and what has changed.

[b]Examples[/b]

Copy remote scans to a local directory:[list]unset XNAT_USER
mkdir OAS1_0010_MR1-mpr-1
cd OAS1_0010_MR1-mpr-1
xnat_sync
init https://central.xnat.org
/data/projects/CENTRAL_OASIS_CS/subjects/OAS1_0010/experiments/OAS1_0010_MR1/scans/mpr-1/resources/2760
xnat_sync status
xnat_sync pull[/list]Synchronize a directory with a resource of your own:[list]export XNAT_USER=yourlogin
export XNAT_PASSWORD=yourpassword
cd /directory/with/data/for/xnat
xnat_sync
init -c http://your.server/xnat
/data/projects/EXISTING_PROJECT/subjects/EXISTING_SUBJECT/experiments/EXISTING_EXPERIMENT/resources/test
xnat_sync status
xnat_sync push

...modify, edit, delete...

xnat_sync status[/list]Please send comments to christian.haselgrove@umassmed.edu.

xnat_extras xnat_sync 0.1-alpha

chcma@stage.nitrcce.org (Christian Haselgrove) — Fri, 02 Dec 2011 16:30:00 GMT

[b]Installation[/b]

Requirements:

[list][url=https://github.com/pyxnat/pyxnat]bleeding edge pyxnat[/url]
[url=http://pypi.python.org/pypi/python-dateutil]python-dateutil[/url]
[url=../download.php/4183/xnat_sync]xnat_sync[/url]
[/list]
[b]Running[/b]

Run xnat_sync with no options for usage.

"xnat_sync init" will make the connection between an XNAT resource and the local directory xnat_sync is run from. Use "init -c" to create the resource on XNAT if it does not exist.

"xnat_sync pull" will pull new or changed files from XNAT to the local directory. Use "pull -f" to force a pull in the case of a conflict.

"xnat_sync push" will push new or changed files to XNAT. Use "push -f" to force a push in the case of a conflict.

"xnat_sync status" will give the synchronization status.

Define the environment variables XNAT_USER and XNAT_PASSWORD for authenticated use. If these are undefined, the connection will be unauthenticated.

If xnat_sync is run with -s, xnat_sync will execute in "dry run" mode: the actions that would be taken are reported, but no changes are made.

All commands must be run in the top-level directory of the local copy of the resource.

xnat_sync uses file modification times to keep track of what has been synchronized and what has changed.

[b]Examples[/b]

Copy remote scans to a local directory:

[list]unset XNAT_USER
mkdir OAS1_0010_MR1-mpr-1
cd OAS1_0010_MR1-mpr-1
xnat_sync init https://central.xnat.org /data/projects/CENTRAL_OASIS_CS/subjects/OAS1_0010/experiments/OAS1_0010_MR1/scans/mpr-1/resources/2760
xnat_sync status
xnat_sync pull
[/list]

Synchronize a directory with a resource of your own:

[list]export XNAT_USER=yourlogin
export XNAT_PASSWORD=yourpassword
cd /directory/with/data/for/xnat
xnat_sync init -c http://your.server/xnat /data/projects/EXISTING_PROJECT/subjects/EXISTING_SUBJECT/experiments/EXISTING_EXPERIMENT/resources/test
xnat_sync status
xnat_sync push

...modify, edit, delete...

xnat_sync status
[/list]
Please send comments to christian.haselgrove@umassmed.edu.

xnat_extras Extra jar for HTTPS XnatPipelineLauncher

chcma@stage.nitrcce.org (Christian Haselgrove) — Thu, 13 Oct 2011 13:58:00 GMT

From Tim O'Keefe: http://groups.google.com/group/xnat_discussion/browse_thread/thread/811635e1d265b15d

xnat_extras XNAT Tools

chcma@stage.nitrcce.org (Christian Haselgrove) — Thu, 13 Oct 2011 13:52:00 GMT

NRG XNAT Tools

xnat_extras FreeSurfer Uploader

chcma@stage.nitrcce.org (Christian Haselgrove) — Wed, 12 Oct 2011 14:12:00 GMT

Scripts for creating and uploading FreeSurfer assessors.

http://groups.google.com/group/xnat_discussion/browse_thread/thread/4e885cc5ba9fff87?hl=en

xnat_extras Metadata Uploader

chcma@stage.nitrcce.org (Christian Haselgrove) — Tue, 11 Oct 2011 12:05:00 GMT