CaTissue

Tags: Lcbru Software Category

THIS SOFTWARE IS NOW DEPRECATED

Overview

From the CaTissue home page: "caTissue Suite is caBIG's biorepository tool for biospecimen inventory management, tracking, and annotation."

​https://cabig.nci.nih.gov/tools/catissuesuite

Notes on the upgrade process from v1.1.p5 to v1.2 are at LEGACY - CaTissueUpgrade.

BRICCS Needs - note that the API client is live, v1.0 released on May 20th, 2011

We need to learn how to use the caTissue API. In particular:

• what would it take to get the 2d bar code reader to feed caTissue with an array of sample barcodes, such that caTissue would check them against the database to verify that the samples are in the right box, and in the right location? Possibly without even knowing the ID of the box?

• what would it take to be able to process more than one participant at a time through the collection protocol? Currently the submission process includes checking for empty data in form elements which presumably have the same ID in each open tab or window, thus throwing an error.

While we work with 1.1.2p5, it might be useful to know that there is a pre-built VM with caTissue 1.2 (the next version) available here:

​https://cabig-kc.nci.nih.gov/Biospecimen/KC/index.php/2010_User_Meeting_VM

This was used during the Houston User Meeting. I know it works on Ubuntu host, using VirtualBox. YMMV.

Demo files for using the caTissue API are here: ​https://cabig-kc.nci.nih.gov/Biospecimen/uploaded_files/4/4c/APIDemo1.1.zip

And files demonstrating the bulk operations feature of caTissue are here: ​https://cabig-kc.nci.nih.gov/Biospecimen/uploaded_files/1/19/BO_-_Loading_Data_Session.zip

The following pages are working notes:

• LEGACY - CaTissueClientAPI
• LEGACY - CaTissueBulkOperations
• LEGACY - CaTissueUseCases
• LEGACY - Collection Protocol amendments for DNA processing
• LEGACY - CaTissue Automatic specimen Labelling

The following is the current work instruction followed by the lab technicians: BRICCS caTissue Work Instruction

User Privileges

A note on user privileges in caTissue from Jeff. It is not our favoured model of privileges, but probably defined in the caBIG CSM (Common Security Model). We'd like more fine-grain privileges, but in the meantime this is how it works:

"It seems from the privileges tab of the admin page for collection protocol, that privileges have to be OK'd from the protocol side too; ie: you can set up privileges for users (and you can see these on the protocol/privileges tab) but there are none in operation (for a protocol) until you enable them from the protocol side."

"I (naively) thought that setting up privileges for each individual user would suffice. Seems reasonable. Then the penny dropped. What if I were doing admin on the protocol and wanted to stop people using it whilst changes were underway? If I were relying upon individual user privileges alone, I would have to go into each user and change their privilege, then do the protocol admin, then go back into each user again to re-enable their use. Very tedious. The way it is set up in caTissue, I can disable / enable wholesale privileges for one protocol with one admin action. Quite clever?"

Storage location structure

Notes on the storage location hierarchy go here.

BRICCS Study Collection Protocol

A BRICCS Study 'initial db' dump was taken during system set-up, after creating the storage hierarchy and CP but before populating with any specimen, and submitted to svn using the following command: svn import -m "Importing caTissue dump of initial db setup " catissue.dump ​svn+ssh://svn.briccs.org.uk/var/local/svn/repo/sysadmin/trunk/scripts/catissue

BRICCS Study Distribution Protocol

For the AS Study cohort to identify lab numbers of suitable participants and their buffycoat samples for DNA, we couldn't use a distribution protocol, since we wanted to be able to block search by BPt number (participant surname). We used a succession of custom searches.

GENVASC Collection Protocol

See the LEGACY - GENVASC Collection Protocol for CaTissue for further details

Configuration issues

Easily forgotten when upgrading to new versions is that the default for CaTissue is to auto-assign barcodes to samples, even before their label etc have been allocated. This plays hell with the API client, among other things.

To fix, edit the LabelGenerator.Properties file either in catissuehome/modules/CaTissue/conf/catissuecore-properties/ before deployment, or in jboss/server/default/catissuecore-properties after deployment, and then restart jboss.

Starting caTissue (temp solution)

Currently caTissue does not start automatically.

To run it:

/usr/local/jboss/bin/run.sh -b 0.0.0.0 &

You need to be root!

caTissue v2.0

Note that a major version upgrade to caTissue is planned for the first quarter of 2012.

Further details are available here:

​https://wiki.nci.nih.gov/display/caTissue/caTissue+Suite+2.0+Development

Search utilities

We should document some search algorithms and suchlike at CaTissue search functions

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