caTissue Suite

Developer / Adopter Weekly Meeting

Thursday, Feb 5, 2009

8:30 AM to 10:00 AM (ET)

**Dial-in Number**: 1-888-790-1566

**International Number**: 1-773-681-5890

**Passcode**: 97195 

**Centra Session Details**:

Guest Attend URL:
<http://mt202.centra.com/GA/main/0000004de3fe0000011d9eec86b40bd9>  

Attendees may enter the event by going to the URL below, and entering
the event ID.

URL: <http://mt202.centra.com/main/Customers/ncicb/>

Event ID: catissue

**Meeting Facilitator**: Linda Schmandt/LiMing Shen

**Participants**: Amber McMahon, Devjani Chatterjee, Jack London, John
Milnes, Ian Fore, Mark Watson, Komal Gulati, Poornima Govindrao,
Srikanth Adiga, Tara McSherry, Michael Krauthammer, Susanne Ragg, Sudha
Chudamani, Sarita Tony

MINUTES

1.  Suggestions for topic items? none

2.  Status and issues

    a.  Yale: Migrated to 1.1 last week and are preparing the public
        instance, including the daily upgrade script, de-id script
        (beyond the standard private-public script) and the trust
        framework. Concerned about whether there is time to accomplish
        this in February. Concern: a daily automated upgrade of the
        public server has to be absolutely fail-proof. The only issues
        that might push beyond February are the trust framework and the
        extra de-id script. Yale also has a use agreement that people
        need to sign.

    b.  Is there documentation of the testing of the std private-public
        scripts? Yes.

    c.  TJU: 1.1 is in production. About 31,000 de-id'd SPRs are loaded
        and 29,000 have been concept-coded. Grid v 1.1 private-public is
        being tested and Jim sent instructions about grouper, which John
        R will implement. Jack is meeting with IRB tomorrow. Everything
        will be up within 2 weeks at the latest.

    d.  **Ian requests that getting a public grid instance running as
        soon as possible is a priority. Getting all of the data into it
        before it is live is not critical.**

    e.  Penn: not finished with migration to Suite 1.1. It will be
        completed tomorrow and then they will set up the grid node. Penn
        will not use Grouper to control access to its own grid node. Per
        later discussion in this call, they will need to administer a
        grid group to be able to establish a trust relationship with the
        other sites.

    f.  Indiana: production instance is up, still loading some DEs. Grid
        node is set up and they requested a stem in NCICB grid grouper.
        As soon as that's available, they will set up the group.

    g.  Pitt: Production node up and grid node up. Need to get API port
        open, which will also make silver API and web UI available.

    h.  WU has a production instance and a public instance behind the
        firewall that Mark is reviewing and then they will open. Mark is
        rewriting the IRB protocol. Feb 20 at the latest. WU will not
        use GG to control access but, like Penn, will set up a group to
        use in trust relationships.

3.  Persistent demo on refreshing public instance - Persistent showed
    how to set up a chron job (Unix scheduled job) to run the
    private-public migration. The script to run the chron job is
    separate from the private-public migration script, which is included
    in the distribution. **ACTION (Persistent): In the final
    distribution package, include the shell script and BAT file, and
    there should be an article about it on the KC. Deployment Guide or
    Admin Guide should provide instructions for running this.**
    Question: How do you trigger a jboss restart on a remote server
    (since that is required to complete the private-to-public migration
    and the job runs on the private server). That's done through the RSA
    server \-- **ACTION: Persistent will document.**

4.  Note: the migration will cause downtime on the grid node. **ACTION:
    Each site track the net downtime on the grid node.** Linda
    questioned whether downtime at 3 am was problematic, but was assured
    that it will be.

5.  Specifications and acceptance criteria for Suite 1.1 deployment :
    The group reviewed the acceptance criteria (revised since last week)
    and the spreadsheet that lists each site's response to each
    criterion. (See below.)

    a.  Summary of the meeting Jeff Weiner (NCI user management) on GG
        and related issues: There is no formal guidance from caBIG or
        NCI yet about operational issues of running a grid node. NCI
        will explore identifying a filter that would enable setting up
        an NCI GG of investigators. Don't expect this to be completely
        top-down -- this group should take some initiative to work this
        out.

    b.  Review updates and build consensus

        i.  If a site isn't going to use Grouper, how do users from
            their sites get to sites that do use Grouper? One approach:
            set up a GG to enter into a trust agreement with other
            nodes, but don't require it for yours.

        ii. **ACTION: Jim post GG information to the TBPT KC**

    c.  Setting up trust relationships with the other adopters:

        i.  TJU: no issues with trusting the other 6 adopter groups
            (column E)

        ii. Pitt: no issues with trusting the other 6 adopter groups
            (column E)

        iii. **ACTION: Yale put their concerns in writing**

        iv. WU: no issues with trusting the other 6 adopter groups

        v.  Indiana: no issues with trusting the other 6 adopter groups

**Revised acceptance criteria for the final 2 deliverables (production
instance and grid node)**

Deliverables:

1.  Production instance of caTissue Suite 1.1

2.  Public instance of caTissue Suite 1.1, accessible through the web,
    API and grid API, deployed under https

    a.  Migrating or re-create accounts for external users

    b.  For Grid Grouper, list criteria for user inclusion in the list

        i.  All investigators?

    c.  Analyze data risk based on DSIC DSSF, to justify the planed
        security measure

    d.  Setup trust relationships among the GGs, define restrictions if
        necessary. Provide formal documentation if an exception is to be
        sought

    e.  Define criteria to setup trust relationships with other
        scientist GGs on the grid

    f.  NCI will setup its own GG, maintained by LiMing Shen from
        SAIC-F, which will enter a trust relationship with other adopter
        GGs. Define conditions for such a relationship, if necessary

    g.  All analysis, conditions, criteria etc. in b through g should be
        put in writing in a document

    h.  It is expected that the public instance will be updated on a
        regular basis even after the ending of the current contract, per
        data sharing agreement

Acceptance Criteria:

1.  Screen shots of the summary page of the production instance after
    initial data loading

2.  URL to access the public instance through the web and Silver APIs

3.  Public instance accessible through the caBIG grid portal

4.  At the end of the contracting period, data in the public instance,
    in terms of specimen collection, type of specimens and number of
    specimens should be comparable to what were defined in the data
    sharing plan created for the contract.

5.  Scripts to refresh public instance will be run daily through
    completion of deliverable ( for a minimum two week period) after
    initial install and grid deployment to allow tracking of activities

6.  Produce weekly report on 1) count of specimen types and 2) count by
    collection protocol numbers of participants with actual specimens
    (till the end of contracts)

**Matrix of adopter responses to acceptance criteria**

  ------------- ------------ ------------ -------- ------------- -------------------
  **Site**      **Notes**    **Suite 1.1  **Use    **Trust the   **Open to group
                             in           the NCI  other 6       filterd from NCI
                             production   GG**     groups? (5    LDAP**
                             use**                 adopters, WU, 
                                                   NCI           
                                                   (LiMing)**    

  **Penn**                   Upgrading to For      Yes           Will need more info
                             1.1 now      trust                  about membership
                                          rel.                   
                                          only                   

  **TJU**                    See notes    yes      yes           Will need more info
                             above                               about membership

  **Pitt**      Waiting for  yes          For      yes           Will need more info
                working port              trust                  about membership
                to enable                 rel.                   
                silver API                only                   
                and UI on                                        
                web.                                             

  **Yale**                                yes      Yes, but need Will need more info
                                                   more info     about membership

  **Indiana**   Loading DEs  yes          yes      yes           Will need more info
                                                                 about membership

  **Wash U**                 Yes, since   For      yes           Will need more info
                             several      trust                  about membership
                             weeks ago    rel.                   
                                          only                   
  ------------- ------------ ------------ -------- ------------- -------------------