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Last Updated: 10/31/2011

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From: Michael.C.Ford.kp Sent: Monday, October 31, 2011 1:55 PM To: Phillips, Lori C. Cc: i2b2 AUG Members Subject: RE: I2B2 Column valuetype_cd in table_access.
added clarification were running 1.4 with plans to move to 1.6
it looks like this column was added in 1.5 and may be part of a Shrine install.

"Phillips, Lori C." <LCPHILLIPS.PARTNERS> Sent: 10/31/2011 10:41 AM To Michael C Ford/CA/KAIPERM.KAIPERM, i2b2 AUG Members cc Subject RE: I2B2 Column valuetype_cd in table_access.
From the Ontology Design Document section 2.3.21:
[Within the metadata] valuetype_cd is a coded value indicating the term type. At present there are two values in use: the type 'DOC' indicates terms that represent documents or notes; the type 'LAB' indicates terms of a laboratory test nature.

From: Michael.C.Ford.kp [Michael.C.Ford.kp] Sent: Monday, October 31, 2011 1:29 PM To: i2b2 AUG Members Subject: I2B2 Column valuetype_cd in table_access.
I was hoping someone in the group could give me some information. We have found a discrepancy in release we have of I2B2.
In the table i2b2metadata.table_access there is a column VALUETYPE_CD. This column is in our development region only.
I find document references to ValueType_cd in Observation_fact but not to i2b2metadata.table.ValueType_cd
is this an erroneous column in one database or should the column be added to our stage server ?

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From: Jack London [jack.london.KimmelCancerCenter] Sent: Monday, October 31, 2011 2:31 PM To: i2b2 AUG Members members Subject: v1.6 web client generates incorrect SQL
I found the source of the problem. I introduced the typo in the metadata table for the ontology. Specifically, in C_COLUMNNAME I had inserted "conecpt_path" rather than "concept_path"
Jack
Jack London, Ph.D. Research Professor Cancer Biology Thomas Jefferson University Director, Informatics Shared Resource Kimmel Cancer Center 808 BLSB, 233 S. 10th St. Philadelphia, PA 19107

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From: Michael.C.Ford.kp Sent: Monday, October 31, 2011 2:45 PM To: i2b2 AUG Members Subject: Odd UI issue
We seem to have an odd UI problem, it only seems to occur with one user and not all of the time.
Sometimes with this one user the set value context menu becomes Lab Values. once this occurs for this user it seems to stay Lab values for a while. But when I go to debug the issue it won't occur. has anyone seen this type of behavior and if so what is causing it.

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From: Murphy, Shawn N. Sent: Thursday, November 03, 2011 6:18 AM To: i2b2 AUG Members Subject: I2b2 1.6.01 is released
Please see release notes for fixes to 1.6.00 and report any issues.
Thanks, Shawn.

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From: Michael.C.Ford.kp Sent: Thursday, November 03, 2011 3:25 PM To: i2b2 AUG Members Subject: Increase the default timeout in 1.4
I have been requested to change the base timeout from 180 seconds to 3600 seconds.
in my initial review it seems that I need to change the following files.
crc.properties index.php jboss-service.xml
standardjboss.xml axis2.xml
WORK_ctrlr_general.js
WORK_view.js
i2b2_cell_communicator.js cell_config_data.js
CRC_ctrlr_History.js
WORK_ctrlr_general.js
is this correct or am I making this more complex then it needs to be ?
because if you don't up the bean life it would create a problem.

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From: Murphy, Shawn N. Sent: Friday, October 28, 2011 7:31 PM To: i2b2 AUG Members Subject: List of Bugs to be fixed in i2b2 1.6.01
Hi All,
Here is the list of bug fixes in 1.6.01 that we will be releasing next week. Are there other critical fixes that that you need?
CRC: Need to escape apostrophe in SQL Statements Zero patients are returned when performing a query using at least one term that contains an apostrophe in the path name.
Temporary fix: Put two single apostrophes in place of one in the c_dim_code entries for patient and providers in the Ontology Cell tables.
Ontology: Need to escape apostrophe when searching for term Terms that contain an apostrophe are not returned when performing a search in the Find Terms view.
Temporary fix: none
Project Management: Not able to add new users An error is returned when trying to add a new user in the Project Management application.
Temporary Fix: Alter that PM_USER_TABLE and add the column IS_ADMIN as a varchar2(50)
Web Client: The "Help" contains references to yui instead of local The links in the on-line help contain references to the external yui. These links should be defined as local.
Temporary fix: Point references to internal site
Web Client: Scrollbar is missing from some analysis plug-ins The horizontal and vertical scrollbars are missing from the following analysis plug-ins: Project Requests, Demographics (1 Patient Set), and Demographics (2 Patient Sets) in Internet Explorer
Temporary fix: none
Thanks, Shawn.

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From: Casale, Marco [Marco_Casale.URMC.Rochester] Sent: Friday, October 28, 2011 3:28 PM To: Murphy, Shawn N.; i2b2 AUG MembersCc: Phillips, Lori C. Subject: RE: ICD-9 to ICD-10 mappings
Hi Shawn,
According to my revenue system manager, there is a leaning towards the CMS reimbursement mapping.
Marco

From: Murphy, Shawn N. [SNMURPHY.PARTNERS] Sent: Friday, October 28, 2011 11:22 AM To: Casale, Marco; i2b2 AUG MembersCc: Phillips, Lori C. Subject: RE: ICD-9 to ICD-10 mappings
That's a good point Marco, which would you recommend?
Thanks,
Shawn.

From: Casale, Marco [Marco_Casale.URMC.Rochester] Sent: Friday, October 28, 2011 10:53 AM To: i2b2 AUG Members Subject: ICD-9 to ICD-10 mappings
Hi everyone, I apologize if this question has already been answered. I spoke to Shawn at the AMIA 2011 Symposium regarding the transition to support ICD-10 mappings in i2b2's CRC. (CONCEPT_DIMENSION) and i2b2metadata schema.
One follow up question I have is regarding the combined mapping of ICD codes where ICD-9 and ICD-10 will co-exist, is this mapping based on GEMs mapping or is it based on the CMS Reimbursement Mappings (see reimbursement mapping reference below)
http://library.ahima.org/xpedio/groups/public/documents/ahima/bok1_043242.hcsp?dDocName=bok1 _043242
Best regards,
Marco
Marco Casale MS
Project Director - Application Integration - ISD Faculty - Medical Informatics urmclogo

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From: Churchill, Susanne E. Sent: Friday, October 28, 2011 1:37 PM To: i2b2 AUG Members Subject: Materials from 10/12 Workshop
Please check out your AUG page (http://www.i2b2.org/work/aug.html) for overall video of the meeting and the individual slide decks for:
i2b2-SHRINE Support for Clinical Trials and Substitutable Medical Applications and Reusable Technologies (SMART) project (Murphy)
i2b2 Software 1.6 (Mendis).
Enjoy!
Susanne

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From: Mendis, Michael E. Sent: Thursday, October 27, 2011 3:56 PM To: i2b2 AUG Members Subject: Add user not working correcting in 1.6.00
When using the webclient add to add a new user, it returns a database error. We are going to be releasing a new 1.6.01 that corrects this and other issues.
As a temporary fix, alter that PM_USER_TABLE and add the column IS_ADMIN as a varchar2(50)
mike

From: jake.cobb.gmail on behalf of Jake Cobb [jake.cobb.gatech] Sent: Tuesday, October 25, 2011 5:06 PM To: i2b2 Subject: Query result after runQueryInstance_fromQueryDefinition
Hello,
I'm trying to understand the messaging protocol for queries. This is against a 1.5 instance. After running a CRC_QRY_runQueryInstance_fromQueryDefinition, I get a result like:
<query_result_instance> <result_instance_id>118</result_instance_id> <query_instance_id>113</query_instance_id> <description>Patient Set - 81 Patients</description> <query_result_type>
<result_type_id>1</result_type_id> <name>PATIENTSET</name> <display_type>LIST</display_type> <visual_attribute_type>LA</visual_attribute_type> <description>Patient list</description>
</query_result_type> <set_size>81</set_size> <start_date>2011-10-25T16:11:02.000-04:00</start_date> <end_date>2011-10-25T16:11:08.000-04:00</end_date> <query_status_type>
<status_type_id>3</status_type_id> <name>FINISHED</name> <description>FINISHED</description>
</query_status_type> </query_result_instance>
Next, I want to get the resulting document, so I send a CRC_QRY_getResultDocument_fromResultInstanceId message using the <result_instance_id> contents:
<ns4:request xsi:type="ns4:result_requestType" xmlns:xsi="http://www.w3.org/2001/XMLSchemainstance"> <query_result_instance_id>118</query_result_instance_id> </ns4:request>
But the server doesn't recognize the id and I get:
<ns4:response xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ns4:crc_xml_result_responseType"> <status> <condition type="ERROR">Query result instance id 118 not found</condition> </status> </ns4:response>

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From: Jack London [jack.london.KimmelCancerCenter] Sent: Wednesday, October 26, 2011 1:56 PM To: Lisa Miao Cc: i2b2 AUG Members Subject: Re: search by name under Find Terms in Release 1.6
We have v1.6 installed from source (not vm) with Oracle 11g: Both "search by name" and "search by code" under "Find Terms" works fine. Jack London

From: Wilson, Brian Sent: Wednesday, October 26, 2011 1:42 PM To: Lisa Miao Cc: i2b2 AUG Members Subject: Re: search by name under Find Terms in Release 1.6
Lisa,
I have a1.6 installed from src not vm connected to sqlserver DB.
the search by code and name work fine for me.
Brian

On Oct 26, 2011, at 1:26 PM, Lisa Miao wrote:
Dear All,
Has anyone tried the "search by name" under the "Find Terms" tab in Release 1.6 (The one that has just been released)? I have the "search by code" working just fine, but when doing the "search by name", it seems like nothing was happening (by looking at the server log). It almost seem like the codes behind the button has been disabled. This was working for RC5. Does anyone have experience on this? Can the i2b2 team comment on this?
Thanks, Lisa.

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From: Murphy, Shawn N. Sent: Tuesday, October 25, 2011 2:40 PM To: Robert Schuff Cc: i2b2 AUG Members Subject: Re: i2b2 versions and issues
We'll post a list when we get back from AMIA and get these fixed within a few weeks. Thank very much for (everyone's) feedback.

On Oct 22, 2011, at 11:31 AM, Robert Schuff wrote:
Hi all,
I am trying to better understand how I tell which bugs have been reported for version 1.6.
Looking at the spreadsheet on the wiki I see issues but I am not able to find version information associated with them. I did notice an ID column (Column A) however when I looked for LEOPARD-11 I saw a totally different issue so it seems the issue Ids do not line up.
Hence this question:
How can I easily get a comprehensive list of outstanding issues for a given version of i2b2?
Thanks
Rob
Robert Schuff - Director, Clinical Research Informatics
Oregon Clinical & Translational Research Institute Oregon Health & Science University http://www.octri.org/http://www.octri.org/

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From: Davis, Michael (Oncology) [davismk.upmc] Sent: Tuesday, October 25, 2011 1:03 PM To: i2b2 AUG Members Subject: i2b2 Web client and IE and Firefox
I'm currently using the plugins (Demographics, simple counts) in the web client with Firefox and these work great. However, most of my user base runs IE 7.x and when testing this same plugin in IE the
scrollbar does not appear in the view results tab. I've tried residing the browser, etc to no avail. Scrollbars do appear in all the other panels except for this one. Anyone experience this or have a workaround, suggestions?
Regards,
Mike

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From: Jack W. London, Ph.D. [Jack.London.KimmelCancerCenter] Sent: Saturday, October 22, 2011 3:30 PM To: Robert Schuff Cc: i2b2 AUG Members Subject: Re: 1.6 VMWare image and admin via webclient
username with admin privilege in the distribution is "i2b2" password, I believe, is demouser
Quoting Robert Schuff <schuffr.ohsu>:
Hi Folks,
I am running the VMWare image on OSX Lion. Regular web client works fine. I cannot authenticate to the http://<<host>>/admin
I must be missing something but I cannot seem to login to the admin web client. First I am not sure what username to use so I have been trying demo, demouser, admin, adminuser, and all other variations I can think of but I keep getting the same result which is a message saying "Requires ADMIN role, please contact your system administrator".
What might be the issue?
Thanks!
Rob
Robert Schuff - Director, Clinical Research Informatics Oregon Clinical & Translational Research Institute Oregon Health & Science University http://www.octri.org/
Jack W. London, Ph.D. Thomas Jefferson University Research Professor, Cancer Biology Kimmel Cancer Center Director, KCC Informatics Core Facility 808 Bluemle Life Science Bldg. 233 S. 10th Street Philadelphia, PA 19107

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From: Anandhi Sowmyan [asowmyan.regenstrief] Sent: Friday, October 21, 2011 4:28 PM To: i2b2 AUG Members Subject: Oracle column missing error
Hello everyone
When I try to add a new user, the application is throwing an exception
Here is the entry from the log file...
Translating SQLException with SQLState '42000' and errorCode '904' and message [ORA-00904: "PUD"."IS_ADMIN": invalid identifier
select distinct case upper(rr.COLUMN_CD) when '@' then pud.USER_ID when 'USER_ID' then pud.USER_ID else null end as USER_ID, case upper(rr.COLUMN_CD) when '@' then pud.FULL_NAME when 'FULL_NAME' then pud.FULL_NAME else null end as FULL_NAME, case upper(rr.COLUMN_CD) when '@' then pud.PASSWORD when 'PASSWORD' then pud.PASSWORD else null end as PASSWORD, case upper(rr.COLUMN_CD) when '@' then pud.EMAIL when 'EMAIL' then pud.EMAIL else null end as EMAIL, case upper(rr.COLUMN_CD)
when '@' then pud.IS_ADMIN when 'IS_ADMIN' then pud.IS_ADMIN else null end as IS_ADMIN from pm_user_data pud, pm_role_requirement rr where rr.status_cd<>'D' and pud.STATUS_CD<>'D' and pud.user_id = ? and
(rr.read_hivemgmt_CD = '@') and upper(rr.table_cd) = 'PM_USER_DATA'
Looks like the IS_ADMIN field is missing in the PM_USER_DATA table. I checked the upgrade scripts and I don't see this field there either. I went ahead and added the column to the table and tried to add the user again and it seems to work but this column is still empty. When I selected Is Admin = true, it just added a record with project_id = @ in the PM_PROJECT_USER_ROLES table.
Thanks
Anandhi

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From: Anandhi Sowmyan [asowmyan.regenstrief] Sent: Friday, October 21, 2011 10:13 AM To: Phillips, Lori C.; i2b2 AUG Members Subject: RE: concept_dimension query - not returning any result
The c_dimcode did have an extra Output Ur at the end. I removed it and it works now.
Thanks Lori....
Anandhi Sowmyan
Regenstrief Institute, Inc.
Medical Informatics
Health Information and Translational Sciences (HITS) Building
410 West 10th Street, Suite 2000
Indianapolis, IN 46202
Email: asowmyan.regenstrief

From: Phillips, Lori C. [LCPHILLIPS.PARTNERS] Sent: Friday, October 21, 2011 9:14 AM To: Anandhi Sowmyan; i2b2 AUG Members Subject: RE: concept_dimension query - not returning any result
Anandi,
What does the corresponding metadata record for OutputUr look like?
In this example, the c_dimcode column should be '\i2b2\VITALS\OUTPUT\Output Ur\'
The following explains how the query is built from the metadata record: https://community.i2b2.org/wiki/display/DevForum/Query+Building+from+Ontology
Lori Phillips

From: Anandhi Sowmyan [asowmyan.regenstrief] Sent: Thursday, October 20, 2011 5:03 PM To: i2b2 AUG Members Subject: concept_dimension query - not returning any result
Hello everyone
We are in the process of setting up the i2b2 system for our organization and we loaded all the concepts and observation_fact data. But when I try to run a query I am not getting any results back.
I checked the log file and the found out that the application does not insert any data into QT_PATIENT_SET_COLLECTION. When I dug further, I found that the following query doesn't return any data select patient_num ,1 as panel_count from ( select /*+ index(observation_fact fact_cnpt_pat_enct_idx) */ patient_num from observation_fact where concept_cd IN (select concept_cd from concept_dimension
where concept_path like '\i2b2\VITALS\OUTPUT\Output Ur\Output Ur%') group by patient_num ) t
For some reason this generated sql appends two 'Output Ur' at the end. But the concept_path in the concept_dimension table has only one 'Output Ur' in the end.
Our two columns values in the concept_dimension record looks like this
CONCEPT_PATH: \i2b2\VITALS\OUTPUT\Output Ur\ NAME_CHAR: Output Ur
When I remove the extra 'Output Ur' from the above query, I get results back (in sql plus). Am I missing something?
Please help!
Thanks Anandhi Sowmyan Regenstrief Institute, Inc. Medical Informatics Health Information and Translational Sciences (HITS) Building 410 West 10th Street, Suite 2000 Indianapolis, IN 46202
Email: asowmyan.regenstrief

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From: Mauro [mauro.bucalo.gmail] Sent: Friday, October 21, 2011 6:38 AM To: i2b2 AUG Members members Subject: c_totalnum use
Hi everyone, I saw that in the latest version of i2b2, ontologies actively using the c_totalnum field. I added a patient with a visit and an observation (ex. DEM|SEX:m). There's an automatic way to update this count?
I try to reboot the vmware but nothing happens.. The count still remains 82 while the query results 83 male.
Ing. Mauro Bucalo, Ext. Collaborator Dipartimento di Informatica e Sistemistica Universita' di Pavia Via Ferrata 1, 27100 Pavia, Italy e-mail: mauro.bucalo.gmail web-page: http://it.linkedin.com/in/maurobucalo

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From: Mendis, Michael E. Sent: Thursday, October 20, 2011 10:33 AM To: Shah, Nimit M.; i2b2 AUG Members Subject: Re: change host of port 8080
That is the default port for oracle xe. To change that you need to logon to sqlplus
sqlplus system/demouser.XE
And enter the following command:
begin dbms_xdb.sethttpport('8080'); end; /
Where 8080 is the new port number
mike

On 10/20/11 9:59 AM, "Shah, Nimit M." <NSHAH11.PARTNERS> wrote:
Inside the VM, is it possible to change the host of port 8080? Thanks Nimit Shah
Informatics Development Co op Sleep Medicine Epidemiology Brigham and Women's Hospital 221 Longwood Avenue Boston, MA 02115 nshah11.partners

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From: Dat Q. Phan [Dat.Q.Phan.uth.tmc] Sent: Wednesday, October 19, 2011 12:01 PM To: Mendis, Michael E.; Robert Schuff; i2b2 AUG Members Subject: RE: LDAP in 1.6 Š WAS Re: i2b2 v1.5.2 AD integration documentation
If you modify the hive parameters it will force all your users to login through your LDAP server. It will not allow local logins. I haven't had much luck with it working well with the hive parameters.
Personally, I prefer configuring it for each individual user, that way it also allows local logins. It's tedious if you add each user through the admin interface but it's much easier to run a SQL script.

Enter parameters for each user
DECLARE
userid varchar(25) := 'user_name';
BEGIN
INSERT INTO PM_USER_PARAMS(DATATYPE_CD, USER_ID, PARAM_NAME_CD, VALUE, CHANGE_DATE, ENTRY_DATE, CHANGEBY_CHAR, STATUS_CD)
VALUES('T', userid, 'authentication_method', 'LDAP', TO_DATE(SYSDATE,'YYYY-MM-DD HH24:MI:SS'), TO_DATE(SYSDATE,'YYYY-MM-DD HH24:MI:SS'), 'i2b2', 'A');
INSERT INTO PM_USER_PARAMS(DATATYPE_CD, USER_ID, PARAM_NAME_CD, VALUE, CHANGE_DATE, ENTRY_DATE, CHANGEBY_CHAR, STATUS_CD)
VALUES('T', userid, 'connection_url', 'ldap://lion.hsc.uth.tmc:389', TO_DATE(SYSDATE,'YYYYMM-DD HH24:MI:SS'), TO_DATE(SYSDATE,'YYYY-MM-DD HH24:MI:SS'), 'i2b2', 'A');
INSERT INTO PM_USER_PARAMS(DATATYPE_CD, USER_ID, PARAM_NAME_CD, VALUE, CHANGE_DATE, ENTRY_DATE, CHANGEBY_CHAR, STATUS_CD)
VALUES('T', userid, 'search_base', 'OU=People,DC=uth,DC=tmc,DC=edu', TO_DATE(SYSDATE,'YYYY-MM-DD HH24:MI:SS'), TO_DATE(SYSDATE,'YYYY-MM-DD HH24:MI:SS'), 'i2b2', 'A');
INSERT INTO PM_USER_PARAMS(DATATYPE_CD, USER_ID, PARAM_NAME_CD, VALUE,
CHANGE_DATE, ENTRY_DATE, CHANGEBY_CHAR, STATUS_CD)
VALUES('T', userid, 'distinguished_name', 'uid=', TO_DATE(SYSDATE,'YYYY-MM-DD HH24:MI:SS'), TO_DATE(SYSDATE,'YYYY-MM-DD HH24:MI:SS'), 'i2b2', 'A'); INSERT INTO PM_USER_PARAMS(DATATYPE_CD, USER_ID, PARAM_NAME_CD, VALUE,
CHANGE_DATE, ENTRY_DATE, CHANGEBY_CHAR, STATUS_CD)
VALUES('T', userid, 'security_authentication', 'simple', TO_DATE(SYSDATE,'YYYY-MM-DD HH24:MI:SS'), TO_DATE(SYSDATE,'YYYY-MM-DD HH24:MI:SS'), 'i2b2', 'A'); COMMIT; END;

From: Mike Mendis [mmendis.partners] Sent: Wednesday, October 19, 2011 10:47 AM To: Robert Schuff; i2b2 AUG Members Subject: Re: LDAP in 1.6 Š WAS Re: i2b2 v1.5.2 AD integration documentation
Yes if you enter it in the hive parameters instead of the user-parmeters. This will need to be on the database side, currently there is no UI admin to hive parameters.
mike

On 10/19/11 11:29 AM, "Robert Schuff" <schuffr.ohsu> wrote:
Hi Johnny/all, In looking at the documentation for LDAP configuration it appears that all of the parameters for an LDAP connection are set up at the user level, meaning quite a bit of configuration work when adding several users and whenever there is a change in LDAP configuration (admittedly rare). Is there some other way I am not seeing that allows setting a global connection or something similar so that the config info is only set once?
Thanks! Rob

On Oct 13, 2011, at 10:23 AM, Dat Q. Phan wrote:
I uploaded some additional documentation that hopefully will help with the installation and
configuration of i2b2 v1.6.
https://community.i2b2.org/wiki/display/community/Community+Postings
Regards,
Johnny Phan Programmer Analyst II UTHealth School of Biomedical Informatics Dat.Q.Phan.uth.tmc

From: Murphy, Shawn N. [SNMURPHY.PARTNERS] Sent: Wednesday, October 05, 2011 12:25 PM To: Phillip Reeder; Michael.C.Ford.kp Cc: Dat Q. Phan; i2b2 AUG Members; travis.nagler.ucdmc.ucdavis Subject: RE: i2b2 v1.5.2 AD integration documentation
Hi Philip,
You can post it on the AUG section of the Community Wiki, I think you should have access but if not let me know.
Thanks for distributing this nice document, Shawn.

From: Phillip Reeder [Phillip.Reeder.uth.tmc] Sent: Tuesday, October 04, 2011 8:38 PM To: <Michael.C.Ford.kp> Cc: Dat Q. Phan; <i2b2 AUG Members>; <travis.nagler.ucdmc.ucdavis> Subject: Re: i2b2 v1.5.2 AD integration documentation
Its supplemental documentation that we have developed at UT Houston based on our experience installing and configuring i2b2. It should work for both the 1.5 and 1.6 releases of i2b2.
If this is helpful to people, is there an official location that we can contribute this and other documentation to?
Phillip

On Oct 4, 2011, at 6:38 PM, <Michael.C.Ford.kp> wrote:
what manual is this from ?

From:: Dat Q. Phan" Sent: 10/04/2011 03:32 PM To: Travis Nagler, i2b2 AUG Members cc: Subject RE: i2b2 v1.5.2 AD integration documentation
Travis, See the attachement.
Johnny Phan Programmer Analyst II UTHealth School of Biomedical Informatics Dat.Q.Phan.uth.tmc

From: Travis Nagler [travis.nagler.ucdmc.ucdavis] Sent: Tuesday, October 04, 2011 5:25 PM To: i2b2 AUG Members Subject: i2b2 v1.5.2 AD integration documentation
We are looking to use Active Directory for logging into i2b2. Does anyone have any documentation they would be willing to share on how they got it done? I have been told to look in the admin web screens where I would find some parameters to employ, but I don't have those parameters pages (I've seen the screenshots).
Is AD setup within Apache or within the web client? How is the integration supposed to work?
Thanks,
Travis

Travis H. Nagler
Senior Database Programmer American Burn Assoc. - Data Coordinating Center UC Davis Division of Burn Surgery UC Davis Health System 2921 Stockton Blvd., Suite 1470 Sacramento, CA, 95817 http://www.ucdmc.ucdavis <http://www.ucdmc.ucdavis/> travis.nagler.ucdmc.ucdavis

From: Remo Mueller <rmueller.rics.bwh.harvard <rmueller.rics.bwh.harvard> To: i2b2 AUG Members <i2b2 AUG Members> Date: 10/04/2011 06:22 AM Subject: i2b2 1.6.rc5 Virtual Machine Question
Hello All,
I'm in the process of setting up my first i2b2 Virtual Machine (1.6.rc5), and I've run into the following error: (I used login:demo pw:demouser). Also of note, I used a bridged connection so that I'd be able to connect to the web service (as NAT was giving me a strange 10.0.2.15 address that was unreachable).
I'm running on a Mac OS X, using Virtual Box 4.1.4
Any help would be appreciated, thanks!
Remo Mueller

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From: Nigam Shah [nigam.stanford] Sent: Tuesday, October 18, 2011 9:02 PM To: kr-sig.mailman.amia; nlp-sig.mailman.amia; public-semweb-lifesci hcls; ncbo
everyone.lists.stanford; bmi-students.lists.stanford; i2b2 AUG Members Subject: Summit on Translational Bioinformatics 2012 – 3 days to panel, podium presentation, poster deadline
Dear Colleagues,
The American Medical Informatics Association (AMIA) invites submissions for the 2012 Summit on Translational Bioinformatics (TBI), which will be held on March 19th-21st 2012 at the Parc 55 Hotel San Francisco, CA. The Summit is part of the Joint Summits on Translational Science and will be followed by the Summit on Clinical Research Informatics (CRI) at the same venue on March 21st – 23rd. This year, we have four tracks at TBI covering research that takes us from base pairs to the bedside, with an emphasis on clinical implications of mining massive data-sets, and on bridging the latest multimodal measurement technologies with large amounts of healthcare data:
Concepts, Tools and Techniques for Translational Bioinformatics
Integrative Analysis of multi modal measurements Base pairs to Bedside Informatics with Big Data
Details at: www.amia.org/jointsummits2012/tbi-submission
Key dates:
Panels, Posters, Podium Abstract Proposals: October 21, 2011
Details on submission types: www.amia.org/jointsummits2012/types-proposals
We anticipate that the TBI Summit will continue to be the venue where the latest informatics research at the dynamic interface of biomedical research and patient care gets showcased. We look forward to your submissions and hope that you will join us in San Francisco in March of 2012.
Nigam H. Shah, Stanford University Chair, 2012 Scientific Program Committee

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From: Shah, Nimit M. Sent: Tuesday, October 18, 2011 4:40 PM To: i2b2 AUG Members Subject: service XE,XEXDB for VMware bridged
Hi,
I am working on VMware for bridged and NAT connections. I am using LSNRCTL to see what my oracle is listening to. In NAT, I see that XE,XEXDB, XE_XEPT are running. It sees Port 8080 for the oracle database:
Whereas, a bridged connection does not have XE, XEXDB, or XE_XPET running. Also I cannot see port 8080 which is needed to access the database.
Is it possible to add XE, XEXDB, and XE_XPT to the bridged connection? Or change the HOST address for the bridged from 127.0.0.1 to its own ip addresss?
Thanks Nimit Shah Informatics Development Co op Sleep Medicine Epidemiology Brigham and Women's Hospital 221 Longwood Avenue Boston, MA 02115
nshah11.partners

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From: Viangteeravat, Dr Tee [tviangte.uthsc] Sent: Tuesday, October 18, 2011 9:15 AM To: Joseph.Bonner.hc.msu; i2b2 AUG Members Subject: RE: Epidemiology Study data put into i2b2
Hi Joe,
Here is what I did for creating a low-level i2b2 ontology (e.g., demographic). Based on "Data Installation Guide" folder structure and information, Directory folder (Metadata), Schema (i2b2metadata), and Project (Demo), once successfully deployed tables for i2b2metadata schema, a low-level ontology tree can be created in i2b2 table to reflect question and answer (tree level 0, 1, or 2) and put the same reference into concept_dimension table (i.e., concept_cd, concept_path). The concept_cd will also have to put into "observation_fact" because this is what query will run against.
Thanks, Tee

From: Natter, Marc [Marc.Natter.childrens.harvard] Sent: Monday, October 17, 2011 5:38 PM To: i2b2 AUG Members Subject: Re: Epidemiology Study data put into i2b2
Hi Joe,
We have done this for our registry efforts and are starting to do it for others. First step for us is constructing a low-level i2b2 ontology (which is just a question and answer ontology tree) based on the form. Then, depending upon the needs of the users, we map this low-level ontology into one or more higher level ontologies by putting the referencing terms in both the ontology cell tables and also the concept_dimension table.
The data we are using now is exported to us in CDISC ODM (PhaseForward InForm flavor) and we have an import pipeline built with help from Griffin Weber and his team that maps terms to our Q&A ontology and then uses XSLT to programmatically generate the SQL inserts needed for ETL into i2b2. It's a bit of a heavy-weight structure, but we are pulling in such data daily and serves our needs.
Soon as we get it a bit more polished (few months?), we'll be open-sourcing it for others too.
Hope this helps,
Marc

From: Joseph Bonner <Joseph.Bonner.hc.msu<Joseph.Bonner.hc.msu> Date: Mon, 17 Oct 2011 16:28:37 -0400 To: "i2b2 AUG Members<i2b2 AUG Members>" <i2b2 AUG Members<i2b2 AUG Members> Subject: Epidemiology Study data put into i2b2
We have a large epidemiology study that we want to put into I2B2 to help investigators find new cohorts for analysis. Is anybody willing to share experience moving survey data (with full meta data) into the i2b2 structure?
Joe B

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From: Brian Ostasiewski [bostasie.wakehealth] Sent: Monday, October 17, 2011 3:14 PM To: i2b2 AUG Members Subject: escaping apostrophes
This seems to be a global issue with 1.6 --queries on concepts that contain apostrophes, such as "Alzheimer's" work fine in our production 1.5 system, but fail on 1.6 (causes sql statement to end prematurely), even when just asking for a patient count.
Has something changed regarding how data is escaped/encoded?
2011-10-17 15:00:37,152 DEBUG [edu.harvard.i2b2.crc.dao.CRCDAO] Executing setfinder query sql [select count(distinct patient_num) as patient_num_count from (
select patient_num from i2b2data.observation_fact where
(( CONCEPT_CD IN (select CONCEPT_CD from i2b2data.CONCEPT_DIMENSION where CONCEPT_PATH LIKE '\WFUBMC\Diagnoses\ICD9\Neurologic Disorders (320-389)\Degenerative diseases (330-337)(331) Other cerebral degenerations(331-0) Alzheimer's disease%') ))
) allitem ] for query instance= 429
2011-10-17 15:00:37,158 ERROR [edu.harvard.i2b2.crc.dao.CRCDAO] Error while executing sql
java.sql.SQLException: ORA-00907: missing right parenthesis
at oracle.jdbc.driver.DatabaseError.throwSqlException(DatabaseError.java:112)
at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:331)
at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:288)
at oracle.jdbc.driver.T4C8Oall.receive(T4C8Oall.java:743)
at oracle.jdbc.driver.T4CStatement.doOall8(T4CStatement.java:207)
at oracle.jdbc.driver.T4CStatement.executeForDescribe(T4CStatement.java:790)
at oracle.jdbc.driver.OracleStatement.executeMaybeDescribe(OracleStatement.java:1037)
at oracle.jdbc.driver.T4CStatement.executeMaybeDescribe(T4CStatement.java:830)
at oracle.jdbc.driver.OracleStatement.doExecuteWithTimeout(OracleStatement.java:1124)
at oracle.jdbc.driver.OracleStatement.executeQuery(OracleStatement.java:1272)
at
org.jboss.resource.adapter.jdbc.WrappedStatement.executeQuery(WrappedStatement.java:226) at edu.harvard.i2b2.crc.dao.setfinder.QueryExecutorHelperDao.executeQuery(Unknown
Source)
at edu.harvard.i2b2.crc.dao.setfinder.QueryExecutorDao.executeSQL(Unknown Source)
at edu.harvard.i2b2.crc.ejb.ExecRunnable.processQueryRequest(Unknown Source)
at edu.harvard.i2b2.crc.ejb.ExecRunnable.execute(Unknown Source)
at edu.harvard.i2b2.crc.ejb.QueryExecutorMDB.onMessage(Unknown Source)
at edu.harvard.i2b2.crc.ejb.QuerySmallExecutorMDB.onMessage(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.jboss.invocation.Invocation.performCall(Invocation.java:359)
at org.jboss.ejb.MessageDrivenContainer
$ContainerInterceptor.invoke(MessageDrivenContainer.java:495)
at org.jboss.resource.connectionmanager.CachedConnectionInterceptor.invoke(CachedConnectionInter
ceptor.java:158)
at org.jboss.ejb.plugins.CallValidationInterceptor.invoke(CallValidationInterceptor.java:63)
at org.jboss.ejb.plugins.AbstractTxInterceptor.invokeNext(AbstractTxInterceptor.java:121)
at
org.jboss.ejb.plugins.AbstractTxInterceptorBMT.invokeNext(AbstractTxInterceptorBMT.java:173) at
org.jboss.ejb.plugins.MessageDrivenTxInterceptorBMT.invoke(MessageDrivenTxInterceptorBMT.java :47)
at org.jboss.ejb.plugins.MessageDrivenInstanceInterceptor.invoke(MessageDrivenInstanceInterceptor.ja va:116)
at org.jboss.ejb.plugins.RunAsSecurityInterceptor.invoke(RunAsSecurityInterceptor.java:109)
at org.jboss.ejb.plugins.LogInterceptor.invoke(LogInterceptor.java:205)
at
org.jboss.ejb.plugins.ProxyFactoryFinderInterceptor.invoke(ProxyFactoryFinderInterceptor.java:138)
at org.jboss.ejb.MessageDrivenContainer.internalInvoke(MessageDrivenContainer.java:402)
at org.jboss.ejb.Container.invoke(Container.java:960)
at org.jboss.ejb.plugins.jms.JMSContainerInvoker.invoke(JMSContainerInvoker.java:1092)
at org.jboss.ejb.plugins.jms.JMSContainerInvoker
$MessageListenerImpl.onMessage(JMSContainerInvoker.java:1392)
at org.jboss.jms.asf.StdServerSession.onMessage(StdServerSession.java:266)
at
org.jboss.mq.SpyMessageConsumer.sessionConsumerProcessMessage(SpyMessageConsumer.jav a:906)
at org.jboss.mq.SpyMessageConsumer.addMessage(SpyMessageConsumer.java:170)
at org.jboss.mq.SpySession.run(SpySession.java:323)
at org.jboss.jms.asf.StdServerSession.run(StdServerSession.java:194)
at EDU.oswego.cs.dl.util.concurrent.PooledExecutor$Worker.run(PooledExecutor.java:761)
at java.lang.Thread.run(Thread.java:619)

From: Brian Ostasiewski Sent: Friday, October 14, 2011 2:45 PM To: i2b2 AUG Members Subject: RE: I2b2 1.6 breakdown problem
The "missing right parenthesis" turns out to have been due to an apostrophe in a concept_path, so adding a new breakdown does work in bullet #3.

From: Brian Ostasiewski Sent: Friday, October 14, 2011 2:28 PM To: i2b2 AUG Members Subject: RE: I2b2 1.6 breakdown problem
If anyone else was wondering:
1. To change the target concept paths for various breakdowns, edit i2b2data.QT_BREAKDOWN_PATH.VALUE for each (this is why the counts were working for the demo data but not our data) I haven't seen a way to target more than one meta table with this, would you just duplicate a row with the same NAME but different VALUE?
2. To remove any that you don't wish to support, delete the relevant row from QT_QUERY_RESULT_TYPE and remove the relevant <entry> xml chunk from CRCApplicationContext.xml
3. To add a new one add a row to QT_QUERY_RESULT_TYPE with a unique RESULT_TYPE_ID, and add another <entry> xml chunk to CRCApplicationContext.xml
To test, I tried adding a Religion breakdown via this method, and when I run a query I get a sql exception "missing right parenthesis", and don't see any other indication in the log of what may be causing it. Am I missing something?
Thanks, Brian

From: Brian Ostasiewski Sent: Tuesday, October 11, 2011 8:36 AM To: i2b2 AUG Members Subject: RE: I2b2 1.6
Thanks for getting this available.
When I run a query in the webclient and ask for the Gender/Race/etc patient breakdowns, it comes back with totals of only 1 or 0 in the categories for race, gender, and vital status. Age breakdown is correct. If I pull this same patient result set into the Demographics analysis plugin it correctly displays the right numbers for race, gender, and vital status.
This 1.6 install I have running on a test box right now, where I've simply overwritten the RC5 webclient files with the newly released files, and I've done a recompile of all the server code with the new release files, so I'm wondering if it may be a result of not doing a complete fresh install – can anyone else verify these problems?
Brian Ostasiewski

From: Murphy, Shawn N. [SNMURPHY.PARTNERS] Sent: Monday, October 10, 2011 6:59 PM To: i2b2 AUG Members Subject: I2b2 1.6
Hi All,
I2b2 1.6.00 has been released at https://www.i2b2.org/software/index.html
Thanks, Shawn.

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From: Kohane, Isaac Samuel [Isaac_Kohane.hms.harvard] Sent: Sunday, October 16, 2011 3:11 PM To: Holden, Nick Cc: i2b2 AUG Members; McMurry, Andrew J. Subject: Re: SHRINE connections for software other than i2b2
We are specifically looking for a non i2b2 site to use a SHRINE adaptor. So far we have worked within the i2b2 community but the adaptors are agnostic as to underlying repository so long as XML payload & authentication semantics are observed. Should not be terribly difficult
Zak
Sent from my iPhone (therefore brief and with iPhone enforced typos)
Isaac S Kohane, MD, PhD Professor of Pediatrics and Health Sciences Technology Harvard Medical School & Children's Hospital http://chip.org/~zak

On Oct 16, 2011, at 1:43 PM, "Holden, Nick" <nrh11.leicester.ac.uk> wrote:
A question which is raised repeatedly in discussions here in the UK surrounds the ability to share data across research institutions. I'm well aware of all the great work being done to facilitate federated querying with SHRINE, but the deployments of SHRINE I have read about so far all seem to be built on a number of institutions deploying i2b2 on a local basis first, and then using SHRINE to share the value locked up in the i2b2 data.
Has anyone done any work on using SHRINE to integrate a site which doesn't use i2b2? Either by connecting other data management applications to SHRINE directly, or by connecting those systems to i2b2 as a filter toward SHRINE connectivity? Do any of the existing SHRINE networks include sites not using i2b2 to support translational research locally?
Thanks,
Nick
Nick Holden BRU Systems and Database Architect Leicester Cardiovascular Biomedical Research Unit Glenfield Hospital +44 (0)116 250 2541

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From: Mendis, Michael E. Sent: Friday, October 14, 2011 5:05 PM To: Shanon Bailey; i2b2 AUG Members Subject: Re: Concepts in same panel to mimic 'OR'
Which version are you using? Also can you provide the xml request message for this. You can get that by clicking on the xml icon on the right side of the query tool.
Thanks mike

On 10/14/11 2:13 PM, "Shanon Bailey" <sbailey1.uw> wrote:
Hi –
Seems I'm unable to drop the same concept in the same panel in the webclient in order to do an 'OR' criteria. I can come up with some inelegant workarounds (create the concept multiple times in the ontology tree). But was hoping there was a cleaner solution.
Thanks, Shanon Bailey
UW Medicine

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From: Michael.C.Ford.kp Sent: Friday, October 14, 2011 4:43 PM To: Mendis, Michael E. Cc: i2b2 AUG Members Subject: Re: Accessing multiple i2b2 regions from a desktop client.
Mike thanks. the change in the screen did not complete, it created a domain_id of fFU1RGPhQjlJCNKxqeHF. once I modified Pm_hive_data the system came up and work correctly thanks.
P.S. I noted a lot of rows in pm_user_session these can all be removed I would think when the system is down correct ?

Mike Mendis <mmendis.partners> 10/14/2011 01:07 PM To: Michael C Ford/CA/KAIPERM.KAIPERM, <i2b2 AUG Members> cc Subject Re: Accessing multiple i2b2 regions from a desktop client.
Try restarting jboss and verify in the database the pm_hive_data that it really is referrring to i2b2test instead of i2b2demo

On 10/14/11 4:04 PM, "Michael.C.Ford.kp" <Michael.C.Ford.kp> wrote:
So I made the following changes and find there is still something referring to i2b2demo as the domain. in the tables CRC_DB_lookup, ont_db_lookup, work_db_lookup I change c_domain_id from i2b2demo to i2b2test.
I then modified i2b2_config.data.js.
name: "Development",
domain: "i2b2test",
debug: true,
urlCellPM: "http://machinename:9090/i2b2/rest/PMService/"
Last I modified the domain in the application and restarted the application.
When I tried to access the system after the restart I found I was still th owing an error. 11:13:09,585 ERROR [ServicesHandler] i2b2test is not associated with this domain i2b2demo. Please check the i2b2workbench.properties file. 11:13:09,585 ERROR [STDERR] java.lang.Exception: i2b2test is not associated with this domain i2b2demo. Please check the i2b2workbench.properties file. 11:13:09,586 ERROR [STDERR] at edu.harvard.i2b2.pm.delegate.ServicesHandler.execute(Unknown Source) 11:13:09,586 ERROR [STDERR] at edu.harvard.i2b2.pm.ws.ExecutorRunnable.run(Unknown Source) 11:13:09,586 ERROR [STDERR] at java.lang.Thread.run(Thread.java:595)
any idea what other item I may have missed, also when I change the hive domain_name where is that stored ?
Thanks Michael C Ford Application Development Project Manager Division of Research 2000 Broadway Oakland Ca
Michael.C.Ford.kp

Michael C Ford/CA/KAIPERM 10/11/2011 04:12 PM To i2b2 AUG Members cc Subject Accessing multiple i2b2 regions from a desktop client.Link
So accessing multiple i2b2 regions is not an issue, making the naming such that the user know what region is being accessed is a little harder.
We currently have a test, stage and production system but there all internally named i2b2demo. so in the desktop client you see the same name on each system i2b2demo.
to change this in each system I would change the domain_name in the hive and c_domain_id in the following tables. CRC_DB_lookup ont_db_lookup work_db_lookup
and the values in i2b2workbench.properties
Did I miss anything ?

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From: Mendis, Michael E. Sent: Friday, October 14, 2011 3:48 PM To: Jack London; i2b2 AUG Members members Subject: Re: v1.6 User Management question
If you click on the user on the left navigation than it will bring up a form where you can change the password or other information about the user.
mike

On 10/14/11 3:16 PM, "Jack London" <jack.london.KimmelCancerCenter> wrote:
I wish to change a user's password. I log into the "admin" web client (http://localhost/admin) as "i2b2" which has an "ADMIN" role.
When I expand "Manage Users" it lists the users' full name, user name, email and "is admin" – but no password column. And clicking on a user row does not bring up that user's data for editing (such as changing password).
I guess that the "i2b2" user is not properly provisioned.
Suggestions please ...
thanks,
Jack

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From: Murphy, Shawn N. Sent: Friday, October 14, 2011 2:50 PM To: Jack London Cc: i2b2 AUG Members Subject: Re: format counts
Thanks for the suggestion Jack.
Shawn Murphy MD Communicating with handheld

On Oct 14, 2011, at 8:15 PM, "Jack London" <jack.london.KimmelCancerCenter> wrote:
This is a suggestion for a minor enhancement to the i2b2 web client, but one which others may also find helpful:
when reporting patient counts, commas would be helpful. That is 11695 would be displayed as 11,
Thanks ....
Jack

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From: Shah, Nimit M. Sent: Friday, October 14, 2011 12:40 PM To: i2b2 AUG Members Subject: trouble with bridged connection
Hi,
While trying to see why the NAT connection works while the bridged connection for i2b2demo works, I decided to try Harvard Demo on bridged connection which works fine. Could the problem lie in the javascript file i2b2_config_data.js located in /var/www/html/admin? I checked all the other areas where i2b2_config_data.js is located and the others have i2b2demo and Harvarddemo in them while the file "/var/www/html/admin/i2b2_config_data.js" has only i2b2demo in it.
Thanks
Nimit

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From: Shah, Nimit M. Sent: Friday, October 14, 2011 10:28 AM To: Mendis, Michael E.; i2b2 AUG Members Subject: RE: message log
That did it. Thanks!
Nimit

From: Mendis, Michael E. Sent: Thursday, October 13, 2011 3:58 PM To: Shah, Nimit M.; i2b2 AUG Members Subject: Re: message log
If you edit the i2b2_config_data.js and change debug from false to true
mike

On 10/13/11 3:38 PM, "Shah, Nimit M." <NSHAH11.PARTNERS> wrote:
Hi,
I was looking at my VM when running on NAT and noticed the message log from i2b2 1.5 version in not in the 1.6 version. It was located next to Analysis Tools before. Is it possible to have this feature put back in?
Thanks Nimit Shah Informatics Development Co op Sleep Medicine Epidemiology Brigham and Women's Hospital 221 Longwood Avenue Boston, MA 02115

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From: Shah, Nimit M. Sent: Thursday, October 13, 2011 2:59 PM To: Mendis, Michael E.; i2b2 AUG Members Subject: RE: VMWare bridged connection
I tired logging into oracle through the steps of VMware guide(Log in to Oracle by going to the following address: http://your ip address:8080/apex/) but I cannot connect to this address. Also how do I check if the listener and xe is up and running? http://172.23.134.136:9090/i2b2/services/listServices shows that all services are all active.
Thanks,
Nimit

From: Mendis, Michael E. Sent: Thursday, October 13, 2011 2:22 PM To: Shah, Nimit M.; i2b2 AUG Members Subject: Re: VMWare bridged connection
Looks like oracle is not running or not listening, can you verify that the listener and xe is up and running.
mike

On 10/13/11 2:18 PM, "Shah, Nimit M." <NSHAH11.PARTNERS> wrote:
Hi Mike,
I did reboot the server after the change. The message log is repeating this one error each time I try to login to i2b2demo on bridged connection. Thanks, Nimit

From: Mend s Michael E. Sent: Thursday, October 13, 2011 12:54 PM To: Shah, Nimit M.; i2b2 AUG Members Subject: Re: VMWare bridged connection
You where able to get to a axis2 screen when you went to h http://172.23.134.136:9090/i2b2/axis2admin/login
Good
I would take a look at the jboss log file /opt/jboss/server/default/log/server.log to see if you see any ERROR: that might point to why you cant login
Also did you reboot the server once you changed from nat to bridge
mike

On 10/13/11 12:47 PM, "Shah, Nimit M." <NSHAH11.PARTNERS> wrote: Hi Mike,
I went to the site but am not able to login to http://172.23.134.136:9090/i2b2/axis2-admin/login . I have tried all the username and passwords from the online guide for the VMware but am not able to login. Is there some way I have to create a username and password? Thank you.
Nimit

From: Mendis, Michael E. Sent: Thursday, October 13, 2011 11:03 AM To: Shah, Nimit M.; i2b2 AUG Members Subject: Re: VMWare bridged connection
Try using a browser and goto http://172.23.134.136:9090/i2b2
It should bring up the axis2 page. If not that check for firewall exceptions.
mike

On 10/13/11 10:04 AM, "Shah, Nimit M." <NSHAH11.PARTNERS> wrote:
Hi,
When using a NAT connection, I am able to connect to the i2b2demo but when I try using a bridged connection, I get an error that says "The PM Cell is down or the address in the properties file is incorrect."
Inside the pm-ds.xml file I have tried using 127.0.0.1 but this does not help.
Thanks Nimit Shah
Informatics Development Co op Sleep Medicine Epidemiology Brigham and Women's Hospital 221 Longwood Avenue Boston, MA 02115 nshah11.partners

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From: Dat Q. Phan [Dat.Q.Phan.uth.tmc] Sent: Thursday, October 13, 2011 1:24 PM To: Murphy, Shawn N.; Phillip Reeder Cc: i2b2 AUG Members Subject: RE: i2b2 v1.5.2 AD integration documentation
I uploaded some additional documentation that hopefully will help with the installation and configuration of i2b2 v1.6.
https://community.i2b2.org/wiki/display/community/Community+Postings
Regards,
Johnny Phan
Programmer Analyst II
UTHealth School of Biomedical Informatics
Dat.Q.Phan.uth.tmc

From: Murphy, Shawn N. [SNMURPHY.PARTNERS] Sent: Wednesday, October 05, 2011 12:25 PM To: Phillip Reeder; Michael.C.Ford.kp Cc: Dat Q. Phan; i2b2 AUG Members; travis.nagler.ucdmc.ucdavis Subject: RE: i2b2 v1.5.2 AD integration documentation
Hi Philip,
You can post it on the AUG section of the Community Wiki, I think you should have access but if not let me know.
Thanks for distributing this nice document,
Shawn.

From: Phillip Reeder [Phillip.Reeder.uth.tmc] Sent: Tuesday, October 04, 2011 8:38 PM To: <Michael.C.Ford.kp> Cc: Dat Q. Phan; <i2b2 AUG Members>; <travis.nagler.ucdmc.ucdavis> Subject: Re: i2b2 v1.5.2 AD integration documentation
Its supplemental documentation that we have developed at UT Houston based on our experience installing and configuring i2b2. It should work for both the 1.5 and 1.6 releases of i2b2.
If this is helpful to people, is there an official location that we can contribute this and other documentation to?
Phillip
Sent from my iPhone

On Oct 4, 2011, at 6:38 PM, <Michael.C.Ford.kp> wrote:
what manual is this from ?

From: Dat Q. Phan Sent: 10/04/2011 03:32 PM To: Travis Nagler, i2b2 AUG Members Subject RE: i2b2 v1.5.2 AD integration documentation
Travis, See the attachement.
Johnny Phan Programmer Analyst II UTHealth School of Biomedical Informatics 713-500-3939
Dat.Q.Phan.uth.tmc

From: Travis Nagler [travis.nagler.ucdmc.ucdavis] Sent: Tuesday, October 04, 2011 5:25 PM To: i2b2 AUG Members Subject: i2b2 v1.5.2 AD integration documentation
We are looking to use Active Directory for logging into i2b2. Does anyone have any documentation they would be willing to share on how they got it done? I have been told to look in the admin web screens where I would find some parameters to employ, but I don't have those parameters pages (I've seen the screenshots).
Is AD setup within Apache or within the web client? How is the integration supposed to work?
Thanks,
Travis
Travis H. Nagler
Senior Database Programmer American Burn Assoc. - Data Coordinating Center UC Davis Division of Burn Surgery UC Davis Health System 2921 Stockton Blvd., Suite 1470 Sacramento, CA, 95817 tel: (916) 703-9215 fax: (916) 703-9124 http://www.ucdmc.ucdavis.edu travis.nagler.ucdmc.ucdavis

From: Remo Mueller <rmueller.rics.bwh.harvard> To: i2b2 AUG Members Date: 10/04/2011 06:22 AM Subject: i2b2 1.6.rc5 Virtual Machine Question
Hello All, I'm in the process of setting up my first i2b2 Virtual Machine (1.6.rc5), and I've run into the following error: (I used login:demo pw:demouser). Also of note, I used a bridged connection so that I'd be able to connect to the web service (as NAT was giving me a strange 10.0.2.15 address that was unreachable).
I'm running on a Mac OS X, using Virtual Box 4.1.4
Any help would be appreciated, thanks!
Remo Mueller

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From: Shah, Nimit M. Sent: Thursday, October 13, 2011 8:51 AM To: Mendis, Michael E.; Law, James; i2b2 AUG Members Subject: RE: logging into i2b2demo through the VMWARE
Hi
I went into the file and changing the IP with 127.0.0.1 allows me to access i2b2demo.
Thanks

From: Mendis, Michael E. Sent: Wednesday, October 12, 2011 6:40 PM To: Law, James; Shah, Nimit M.; i2b2 AUG Members Subject: Re: logging into i2b2demo through the VMWARE
Thanks james.
There is a error in the pm-ds.xml file that containted a hardcoded IP address. And because the Vmware server gives you a unique IP this will not work. It should be either (127.0.0.1 or localhost)
I am updating the VM image now. You can either download the new one or replace the
192.168.175.130 with 127.0.0.1.
Sorry ,mike

On 10/12/11 11:10 AM, "Law, James" <jlaw.med.umich> wrote:
Hi,
In the 1.60 release of the VM, I noticed the the PM-ds.xml file inside the /opt/jboss/server/default/deploy directory had an invalid IP address, you may want to check this file and make sure it is pointed to localhost.
Thanks, James

From: Shah, Nimit M. [NSHAH11.PARTNERS] Sent: Wednesday, October 12, 2011 10:50 AM To: i2b2 AUG Members Subject: logging into i2b2demo through the VMWARE
Hello,
I seem to be having some trouble using the VWware. The problems I am facing occur when trying to login to i2b2demo. I had to put the login and password which were login:demo password:demouser
I then tried to login but received this error.
I then tried the same credential in harvard demo which after some time loaded. Is i2b2demo not supposed to work under VMware? Also I the network is a NAT connection but I face the same problem with a bridged connection.
Thanks Nimit Shah Informatics Development Co op Sleep Medicine Epidemiology Brigham and Women's Hospital 221 Longwood Avenue Boston, MA 02115 Tel: 857-307-0358 nshah11.partners

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From: Donahoe, Janice M Sent: Wednesday, October 12, 2011 12:01 PM To: Joseph Bonner; i2b2 AUG Members Subject: RE: Workbench Working - but where is Data Import Plug In
Hi Joe,
The import plug-in is an optional feature. In chapter 4 of the i2b2Workbench_Install_Guide we explain how to install the optional plug-ins.
Attached is a document with just the chapter on features and how to install them. If you haven't already done so you can download the full version of the guide from the software page of the i2b2 website.
Thanks.
Janice
From: Joseph Bonner [Joseph.Bonner.hc.msu] Sent: Wednesday, October 12, 2011 11:06 AM To: i2b2 AUG Members Subject: Workbench Working - but where is Data Import Plug In
I have workbench working thanks so much to James and Lori. Now that it is here - I am trying to find to find the Data Import Plug In. The main i2b2.org site says that it is downloaded through workbench but I cannot seem to find out how to do this. Sorry for being a pest.
Joe B

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From: Phillips, Lori C. Sent: Wednesday, October 12, 2011 11:04 AM To: Joseph Bonner; i2b2 AUG Members Subject: RE: Workbench 1.6
Hi Joe,
You should be trying to import the file i2b2Workbench-src-16.zip into eclipse.
The file i2b2Workbench-win-16.zip is the packaged executable that is described in the document i2b2workbench_install_guide_1-6-1.doc. If you have no reason to either run i2b2 from eclipse or to look at the source code then use this setup.
Lori Phillips

From: Joseph Bonner [Joseph.Bonner.hc.msu] Sent: Wednesday, October 12, 2011 9:54 AM To: i2b2 AUG Members Subject: Workbench 1.6
I cannot get the workbench (i2b2Workbench-win-16.zip) to import into Eclipse beyond step 2.1.2#8 of the documentation.
When I try to import the file into a eclipse project there no entries in the project window as show in the documentation screenshot for step 2.1.2#8.
I have downloaded the .zip several times each time it want to take a bit too long when moving from the temp to a permanent file on my desktop. Being a newbie I don't know if there is a problem with the file, a problem with the instructions or a mixture of the two.
Can anybody help me beyond this step?
Joe B Michigan State University

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From: Mendis, Michael E. Sent: Tuesday, October 11, 2011 9:54 AM To: Dan Connolly; Dat.Q.Phan.uth.tmc.edu Cc: i2b2 AUG Members; Arvinder Choudhary Subject: Re: new 1.6 installation - Web client
There are two webclients, one in the i2b2 core source called admin and the regular webclient. Yes they are actually the same, with the admin have adminOnly: true and in the i2b2_plugin file it does not load the modules (CRC, WORK, and ONT).
You could if you wanted just have one client and add a admin domain also in the list such as:(2b2 _config_data.js) {
domain: "i2b2demo", name: "I2B2 1.6 Demo", urlCellPM: "http://127.0.0.1:8080/i2b2/rest/PMService/", allowAnalysis: true,
adminOnly: false,
debug: true, isSHRINE: false
}, {
domain: "i2b2demo", name: "I2B2 1.6 ADMIN", urlCellPM: "http://127.0.0.1:8080/i2b2/rest/PMService/", allowAnalysis: true,
adminOnly: true,
debug: true, isSHRINE: false
}
mike

On 10/11/11 9:48 AM, "Dan Connolly" <dconnolly.kumc.edu> wrote:
Is this documented? I thought we looked pretty carefully.

On Mon, 2011?10?10 at 22:04 +0000, Dat Q. Phan wrote:
In 1.6 they are separate webclients.
Leave adminOnly: false in the webclient folder and then make a copy of the webclient folder and name it admin and change adminOnly: true.

From: Arvinder Choudhary [achoudhary.kumc] Sent: Monday, October 10, 2011 4:44 PM To: i2b2 AUG Members Subject: new 1.6 installation ?Web client
Team:
In i2b2 1.6 R4 do we have separate webclients for Admin and regular users or it is same as we have in 1.4. What file I have to manipulate to have both find Patient and Admin tab in the same web client.
Only file that I see is i2b2_config_data.js
===============
{ urlProxy: "index.php", urlFramework: "js?i2b2/", //??????????????????????????????????????????????????????????????????????????????????????????// THESE ARE ALL THE DOMAINS A USER CAN LOGIN TO lstDomains: [
{ domain: "i2b2demo",
name: "I2B2 1.6 Demo", urlCellPM: "http://127.0.0.1:8080/i2b2/rest/PMService/", allowAnalysis: true, adminOnly: false, debug: true, isSHRINE: false
} ] //??????????????????????????????????????????????????????????????????????????????????????????
}
===============
if I change the AdminOnly to True and isSHRINE to True... I get Admin webclient with no find patient tab .
Arvinder

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From: Brian Ostasiewski [bostasie.wakehealth] Sent: Tuesday, October 11, 2011 8:36 AM To: i2b2 AUG Members Subject: RE: I2b2 1.6
Thanks for getting this available.
When I run a query in the webclient and ask for the Gender/Race/etc patient breakdowns, it comes back with totals of only 1 or 0 in the categories for race, gender, and vital status. Age breakdown is correct. If I pull this same patient result set into the Demographics analysis plugin it correctly displays the right numbers for race, gender, and vital status.
This 1.6 install I have running on a test box right now, where I've simply overwritten the RC5 webclient files with the newly released files, and I've done a recompile of all the server code with the new release files, so I'm wondering if it may be a result of not doing a complete fresh install – can anyone else verify these problems?
Brian Ostasiewski

From: Murphy, Shawn N. [SNMURPHY.PARTNERS] Sent: Monday, October 10, 2011 6:59 PM To: i2b2 AUG Members Subject: I2b2 1.6
Hi All,
I2b2 1.6.00 has been released at https://www.i2b2.org/software/index.html
Thanks, Shawn.

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From: Murphy, Shawn N. Sent: Tuesday, October 11, 2011 7:46 AM To: Jack London Cc: i2b2 AUG Members Subject: RE: i2b2 1.6 Release on Monday
Hi Jack,
Although the components are interchangeable, the final release has some bug fixes and new functionality in most of the modules. The web client has been cleaned up substantially from RC5.
Thanks, Shawn.

From: Jack London [jack.london.KimmelCancerCenter] Sent: Monday, October 10, 2011 10:01 AM To: Murphy, Shawn N. Cc: i2b2 AUG Members Subject: Re: i2b2 1.6 Release on Monday
Shawn,
If we already have the i2b2 web client v1.6 RC5 deployed, will we need to do a complete install of the v1.6 Release, or can we just replace a few modules of RC5?
Jack

On Oct 7, 2011, at 8:36 PM, Murphy, Shawn N. wrote:
Hi All,
We're going to need to take the weekend to clean up some details and do the release on Monday.
Thanks, Shawn.

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From: Dan Connolly [dconnolly.kumc] Sent: Monday, October 10, 2011 5:54 PM To: Mendis, Michael E. Cc: i2b2 AUG Members Subject: Re: help diagnose IncorrectResultSizeDataAccessException in new 1.6 installation?
Thanks for taking a quick look, Mike. It turns out that the big metadata query wasn't actually the relevant one.
The problem was that we somehow loaded the QT_PRIVILEGE and QT_BREAKDOWN_PATH tables twice, causing this query to fail:
2011-10-10 16:35:59,588 DEBUG [org.springframework.jdbc.core.JdbcTemplate] Executing SQL query [select * from i2b2_16demodata.qt_privilege where protection_label_cd = ? and plugin_id is NULL]

On Mon, 2011-10-10 at 17:31 -0400, Mike Mendis wrote:
Take a look at the table: i2b2_16metadata.I2B2 seems like you have a duplicate entry in it.
mike

On 10/10/11 5:20 PM, "Dan Connolly" <dconnolly.kumc> wrote:
Hi,
We're trying to get i2b2 1.6 R4 running. We made life hard for ourselves by re-using an oracle instance that hosts 1.4, so we renamed all the schema/user names to i2b2_16hive, i2b2_16pm, i2b2_16metadata, etc. We think we did that in all the right places, but it's entirely possible that we missed a few.
We've got the web client to come up and show us the concept hierarchy and such, but when we run a query, we lose. The relevant part of the debug log seems to be:
15:42:35,523 INFO [ConceptDao] findMods: select c_hlevel, c_fullname, c_name, c_synonym_cd, c_visualattributes, c_totalnum, c_basecode, c_facttablecolumn, c_tablename, c_columnname, c_columndatatype, c_operator, c_dimcode, c_tooltip, m_applied_path from i2b2_16metadata.I2B2 where m_exclusion_cd is null and c_fullname in (select c_fullname from i2b2_16metadata.I2B2 where m_applied_path = '\i2b2\Labtests\' and c_hlevel = 1 and m_exclusion_cd is null union all (select c_fullname from i2b2_16metadata.I2B2 where m_applied_path = '\i2b2\Labtests%' and c_hlevel = 1 and m_exclusion_cd is null) union all (select c_fullname from i2b2_16metadata.I2B2 where m_applied_path = '\i2b2%' and c_hlevel = 1 and m_exclusion_cd is null) union all (select c_fullname from i2b2_16metadata.I2B2 where m_applied_path = '%' and c_hlevel = 1 and m_exclusion_cd is null) MINUS (select c_fullname from i2b2_16metadata.I2B2 where m_applied_path = '\i2b2\Labtests\' and m_exclusion_cd is not null union all (select c_fullname from i2b2_16metadata.I2B2 where m_applied_path = '\i2b2\Labtests%' and m_exclusion_cd is not null) union all (select c_fullname from i2b2_ 16metadata.I2B2 where m_applied_path = '\i2b2%' and m_exclusion_cd is not null) union all (select c_fullname from i2b2_16metadata.I2B2 where m_applied_path = '%' and m_exclusion_cd is not null))) order by c_name 15:42:42,321 INFO [DataSourceLookupHelper] Located DataSource for hiveId=[i2b2demo] projectId=[/Demo/] 15:42:42,322 INFO [STDOUT] Roles from get i2b2demo/Demo/dconnolly 15:42:42,322 INFO [STDOUT] Roles from size 2 15:42:42,322 INFO [OracleDAOFactory] Using datasource java:QueryToolDemoDS 15:42:42,327 ERROR [QueryRequestDelegate] Throwable javax.ejb.EJBException: org.springframework.dao.IncorrectResultSizeDataAccessException: Incorrect result size: expected 1, actual 2
Clues, anyone?

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From: Mendis, Michael E. Sent: Friday, October 07, 2011 9:22 AM To: Robert Schuff; i2b2 AUG Members Subject: Re: issue status with two reported bugs
I checked and both of these where fixed in 1.5.2.
mike

From: Robert Schuff [schuffr.ohsu] Sent: Thursday, October 06, 2011 6:21 PM To: Mendis, Michael E.; i2b2 AUG Members Subject: Re: issue status with two reported bugs
Great! Thanks Mike. If they are can Jira also be updated? Could a patch for these be applied to 1.4?
Robert Schuff - Director, Clinical Research Informatics Oregon Clinical & Translational Research Institute Oregon Health & Science University http://www.octri.org/

On 10/6/11 3:10 PM, "Mendis, Michael E." <MMENDIS.PARTNERS> wrote:
Rob, I believe that these are resolved in the final 1.6, but will double check
Mike

On 10/6/11 6:06 PM, "Robert Schuff" <schuffr.ohsu> wrote:
Hi Folks,
There are two reported bugs in i2b2 that I am curious about with respect to resolution status. I checked the Jira site and it doesn't show any activity on these issues except from the user community about 1 year ago so I am curious if the team has addressed them yet or not. They represent pretty serious issues in that fairly common usage scenarios will lead to incorrect counts. We are using version 1.4. Here are the issues:
LEOPARD?21 – in the web client the <= and >= operators do not appear to be functioning properly, however the < and > operators do function as expected.
LEOPARD?52 – when a saved query has query by value components and the saved query is executed, the query by value criteria are not applied to the query and erroneously high counts are returned. If the "set value" dialog is invoked for each of the parameters and then closed (no need to change anything) and the query is executed, then the correct values are returned.
These were reported almost a year ago and are (arguably) pretty serious so I am guessing they have been addressed, but I cannot tell from Jira if that's the case. There is a note that as of 1.6 RC2 in december 2010, LEOPARD?21 still was unresolved.
Can anyone verify if these behaviors exist in 1.5 and 1.6? If so, is there a patch that can be applied to 1.4? I'd rather not "educate" our users around these bugs if we can avoid it!
BTW, we are (finally!) going live with our installation this month. Interest (and expectations!) are high and our first trained cohort will be about 20 investigators.
Thanks! Rob
Robert Schuff ?Director, Clinical Research Informatics
Oregon Clinical & Translational Research Institute Oregon Health & Science University http://www.octri.org/

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From: Phillips, Lori C. Sent: Thursday, October 06, 2011 11:33 AM To: Murphy, Shawn N.; Huser, Vojtech (NIH/CC/OD) [E]; i2b2 AUG Members Subject: RE: demo vs. demo2 dataset - short description of what are the differences between them
One set had expression profile data and the other didnt. I believe that demo had the data and demo2 did not.
Lori

From: Murphy, Shawn N. Sent: Thursday, October 06, 2011 11:19 AM To: Huser, Vojtech (NIH/CC/OD) [E]; i2b2 AUG Members Subject: RE: demo vs. demo2 dataset - short description of what are the differences between them
Hi Vojtech,
The second project was stood up in the demo only to provide an example of how to set up two projects. There was a lot of questions about that back in the 1.3 days. We agree that now it creates more confusion than it solves, so in 1.6 we will no longer support the smaller project and just have one project in the demo.
Thanks, Shawn.

From: Huser, Vojtech (NIH/CC/OD) [E] [vojtech.huser.nih.gov] Sent: Thursday, October 06, 2011 11:05 AM To: i2b2 AUG Members Subject: demo vs. demo2 dataset - short description of what are the differences between them
Hi, This may be in some other source, but could someone, please, provide any brief description on how are the two demo sets different.
E.g., demo2 has more types of data or more patients?
Vojtech
p.s.
I write 10-20 queries to research it myself; however getting it from the source (creator of the demo data sets) produces more accurate description (insights)
Vojtech Huser, MD PhD Laboratory for Informatics Development NIH Clinical Center, Bethesda, MD 20892 Bld 10, Rm 6-5561 Email: vojtech.huser.nih.gov

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From: Dat Q. Phan [Dat.Q.Phan.uth.tmc] Sent: Thursday, October 06, 2011 10:39 AM To: Remo Mueller Cc: i2b2 AUG Members Subject: RE: i2b2 1.6.rc5 Oracle Connection
From your previous post, didn't you mention port 8080 is being used by another process? If so, can you temporarily disable the other service that is utilizing port 8080 just to test that the oracle interface is working? Besides this, everything else is working right webclient, etc?
Johnny
From: Mendis, Michael E. Sent: Thursday, October 06, 2011 10:04 AM To: Sebastian Mate; 'Remo Mueller' Cc: 'Dat Q. Phan'; 'Peter Beninato'; i2b2 AUG Members Subject: Re: AW: i2b2 1.6.rc5 Oracle Connection
If you have set the VM to bridge connection, than to access the oracle XE web interface you will need to execute the following command in sqlplus exec dbms_xdb.setListenerLocalAccess(false);
Login as sqlplus system/demouser
mike

On 10/6/11 9:51 AM, "Sebastian Mate" <Sebastian.Mate.imi.med.uni?erlangen.de> wrote:
Hi Remo,
please note that the Oracle web interface (/apex) is ONLY accessible from "localhost", that means from inside your VM. If you want to access it from the outside, you have to change a setting inside the web interface. To be able to do this, you need a graphical web browser on you VM. So this a kind of a hen/egg problem.
Regarding the NAT interface: you need two network interfaces when using VirtualBox:
?NAT: to access the internet from your VM
?"Host Only Network": to access your VM from your host machine
Sebastian

From: Remo Mueller [rmueller.rics.bwh.harvard] Sent: Thursday, October 06, 2011 8:29 AM To: i2b2 AUG Members Cc: Dat Q. Phan; Peter Beninato Subject: Re: i2b2 1.6.rc5 Oracle Connection
Hi,
I tried a fresh install using Virtual Box, and setting to a Bridged connection without trying a NAT setup first.
I'm able to access the web client login screen, however http://_______:8080/apex/ still fails to load the oracle interface.
Has anyone successfully booted i2b2 in a VirtualBox environment (or in a bridged environment)?
Thanks,
Remo

On Oct 5, 2011, at 4:07 PM, Remo Mueller wrote:
Ok thanks Johnny, I'll give that a try!
Remo

On Oct 5, 2011, at 4:04 PM, Dat Q. Phan wrote:
The reason why I mentioned it is because with the default VM image from i2b2, you shouldn't have to configure anything because it is already configured for you.
Unless you want to reload the default image but set it as a bridge connection instead of NAT and then the VM will assign you an IP that you can access. I'm just thinking changing it from NAT initially to bridge is what is giving you so much trouble. If you start it off as a bridged connection before starting the VM that might help.

From: Remo Mueller [rmueller.rics.bwh.harvard] Sent: Wednesday, October 05, 2011 1:33 PM To: Dat Q. Phan; Peter Beninato Cc: i2b2 AUG Members Subject: Re: i2b2 1.6.rc5 Oracle Connection
Hi Johnny,
I was never able to connect through NAT. NAT gave me an address 10.0.2.15, which I tried in my web browser, however it never allowed me to connect to the web client. I was also unable to connect to the virtual machine using ssh.
I did try the initial NAT setup when I extracted from the zip file initially. Is there a reason why NAT is preferred over a bridged connection?
Thanks!
Remo
Remo Mueller, Ph.D. Director of Informatics Sleep Medicine Epidemiology Brigham and Women's Hospital 221 Longwood Avenue, BL 231A Boston, MA 02115
rmueller.rics.bwh.harvard
https://sleepepi.partners.org

On Oct 5, 2011, at 2:26 PM, Dat Q. Phan wrote:
Remo,
What is wrong with leaving it in NAT mode? You mentioned you are running this VM through your Mac correct? If you are also accessing the webclient through your Mac's browser then NAT mode will be fine even though it assigns a weird IP address for your VM. Since you are running that VM from your Mac, you will still be able to access it locally from your Mac.
You will not be able to access it from another machine to the VM on your Mac though.
If you are just accessing it through your Mac and the VM is ran from the same machine then I suggest you delete your current VM and reload the default VM from i2b2 and leave it in NAT mode. With the VM from i2b2, you really don't need to make any modifications to the VM to get it to run.
Johnny

From: Remo Mueller [rmueller.rics.bwh.harvard] Sent: Wednesday, October 05, 2011 1:24 PM To: Peter Beninato Cc: i2b2 AUG Members Subject: Re: i2b2 1.6.rc5 Oracle Connection
Hi Peter,
I'm forwarding the port 8080 to 3088 on my local computer using the ssh -L parameter (since 8080 is already taken by a different process).
For example, I forward the default 80 port to 3000 on my local machine (and that is working fine).
Remo

On Oct 5, 2011, at 2:13 PM, Peter Beninato wrote:
Hi,
The default port for apex is generally 8080, so not sure the apex URL with port 3088 is correct.

From: Remo Mueller [rmueller.rics.bwh.harvard] Sent: Wednesday, October 05, 2011 11:09 AM To: i2b2 AUG Members Subject: i2b2 1.6.rc5 Oracle Connection
Hello All,
I've gotten a bit farther in getting a virtual machine for i2b2 1.6.rc5 up and running. (All I'm trying to do is get a sample i2b2 web client running with the default demo user login).
I start the VM in bridged mode so I can connect to it from my computer:
ssh -L 3080:127.0.0.1:80 -L 3088:127.0.0.1:8080 root.172.23.134.198
This way on my local machine browser I can type:
http://localhost:3080/webclient/index.php
Which gets me to the login.
However http://localhost:3088/apex/
which should allow me to view the Oracle login gives me:
No Data Received
And the following in the virtual machine
channel 5: open failed: connect failed: Connection refused channel 6: open failed: connect failed: Connection refused
Additionally, when I try logging in to the web client, it gives me:
ERROR: Database error in getting environment data
I assume the two are related, but I don't see how I can get access to Oracle database to fix the access issue for my demo user.
Thanks, Remo
Remo Mueller, Ph.D. Director of Informatics Sleep Medicine Epidemiology Brigham and Women's Hospital 221 Longwood Avenue, BL 231A Boston, MA 02115
rmueller.rics.bwh.harvard https://sleepepi.partners.org
Dump:
13:59:17,658 ERROR [STDERR] Caused by: java.sql.SQLException: Listener refused the connection with the following error: ORA-12505, TNS:listener does not currently know of SID given in connect descriptor The Connection descriptor used by the client was:
localhost:1521:xe 13:59:17,658 ERROR [STDERR] at oracle.jdbc.driver.DatabaseError.throwSqlException(DatabaseError.java:112)
13:59:17,658 ERROR [STDERR] at
oracle.jdbc.driver.DatabaseError.throwSqlException(DatabaseError.java:261) 13:59:17,658 ERROR [STDERR] at oracle.jdbc.driver.T4CConnection.logon(T4CConnection.java:387)
13:59:17,659 ERROR [STDERR] at
oracle.jdbc.driver.PhysicalConnection.<init>(PhysicalConnection.java:420) 13:59:17,659 ERROR [STDERR] at oracle.jdbc.driver.T4CConnection.<init>(T4CConnection.java:165)
13:59:17,659 ERROR [STDERR] at oracle.jdbc.driver.T4CDriverExtension.getConnection(T4CDriverExtension.java:35)
13:59:17,659 ERROR [STDERR] at oracle.jdbc.driver.OracleDriver.connect(OracleDriver.java:801) 13:59:17,660 ERROR [STDERR] at
org.jboss.resource.adapter.jdbc.local.LocalManagedConnectionFactory.createManagedConnection(L ocalManagedConnectionFactory.java:171) 13:59:17,660 ERROR [STDERR] ... 18 more 13:59:17,660 ERROR [STDERR] edu.harvard.i2b2.common.exception.I2B2DAOException: Database error 13:59:17,660 ERROR [STDERR] Source) at edu.harvard.i2b2.pm.dao.PMDbDao.getEnvironment(Unknown
13:59:17,661 ERROR [STDERR] at edu.harvard.i2b2.pm.delegate.ServicesHandler.execute(Unknown Source)
13:59:17,661 ERROR [STDERR] at edu.harvard.i2b2.pm.ws.ExecutorRunnable.run(Unknown Source) 13:59:17,661 ERROR [STDERR] at java.lang.Thread.run(Thread.java:619) 13:59:17,661 ERROR [ServicesHandler] Database error in getting environment data 13:59:17,661 ERROR [STDERR] java.lang.Exception: Database error in getting environment data 13:59:17,662 ERROR [STDERR] at
edu.harvard.i2b2.pm.delegate.ServicesHandler.execute(Unknown Source)
13:59:17,662 ERROR [STDERR] at edu.harvard.i2b2.pm.ws.ExecutorRunnable.run(Unknown Source) 13:59:17,662 ERROR [STDERR] at java.lang.Thread.run(Thread.java:619) 13:59:17,767 DEBUG [PMService] my pm repsonse is: <?xml version="1.0" encoding="UTF-8"
standalone="yes"?> <ns2:response xmlns:ns2="http://www.i2b2.org/xsd/hive/msg/1.1/" xmlns:ns4 ="http://www.i2b2.org/xsd/cell/pm/1.1/" xmlns:ns3="http://www.i2b2.org/xsd/hive/msg/version/">
<message_header> <i2b2_version_compatible>1.1</i2b2_version_compatible> <hl7_version_compatible>2.4</hl7_version_compatible> <sending_application>
<application_name>PM Cell</application_name> <application_version>1.5</application_version>
</sending_application> <sending_facility>
<facility_name>i2b2 Hive</facility_name> </sending_facility> <receiving_application>
<application_name>PM Cell</application_name>
<application_version>1.5</application_version> </receiving_application> <receiving_facility>
<facility_name>i2b2 Hive</facility_name> </receiving_facility> <datetime_of_message>2011-10-05T13:59:17.671-04:00</datetime_of_message> <message_control_id>
<message_num>l1R92V7F91orDXL0pvYoe</message_num>
<instance_num>1</instance_num> </message_control_id> <processing_id>
<processing_id>P</processing_id>
<processing_mode>I</processing_mode> </processing_id> <accept_acknowledgement_type>AL</accept_acknowledgement_type> <application_acknowledgement_type>AL</application_acknowledgement_type> <country_code>US</country_code> <project_id>undefined</project_id>
</message_header> <response_header> <result_status>
<status type="ERROR">Database error in getting environment data</status> </result_status> </response_header> </ns2:response>
13:59:17,769 DEBUG [PMService] my return is: <ns2:response xmlns:ns2 ="http://www.i2b2.org/xsd/hive/msg/1.1/" xmlns:ns4="http://www.i2b2.org/xsd/cell/pm/1.1/" xmlns:ns3 ="http://www.i2b2.org/xsd/hive/msg/version/">
<message_header> <i2b2_version_compatible>1.1</i2b2_version_compatible> <hl7_version_compatible>2.4</hl7_version_compatible> <sending_application>
<application_name>PM Cell</application_name>
<application_version>1.5</application_version> </sending_application> <sending_facility>
<facility_name>i2b2 Hive</facility_name> </sending_facility> <receiving_application>
<application_name>PM Cell</application_name>
<application_version>1.5</application_version> </receiving_application> <receiving_facility>
<facility_name>i2b2 Hive</facility_name> </receiving_facility> <datetime_of_message>2011-10-05T13:59:17.671-04:00</datetime_of_message> <message_control_id>
<message_num>l1R92V7F91orDXL0pvYoe</message_num>
<instance_num>1</instance_num> </message_control_id> <processing_id>
<processing_id>P</processing_id>
<processing_mode>I</processing_mode> </processing_id> <accept_acknowledgement_type>AL</accept_acknowledgement_type> <application_acknowledgement_type>AL</application_acknowledgement_type> <country_code>US</country_code> <project_id>undefined</project_id>
</message_header> <response_header> <result_status>
<status type="ERROR">Database error in getting environment data</status> </result_status>
</response_header> </ns2:response> [root.dhcp-172-23-134-198 ~]# service oracle restart13:59:25,399 DEBUG [IdleRemover] run:
IdleRemover notifying pools, interval: 30000
13:59:25,873 INFO [JMSContainerInvoker] Trying to reconnect to JMS provider for querytool.QueryExecutorMDB 13:59:25,878 DEBUG [JMSContainerInvoker] Initializing 13:59:25,878 DEBUG [JMSContainerInvoker] Looking up provider adapter: java:/DefaultJMSProvider 13:59:25,879 DEBUG [JMSContainerInvoker] Provider adapter:
org.jboss.jms.jndi.JNDIProviderAdapter.1747f59
13:59:25,879 DEBUG [DLQHandler] Creating DLQHandler 13:59:25,879 DEBUG [DLQHandler] Initialization failed DLQHandler
javax.naming.NameNotFoundException: XAConnectionFactory not bound at org.jnp.server.NamingServer.getBinding(NamingServer.java:529) at org.jnp.server.NamingServer.getBinding(NamingServer.java:537) at org.jnp.server.NamingServer.getObject(NamingServer.java:543) at org.jnp.server.NamingServer.lookup(NamingServer.java:296) at org.jnp.interfaces.NamingContext.lookup(NamingContext.java:667) at org.jnp.interfaces.NamingContext.lookup(NamingContext.java:627) at javax.naming.InitialContext.lookup(InitialContext.java:392) at org.jboss.ejb.plugins.jms.DLQHandler.createService(DLQHandler.java:182) at
org.jboss.system.ServiceMBeanSupport.jbossInternalCreate(ServiceMBeanSupport.java:260) at org.jboss.system.ServiceMBeanSupport.create(ServiceMBeanSupport.java:188) at
org.jboss.ejb.plugins.jms.JMSContainerInvoker.innerStartDelivery(JMSContainerInvoker.java:510) at org.jboss.ejb.plugins.jms.JMSContainerInvoker$ExceptionListenerImpl $ExceptionListenerRunnable.run(JMSContainerInvoker.java:1428) at java.lang.Thread.run(Thread.java:619)
13:59:25,879 ERROR [JMSContainerInvoker] Reconnect failed: JMS provider failure detected for querytool.QueryExecutorMDB javax.naming.NameNotFoundException: XAConnectionFactory not bound
at org.jnp.server.NamingServer.getBinding(NamingServer.java:529)

NEXT EMAIL
From: Murphy, Shawn N. Sent: Wednesday, October 05, 2011 1:30 PM To: Peter Beninato; Phillip Reeder; Michael.C.Ford.kp Cc: Dat Q. Phan; i2b2 AUG Members; travis.nagler.ucdmc.ucdavis Subject: RE: i2b2 v1.5.2 AD integration documentation
Sure, I think Mike may be working on that now.
Thanks, Shawn.

From: Peter Beninato [beninato.ohsu] Sent: Wednesday, October 05, 2011 1:26 PM To: Murphy, Shawn N.; Phillip Reeder; Michael.C.Ford.kp Cc: Dat Q. Phan; i2b2 AUG Members; travis.nagler.ucdmc.ucdavis Subject: RE: i2b2 v1.5.2 AD integration documentation
Could it also be added to the distribution documentation that comes with the software?

From: Murphy, Shawn N. [SNMURPHY.PARTNERS] Sent: Wednesday, October 05, 2011 10:25 AM To: Phillip Reeder; Michael.C.Ford.kp Cc: Dat Q. Phan; i2b2 AUG Members; travis.nagler.ucdmc.ucdavis Subject: RE: i2b2 v1.5.2 AD integration documentation
Hi Philip,
You can post it on the AUG section of the Community Wiki, I think you should have access but if not let me know.
Thanks for distributing this nice document,
Shawn.

From: Phillip Reeder [Phillip.Reeder.uth.tmc] Sent: Tuesday, October 04, 2011 8:38 PM To: <Michael.C.Ford.kp> Cc: Dat Q. Phan; <i2b2 AUG Members>; <travis.nagler.ucdmc.ucdavis> Subject: Re: i2b2 v1.5.2 AD integration documentation
Its supplemental documentation that we have developed at UT Houston based on our experience installing and configuring i2b2. It should work for both the 1.5 and 1.6 releases of i2b2.
If this is helpful to people, is there an official location that we can contribute this and other documentation to?
Phillip

On Oct 4, 2011, at 6:38 PM, <Michael.C.Ford.kp> wrote:
what manual is this from ?

From: "Dat Q. Phan" <Dat.Q.Phan.uth.tmc> Sent: 10/04/2011 03:32 PM To:
Travis Nagler <travis.nagler.ucdmc.ucdavis>, i2b2 AUG Members Subject RE: i2b2 v1.5.2 AD integration documentation
Travis, See the attachement.
Johnny Phan Programmer Analyst II UTHealth School of Biomedical Informatics Dat.Q.Phan.uth.tmc

From: Travis Nagler [travis.nagler.ucdmc.ucdavis] Sent: Tuesday, October 04, 2011 5:25 PM To: i2b2 AUG Members Subject: i2b2 v1.5.2 AD integration documentation
We are looking to use Active Directory for logging into i2b2. Does anyone have any documentation they would be willing to share on how they got it done? I have been told to look in the admin web screens where I would find some parameters to employ, but I don't have those parameters pages (I've seen the screenshots).
Is AD setup within Apache or within the web client? How is the integration supposed to work?
Thanks,
Travis
Travis H. Nagler
Senior Database Programmer American Burn Assoc. - Data Coordinating Center UC Davis Division of Burn Surgery UC Davis Health System 2921 Stockton Blvd., Suite 1470 Sacramento, CA, 95817 http://www.ucdmc.ucdavis travis.nagler.ucdmc.ucdavis

From: Remo Mueller <rmueller.rics.bwh.harvard> To: i2b2 AUG Members Date: 10/04/2011 06:22 AM Subject: i2b2 1.6.rc5 Virtual Machine Question
Hello All,
I'm in the process of setting up my first i2b2 Virtual Machine (1.6.rc5), and I've run into the following error: (I used login:demo pw:demouser). Also of note, I used a bridged connection so that I'd be able to connect to the web service (as NAT was giving me a strange 10.0.2.15 address that was unreachable).
I'm running on a Mac OS X, using Virtual Box 4.1.4
Any help would be appreciated, thanks!
Remo Mueller

NEXT EMAIL
From: Murphy, Shawn N. Sent: Monday, October 03, 2011 8:53 PM To: Lusted, Jeff; i2b2 AUG Members Subject: RE: Optional columns on the patient_dimension...
Hi Jeff,
Although the optional columns are allowed in 1.5.x, the query tools and metadata that utilize these columns are implemented starting in 1.6. Optional columns can also be returned in the PDO (other than just the hardcoded ones) starting in
1.6.
Thanks, Shawn.

From: Lusted, Jeff [jl99.leicester.ac.uk] Sent: Monday, October 03, 2011 6:43 AM To: i2b2 AUG Members Subject: Optional columns on the patient_dimension...
Hi Colleagues!
We here at Leicester have managed to install 1.5.2 on a test basis on two separate infrastructures (university and hospital) and in both have installed another project alongside the two demo projects.
The questions I have concern optional columns on the patient_dimension and visit_dimension. The docs say "The patient_dimension table may have an unlimited number of optional columns and their data types and coding systems are specific to the local implementation." The patient_dimension for the two demo projects has the following optional columns:
sex_cd, age_in_years_num language_cd race_ cd marital_Status_cd religion_cd zip_cd stateCityZip_Path
Some of these seem to be related to choosing analysis items when making a query. What are the implications of changing the columns: eg: removing a column or changing the name of a column?
I've done a grep of the source and it seems there are references within java code, javascript and some xsd files. For example:
(a) edu.harvard.i2b2.crc.dao.pdo.TablePdoQueryPatientDao.java
(b) Dem1Set_ctrlr.js and Dem2Set_ctrlr.js
(c) i2b2_PDO.xsd and i2b2_PDO_fields.xsd
I've not undertaken any searching within the workbench source yet.
Can anyone give me an idea of what I'm letting myself in for if we change column details? How much local implementation is involved? How difficult does it make setting up numbers of different projects? Do all projects within a domain need to share the same patient_dimension details?
I'm eager to hear your experiences. Kindest regards Jeff
Jeff Lusted, Senior Programmer (RCS, IT Services) University of Leicester Mob: 07941599062 Glenfield Email: jl99.le.ac.uk
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