AUG Email 2011-Nov

Last Updated: 11/30/2011

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From: Michael.C.Ford.kp Sent: Wednesday, November 30, 2011 12:47 PM To: i2b2 AUG Members Subject: 1.6 upgrade from 1.4
I was hoping someone could give me some pointers.
we are planning on doing a jump from our current 1.4 release to a 1.6 release, it will use the same database but be a completely clean install on the server.
at this time I am trying to identify tasks and times associated.
I noted there is one Database upgrade required Project_Management_Installation_Guide.pdf Page 14
I looked at the 1.5 PM and it looks like there was a need to do some change from 1.3 but not 1.4 so this seems to be all of the database changes required.
is there any other data changes I need to look into that I may have missed?
The following statement confused me from page 14 "The following steps are to be followed when upgrading from 1.5 when the 1.5 PM cell and other cells do not exist on the same server."
If your upgrading to 1.6 would you not always do this?
Any other major items I may have missed that I need to be concerned about?

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From: Russ Waitman [rwaitman.kumc] Sent: Tuesday, November 29, 2011 3:32 PM To: Bill Adams; i2b2 AUG Members Cc: Dustin Key; Jack London Subject: Re: METRiQ cancer registry data schema/mapping experience?
Hi Bill,
We're right in the middle of that now. Dan and Arvinder on our team have been working on incorporating the tumor registry following the NAACCR file format http://www.naaccr.org/. Since most registries have to export NAACCR files to go to the state or elsewhere, we worked off that standard. Also because we could base our work on the efforts of Jack London (Kimmel Cancer Center) and Dustin Key (Group Health Cooperative). They shared their approaches to building off that file format. I think if you look at the i2b2 message archive you'll see the communications.
We just released a draft version last week and the tickets related to this work are at the top of our blog post: http://informatics.kumc.edu/work/blog/2011/11/heron-tuttlecreek-release
We need to do a bit more clean up and we hope of have a better than draft release before Christmas.
Right now, some parts of our ontology don't yet fully map NAACCR codes to their corresponding text and we'd also like to get a better approach for combining primary site and histology. Dan's probably better to comment but most of our code is under http://informatics.kumc.edu/work/browser/heron_load http://informatics.kumc.edu/work/browser/heron_load/epic_concepts_load.sql http://informatics.kumc.edu/work/browser/heron_load/naaccr_load.sql http://informatics.kumc.edu/work/browser/heron_load/naaccr_txform.sql
Russ Waitman Associate Professor Director of Medical Informatics Department of Biostatistics University of Kansas Medical Center
rwaitman.kumc http://informatics.kumc.edu

"Adams, Bill" <Bill.Adams.bmc> 11/29/2011 12:41 PM
Dear Colleagues;
We are hoping to add a cancer registry ontology to our i2b2 for the BU-CTSI and include as much data from our hospital cancer registry as possible. We are using the METRiQ (vendor is Elekta) for our local registry.
The data schema documentation for METRiQ has been hard to come by and we would prefer not to re-invent the wheel.
Anyone already have experience, documentation, and/or hopefully an ontology for METRiQ that they could share?
Thanks in advance,
Bill Adams, MD
BU-CTSI

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From: Petruc, Marius [PetrucM.health.missouri] Sent: Tuesday, November 29, 2011 12:44 PM To: Askar Ibragimov; i2b2 AUG Members Subject: Re: comments about installation docs of i2b2
Askar Ibragimov <askar.ibragimov.gmail> wrote:
Hello,
as I am installing now i2b2 on my Centos x64, thought I would share some concerns with the installation documentation. Rather well written but sometimes a certain omissions and inconsistencies happen.. My task is to evaluate i2b2 for our institute so I am documenting the issues and thought I share these here.
It is probably worth noting that Oracle 10g is not the very latest now. I tried first to install most recent 11g but it meets some complications so I used suggested 10g. It is worth noting in the documentation that Oracle 10g on x64 linux kernel simply won't work out of the box, because it relies on some library and wants 32 bit version. So libaio package (http://www.nic.funet.fi/pub/Linux/INSTALL/Centos/6/os/i386/Packages/libaio-0.3.107-10.el6.i686.rpm ) should be installed in 32 bit version on linux x64 to make oracle work, otherwise nothing will function.
Data installation:
Installation documentation is large and I have a strong feeling that most stuff there can be put in a shell script. It is quite clear that data installation (six folders or so) can be authomatized.
Data installation guide contains quite a confusion with passwords for i2b2 users. For Ms SQL server suggested passwords are demouser. For Oracle the passwords = usernames, for some reason.
In addition, some of data packages come with db.properties files that specify passwords as "i2b2metadata_pswd" while in some others "pswd" letters in passwords are omitted. Steps 9 and 10 in section 2.3 of data installations do not tell which passwords to set for demodata, workdata, hive and pm users. If we follow the Data installation guide for oracle (by setting passwords=usernames) then we have to fix manually some half of db.properties files.
Note that in Oracle 11g by default you can not set password=username, as there is a protection against weak passwords. This said, if a company runs 11g, then i2b2 installation will be kinda complex.

Hive cells installation doc:
the whole istallation of cells part is 0.3 page long while other parts concering programs to run are repeated in other docs. It is unclear why TOMCAT and CATALINA are mentioned on page 7 and if user ever needs these (these words also appear in actual config files). Here, I have a feeling that one istallation document will be of more convenience than several PDFs that you have to order yourself. By the way main installation doc "Hive cells" is not available via browser before you download a certain archive, unpack and check out, and some of the links f shown online on i2b2 webpage in Documentation -> List result in a broken links.

PM installation doc issues:
again features "pswd" issue in pm-ds.xml file, contrary to the docs.
2.1.6.1 START JBOSS. To start JBOSS run the following: $JBOSS_HOME/bin/run.sh -b 0.0.0.0 Earlier, documentation does not mention that JBOSS and oracle web interface will want the same port 8080, and I see errors such as
07:44:24,378 ERROR [Catalina] Catalina.start LifecycleException: Protocol handler initialization failed: java.net.BindException: Address already in use:8080 07:44:27,882 ERROR [Http11Protocol] Error starting endpoint java.net.BindException: Address already in use:8080
so essentially one needs to go back and reconfigure it to something else, while documentaion does not poit out that it's necessary. It's only says "If default port 8080 is unavailable because another application is using this port then edit the server.xml file' while user himself setups that another application (oracle) a bit later, following the installation docs.

2.1.5 Install the WebClient
1. Copy the admin directory, which is in the root directory of the core server source code to your httpd directory; on Centos Linux this is typically located in /var/www/html. The webclient is pre-configured for a localhost domain of 'i2b2demo'. If you are upgrading from a system with a different domain or want to specify a different domain, edit the file admin/i2b2_config_data.js accordingly. {name: "localhost", domain: "yourDomain", debug: true, urlCellPM: "http://localhost:9090/i2b2/rest/PMService/" }
for some reason, in actual config file :9090 is omitted in the real config.
Apart from that, some case study guide for users would be really desirable. The likely suggestion of such kick-start doc would be how I could preload my patients/samples/ontology to the i2b2?
Cheers,
Askar

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From: Luke Vincent Rasmussen [luke.rasmussen.northwestern] Sent: Tuesday, November 29, 2011 9:05 AM To: Askar Ibragimov; i2b2 AUG Members Subject: Re: Further help with install?
Hi Askar -
There is a Google Group available for installation help, which would probably be the best resource for some of these questions: http://groups.google.com/group/i2b2-install-help The i2b2 community is really good at trying to help out whenever possible, and sharing learned experiences.
Your last question is a good one, as the most common response to a problem is "what does the log say?". The Jboss log on the VM will provide you with a lot of information regarding the problems you're seeing, although the information may seem a little cryptic at first until you become more familiar with i2b2. I am in the process of getting the VM loaded on a new machine, so unfortunately I can't tell you the exact path but I'm guessing you should be able to track it down.
I hope this helps partially point you in the right direction.
Luke Rasmussen Systems Analyst/Programmer Senior Northwestern University Division of Health and Biomedical Informatics

On 11/29/11 7:46 AM, "Askar Ibragimov" <askar.ibragimov.gmail> wrote:
Dear colleagues,
apologies if you receiving many messages from me recently. Is there a specific helpdesk where basic installation questions can be addressed? Please let me know whom from this long list I can address all my technical questions: https://www.i2b2.org/about/contact.html
I managed to follow installation instructions for obligatory cells, but presently I would need at least importData installed as well as Workbench and Web client. here's where I am rather confused:
installation guides are missing for all three cases. importData cell apparently do not istalls with command that is same for main cells.
webclient was copied to server, local login configured as in here:
https://www.i2b2.org/software/files/PDF/current/i2b2_Web_Client_Startup_Guide.pdf but I only getting message that there is no i2b2 projects and login screen again. Giving the issue with 1.6 (that persists also with demo VMWare image), could somebody help me to get this to work?
is there any kind of error log for i2b2, so if some problem with configuration appears, I can see it there?
I might be also interested in PFT cell, but its installation guide, for example, is 4 years old and it's for 1.3 version of i2b2. Will it work with 1.6 and what are adjustments to install it into 1.6 ?
Thanks in advance!
Askar

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From: Mauro [mauro.bucalo.gmail] Sent: Monday, November 28, 2011 10:15 AM To: Chan, Wayne Cc: Joe.Terdiman.kp; i2b2 AUG Members Subject: Re: i2b2 questions
Hope it helps me too
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

2011/11/28 Chan, Wayne <Wayne.Chan.umassmed>
Joe,
For your Q1, you may want to look into the ExportXLS webclient plugin developed by Mauro Bucalo of Universite de Pavia in Italy, available at http://code.google.com/p/i2b2-export-xlsplugin/downloads/list.
For your reference, below is the screenshot of it on my development server (I modified it very
slightly for our own use here in UMassMed) – Notice the "Excel Export" button:
Hope this helps.
Wayne
S. Wayne Chan, MSEE, MSME
Biomedical Research Informatics Development Group (BRIDG) and Biomedical Research Informatics Consultation & Knowledge Service (BRICKS), Division of Health Informatics & Implementation Science (HIIS), Department of Quantitaive Health Sciences (QHS), University of Massachusetts Medical School (UMMS) at Worcester, MA 01655

From: Joe.Terdiman.kp.org [Joe.Terdiman.kp.org] Sent: Wednesday, November 23, 2011 4:46 PM To: i2b2 AUG Members Subject: i2b2 questions
We are running i2b2 version 1.4 in a Unix environment. Two questions:
If a query is run with Patient Set selected as a query result, the list of patients that match the query criteria can only be viewed in the Previous Queries window. Is there a tool within i2b2 or has anyone developed a method for outputting a Patient Set into a text file or spreadsheet?
In our deployment of i2b2, we currently create separate accounts for each user, with a userID and password. It appears that in i2b2 v.1.4, only a user with the role of Admin can enter or change passwords, and non-Admin users cannot change their own passwords. Is that correct? Is this also true in later versions?
Joe
Joe Terdiman, MD, PhD Division of Research Kaiser Permanente 2000 Broadway Oakland, CA 94612

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From: Phillips, Lori C. Sent: Monday, November 28, 2011 9:06 AM To: Dat Q. Phan; i2b2 AUG Members Subject: RE: Optional Columns (C_PATH and C_FULLNAME) for Support of External Tools
These columns were created to support the NCBO ontology extraction tool. https://community.i2b2.org/wiki/display/NCBO/NCBO+Ontology+Tools

From: Dat Q. Phan [Dat.Q.Phan.uth.tmc] Sent: Wednesday, November 23, 2011 11:22 AM To: i2b2 AUG Members Subject: Optional Columns (C_PATH and C_FULLNAME) for Support of External Tools
Hi,
In 'Ontology_Architecture.pdf', page 25, section '4.2.2 Metadata tables', the last paragraph states:
"Finally, in Release 1.6, we added two optional columns in support of external tools. The column 'c_path' contains the c_fullname of a node's parent. The column 'c_symbol' is a unique, abbreviated form of the node's c_name. A node's c_path, concatenated with its c_symbol form the node's c_fullname."
Can someone explain to me what these external tools are so we can decide whether or not to implement these columns or just ignore them?
Thanks,
Johnny Phan
Programmer Analyst II UTHealth School of Biomedical Informatics Dat.Q.Phan.uth.tmc

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From: Sebastian Mate [Sebastian.Mate.imi.med.uni-erlangen.de] Sent: Thursday, November 24, 2011 6:12 AM To: Mendis, Michael E. Cc: i2b2 AUG Members Subject: AW: Running 1.5 project in 1.6
Hi Mike,
found it: the AGG_SERVICE_ACCOUNT entry in I2B2PM was missing when a new project was created. It's working!
Cheers, Sebastian

Von: i2b2 AUG Members Im Auftrag von Mendis, Michael E. Gesendet: Mittwoch, 23. November 2011 15:19 An: Sebastian Mate; i2b2 AUG Members Betreff: RE: Running 1.5 project in 1.6
Did you run the update script located in the createdb_1.6.zip file?
mike

From: Sebastian Mate [Sebastian.Mate.imi.med.uni-erlangen.de] Sent: Wed 11/23/2011 6:56 AM To: i2b2 AUG Members Subject: Running 1.5 project in 1.6
Hi all,
I'm experiencing an issue with i2b2 1.6 when using a project that has been originally created for i2b2 1.5 - see log below. The error happens when I press the "Run Query" button in the webclient. ONT and WORK seem to work fine.
So far I have added the missing columns to the various tables (I2B2, OBSERVATION_FACT). Is there anything else I have to update?
I need this information in order to complete the new i2b2 Wizard which will support i2b2 1.6. The Demodata and everything else already works . J
Any help would be highly appreciated
Thanks, Sebastian
Dipl.-Inf. Univ. Sebastian Mate
Chair of Medical Informatics, Friedrich-Alexander-University Erlangen-Nuremberg, Germany
Krankenhausstrasse 12, 91054 Erlangen
12:48:38,200 INFO [OracleDAOFactory] Using datasource java:QueryToolMyProjectDS
12:48:39,276 ERROR [STDERR] edu.harvard.i2b2.common.exception.I2B2DAOException: Error when getting metadata from ontology [User was not validated]
12:48:39,276 ERROR [STDERR] at edu.harvard.i2b2.crc.delegate.ontology.CallOntologyUtil.getConceptFromRespon se(Unknown Source)
12:48:39,276 ERROR [STDERR] at edu.harvard.i2b2.crc.delegate.ontology.CallOntologyUtil.callOntology(Unknown Source)
12:48:39,276 ERROR [STDERR] at edu.harvard.i2b2.crc.dao.setfinder.querybuilder.SortPanel.sortedPanelList(Un known Source)
12:48:39,276 ERROR [STDERR] at edu.harvard.i2b2.crc.dao.setfinder.querybuilder.QueryToolUtilNew.generateSql ForGroupedPanelList(Unknown Source)
12:48:39,276 ERROR [STDERR] at edu.harvard.i2b2.crc.dao.setfinder.querybuilder.QueryToolUtilNew.getSetfinde rSqlForQueryDefinition(Unknown Source) 12:48:39,276 ERROR [STDERR] at edu.harvard.i2b2.crc.dao.setfinder.querybuilder.RecursiveBuild.execQuery(Unk nown Source)
12:48:39,276 ERROR [STDERR] at edu.harvard.i2b2.crc.dao.setfinder.querybuilder.RecursiveBuild.startSqlBuild (Unknown Source)
12:48:39,276 ERROR [STDERR] at edu.harvard.i2b2.crc.dao.setfinder.QueryRequestSpringDao.buildSql(Unknown Source)
12:48:39,276 ERROR [STDERR] at edu.harvard.i2b2.crc.dao.setfinder.QueryExecutorDao.executeSQL(Unknown Source)
12:48:39,276 ERROR [STDERR] at edu.harvard.i2b2.crc.ejb.ExecRunnable.processQueryRequest(Unknown Source)

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From: Murphy, Shawn N. Sent: Wednesday, November 23, 2011 9:20 AM To: Juha Muilu Cc: Askar Ibragimov; i2b2 AUG Members Subject: RE: getting started with i2b2 devel
I see Juha, will talk to the team to see what they want to do.
Thanks, Shawn.

From: Juha Muilu [juha.muilu.helsinki.fi] Sent: Tuesday, November 22, 2011 11:28 PM To: Murphy, Shawn N. Cc: Askar Ibragimov; i2b2 AUG Members Subject: Re: getting started with i2b2 devel
Hi Shawn
Looks like the latest vmware image of v.1.6 do not have development tools and gnome/kde installed. Would be great to have full development version available as well as shown in the video. ...In that video i2b2 1.4 version vas used.
Best,
Juha

On 23 Nov 2011, at 00:10, Murphy, Shawn N. wrote:
Hi Askar,
It sounds like you already watched the tutorial on the i2b2 Software page? The PFT Processing cell is a good starting point for building a cell. It has a lot of the "skeleton" you will need.
Thanks,
Shawn.

From: Askar Ibragimov [askar.ibragimov.gmail] Sent: Tuesday, November 22, 2011 4:15 PM To: i2b2 AUG Members Subject: getting started with i2b2 devel
Dear all,
I am an IT specialist in Finnish Institute for Molecular Medicine and we're evaluating i2b2 for our needs. I will perhaps post more specific questions later, but now I would just appreciate if you could suggest me a best way to start developing for i2b2.
Are there any matherials that I can read which describe step-by-step what should be done to create a new "cell"? Shall I use provided VMWare image for that?
Also, on my Mac the VMWare image I have started produces text console, while in video presentation on i2b2 I saw graphical image. Apparently graphic tools are needed to develop, so how I can start graphical console, or shall I connect via remote X terminal to the image?
Summarizing, all that can help me get started with the development (I intent to build some "adapters" that query our principal lab database for various stuff such as patients/ontology/samples and present results in i2b2) is much appreciated. Any kind of matherial is welcome.
Cheers,
Askar Ibragimov
IT Specialist, PhD, FIMM

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From: Murphy, Shawn N. Sent: Tuesday, November 22, 2011 5:13 PM To: Robert Schuff; i2b2 AUG Members Subject: RE: Different versions of 1.5.x available?
Hi Rob,
Most of the sub-versions are bug fixes, but we do want to make the latest of each major version available.
Thanks,
Shawn.

From: Robert Schuff [schuffr.ohsu] Sent: Tuesday, November 22, 2011 4:44 PM To: i2b2 AUG Members Subject: Re: Different versions of 1.5.x available?
Perhaps we can maintain links to *all* released versions as there does seems to be a variety of versions in use.
Rob
Robert Schuff - Director, Clinical Research Informatics Oregon Clinical & Translational Research Institute Oregon Health & Science University http://www.octri.org/

On 11/22/11 1:24 PM, "Mendis, Michael E." <MMENDIS.PARTNERS> wrote:
I have updated the archive software with the latest in the 1.5 series
https://www.i2b2.org/software/archive.html
Web Client Source v1.5.4
Core Source Code Client v1.5.4
Core Source Code Server v1.5.5
Thanks
Mike

From: Murphy, Shawn N. Sent: Tue 11/22/2011 4:04 PM To: Travis Nagler; i2b2 AUG Members Subject: RE: Different versions of 1.5.x available?
Hi Travis,
The archive will be updated in a few minutes to have the 1.5.5 release. Mike will send out a message as soon as it is done.
Thanks,
Shawn.

From: Travis Nagler [travis.nagler.ucdmc.ucdavis] Sent: Tuesday, November 22, 2011 3:53 PM To: i2b2 AUG Members Subject: Different versions of 1.5.x available?
I am looking for the most recent version of 1.5. On the i2b2 website, you can download an archived version of 1.5, but I don't see 1.5.2 or 1.5.5 or any other updated version. I don't see any updates in the Subversion info on the website, either.
Could someone please tell me where can I get my hands on a download of the latest 1.5 version? We are installing 1.5.2 right now, but are having a problem with the result set count for "less than 10" actually showing a number, which was my understanding that anything less than 10 results would just say "< 10", or something to that effect and not actually give the number, even if it's obfuscated.
I was told later versions of 1.5 might have a fix for this problem.
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.edu <http://www.ucdmc.ucdavis.edu/> travis.nagler.ucdmc.ucdavis

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From: Michael.C.Ford.kp Sent: Tuesday, November 22, 2011 4:55 PM To: i2b2 AUG Members Subject: Lab value set - Context menu issue
I hope someone can give me some insight into an issue we have randomly.
Once in a while when you bring up a context menu it shows lab values when it should show set value.
it seems in be in the CRC_view_QryTool.js module it does not seem to have a valid or correct ont_tid-* when it's working correctly it shows ont_tid-57 ( some number between 50 - 69 ) when it fails it shows it has ont_tid-672.
it's very random and had to track, anyone have any idea on what may be the issue ?
code // ====================================================== ======= //
i2b2.CRC.view.QT.ContextMenuPreprocess = function(p_oEvent) { var clickId = false; var clickPanel = false; var isDone = false; var currentNode = this.contextEventTarget; var doNotShow = false;
console.group('enter while i2b2.CRC.view.QT.ContextMenuPreprocess with event' + p_oEvent); console.time('execute time');
while (!isDone) { // save the first DOM node found with an ID if (currentNode.id && !clickId) {
clickId = currentNode.id;
console.group('set clickID to ' + clickId); } // save and exit when we find the linkback to the panel controller if (currentNode.linkbackPanelController) {
// we are at the tree root... var clickPanel = currentNode.linkbackPanelController; isDone = true; console.group('set isDone 1 linkbackpanel ' + clickPanel);
} if (currentNode.parentNode) { currentNode = currentNode.parentNode;
} else { // we have recursed up the tree to the window/document DOM... isDone = true; console.group('set isDone 2');
} } if (!clickId || !clickPanel) {
// something is missing, exit console.group('exit !!!!'); this.cancel(); return;
} // see if the ID maps back to a treenode with SDX data var tvNode = clickPanel.yuiTree.getNodeByProperty('nodeid', clickId); console.group('tvNode ' + tvNode); if (tvNode) {
console.group('tvNode 1' ); if (!Object.isUndefined(tvNode.data.i2b2_SDX)) {
console.group('tvNode 2' ); // Make sure the clicked node is at the root level if (tvNode.parent == clickPanel.yuiTree.getRoot()) {
console.group('tvNode 3' ); if (p_oEvent == "beforeShow") {
console.group('tvNode beforeShow' ); i2b2.CRC.view.QT.contextRecord = tvNode.data.i2b2_SDX; i2b2.CRC.view.QT.contextPanelCtrlr = clickPanel; // custom build the context menu according to the concept that was clicked var mil = []; var op = i2b2.CRC.view.QT; // all nodes can be deleted mil.push( { text: "Delete", onclick: { fn: op.ContextMenuRouter, obj: 'delete' }} ); // For lab tests...
var lvMetaDatas = i2b2.h.XPath(i2b2.CRC.view.QT.contextRecord.origData.xmlOrig, 'metadataxml/ValueMetadata[string-length(Loinc)>0]'); if (lvMetaDatas.length > 0) {
mil.push( { text: "Set Value...", onclick: { fn: op.ContextMenuRouter, obj: 'labvalues' }} ); } i2b2.CRC.view.QT.ContextMenu.clearContent(); i2b2.CRC.view.QT.ContextMenu.addItems(mil); i2b2.CRC.view.QT.ContextMenu.render();
}
} else { // not root level node console.group('not show 1'); doNotShow = true;
}
} else { // no SDX data console.group('not show 2'); doNotShow = true;
} } else {
// not a treenode console.group('not show 3'); doNotShow = true;
} if (doNotShow) {
console.group('not show if with value ' + p_oEvent); if (p_oEvent == "beforeShow") { i2b2.CRC.view.QT.ContextMenu.clearContent(); } if (p_oEvent == "triggerContextMenu") { this.cancel(); }
} }
Log messages

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From: Russ Waitman [rwaitman.kumc] Sent: Monday, November 21, 2011 6:07 PM To: Matvey Palchuk Cc: i2b2 AUG Members; schuffr.ohsu Subject: Re: Medications hierarchy?
Hi Matvey,
I enjoyed your article today as it outlined and accomplished what I'd think would be the desired way to create interoperable medication data across EMR vendor sources.
It did raise some follow up thoughts:
You mention that you were able map 93% from UMMHC and 83% of the BMC data to RxNorm but didn't evaluate the mapping discrepancies at the time of your paper.
After enriching, you got 93% of meds mapped to RxNorm to have a linkage with the NDFRT hierarchies (dramatically better than the initial 37% for BMC and 65% for UMMHC).
I'd still worry that's leaving a bunch of meds on the floor, not mapped to the ontology and thus potentially unsearchable.
I need to spend more time verifying our data here but I think all the meds in file we use (CLARITY_MEDICATION) to build our hierarchy have entries for all the medication records.
Q: Are the meds which couldn't be mapped to RxNorm due to things like extemp meds dispensed by the hospital pharmacy that have ficitious NDCs? Other sources of error?
It also seems that NDF-RT doesn't have complete mapping to all the drugs in RxNorm at the time you did this work. Have things improved? Do the two hospital use the RxNorm/NDF-RT view of things or do they use locally derived ontologies based on the drug frameworks internal to their EMR vendors?
Russ

Matvey Palchuk <MPalchuk.recomdata> 11/10/2011 9:36 AM
We developed an RxNorm/NDF-RT hierarchy for SHRINE at Harvard Catalyst. It was subsequently refined - see citation below.
We used VA product classes - something the VA folks were not happy about. Apparently they are focusing on things like Mechanism of Action and such for FDA structured labeling, and not maintaining the therapeutic classification.
I am not sure about AHFS - believe the sell a mapping to RxNorm.
Matvey
AMIA Annu Symp Proc. 2010; vol. 2010 pp. 577-81
Enabling Hierarchical View of RxNorm with NDF-RT Drug Classes.
Palchuk MB, Klumpenaar M, Jatkar T, Zottola RJ, Adams WG, Abend AH
NDF-RT is the proposed source of drug classification information. We set out to construct a hierarchy of NDF-RT drug classes and RxNorm medications and evaluate it on medication records data. NDFRT and RxNorm are distributed in different file formats, require different tools to manipulate and linking the two into a hierarchy is a non-trivial exercise. Medication data in RxNorm from two institutions was constrained by the hierarchy. Only 37% of records from one and 65% from another institution were accessible. We subsequently enriched the RxNorm mapping in NDF-RT by exploiting relationships between concepts for branded and generic drugs. Coverage improved dramatically to 93% for both institutions. To improve usability of the resulting hierarchy, we grouped clinical drugs by corresponding clinical drug form.
PMID: 21347044
PMCID: PMC3041416 URL -http://www.ncbi.nlm.nih.gov/pubmed/21347044?dopt=Citation

On Nov 10, 2011, at 9:03 AM, "Russ Waitman" <rwaitman.kumc> wrote:
We need to revisit meds. That said, currently we use the hierarchy we pull out of the Epic meta data. I think it's based on FDB. In a future ideal state, I'd map that to RxNorm and then give people options for NDF-RT or AHFS.
Russ

Robert Schuff 11/10/11 1:28 AM
Hi folks,
I am curious what you all are using for your meds hierarchy and encoding. So far we've just populated using med orders, but we'll also soon be including medication list data. As our first cut we've just used the very basic hierarchy contained within our epic installation which is
Pharm Class Pharm Subclass
Drug Name This is a bit sub-optimal so we're investigating other options. Although I haven't validated it fully
yet, it appears that there may be a mapping done to UDDF which may get us to a hierarchy through RxNorm. Is there an emerging standard ontology used in i2b2 for meds? 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: Brian Ostasiewski [bostasie.wakehealth] Sent: Monday, November 21, 2011 12:15 PM To: Lisa Miao; i2b2 AUG Members Subject: RE: Analysis Breakdowns in Release 1.6
This is what I mailed out earlier regarding how to modify the breakdowns, they key off concept paths. You can add entirely new ones or delete the existing ones if you want.
To change the target concept paths for various breakdowns, edit i2b2data.QT_BREAKDOWN_PATH.VALUE for each
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
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

From: Lisa Miao [lmiao.regenstrief] Sent: Monday, November 21, 2011 10:45 AM To: i2b2 AUG Members Subject: FW: Analysis Breakdowns in Release 1.6
Could someone in the i2b2 team answer this question? We would like to know how to load patient demographic information so that the analysis breakdowns work.
Thanks,
Lisa.

From: Phillips, Lori C. [LCPHILLIPS.PARTNERS] Sent: Tuesday, November 01, 2011 11:13 AM To: Lisa Miao Subject: RE: Analysis Breakdowns in Release 1.6
Lisa,
I am not sure I know the answer to this; I forwarded your questions to others who might be able to answer them.

From: Lisa Miao [lmiao.regenstrief] Sent: Tuesday, November 01, 2011 11:02 AM To: Phillips, Lori C. Cc: John Hook Subject: Analysis Breakdowns in Release 1.6
Lori,
In the release note for Release 1.6, it was mentioned that some "Analysis Breakdowns" were added to web client (I appended them at the end of the email). When I looked at the i2b2metadata.i2b2 table, it seems like only the "Age" portion of the demographic information points to "patient_dimension" (as c_tablename). My guess is, in order to make the "Analysis Breakdowns" work, we will still need to load the demographic information (except Age) in the old way, by which I mean load them into observation_fact table (for one patient, there will be one entry for gender, one entry for race, etc). Is that correct?
How should we populate our demographic information in Release 1.6? Is it enough just to load the patient_dimension table?
Thanks,
Lisa.
Analysis Breakdowns Added to Web Client
In the 1.6 Release the following Analysis breakdowns have been added to the web client.
Gender patient breakdown
Vital Status patient breakdown
Race patient breakdown
Age patient breakdown

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From: Schulte, Gregory [Gregory.Schulte.childrenscolorado] Sent: Friday, November 18, 2011 5:28 PM To: 'Jack London'; Jennifer Cai Cc: i2b2 AUG Members members Subject: RE: PM 1.6 installation and requires ADMIN role
The "Requires ADMIN role .... " error is pretty generic, you'll get this even if your PM webservice isn't running, or the urlCellPM in i2b2_config_data.js isn't pointing to the correct webservice url, don't ask me how I know that . The server.log under "JBOSS_HOME"/server/default/log might be more helpful in pointing you to the problem.
As for the "file does not exist " errors, in my apache error log, I have the same errors and my admin webclient seems to be functioning fine.
Greg

From: Jack London [jack.london.KimmelCancerCenter] Sent: Friday, November 18, 2011 3:16 PM To: Jennifer Cai Cc: i2b2 AUG Members members Subject: Re: PM 1.6 installation and requires ADMIN role
What I meant was that – specifically – the PM_PROJECT_USER_ROLES table should have a row for user_id "i2b2" with project_id = "@" and user_role_cd = "ADMIN"
The status_cd on this row must also be "A" (active).
If this is the case, then this is not the problem.
jack

On Nov 18, 2011, at 5:03 PM, Jennifer Cai wrote: Jack,
There is no PM_User table. There are a few PM user related tables. in PM_PROJECT_USER_ROLES table, the project_id is "@" instead of "*" for i2b2 user.
By the way, we are using Oracle 11g.
Thanks,
Jennifer

From: Jack London [jack.london.KimmelCancerCenter] Sent: Friday, November 18, 2011 3:40 PM To: Jennifer Cai Cc: i2b2 AUG Members Subject: Re: PM 1.6 installation and requires ADMIN role
Check the PM USER table to make sure there is a row for user "i2b2" with an "*" (asterisk) for project.

On Nov 18, 2011, at 4:14 PM, Jennifer Cai wrote:
Hello,
We are installing the 1.6 PM on the windows server (New installation). When we tried to login to PM tool, http://localhost/admin by using "i2b2' and password "demouser", we got the message "Requires ADMIN role, please contact your system administrator". The database table PM_PROJECT_USER_ROLES has the user i2b2 as AMDIN. The "admin" folder was copied from the source 1.6 download into the apache's htdocs directory. We do not see missing files complained in the log from original download.
Here is some log from apache "error.log":
[Fri Nov 18 13:54:26 2011] [error] [client 127.0.0.1] File does not exist: C:/Program Files/Apache Software Foundation/Apache2.2/htdocs/admin/null.gif, referer: https://localhost/admin/
[Fri Nov 18 14:42:56 2011] [error] [client 127.0.0.1] File does not exist: C:/Program Files/Apache Software Foundation/Apache2.2/htdocs/admin/js-ext/yui/build/element/element-beta.js, referer:https://localhost/admin/
[Fri Nov 18 14:42:59 2011] [error] [client 127.0.0.1] File does not exist: C:/Program Files/Apache Software Foundation/Apache2.2/htdocs/admin/js-ext/yui/build/treeview/assets/treeview.css, referer:https://localhost/admin/
[Fri Nov 18 14:43:00 2011] [error] [client 127.0.0.1] File does not exist: C:/Program Files/Apache Software Foundation/Apache2.2/htdocs/admin/null.gif, referer: https://localhost/admin/
Thanks,
Jennifer

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From: Travis Nagler [travis.nagler.ucdmc.ucdavis] Sent: Friday, November 18, 2011 4:40 PM To: i2b2 AUG Members Subject: Data coming up non-obfuscated
I was running a few queries, just checking things out on my dev install of v1.5.2, when I ran one that ended up with 1 record. It told me that at the bottom of the screen (screenshot below). I thought the answers were automatically obfuscated?
I was logged in as me through my AD account, and my user role on this project are USER, DATA_OBFSC, and DATA_AGG. I got the answer shown to me, as well, when I was just USER and DATA_OBFSC. The USER and DATA_OBFSC are what the Project Management installation PDF showed as it's example, so that's what I did.
The problem is not the obfuscation, which sometimes it showed 0 and sometimes it showed 1. It's that it showed anything at all. My understanding was that if the result set was less than 10, it just returns an answer of "<10" instead of the obfuscated result.
Is there something I need to turn on within the v1.5.2 code to get it obfuscated for less than 10 results?
Thanks,
Travis
P.S. Don't mind the 29.8 seconds. I was running some other scripts on the db at the same time. It usually only takes 3-5 seconds.
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

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From: Chan, Wayne [Wayne.Chan.umassmed] Sent: Friday, November 18, 2011 12:31 PM To: i2b2 AUG Members Cc: Sadasivam, Rajani; Houston, Thomas; Zottola, Ralph; Ranauro, Paul; Kinney, Rebecca;
Phillips, Barrett D Subject: 2 Workplace Items Sharing Enhancement plugins (for webclient) from UMass Med School
Folks,
We at University of Massachusetts Medical School are glad to announce that the 2 Workplace Items Sharing Enhancement (WISE) plugins (for webclient) that we presented in this past CTSA 2011 Annual Informatics Meeting, DC, on 10/13/2011, are finally available to be downloaded from our website: http://micard.umassmed/downloads.php
These 2 plugins are:
Workplace Items Sharing Enhancement - Tagger / Annotator
This plugin facilitates the annotation (with tags or notes) of a Workplace item (folder, query, patient set, etc.) within the web client framework.
Workplace Items Sharing Enhancement - Searcher
This plugin facilitates searching for similar Workplace items (folder, query, patient set, etc.) within the web client framework.
This was the handout we provided during the presentation.
Note that each downloadable kit contains its own "installation document", for easy reference.
Please don't hesitate to contact us regarding any questions, problems, feedbacks, or suggestions for improvements.
Wayne
Wayne Chan, MSEE, MSME
Biomedical Research Informatics Development Group (BRIDG) and Biomedical Research Informatics Consultation & Knowledge Service (BRICKS),
Division of Health Informatics & Implementation Science (HIIS),
Department of Quantitaive Health Sciences (QHS),
University of Massachusetts Medical School (UMMS) at Worcester, MA 01655

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From: Chanchai McDonald [cmcdon12.uthsc] Sent: Friday, November 18, 2011 10:08 AM To: Russ Waitman Cc: Parth Divekar; Dan Connolly; petrucm.health.missouri; i2b2 AUG Members;
Mendis, Michael E. Subject: Re: I2B2 webserver
Russ, I will running into the same issue as yours since the team plan to operates to having our researchers using i2b2 for their research questions and explore the hypothesis. Thank you. I am interested to talk to you more about this issue.
Chanchai

On Nov 18, 2011, at 8:56 AM, Russ Waitman wrote:
Chanchai and all, I suppose it all depends on your definition of "acceptable", how big your audience of simultaneous users will be, and knowing if 1.6 really boosts performance.
We have ~ half a billion facts on 250,000 to 500,000 people depending on what you're looking for. We're running 1.4.
Prior to the fusionio cards, we'd have queries which would never return data. I'd set a lab threshold like potassium < 3.5 and loop diuretic medicaiton exposure: not even sophisticated queries. It was embarrassing. I had to do puppet shows on projector when I was demoing things.
We also noticed that on local SAS storage, we were completely disk bound such that one user was consuming all disk utilization.
Now one user typically runs less than 10% disk utilization which means we can support simultaneous queries. That's important because when we hold classes we've had 6-8 people hitting "run query" at the same time. Simple queries resolve in less than 20 seconds. Still, we hit spots where queries can take over 40 seconds but I am hoping improved performance with 1.6 will help.
For me, I think you want the system to be pretty responsive so that people can really do hypothesis exploration and not get frustrated. Based on my experience running CPOE, clinicians and researchers (and I) are inherently impatient so anything over 15 or 20 seconds is not great. But when they realize what the computer is doing for them, I suppose you can take a sip of coffee during the delay. If it gets over 60 seconds or hangs up on a simple query, they will think it's broken.
We're now getting to the point where people are beginning to use i2b2 for real research questions (4-10 groups, labs, diagnoses, flowsheet data, demographics multiple occurrence thresholds, over 20 exclusion criteria). Those larger queries are running over 20 seconds and in some cases still take a long time to resolve. one example I just did has 3 groups: first with 25 items, second with 45 exclusion concepts, and third with over 100: query takes 154 seconds. But, I am fairly sure these may have taken forever without the memory cards or we'd spend a ton of hours learning how to configure Oracle. Actually, it often takes longer for them to reload in the web client from the shared folder than it takes to actually run the query.
I've always worried that a conventional relational database like Oracle or SqlServer would choke on big data compared to other DBs like column stores but that was just based on academic reading. But I think the cards allowed us to use off the shelf oracle and move on to the fun stuff instead of spending our time loading interesting data.
Russ Waitman Associate Professor Director of Medical Informatics Department of Biostatistics University of Kansas Medical Center rwaitman.kumc http://informatics.kumc.edu

"Parth Divekar" <Parth.Divekar.cchmc> 11/18/2011 7:02 AM
Chanchai,
Whether you need SSD or not will depend upon amount of data and number of users accessing data. We have SSD for ETL but not for application database. We are currently porting in excess of 50 mill rows in fact table and the performance is acceptable. We have tuned our database for memory and have made some changes in the query that gets executed when you hit "run query from application. FYI: we are using Oracle 11gR2.
Regards Parth
Parth Divekar Database Administrator II Cincinnati Children's Hospital Medical Center Ph: - 513-636-1004 (O)

Chanchai McDonald <cmcdon12.uthsc> 11/17/2011 6:25 PM
We concern if the Database storage really requires using Solid state Storage (Fusion-io Cards). We do not currently use/have this type of storage. Will it impact performance adversely if we won't use it?
Chanchai
Chanchai Singhanayok McDonald, Ph.D. Director Biomedical Informatics The Office of Research, UTHSC 910 Madison Building Suite 620

On Jul 20, 2011, at 3:17 PM, Dan Connolly wrote:
Marius,
Mike answered the specific question about threading, but if your question is really "will end users see a speed difference if I give the hive more CPUs/cores?" then I'd say: I doubt it; I suspect the rate-limiting-factor is the database.
We've tried various approaches to improve performance. For many queries, the biggest performance impact comes from giving more RAM to the oracle database server (I think we're giving Oracle 12GB of SGA and 6GB of PGA; we have more RAM on the server, but we're juggling various Oracle instances, so we haven't given any one of them much more than that).
But since the observation_fact table is too big for RAM (even the indexes are too big), we just recently deployed solid state storage (fusion-io cards).

On Wed, 2011-07-20 at 14:46 -0400, Mike Mendis wrote:
Yes it is multithreaded and multiple cores/cpu will increase the
performance. Make sure the OS and java is configured to handle it.
mike

On 7/20/11 2:40 PM, "Marius Petruc" <petrucm.health.missouri> wrote:
Dan, do you know if the i2b2 hive is multithreaded? assuming 10 concurrent users, will a multi core/multi cpu system provide a significant performance increase (i.e. faster response time) than a single CPU system?
thanks a lot
Marius Petruc

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From: John Kilian [Jkilian.harthosp] Sent: Friday, November 18, 2011 9:24 AM To: Jack London Cc: <i2b2 AUG Members> Subject: Re: Client still looking for Oracle?
Found it.
CRCApplicationContext.xml in the server/conf/crcapp dir was the last remaining holdout. I bet the build scripts take care of this for you, but I was working of the VM image.
John Kilian, RN, BSCS, BSED
Senior Distributed Applications Programmer/Analyst Hartford Hospital W:(860)545-4213

Jack London <jack.london.KimmelCancerCenter> 11/16/2011 7:28 PM
John, I know nothing about MSSQL, but I know the connection to Oracle XE is 1521:xe. Is this true for MSSQL? Of not, fix your db.properties files across the board.
Jack

On Nov 16, 2011, at 1:54 PM, "John Kilian" <Jkilian.harthosp> wrote:
I am trying to point to MSSQL. I have updated all my ds files to contain mssql entries and comment out oracle entries. I have added crc-mssql-jdbc2-service.xml to deploy/jms and removed the oracle equivalent.
I2B2 is still looking for Oracle on the localhost. On startup I get: 14:42:09,489 ERROR [TimerImpl] Error invoking ejbTimeout: javax.ejb.EJBException:
org.springframework.jdbc.CannotGetJdbcConnectionException: Could not get JDBC Connection; nested exception is org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (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: 127.0.0.1:1521:XE )
I may have something left to config on the client, I get this when I invoke the gui:
2011-11-16 14:27:23,509 ERROR [org.jboss.ejb.txtimer.TimerImpl] Error invoking ejbTimeout: javax.ejb.EJBException: org.springframework.jdbc.CannotGetJdbcConnectionException: Could not get JDBC Connection; nested exception is org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (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: 127.0.0.1:1521:XE
John Kilian, RN, BSCS, BSED
Senior Distributed Applications Programmer/Analyst Hartford Hospital W:(860)545-4213

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From: John Kilian [Jkilian.harthosp] Sent: Friday, November 18, 2011 9:18 AM To: Andrew J. McMurry; Nick Holden Cc: i2b2 AUG Members; Shah, Nimit M. Subject: Re: i2b2 mysql
Our Clinical Data Warehouse is in MySql. We certainly would be interested in a version of I2B2 that supported MySql.
John Kilian, RN, BSCS, BSED
Senior Distributed Applications Programmer/Analyst Hartford Hospital W:(860)545-4213
Nick Holden <nrh11.leicester.ac.uk> 11/17/2011 4:44 AM
On 07/11/11 20:51, McMurry, Andrew J. wrote:
There isn't a MySQL version – the lack of real stored procedures makes MySQL query optimization really tough. There have been attempts at this before with varying degrees of success, though to my knowledge, no one has MySQL i2b2 running in production hope this helps,
andy
Hi Andy,
I understood that later versions of MySQL do support stored procedures, which might make a MySQL back end for i2b2 more of a realistic possibility? We're certainly interested, here at Leicester, in exploring the options, given that we deploy i2b2 as part of a suite of software to support the research process, the other components of which all use MySQL as their back-end and consistency is attractive.
Perhaps someone could take the initiative to lead a little collaboration to explore this?
Nick

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From: Peter Beninato [beninato.ohsu] Sent: Thursday, November 17, 2011 6:21 PM To: Chanchai McDonald; Jack London Cc: Lisa Miao; i2b2 AUG Members Subject: RE: search by name under Find Terms in Release 1.6
Yes. It's true.
https://forums.oracle.com/forums/thread.jspa?threadID=840451

From: Chanchai McDonald [cmcdon12.uthsc] Sent: Thursday, November 17, 2011 3:13 PM To: Jack London Cc: Lisa Miao; i2b2 AUG Members Subject: Re: search by name under Find Terms in Release 1.6
Is it true that the Express edition has a limited database size of around 4gb?
Chanchai
Chanchai Singhanayok McDonald, Ph.D. Director Biomedical Informatics The Office of Research, UTHSC 910 Madison Building Suite 620 Telephone: (901) 448-2088

On Oct 26, 2011, at 12:56 PM, Jack London wrote:
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

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: Lisa Miao [lmiao.regenstrief] Sent: Thursday, November 17, 2011 2:24 PM To: i2b2 AUG Members Subject: bug report
Dear i2b2 team,
I would like to report a bug so that it can be fixed in future releases.
In the concept definition, special characters such as '&' are now allowed. This is in both i2b2 table and concept_dimension tbale. I hope this can be fixed in future release.
Thanks,
Lisa.

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From: Jack London [jack.london.KimmelCancerCenter] Sent: Thursday, November 17, 2011 12:17 PM To: Bill Adams Cc: Wilson, Brian; i2b2 AUG Members members; Herring, Neil C. Subject: Re: Freezer Works Specimen Repository and i2b2?
Bill,
We have now updated our caTissue biospecimen i2b2 ontology (and E-T-L) to incorporate v1.6 concept modifiers. I also would be glad to help out.
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

On Nov 17, 2011, at 10:59 AM, Herring, Neil C. wrote:
Hi Brian and Bill I'd be glad to help as well. Neil Neil C. Herring
Program Director, BWH Crimson Bio-Specimen Core
From: Wilson, Brian Sent: Thursday, November 17, 2011 10:43 To: Adams, Bill Cc: i2b2 AUG Members Subject: Re: Freezer Works Specimen Repository and i2b2?
Hi Bill,
We are working on an infrastructure as part of the Crimson-SMP project (PI: Dr. Lynn Bry) that imports samples/specimens (Currently looking at Daedalus & StarLIMS) but also allows for the possibility of 'broadcasting' a request for specimens to target LIMS systems. We are currently reworking our ontology to take advantage of the new concept modifiers within i2b2 1.6 and updating our ETL accordingly.
Happy to talk further
Brian

On 11/17/2011 10:36 AM, Adams, Bill wrote:
Dear Colleagues;
We are in the process of figuring out the best way to get our specimen repository data into i2b2. We are "Freezer Works". Has anyone already done this and willing to offer a bit of advice (and ideally share an ontology) so we don't have to recreate the wheel?
Thanks in advance,
Bill Adams, MD BU-CTSI
Brian Wilson Senior IS Programmer AnalystNational Center For Biomedical ComputingI2B2 http://www.i2b2 Email:
bwilson6.partners bwilson3.bics.bwh.harvard
Brigham & Women's Hospital75 Francis Street Boston, MA 02115 http://www.brighamandwomens.org

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From: Peter Beninato [beninato.ohsu] Sent: Thursday, November 17, 2011 10:53 AM To: Nick Holden; McMurry, Andrew J. Cc: Shah, Nimit M.; i2b2 AUG Members Subject: RE: i2b2 mysql
http://dev.mysql.com/doc/refman/5.0/en/stored-routines.html

From: Nick Holden [nrh11.leicester.ac.uk] Sent: Thursday, November 17, 2011 1:45 AM To: McMurry, Andrew J. Cc: Shah, Nimit M.; i2b2 AUG Members Subject: Re: i2b2 mysql
On 07/11/11 20:51, McMurry, Andrew J. wrote:
There isn't a MySQL version – the lack of real stored procedures makes MySQL query optimization really tough. There have been attempts at this before with varying degrees of success, though to my knowledge, no one has MySQL i2b2 running in production hope this helps,
andy
Hi Andy,
I understood that later versions of MySQL do support stored procedures, which might make a MySQL back end for i2b2 more of a realistic possibility? We're certainly interested, here at Leicester, in exploring the options, given that we deploy i2b2 as part of a suite of software to support the research process, the other components of which all use MySQL as their back-end and consistency is attractive.
Perhaps someone could take the initiative to lead a little collaboration to explore this?
Nick

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From: Schulte, Gregory [Gregory.Schulte.childrenscolorado] Sent: Wednesday, November 16, 2011 1:33 PM To: 'John Kilian'; i2b2 AUG Members Subject: RE: Could not resolve uncommited transactions
John,
In my deploy/jms folder I have a crc-mssql-jdbc2-service.xml file.
I believe this is being built by setting the "jboss.jms.persistance" variable in the build.properties file from "oracle" to "mssql"
Greg

From: John Kilian [Jkilian.harthosp] Sent: Wednesday, November 16, 2011 11:17 AM To: i2b2 AUG Members Subject: Could not resolve uncommited transactions
I am pointing to MSSql, and getting an issue with the persistence manager (see below)
2011-11-16 12:30:48,235 INFO [org.jboss.resource.connectionmanager.ConnectionFactoryBindingService] Bound ConnectionManager 'jboss.jca:service=DataSourceBinding,name=QueryToolDemoDS_ora' to JNDI name 'java:QueryToolDemoDS_ora' 2011-11-16 12:30:48,239 INFO [org.jboss.resource.connectionmanager.ConnectionFactoryBindingService] Bound ConnectionManager 'jboss.jca:service=DataSourceBinding,name=QueryToolDemoDS' to JNDI name 'java:QueryToolDemoDS' 2011-11-16 12:30:49,015 INFO [org.jboss.resource.connectionmanager.ConnectionFactoryBindingService] Bound ConnectionManager 'jboss.jca:service=DataSourceBinding,name=DefaultDS' to JNDI name 'java:DefaultDS' 2011-11-16 12:30:50,908 WARN [org.jboss.system.ServiceController] Problem starting service jboss.mq:service=PersistenceManager org.jboss.mq.SpyJMSException: Could not resolve uncommited transactions. Message recovery may not be accurate; - nested throwable: (com.microsoft.sqlserver.jdbc.SQLServerException: Incorrect syntax near ')'.)
at org.jboss.mq.pm.jdbc2.PersistenceManager.resolveAllUncommitedTXs(PersistenceManager.java:48 8)
I notice there is a file deploy/jms/crc-oracle-jdbc2-service.xml that contains
Should there be afile out there for mssql?
Do I need to edit the crc-oracle-jdbc2-service.xml file?
<mbean code="org.jboss.mq.pm.jdbc2.PersistenceManager" name="jboss.mq:service=PersistenceManager"> <depends optional-attribute-name="ConnectionManager"> jboss.jca:service=DataSourceBinding,name=DefaultDS</depends>
<attribute name="SqlProperties"> BLOB_TYPE=BINARYSTREAM_BLOB INSERT_TX = INSERT INTO JMS_TRANSACTIONS (TXID) values INSERT_MESSAGE = INSERT INTO JMS_MESSAGES (MESSAGEID, DESTINATION,
MESSAGEBLOB, TXID, TXOP) VALUES(?,?,?,?,?) SELECT_ALL_UNCOMMITED_TXS = SELECT TXID FROM JMS_TRANSACTIONS SELECT_MAX_TX = SELECT MAX(TXID) FROM (SELECT MAX(TXID) AS TXID FROM
JMS_TRANSACTIONS UNION SELECT MAX(TXID) AS TXID FROM JMS_MESSAGES) DELETE_ALL_TX = DELETE FROM JMS_TRANSACTIONS SELECT_MESSAGES_IN_DEST = SELECT MESSAGEID, MESSAGEBLOB FROM
JMS_MESSAGES WHERE DESTINATION=? SELECT_MESSAGE = SELECT MESSAGEID, MESSAGEBLOB FROM JMS_MESSAGES WHERE MESSAGEID=? AND DESTINATION=? MARK_MESSAGE = UPDATE JMS_MESSAGES SET TXID=?, TXOP=? WHERE MESSAGEID=? AND DESTINATION=? UPDATE_MESSAGE = UPDATE JMS_MESSAGES SET MESSAGEBLOB=? WHERE MESSAGEID=? AND DESTINATION=? UPDATE_MARKED_MESSAGES = UPDATE JMS_MESSAGES SET TXID=?, TXOP=? WHERE TXOP=? UPDATE_MARKED_MESSAGES_WITH_TX = UPDATE JMS_MESSAGES SET TXID=?, TXOP=? WHERE TXOP=? AND TXID=?
DELETE_MARKED_MESSAGES_WITH_TX = DELETE FROM JMS_MESSAGES MESS WHERE TXOP=:1 AND EXISTS (SELECT TXID FROM JMS_TRANSACTIONS TX WHERE TX.TXID = MESS.TXID)
DELETE_TX = DELETE FROM JMS_TRANSACTIONS WHERE TXID = ? DELETE_MARKED_MESSAGES = DELETE FROM JMS_MESSAGES WHERE TXID=? AND
TXOP=? DELETE_TEMPORARY_MESSAGES = DELETE FROM JMS_MESSAGES WHERE TXOP='T' DELETE_MESSAGE = DELETE FROM JMS_MESSAGES WHERE MESSAGEID=? AND
DESTINATION=? CREATE_MESSAGE_TABLE = CREATE TABLE JMS_MESSAGES ( MESSAGEID INTEGER
NOT NULL, \ DESTINATION VARCHAR(255) NOT NULL, TXID INTEGER, TXOP CHAR(1), \ MESSAGEBLOB BLOB, PRIMARY KEY (MESSAGEID, DESTINATION) )
CREATE_IDX_MESSAGE_TXOP_TXID = CREATE INDEX JMS_MESSAGES_TXOP_TXID ON JMS_MESSAGES (TXOP, TXID) CREATE_IDX_MESSAGE_DESTINATION = CREATE INDEX JMS_MESSAGES_DESTINATION ON JMS_MESSAGES (DESTINATION) CREATE_TX_TABLE = CREATE TABLE JMS_TRANSACTIONS ( TXID INTEGER, PRIMARY KEY (TXID) )
CREATE_TABLES_ON_STARTUP = TRUE </attribute> 
<target name="jaxb_gen" depends="init" description="Generate JAXB classes for i2b2 and Vocab Data messages"> <xjc destdir="${gensrc}" removeOldOutput="no">
<schema dir="../${i2b2xmlproject}/xsd/cell/ont_1.1" includes="ONT_QRY.xsd" />
<schema dir="../${i2b2xmlproject}/xsd/cell/ont_1.1" includes="ONT_RESP.xsd" />
<schema dir="../${i2b2xmlproject}/xsd/cell/pm_1.1" includes="PM_USER.xsd" />
<schema dir="../${i2b2xmlproject}/xsd/hive/msg_1.1" includes="i2b2_response.xsd" />
<schema dir="../${i2b2xmlproject}/xsd/cell/fr_1.0" includes="FR_QRY.xsd" />
<schema dir="../${i2b2xmlproject}/xsd/cell/crc/loader_1.1" includes="CRC_UPLOADER_QRY.xsd" />
<schema dir="../${i2b2xmlproject}/xsd/cell/crc/psm_1.1" includes="CRC_PSM_QRY.xsd" />
< <schema dir="../${i2b2xmlproject}/xsd/cell/crc/psm_1.1" includes="CRC_PSM_QRY_analysis_definition.xsd.xsd" />
<schema dir="../${i2b2xmlproject}/xsd/cell/crc/psm_1.1"
includes="CRC_PSM_QRY_query_definition.xsd" />
<binding dir="." includes="etc/xsd_1.1/i2b2_vdo_bindings.xjb" />
<binding dir="." includes="etc/xsd_1.1/i2b2_rspdo_bindings.xjb" />
<binding dir="." includes="etc/xsd_1.1/i2b2_response_message_bindings.xjb" />
<binding dir="." includes="etc/xsd_1.1/i2b2_pm_bindings.xjb" />
<binding dir="." includes="etc/xsd_1.1/i2b2_fr_bindings.xjb" />
<binding dir="." includes="etc/xsd_1.1/i2b2_crcloader_bindings.xjb" />
<binding dir="." includes="etc/xsd_1.1/i2b2_crc_psm_bindings.xjb" />
<binding dir="." includes="etc/xsd_1.1/i2b2_psm_analysisdefinition_bindings.xjb" />
<binding dir="." includes="etc/xsd_1.1/i2b2_psm_querydefinition_bindings.xjb" />
</xjc> </target>
Duane Steward, DVM, MSIE, PhD Chief Computer Scientist for Health Informatics Nemours

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From: Mendis, Michael E. Sent: Tuesday, November 15, 2011 12:21 PM To: Yves Thorrez; 'Schulte, Gregory'; Arnold, Garth; i2b2 AUG Members Subject: Re: 64bit sql server connection issue
The speed will be the same for 32 vs 64bit
mike

On 11/15/11 12:16 PM, "Yves Thorrez" <Yves.Thorrez.uzbrussel.be> wrote:
Hi everyone,
Just curious: can anyone testify of a better performance of the i2b2 stack using 64 bit Java? (we have the same setup as what Greg describes here; we compiled v1.6 with both 32 and 64 bit java and observed no issues during early testing)
Thanks,
Yves

From: Schulte, Gregory [Gregory.Schulte.childrenscolorado] Sent: dinsdag 15 november 2011 15:34 To: Arnold, Garth; i2b2 AUG Members Subject: RE: 64bit sql server connection issue
Thanks Garth!
I'm running two 64 bit windows servers, one for SQL Server 2008 and the other for the i2b2 stack.
I removed the 64 bit java and installed 32 bit Java, recompiled and it seems to have gotten me past this issue.
Thanks again,
Greg

From: Arnold, Garth [arnold.g.ghc] Sent: Monday, November 14, 2011 3:01 PM To: Schulte, Gregory; i2b2 AUG Members Subject: RE: 64bit sql server connection issue
Hi Greg ?I'm not clear whether your SQL and i2b2 stack (tomcat, etc) boxes are one and same or whether SQL is on a separate box. We've had no problem using 64?bit Windows and SQL Server, running SQL Server and v1.4 of the i2b2 stack on the same box. One thing we did do was to stick with 32?bit versions of java, apache, php, etc ?for java we used 'jdk?6u16?windows?i586', for apache the 'httpd?2.2.16?32 bit no_ssl' distribution, and for php the 'php?5.2.14?Win32?VC6?x86' compilation.
Hope this helps,
Garth
Garth Arnold | MANAGER, TECHNICAL INFRASTRUCTURE Group Health Research Institute
E?MAIL arnold.g.ghc www.ghc.org

From: Schulte, Gregory [Gregory.Schulte.childrenscolorado] Sent: Monday, November 14, 2011 1:49 PM
To: i2b2 AUG Members Subject: 64bit sql server connection issue
Hello everyone, I'm an i2b2 newbie here at children's Colorado hospital and running into an issue with
connecting to a 64 bit sql server instance.
I'm been able to successfully install 1.6 final onto a 32 bit windows environment running sql server but having issues when setting up the 64 bit environment.
Whenever I launch the admin web client "i2b2_pm" tries to connect to "MASTER" database instead of its set default database. This of course causes a failure when running the first select statement.
When I run the same code on my 32 bit windows web server connecting to the 64 bit sql server instance it runs fine, so I'm guessing it has to be a php apache versioning issue?
Any one run into issues with 64 sql server connectivity?
Thanks,
Greg Schulte | Clinical Research Data Warehouse Database Analyst
13123 East 16th Avenue, Box 485 | Aurora, CO 80045 | Gregory.Schulte.childrenscolorado <schulte.kelly.tchden>

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From: Peter Beninato [beninato.ohsu] Sent: Monday, November 14, 2011 6:11 PM To: Michael.C.Ford.kp; i2b2 AUG Members Subject: RE: Clearing the query queues
I'm not sure exactly how it works, but you might want to better understand how saved queries are reused.
If someone saves a query to the workplace and goes to re-run it, but the query is deleted from the tables you describe below then it might not work so well?

From: Michael.C.Ford.kp [Michael.C.Ford.kp] Sent: Monday, November 14, 2011 2:51 PM To: i2b2 AUG Members Subject: Clearing the query queues
We have been running for a while and I was wondering if anyone has written a script for this.
I would like to clear out all queries that are over say 30 days old. I think I can just delete all rows meeting my criteria from the following
QT_Query_INSTANCE
QT_QUERY_MASTER QT_QUERY_RESULT_INSTANCE QT_XML_RESULT
but would like some feedback - other things to think about, other tables I should be concerned with.

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From: Brian Ostasiewski [bostasie.wakehealth] Sent: Monday, November 14, 2011 10:49 AM To: i2b2 AUG Members Subject: bug with Dates contraint on dimensional queries?
In 1.6.01, we had a user attempt to filter the Dates on a query of Age now, which is a dimensional query against the patient_dimension. The resulting query underneath appears to assume it is going against the observation_fact table.
Can someone verify this is an issue? Also, is there a way to disable use of the Dates filter for specific concepts via c_metadataxml?
Brian Ostasiewski
The sql from qt_query_master:
select count(distinct patient_num) as patient_num_count from (
(select patient_num ,1 as panel_count from ( select /*+ index(observation_fact fact_cnpt_pat_enct_idx) */ patient_num from i2b2data.patient_dimension where patient_num IN (select patient_num from i2b2data.patient_dimension where birth_date <= sysdate ?(365.25*65) ) AND ( start_date >= to_date('31?Dec?2010 19:00:00','DD?MON?YYYY HH24:MI:SS') ) group by patient_num ) t ) INTERSECT
(select patient_num ,1 as panel_count from ( select /*+ index(observation_fact fact_cnpt_pat_enct_idx) */ patient_num from i2b2data.observation_fact where CONCEPT_CD IN (select CONCEPT_CD from i2b2data.CONCEPT_DIMENSION where CONCEPT_PATH LIKE '\WFUBMC\Diagnoses \ICD9\Circulatory system (390?459)\Hypertensive disease (401?405)(401) Essential hypertension (401?1) Benign essential hyperten~%') group by patient_num ) t
UNION ALL select patient_num ,1 as panel_count from ( select /+ index(observation_fact fact_cnpt_pat_enct_idx) */ patient_num from i2b2data.observation_fact where CONCEPT_CD IN (select CONCEPT_CD from i2b2data.CONCEPT_DIMENSION where CONCEPT_PATH LIKE '\WFUBMC\Diagnoses \ICD9\Circulatory system (390?459)\Hypertensive disease (401?405)(401) Essential hypertension (401?9) Unspecified essential hyp~%') group by patient_num ) t UNION ALL select patient_num ,1 as panel_count from ( select /+ index(observation_fact fact_cnpt_pat_enct_idx) */ patient_num from i2b2data.observation_fact where CONCEPT_CD IN (select CONCEPT_CD from i2b2data.CONCEPT_DIMENSION where CONCEPT_PATH LIKE '\WFUBMC\Diagnoses \ICD9\Endocrine disorders (240?259)\Other endocrine gland diseases (250?259)(250) Diabetes mellitus(250?0) Diabetes mellitus without~%') group by patient_num ) t )
) allitem
Results in logged exception:
2011?11?14 10:34:50,763 ERROR [edu.harvard.i2b2.crc.dao.CRCDAO] Error while executing sql java.sql.SQLException: ORA?00904: "START_DATE": invalid identifier
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(CachedConnectionIntercept or.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
$MessageListenerImpl.onMessage(JMSContainerInvoker.java:1392) at org.jboss.jms.asf.StdServerSession.onMessage(StdServerSession.java:266) at
org.jboss.mq.SpyMessageConsumer.sessionConsumerProcessMessage(SpyMessageConsumer.java:906) at org.jboss.mq.SpyMessageConsumer.addMessage(SpyMessageConsumer.java:170) at org.jboss.mq.SpySession.run(SpySession.java:323) at org.jboss.jms.asf.StdServerSession.run(StdServerSession.java:194) at EDU.oswego.cs.dl.util.concurrent.PooledExecutor$Worker.run(PooledExecutor.java:761) at java.lang.Thread.run(Thread.java:619)

NEXT EMAIL
From: John Kilian [Jkilian.harthosp] Sent: Monday, November 14, 2011 10:35 AM To: Seth Lenzi; John Kilian; Christopher P Heilala; Phillips, Lori C. Cc: i2b2 AUG Members Subject: Re: JMS provider failure trying to use mssql (Correction)
Sorry for the extra email. To be clear, I am using MSSql as my datasource.
John Kilian, RN, BSCS, BSED
Senior Distributed Applications Programmer/Analyst Hartford Hospital W:(860)545-4213

"John Kilian" <Jkilian.harthosp> 11/14/2011 10:29 AM
I am trying to use mssql, and have modified the various db.properties files and ds files. When I start the jboss server I get this, and I am not able to get anywhere via the gui. Has anyone run into and resolved this problem?
15:59:58,944 INFO [JMSContainerInvoker] Trying to reconnect to JMS provider for querytool.QueryExecutorSmallMDB 15:59:58,945 ERROR [JMSContainerInvoker] Reconnect failed: JMS provider failure detected for querytool.QueryExecutorSmallMDB javax.naming.NameNotFoundException: XAConnectionFactory not bound
John Kilian, RN, BSCS, BSED
Senior Distributed Applications Programmer/Analyst Hartford Hospital

NEXT EMAIL
From: Mendis, Michael E. Sent: Monday, November 14, 2011 9:54 AM To: Yves Thorrez; i2b2 AUG Members Subject: Re: Updated i2b2createdb601.zip
Thanks Yves,
I thought I got them all and but missed that one. Thanks has been fixed.
mike

On 11/14/11 5:41 AM, "Yves Thorrez" <Yves.Thorrez.uzbrussel.be> wrote:
My download is Nov 10. There is still one faulty occurrence of 'VARCHAR2' in 'CREATE TABLE PM_APPROVALS'.
Yves

From: Mike Mendis [mmendis.partners] Sent: dinsdag 8 november 2011 21:53 To: i2b2 AUG Members Subject: Updated i2b2createdb601.zip
Due to a error in the build create db scripts on the sql server side. I have replaced the file on the i2b2 server with a working version. If you have downloaded the recent i2b2createdb601.zip from Nov 2 to Nov 8, can you reddownload it again.
Thanks mike

On 11/8/11 9:24 AM, "m m" <mmendis.partners> wrote:
Thanks johnny, updated the pm install scripts and will be in the next minor release.
Thanks again mike

On 11/7/11 7:00 PM, "Murphy, Shawn N." <SNMURPHY.PARTNERS> wrote:
Thanks Johnny.

From: Dat Q. Phan [Dat.Q.Phan.uth.tmc] Sent: Monday, November 07, 2011 12:43 PM To: i2b2 AUG Members Subject: Error in create_sqlserver_i2b2pm_tables.sql
I'm not sure if this has been reported yet, but in the create_sqlserver_i2b2pm_tables.sql script it should be VARCHAR and not VARCHAR2 for 'CREATE TABLE PM_APPROVALS', 'CREATE TABLE PM_APPROVALS_PARAMS', and 'CREATE TABLE PM_PROJECT_REQUEST'.
Johnny Phan Programmer Analyst II UTHealth School of Biomedical Informatics Dat.Q.Phan.uth.tmc

NEXT EMAIL
From: Wilson, Brian Sent: Saturday, November 12, 2011 5:02 PM To: dsteward.NEMOURS Cc: i2b2 AUG Members Subject: re:build.xml problem building the ontology cell v1.601
Duane,
I got something similar. The current installation guide suggests installing the ONT cell before CRC, however the ONT cell now has a dependency on the CRC - re c_totalnum field.
I simply installed the CRC and reran the ONT ant build for good measure, and was good to go.
Rian

Subject: build.xml problem building the ontology cell v1.601 Date: Fri, 11 Nov 2011 18:32:43 -0500 From: Steward, Duane To: i2b2 AUG Members CC: MMENDIS.PARTNERS
Line 52 in i2b2core-src-1601/Server/edu.harvard.i2b2.ontology/build.xml is currently as follows.
<schema dir="../${i2b2xmlproject}/xsd/cell/crc/psm_1.1" includes="CRC_PSM_QRY_analysis_definition.xsd.xsd" />
Has anyone had difficulty building the 1.601 ontology cell with this ant script? The redundant extension in the file name seems to be a typo, albeit something that would only result in an omission, but still a successful build with Ant. However, I am getting a NullPointerException attributed to line 44, which is the opening xjc tag above this line when I attempt to build the "build-all" target following the i2b2 Hive_Installation_Guide (Linus) v1.6.1, Data_Installation_Guide, Project_Management_Installation_Guide and Ontology_Installation_Guide on a Ubuntu platform that is successful up to this point. I suspect the true source of the NPE is within one of the schemas or binding files, but presumptive editing of line 52 results in an unreadable schema exception and commenting out one binding tag at a time to otherwize localize the problem turns into a good wrapping around the axle.
Any shared experience or help on what I am doing wrong?
? <!=================================================================== ->
<!COMMON JAXB GENERATION ->
<!=================================================================== ->
<target name="jaxb_gen" depends="init" description="Generate JAXB classes for i2b2 and Vocab Data messages">
<xjc destdir="${gensrc}" removeOldOutput="no">
<schema dir="../${i2b2xmlproject}/xsd/cell/ont_1.1" includes="ONT_QRY.xsd" />
<schema dir="../${i2b2xmlproject}/xsd/cell/ont_1.1" includes="ONT_RESP.xsd" />
<schema dir="../${i2b2xmlproject}/xsd/cell/pm_1.1" includes="PM_USER.xsd" />
<schema dir="../${i2b2xmlproject}/xsd/hive/msg_1.1" includes="i2b2_response.xsd"
/>
<schema dir="../${i2b2xmlproject}/xsd/cell/fr_1.0" includes="FR_QRY.xsd" />
<schema dir="../${i2b2xmlproject}/xsd/cell/crc/loader_1.1" includes="CRC_UPLOADER_QRY.xsd" />
<schema dir="../${i2b2xmlproject}/xsd/cell/crc/psm_1.1" includes="CRC_PSM_QRY.xsd" />
< <schema dir="../${i2b2xmlproject}/xsd/cell/crc/psm_1.1" includes="CRC_PSM_QRY_analysis_definition.xsd.xsd" />
<schema dir="../${i2b2xmlproject}/xsd/cell/crc/psm_1.1" includes="CRC_PSM_QRY_query_definition.xsd" />
<binding dir="." includes="etc/xsd_1.1/i2b2_vdo_bindings.xjb" /> <binding dir="." includes="etc/xsd_1.1/i2b2_rspdo_bindings.xjb" /> <binding dir="." includes="etc/xsd_1.1/i2b2_response_message_bindings.xjb" /> <binding dir="." includes="etc/xsd_1.1/i2b2_pm_bindings.xjb" /> <binding dir="." includes="etc/xsd_1.1/i2b2_fr_bindings.xjb" /> <binding dir="." includes="etc/xsd_1.1/i2b2_crcloader_bindings.xjb" /> <binding dir="." includes="etc/xsd_1.1/i2b2_crc_psm_bindings.xjb" /> <binding dir="." includes="etc/xsd_1.1/i2b2_psm_analysisdefinition_bindings.xjb"
/> <binding dir="." includes="etc/xsd_1.1/i2b2_psm_querydefinition_bindings.xjb" /> </xjc> </target>
Duane Steward, DVM, MSIE, PhD Chief Computer Scientist for Health Informatics Nemours

NEXT EMAIL
From: Patibandla, Nandan [Nandan.Patibandla.childrens.harvard] Sent: Friday, November 11, 2011 5:10 PM To: i2b2 AUG Members Cc: Mendis, Michael E. Subject: FW: Not generating the Patient sets
HI,
With respect to the same issue as below, I found this in the error log, Is there a fix around for this issue:
2011-11-11 16:45:48,536 DEBUG [org.jboss.mq.il.uil2.ServerSocketManagerHandler] Exiting on IOE
java.net.SocketException: socket closed
at java.net.SocketInputStream.socketRead0(Native Method)
at java.net.SocketInputStream.read(SocketInputStream.java:129)
at java.io.BufferedInputStream.fill(BufferedInputStream.java:218)
at java.io.BufferedInputStream.read(BufferedInputStream.java:237)
at org.jboss.util.stream.NotifyingBufferedInputStream.read(NotifyingBufferedInputStream.java:79)
at java.io.ObjectInputStream$PeekInputStream.peek(ObjectInputStream.java:2248)
at java.io.ObjectInputStream
$BlockDataInputStream.readBlockHeader(ObjectInputStream.java:2428)
at java.io.ObjectInputStream$BlockDataInputStream.refill(ObjectInputStream.java:2498) at java.io.ObjectInputStream$BlockDataInputStream.read(ObjectInputStream.java:2570) at java.io.ObjectInputStream
$BlockDataInputStream.readByte(ObjectInputStream.java:2719) at java.io.ObjectInputStream.readByte(ObjectInputStream.java:894) at org.jboss.mq.il.uil2.SocketManager$ReadTask.run(SocketManager.java:340) at java.lang.Thread.run(Thread.java:662)
Thank you Nandan

From: Patibandla, Nandan Sent: Friday, November 11, 2011 12:38 PM To: i2b2 AUG Members Cc: 'Mike Mendis' Subject: Not generating the Patient sets
Hi, I am able to deploy the i2b2 v 1.6 successfully but not able to get the patient set after running the query, and if I click on the sub tree of the patient set in the previous queries, the wait symbol is there
forever. By seeing the error log, I am see the below message and might be the possible cause for not generating the patient sets. Can you guys please let me know fix for this issue.
Thank you Nandan
ERROR 2011-11-11 12:29:39,851 DEBUG [org.springframework.core.CollectionFactory] Creating [java.util.LinkedHashMap]
2011-11-11 12:29:39,851 DEBUG [org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory $ConstructorResolverAdapter] Ignoring constructor [public java.lang.String(byte[],int,int,int)] of bean 'defaultSetfinderResultType': Error creating bean with name 'defaultSetfinderResultType' defined in URL [file:C:/prod/jboss-4.2.2.GA/server/default/conf/crcapp/CRCApplicationContext.xml]: Unsatisfied dependency expressed through constructor argument with index 0 of type [byte[]]: Ambiguous constructor argument types - did you specify the correct bean references as constructor arguments?
2011-11-11 12:29:39,851 DEBUG [org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory $ConstructorResolverAdapter] Ignoring constructor [public java.lang.String(byte[],int,int,int)] of bean 'defaultSetfinderResultType': Error creating bean with name 'defaultSetfinderResultType' defined in URL [file:C:/prod/jboss-4.2.2.GA/server/default/conf/crcapp/CRCApplicationContext.xml]: Unsatisfied dependency expressed through constructor argument with index 0 of type [byte[]]: Ambiguous constructor argument types - did you specify the correct bean references as constructor arguments?
2011-11-11 12:29:39,851 DEBUG [org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory $ConstructorResolverAdapter] Ignoring constructor [public java.lang.String(byte[],int,int,java.lang.String) throws java.io.UnsupportedEncodingException] of bean 'defaultSetfinderResultType': Error creating bean with name 'defaultSetfinderResultType' defined in URL [file:C:/prod/jboss-4.2.2.GA/server/default/conf/crcapp/CRCApplicationContext.xml]: Unsatisfied dependency expressed through constructor argument with index 0 of type [byte[]]: Ambiguous constructor argument types - did you specify the correct bean references as constructor arguments?
2011-11-11 12:29:39,851 DEBUG [org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory $ConstructorResolverAdapter] Ignoring constructor [public java.lang.String(byte[],int,int,java.lang.String) throws java.io.UnsupportedEncodingException] of bean 'defaultSetfinderResultType': Error creating bean with name 'defaultSetfinderResultType' defined in URL [file:C:/prod/jboss-4.2.2.GA/server/default/conf/crcapp/CRCApplicationContext.xml]: Unsatisfied dependency expressed through constructor argument with index 0 of type [byte[]]: Ambiguous constructor argument types - did you specify the correct bean references as constructor arguments?

NEXT EMAIL
From: Lisa Miao [lmiao.regenstrief] Sent: Monday, November 07, 2011 2:48 PM To: Phillips, Lori C.; i2b2 AUG Members Subject: RE: search by name
Thanks for the help Lori!
I got rid of '-', ':' characters in the c_table_cd column, now it's fully working!
Thanks!
Lisa.

From: Phillips, Lori C. [LCPHILLIPS.PARTNERS] Sent: Monday, November 07, 2011 2:36 PM To: Phillips, Lori C.; i2b2 AUG Members Subject: RE: search by name
Lisa,
I just ran a test locally with 21 categories and it worked fine. Is there anything unusual about the 11th or 12th category being returned by get_categories ?
Lori

From: Peter Beninato [beninato.ohsu] Sent: Monday, November 07, 2011 2:03 PM To: Phillips, Lori C.; i2b2 AUG Members Subject: RE: search by name
On the top of search functionality, Is there a mechanism to clear the results in the new version?
In 1.4, the only way to clear the results from the search is to logout.
If a mechanism to clear does not yet exist in v1.6, could this be added to the codebase? Does a JIRA issue need to be created for this functionality request?
Thanks.
Peter

From: Phillips, Lori C. Sent: Monday, November 07, 2011 1:55 PM To: i2b2 AUG Members Subject: FW: search by name
Lisa,
Am forwarding this to the community to see if others have experienced this problem in the web client and if there is a fix available ... in addition the problem will get logged properly as well.
Thanks, Lori

From: Lisa Miao [lmiao.regenstrief] Sent: Monday, November 07, 2011 1:49 PM To: Phillips, Lori C. Cc: Donahoe, Janice M; Mendis, Michael E. Subject: RE: search by name
Lori,
Thanks for the help!
After I tried the things you suggested, we do have things coming back for the GetCategory call. The dropdown seem to have a limit on how many it can contain. We have about 35, the dropdown is only displaying 11 of them.
When selecting "Any Category", the search doesNOT work.
Thanks,
Lisa.

From: Phillips, Lori C. [LCPHILLIPS.PARTNERS] Sent: Thursday, November 03, 2011 10:28 AM To: Lisa Miao Cc: Donahoe, Janice M; Mendis, Michael E. Subject: RE: search by name
Lisa,
I was able to track down your problem.
The webclient does not like spaces or '&' in the c_table_cd col of the table_access table.
Try shortening your c_table_cd entries to something like
BLOOD_BANK or BLOOD
CHROMOSOME etc...
Lori

From: Lisa Miao [lmiao.regenstrief] Sent: Thursday, October 27, 2011 11:23 AM To: Phillips, Lori C. Subject: RE: search by name
Thanks Lori!
Lisa.

From: Phillips, Lori C. [LCPHILLIPS.PARTNERS] Sent: Thursday, October 27, 2011 11:19 AM To: Lisa Miao Subject: RE: search by name
Ok – the problem is related to the fact that your drop down is not getting populated.
When you do a find 'any' it iterates through all the categories; you have none so it doesnt make the find request.
get_categores is called on startup – so , yes, you are correct it will only show up once.
You are getting results back that should populate the categories drop box.
I am going to have to consult with the web client developer to find out why your categories are not getting populated.
Lori

From: Lisa Miao [lmiao.regenstrief] Sent: Thursday, October 27, 2011 10:49 AM To: Phillips, Lori C. Subject: RE: search by name
I am using webclient.
I don't see anything in the server.log.
When I do "search by name", there are two messages in XML message history. Here're the two messages: Get Schemes and Get Categories. (However if I clear the history, and hit Find again, nothing showed up in the history, so it looks like it only shows something for the first time.)
The Get Categories looks like the following:
Thanks,
Lisa.
<message_body>
<ns6:concepts>
<concept>
<level>1</level>
<key>
BLOOD BANK:\i2b2\BLOOD BANK:{color:#0000ff}</key>
<name>BLOOD BANK:</name>
<synonym_cd>N</synonym_cd>
<visualattributes>FA </visualattributes>
<totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true" />
<basecode>Local Concept::16550</basecode>
<facttablecolumn>concept_cd</facttablecolumn>
<tablename>concept_dimension</tablename>
<columnname>concept_path</columnname>
<columndatatype>T</columndatatype>
<operator>like</operator>
<dimcode>\i2b2\BLOOD BANK:{color:#0000ff}</dimcode>
<tooltip>BLOOD BANK:</tooltip>
</concept>
<concept>
<level>1</level>
<key>
CARDIOLOGY STUDIES\i2b2\CARDIOLOGY STUDIES{color:#0000ff}</key>
<name>CARDIOLOGY STUDIES</name>
<synonym_cd>N</synonym_cd>
<visualattributes>FA </visualattributes>
<totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true" />
<basecode>Local Concept::7496</basecode>
<facttablecolumn>concept_cd</facttablecolumn>
<tablename>concept_dimension</tablename>
<columnname>concept_path</columnname>
<columndatatype>T</columndatatype>
<operator>like</operator>
<dimcode>\i2b2\CARDIOLOGY STUDIES{color:#0000ff}</dimcode>
<tooltip>CARDIOLOGY STUDIES</tooltip>
</concept>
<concept>
<level>1</level>
<key>
CHEMISTRY STUDIES\i2b2\CHEMISTRY STUDIES{color:#0000ff}</key>
<name>CHEMISTRY STUDIES</name>
<synonym_cd>N</synonym_cd>
<visualattributes>FA </visualattributes>
<totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true" />
<basecode>Local Concept::4011</basecode>
<facttablecolumn>concept_cd</facttablecolumn>
<tablename>concept_dimension</tablename>
<columnname>concept_path</columnname>
<columndatatype>T</columndatatype>
<operator>like</operator>
<dimcode>\i2b2\CHEMISTRY STUDIES{color:#0000ff}</dimcode>
<tooltip>CHEMISTRY STUDIES</tooltip>
</concept>
<concept>
<level>1</level>
<key>
CHROMOSOME&MOLECULAR PATHOLOGY\i2b2
\CHROMOSOME&MOLECULAR PATHOLOGY\
</key>
<name>CHROMOSOME&MOLECULAR PATHOLOGY</name>
<synonym_cd>N</synonym_cd>
<visualattributes>FA </visualattributes>
<totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true" />
<basecode>Local Concept::26134</basecode>
<facttablecolumn>concept_cd</facttablecolumn>
<tablename>concept_dimension</tablename>
<columnname>concept_path</columnname>
<columndatatype>T</columndatatype>
<operator>like</operator>
<dimcode>\i2b2\CHROMOSOME&MOLECULAR PATHOLOGY{color:#0000ff}</dimcode>
<tooltip>CHROMOSOME&MOLECULAR PATHOLOGY</tooltip>
</concept>
<concept>
<level>1</level>
<key>
CSF&OTHER FLUID (COUNTS & CHEM)\i2b2\CSF&OTHER FLUID
(COUNTS & CHEM)\
</key>
<name>CSF&OTHER FLUID (COUNTS & CHEM)</name>
<synonym_cd>N</synonym_cd>
<visualattributes>FA </visualattributes>
<totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true" />
<basecode>Local Concept::16962</basecode>
<facttablecolumn>concept_cd</facttablecolumn>
<tablename>concept_dimension</tablename>
<columnname>concept_path</columnname>
<columndatatype>T</columndatatype>
<operator>like</operator>
<dimcode>\i2b2\CSF&OTHER FLUID (COUNTS & CHEM){color:#0000ff}</dimcode>
<tooltip>CSF&OTHER FLUID (COUNTS & CHEM)</tooltip>
</concept>
<concept>
<level>1</level>
<key>\\Demographics\i2b2\Demographics{color:#0000ff}</key>
<name>DEMOGRAPHICS</name>
<synonym_cd>N</synonym_cd>
<visualattributes>CA </visualattributes>
<totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true" />
<facttablecolumn>concept_cd</facttablecolumn>
<tablename>concept_dimension</tablename>
<columnname>concept_path</columnname>
<columndatatype>T</columndatatype>
<operator>LIKE</operator>
<dimcode>\i2b2\Demographics{color:#0000ff}</dimcode>
<tooltip>DEMOGRAPHICS</tooltip>
</concept>
<concept>
<level>1</level>
<key>
ENCOUNTER DATA\i2b2\ENCOUNTER DATA{color:#0000ff}</key>
<name>ENCOUNTER DATA</name>
<synonym_cd>N</synonym_cd>
<visualattributes>FA </visualattributes>
<totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true" />
<basecode>Local Concept::18282</basecode>
<facttablecolumn>concept_cd</facttablecolumn>
<tablename>concept_dimension</tablename>
<columnname>concept_path</columnname>
<columndatatype>T</columndatatype>
<operator>like</operator>
<dimcode>\i2b2\ENCOUNTER DATA{color:#0000ff}</dimcode>
<tooltip>ENCOUNTER DATA</tooltip>
</concept>
<concept>
<level>1</level>
<key>
EYE & EAR STUDIES\i2b2\EYE & EAR STUDIES{color:#0000ff}</key>
<name>EYE & EAR STUDIES</name>
<synonym_cd>N</synonym_cd>
<visualattributes>FA </visualattributes>
<totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true" />
<basecode>Local Concept::26669</basecode>
<facttablecolumn>concept_cd</facttablecolumn>
<tablename>concept_dimension</tablename>
<columnname>concept_path</columnname>
<columndatatype>T</columndatatype>
<operator>like</operator>
<dimcode>\i2b2\EYE & EAR STUDIES{color:#0000ff}</dimcode>
<tooltip>EYE & EAR STUDIES</tooltip>
</concept>
<concept>
<level>1</level>
<key>
GASTROENTEROLOGY STUDIES\i2b2\GASTROENTEROLOGY STUDIES
\
</key>
<name>GASTROENTEROLOGY STUDIES</name>
<synonym_cd>N</synonym_cd>
<visualattributes>FA </visualattributes>
<totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true" />
<basecode>Local Concept::2246</basecode>
<facttablecolumn>concept_cd</facttablecolumn>
<tablename>concept_dimension</tablename>
<columnname>concept_path</columnname>
<columndatatype>T</columndatatype>
<operator>like</operator>
<dimcode>\i2b2\GASTROENTEROLOGY STUDIES{color:#0000ff}</dimcode>
<tooltip>GASTROENTEROLOGY STUDIES</tooltip>
</concept>
<concept>
<level>1</level>
<key>
HEMATOLOGY STUDIES:\i2b2\HEMATOLOGY STUDIES:{color:#0000ff}</key>
<name>HEMATOLOGY STUDIES:</name>
<synonym_cd>N</synonym_cd>
<visualattributes>FA </visualattributes>
<totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true" />
<basecode>Local Concept::16540</basecode>
<facttablecolumn>concept_cd</facttablecolumn>
<tablename>concept_dimension</tablename>
<columnname>concept_path</columnname>
<columndatatype>T</columndatatype>
<operator>like</operator>
<dimcode>\i2b2\HEMATOLOGY STUDIES:{color:#0000ff}</dimcode>
<tooltip>HEMATOLOGY STUDIES:</tooltip>
</concept>
<concept>
<level>1</level>
<key>
Hospital Quality Management\i2b2\Hospital Quality Management{color:#0000ff}</key>
<name>Hospital Quality Management</name>
<synonym_cd>N</synonym_cd>
<visualattributes>FA </visualattributes>
<totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true" />
<basecode>Local Concept::30964</basecode>
<facttablecolumn>concept_cd</facttablecolumn>
<tablename>concept_dimension</tablename>
<columnname>concept_path</columnname>
<columndatatype>T</columndatatype>
<operator>like</operator>
<dimcode>\i2b2\Hospital Quality Management{color:#0000ff}</dimcode>
<tooltip>Hospital Quality Management</tooltip>
</concept>
<concept>
<level>1</level>
<key>
MED DOSES-SUPPLIES-VACC-SKIN TST\i2b2\MED DOSES-SUPPLIES-VACC¬SKIN TST{color:#0000ff}</key>
<name>MED DOSES-SUPPLIES-VACC-SKIN TST</name>
<synonym_cd>N</synonym_cd>
<visualattributes>FA </visualattributes>
<totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true" />
<basecode>Local Concept::26259</basecode>
<facttablecolumn>concept_cd</facttablecolumn>
<tablename>concept_dimension</tablename>
<columnname>concept_path</columnname>
<columndatatype>T</columndatatype>
<operator>like</operator>
<dimcode>\i2b2\MED DOSES-SUPPLIES-VACC-SKIN TST{color:#0000ff}</dimcode>
<tooltip>MED DOSES-SUPPLIES-VACC-SKIN TST</tooltip>
</concept>
<concept>
<level>1</level>
<key>
MICROBIOLOGY STUDIES:\i2b2\MICROBIOLOGY STUDIES:{color:#0000ff}</key>
<name>MICROBIOLOGY STUDIES:</name>
<synonym_cd>N</synonym_cd>
<visualattributes>FA </visualattributes>
<totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true" />
<basecode>Local Concept::16554</basecode>
<facttablecolumn>concept_cd</facttablecolumn>
<tablename>concept_dimension</tablename>
<columnname>concept_path</columnname>
<columndatatype>T</columndatatype>
<operator>like</operator>
<dimcode>\i2b2\MICROBIOLOGY STUDIES:{color:#0000ff}</dimcode>
<tooltip>MICROBIOLOGY STUDIES:</tooltip>
</concept>
<concept>
<level>1</level>
<key>
NEUROLOGY STUDIES\i2b2\NEUROLOGY STUDIES{color:#0000ff}</key>
<name>NEUROLOGY STUDIES</name>
<synonym_cd>N</synonym_cd>
<visualattributes>FA </visualattributes>
<totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true" />
<basecode>Local Concept::21929</basecode>
<facttablecolumn>concept_cd</facttablecolumn>
<tablename>concept_dimension</tablename>
<columnname>concept_path</columnname>
<columndatatype>T</columndatatype>
<operator>like</operator>
<dimcode>\i2b2\NEUROLOGY STUDIES{color:#0000ff}</dimcode>
<tooltip>NEUROLOGY STUDIES</tooltip>
</concept>
<concept>
<level>1</level>
<key>\\OB/GYN/PERINATAL:\i2b2\OB/GYN/PERINATAL:{color:#0000ff}</key>
<name>OB/GYN/PERINATAL:</name>
<synonym_cd>N</synonym_cd>
<visualattributes>FA </visualattributes>
<totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true" />
<basecode>Local Concept::26232</basecode>
<facttablecolumn>concept_cd</facttablecolumn>
<tablename>concept_dimension</tablename>
<columnname>concept_path</columnname>
<columndatatype>T</columndatatype>
<operator>like</operator>
<dimcode>\i2b2\OB/GYN/PERINATAL:{color:#0000ff}</dimcode>
<tooltip>OB/GYN/PERINATAL:</tooltip>
</concept>
<concept>
<level>1</level>
<key>\\OTHER\i2b2\OTHER{color:#0000ff}</key>
<name>OTHER</name>
<synonym_cd>N</synonym_cd>
<visualattributes>FA </visualattributes>
<totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true" />
<basecode>Local Concept::1913</basecode>
<facttablecolumn>concept_cd</facttablecolumn>
<tablename>concept_dimension</tablename>
<columnname>concept_path</columnname>
<columndatatype>T</columndatatype>
<operator>like</operator>
<dimcode>\i2b2\OTHER{color:#0000ff}</dimcode>
<tooltip>OTHER</tooltip>
</concept>
<concept>
<level>1</level>
<key>
PREVENTIVE CARE\i2b2\PREVENTIVE CARE{color:#0000ff}</key>
<name>PREVENTIVE CARE</name>
<synonym_cd>N</synonym_cd>
<visualattributes>FA </visualattributes>
<totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true" />
<basecode>Local Concept::7495</basecode>
<facttablecolumn>concept_cd</facttablecolumn>
<tablename>concept_dimension</tablename>
<columnname>concept_path</columnname>
<columndatatype>T</columndatatype>
<operator>like</operator>
<dimcode>\i2b2\PREVENTIVE CARE{color:#0000ff}</dimcode>
<tooltip>PREVENTIVE CARE</tooltip>
</concept>
<concept>
<level>1</level>
<key>
PROVIDER NOTES\i2b2\PROVIDER NOTES{color:#0000ff}</key>
<name>PROVIDER NOTES</name>
<synonym_cd>N</synonym_cd>
<visualattributes>FA </visualattributes>
<totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true" />
<basecode>Local Concept::23171</basecode>
<facttablecolumn>concept_cd</facttablecolumn>
<tablename>concept_dimension</tablename>
<columnname>concept_path</columnname>
<columndatatype>T</columndatatype>
<operator>like</operator>
<dimcode>\i2b2\PROVIDER NOTES{color:#0000ff}</dimcode>
<tooltip>PROVIDER NOTES</tooltip>
</concept>
<concept>
<level>1</level>
<key>\\Providers\i2b2\Providers{color:#0000ff}</key>
<name>PROVIDERS</name>
<synonym_cd>N</synonym_cd>
<visualattributes>FA </visualattributes>
<totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true" />
<basecode>LCS-I2B2:PROVIDERS</basecode>
<facttablecolumn>provider_id</facttablecolumn>
<tablename>provider_dimension</tablename>
<columnname>provider_path</columnname>
<columndatatype>T</columndatatype>
<operator>LIKE</operator>
<dimcode>\i2b2\Providers{color:#0000ff}</dimcode>
<tooltip>PROVIDERS</tooltip>
</concept>
<concept>
<level>1</level>
<key>
PSYCHIATRIC DATA:\i2b2\PSYCHIATRIC DATA:{color:#0000ff}</key>
<name>PSYCHIATRIC DATA:</name>
<synonym_cd>N</synonym_cd>
<visualattributes>FA </visualattributes>
<totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true" />
<basecode>Local Concept::36793</basecode>
<facttablecolumn>concept_cd</facttablecolumn>
<tablename>concept_dimension</tablename>
<columnname>concept_path</columnname>
<columndatatype>T</columndatatype>
<operator>like</operator>
<dimcode>\i2b2\PSYCHIATRIC DATA:{color:#0000ff}</dimcode>
<tooltip>PSYCHIATRIC DATA:</tooltip>
</concept>
<concept>
<level>1</level>
<key>
PULMONARY STUDIES\i2b2\PULMONARY STUDIES{color:#0000ff}</key>
<name>PULMONARY STUDIES</name>
<synonym_cd>N</synonym_cd>
<visualattributes>FA </visualattributes>
<totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true" />
<basecode>Local Concept::2230</basecode>
<facttablecolumn>concept_cd</facttablecolumn>
<tablename>concept_dimension</tablename>
<columnname>concept_path</columnname>
<columndatatype>T</columndatatype>
<operator>like</operator>
<dimcode>\i2b2\PULMONARY STUDIES{color:#0000ff}</dimcode>
<tooltip>PULMONARY STUDIES</tooltip>
</concept>
<concept>
<level>1</level>
<key>\\QUESTIONNAIRES\i2b2\QUESTIONNAIRES{color:#0000ff}</key>
<name>QUESTIONNAIRES</name>
<synonym_cd>N</synonym_cd>
<visualattributes>FA </visualattributes>
<totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true" />
<basecode>Local Concept::30739</basecode>
<facttablecolumn>concept_cd</facttablecolumn>
<tablename>concept_dimension</tablename>
<columnname>concept_path</columnname>
<columndatatype>T</columndatatype>
<operator>like</operator>
<dimcode>\i2b2\QUESTIONNAIRES{color:#0000ff}</dimcode>
<tooltip>QUESTIONNAIRES</tooltip>
</concept>
<concept>
<level>1</level>
<key>
RADIOLOGY&NUCLEAR MEDICINE\i2b2\RADIOLOGY&NUCLEAR
MEDICINE\
</key>
<name>RADIOLOGY&NUCLEAR MEDICINE</name>
<synonym_cd>N</synonym_cd>
<visualattributes>FA </visualattributes>
<totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true" />
<basecode>Local Concept::26135</basecode>
<facttablecolumn>concept_cd</facttablecolumn>
<tablename>concept_dimension</tablename>
<columnname>concept_path</columnname>
<columndatatype>T</columndatatype>
<operator>like</operator>
<dimcode>\i2b2\RADIOLOGY&NUCLEAR MEDICINE{color:#0000ff}</dimcode>
<tooltip>RADIOLOGY&NUCLEAR MEDICINE</tooltip>
</concept>
<concept>
<level>1</level>
<key>
REFERRAL LAB\i2b2\REFERRAL LAB{color:#0000ff}</key>
<name>REFERRAL LAB</name>
<synonym_cd>N</synonym_cd>
<visualattributes>FA </visualattributes>
<totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true" />
<basecode>Local Concept::22108</basecode>
<facttablecolumn>concept_cd</facttablecolumn>
<tablename>concept_dimension</tablename>
<columnname>concept_path</columnname>
<columndatatype>T</columndatatype>
<operator>like</operator>
<dimcode>\i2b2\REFERRAL LAB{color:#0000ff}</dimcode>
<tooltip>REFERRAL LAB</tooltip>
</concept>
<concept>
<level>1</level>
<key>
SEROLOGY STUDIES:\i2b2\SEROLOGY STUDIES:{color:#0000ff}</key>
<name>SEROLOGY STUDIES:</name>
<synonym_cd>N</synonym_cd>
<visualattributes>FA </visualattributes>
<totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true" />
<basecode>Local Concept::16549</basecode>
<facttablecolumn>concept_cd</facttablecolumn>
<tablename>concept_dimension</tablename>
<columnname>concept_path</columnname>
<columndatatype>T</columndatatype>
<operator>like</operator>
<dimcode>\i2b2\SEROLOGY STUDIES:{color:#0000ff}</dimcode>
<tooltip>SEROLOGY STUDIES:</tooltip>
</concept>
<concept>
<level>1</level>
<key>
SURGICAL PATHOLOGY & CYTOLOGY\i2b2\SURGICAL PATHOLOGY
& CYTOLOGY\
</key>
<name>SURGICAL PATHOLOGY & CYTOLOGY</name>
<synonym_cd>N</synonym_cd>
<visualattributes>FA </visualattributes>
<totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true" />
<basecode>Local Concept::26107</basecode>
<facttablecolumn>concept_cd</facttablecolumn>
<tablename>concept_dimension</tablename>
<columnname>concept_path</columnname>
<columndatatype>T</columndatatype>
<operator>like</operator>
<dimcode>\i2b2\SURGICAL PATHOLOGY & CYTOLOGY{color:#0000ff}</dimcode>
<tooltip>SURGICAL PATHOLOGY & CYTOLOGY</tooltip>
</concept>
<concept>
<level>1</level>
<key>
SYMPTOMS & FINDINGS:\i2b2\SYMPTOMS & FINDINGS:{color:#0000ff}</key>
<name>SYMPTOMS & FINDINGS:</name>
<synonym_cd>N</synonym_cd>
<visualattributes>FA </visualattributes>
<totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true" />
<basecode>Local Concept::7509</basecode>
<facttablecolumn>concept_cd</facttablecolumn>
<tablename>concept_dimension</tablename>
<columnname>concept_path</columnname>
<columndatatype>T</columndatatype>
<operator>like</operator>
<dimcode>\i2b2\SYMPTOMS & FINDINGS:{color:#0000ff}</dimcode>
<tooltip>SYMPTOMS & FINDINGS:</tooltip>
</concept>
<concept>
<level>1</level>
<key>
TDM & TOXICOLOGY STUDIES\i2b2\TDM & TOXICOLOGY STUDIES
\
</key>
<name>TDM & TOXICOLOGY STUDIES</name>
<synonym_cd>N</synonym_cd>
<visualattributes>FA </visualattributes>
<totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true" />
<basecode>Local Concept::16559</basecode>
<facttablecolumn>concept_cd</facttablecolumn>
<tablename>concept_dimension</tablename>
<columnname>concept_path</columnname>
<columndatatype>T</columndatatype>
<operator>like</operator>
<dimcode>\i2b2\TDM & TOXICOLOGY STUDIES{color:#0000ff}</dimcode>
<tooltip>TDM & TOXICOLOGY STUDIES</tooltip>
</concept>
<concept>
<level>1</level>
<key>
TRANSPLANT/ STEM CELL LEUKEMIA\i2b2\TRANSPLANT/ STEM CELL
LEUKEMIA\
</key>
<name>TRANSPLANT/ STEM CELL LEUKEMIA</name>
<synonym_cd>N</synonym_cd>
<visualattributes>FA </visualattributes>
<totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true" />
<basecode>Local Concept::26106</basecode>
<facttablecolumn>concept_cd</facttablecolumn>
<tablename>concept_dimension</tablename>
<columnname>concept_path</columnname>
<columndatatype>T</columndatatype>
<operator>like</operator>
<dimcode>\i2b2\TRANSPLANT/ STEM CELL LEUKEMIA{color:#0000ff}</dimcode>
<tooltip>TRANSPLANT/ STEM CELL LEUKEMIA</tooltip>
</concept>
<concept>
<level>1</level>
<key>
TREE POSITION NOT ESTABLISHED\i2b2\TREE POSITION NOT ESTABLISHED
\
</key>
<name>TREE POSITION NOT ESTABLISHED</name>
<synonym_cd>N</synonym_cd>
<visualattributes>FA </visualattributes>
<totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true" />
<basecode>Local Concept::30719</basecode>
<facttablecolumn>concept_cd</facttablecolumn>
<tablename>concept_dimension</tablename>
<columnname>concept_path</columnname>
<columndatatype>T</columndatatype>
<operator>like</operator>
<dimcode>\i2b2\TREE POSITION NOT ESTABLISHED{color:#0000ff}</dimcode>
<tooltip>TREE POSITION NOT ESTABLISHED</tooltip>
</concept>
<concept>
<level>1</level>
<key>\\URINALYSIS:\i2b2\URINALYSIS:{color:#0000ff}</key>
<name>URINALYSIS:</name>
<synonym_cd>N</synonym_cd>
<visualattributes>FA </visualattributes>
<totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true" />
<basecode>Local Concept::16544</basecode>
<facttablecolumn>concept_cd</facttablecolumn>
<tablename>concept_dimension</tablename>
<columnname>concept_path</columnname>
<columndatatype>T</columndatatype>
<operator>like</operator>
<dimcode>\i2b2\URINALYSIS:{color:#0000ff}</dimcode>
<tooltip>URINALYSIS:</tooltip>
</concept>
<concept>
<level>1</level>
<key>
URINE STUDIES\i2b2\URINE STUDIES{color:#0000ff}</key>
<name>URINE STUDIES</name>
<synonym_cd>N</synonym_cd>
<visualattributes>FA </visualattributes>
<totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true" />
<basecode>Local Concept::16969</basecode>
<facttablecolumn>concept_cd</facttablecolumn>
<tablename>concept_dimension</tablename>
<columnname>concept_path</columnname>
<columndatatype>T</columndatatype>
<operator>like</operator>
<dimcode>\i2b2\URINE STUDIES{color:#0000ff}</dimcode>
<tooltip>URINE STUDIES</tooltip>
</concept>
<concept>
<level>1</level>
<key>
Visit Details\i2b2\Visit Details{color:#0000ff}</key>
<name>VISIT DETAILS</name>
<synonym_cd>N</synonym_cd>
<visualattributes>CA </visualattributes>
<totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true" />
<facttablecolumn>concept_cd</facttablecolumn>
<tablename>concept_dimension</tablename>
<columnname>concept_path</columnname>
<columndatatype>T</columndatatype>
<operator>LIKE</operator>
<dimcode>\i2b2\Visit Details{color:#0000ff}</dimcode>
<tooltip>VISIT DETAILS</tooltip>
</concept>
<concept>
<level>1</level>
<key>\\VITALS\i2b2\VITALS{color:#0000ff}</key>
<name>VITALS</name>
<synonym_cd>N</synonym_cd>
<visualattributes>FA </visualattributes>
<totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true" />
<basecode>Local Concept::64</basecode>
<facttablecolumn>concept_cd</facttablecolumn>
<tablename>concept_dimension</tablename>
<columnname>concept_path</columnname>
<columndatatype>T</columndatatype>
<operator>like</operator>
<dimcode>\i2b2\VITALS{color:#0000ff}</dimcode>
<tooltip>VITALS</tooltip>
</concept>
</ns6:concepts>
</message_body>

From: Phillips, Lori C. [LCPHILLIPS.PARTNERS] Sent: Thursday, October 27, 2011 10:29 AM To: Lisa Miao Subject: RE: search by name
I meant the XML message history – are you running web client or workbench ?
Is there an XML message for get_categories? what does the response look like?
You dont see a request for the (outgoing) search message?

From: Lisa Miao [lmiao.regenstrief] Sent: Thursday, October 27, 2011 10:24 AM To: Phillips, Lori C. Subject: RE: search by name
After I hit the "Find" button, nothing happened. There is nothing in the XML message history either.
Is that what you meant by "sent/recvd messages on the clinet"? Where do I see those?
Thanks,
Lisa.

From: Phillips, Lori C. [LCPHILLIPS.PARTNERS] Sent: Thursday, October 27, 2011 10:19 AM To: Lisa Miao Subject: RE: search by name
Let me look at the code and figure out why you are not getting any categories.
If there is anything in the log related to this let me know.
The sent/recvd messages on the client == what do you see ? Also = does the client say "working" only or do you get "No terms were found"
Lori

From: Lisa Miao [lmiao.regenstrief] Sent: Thursday, October 27, 2011 10:12 AM To: Phillips, Lori C. Subject: RE: search by name
What's the query that will be executed when we do "search by name"? Perhaps I could try to run those query and see why it is NOT returning anything?
Thanks,
Lisa.

From: Phillips, Lori C. [LCPHILLIPS.PARTNERS] Sent: Thursday, October 27, 2011 10:03 AM To: Lisa Miao Subject: RE: search by name
Lisa
You arent going to find anything in log related to "search by name"
Try looking for "ERROR" around the time you made the query - or - look for the name (word) you searched for.
I am looking at your file... When I designed this I did not anticipate that the c_table_cd would be a phrase.
I will have to investigate if this is the issue or not. Which terms are showing up twice?
And you say these entries were working in RC5? In RC5 did the categories show up under Any category?
Thanks
Lori

From: Lisa Miao [lmiao.regenstrief] Sent: Thursday, October 27, 2011 9:49 AM To: Phillips, Lori C. Subject: RE: search by name
Thank you so much Lori!
We are using oracle server.
There is NO messages in the server.log when I do "search by name". I suspect it's just nothing has been brought back. This makes it harder to debug, since I don't know what's going on behind the scene.
I have attached our table_access data. The data in c_dimcode and c_tooltip may not be exactly what we want (there're some name double showing), but I think that won't affect this, will it? (I can fix it if necessary).
Thanks,
Lisa.

From: Phillips, Lori C. [LCPHILLIPS.PARTNERS] Sent: Thursday, October 27, 2011 9:40 AM
To: Lisa Miao Subject: RE: search by name
Hi Lisa,
Could you tell me if there is anything in the jboss server log related to this?
Is your database Oracle or SQLServer?
Can you also send me your table_access entries?
Lori

From: Lisa Miao [lmiao.regenstrief] Sent: Wednesday, October 26, 2011 3:25 PM To: Phillips, Lori C. Subject: search by name
Lori,
In RC5, the search by name (under Find Terms tab) had been working for us. When we installed Release1.6, this stopped working. I'm trying to figure out why.
There is the drop down (on the right handside of the find button), for ours, it only has "Any Category"; for the i2b2demo system, it has a few more below "Any Category", such as "Clinical Trials", "Custom Metadata:, etc.
I have removed all entries in the table_access (of the original data), and made it up of our own data. It seems to have shown up in the term tree ok, but I'm wondering if there is other requirements (that breaks the search by name).
Could you pelase help?
Thanks,
Lisa.

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From: Michael.C.Ford.kp Sent: Monday, November 07, 2011 4:09 PM To: Shah, Nimit M. Cc: i2b2 AUG Members Subject: Re: i2b2 mysql
You could pull mysql-connector-java-5.1.7-bin.jar drop in the lib and then db.driver=org.gjt.mm.mysql.Driver
but as another stated it would have trouble with stored procedures if there are any.

From: Shah, Nimit M. Sent: Monday, November 07, 2011 4:07 PM To: John Kilian; Andrew J. McMurry Cc: i2b2 AUG Members Subject: RE: i2b2 mysql
Thanks for the info. I will give sqlserver a try.
Nimit

From: John Kilian [Jkilian.harthosp] Sent: Monday, November 07, 2011 3:57 PM To: Andrew J. McMurry; Shah, Nimit M. Cc: i2b2 AUG Members Subject: Re: i2b2 mysql
I believe the reason you can not simply plug and play a set of database options is because the client uses proprietary (harvard) code to get at the data sources.
Right now I am having a class loading issue when I try to use SqlServer:
13:07:50,999 ERROR [QueryService] Throwable java.lang.NoClassDefFoundError: edu/harvard/i2b2/crc/datavo/CRCJAXBUtil
Where does this class live? Is it new to 1.6? I am still running 1.5, and get this problem. Not sure in i2b2 links dictate use of a class that is not in 1.5.
John Kilian, RN, BSCS, BSED Senior Distributed Applications Programmer/Analyst Hartford Hospital

"McMurry, Andrew J." <Andrew_McMurry.hms.harvard> 11/7/2011 3:51 PM
There isn't a MySQL version – the lack of real stored procedures makes MySQL query optimization really tough.
There have been attempts at this before with varying degrees of success, though to my knowledge, no one has MySQL i2b2 running in production
hope this helps,
andy

On Nov 7, 2011, at 3:43 PM, Shah, Nimit M. wrote:
Hi,
I am trying to get i2b2 to work with mysql on a linux machine. The Data_Installation_Guide states that in order to load data, I have to modify db.properties within edu.harvard.i2b2.data/Release_ 1-6/NewInstall/Metadata. However, these instructions were made primarily for oracle and sql server. Does anyone have an idea what the following properties should be for mysql?
db.server=localhost:1521:xe db.driver=oracle.jdbc.driver.OracleDriver db.url=jdbc:oracle:thin:@localhost:1521.xe
Thank you
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: Mendis, Michael E. Sent: Tuesday, November 08, 2011 9:25 AM To: Murphy, Shawn N.; Dat Q. Phan; i2b2 AUG Members Cc: Donahoe, Janice M Subject: Re: Error in create_sqlserver_i2b2pm_tables.sql
Thanks johnny, updated the pm install scripts and will be in the next minor release.
Thanks again
mike

On 11/7/11 7:00 PM, "Murphy, Shawn N." <SNMURPHY.PARTNERS> wrote:
Thanks Johnny.

From: Dat Q. Phan [Dat.Q.Phan.uth.tmc] Sent: Monday, November 07, 2011 12:43 PM To: i2b2 AUG Members Subject: Error in create_sqlserver_i2b2pm_tables.sql
I'm not sure if this has been reported yet, but in the create_sqlserver_i2b2pm_tables.sql script it should be VARCHAR and not VARCHAR2 for 'CREATE TABLE PM_APPROVALS', 'CREATE TABLE PM_APPROVALS_PARAMS', and 'CREATE TABLE PM_PROJECT_REQUEST'.
Johnny Phan Programmer Analyst II UTHealth School of Biomedical Informatics Dat.Q.Phan.uth.tmc

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From: Brian Ostasiewski [bostasie.wakehealth] Sent: Tuesday, November 08, 2011 2:41 PM To: i2b2 AUG Members members Subject: ontology c_operator values
Can the ontology c_operator/c_dimcode combo handle the case where I want to query a dimension column for IS NULL? I don't see this mentioned in the design doc, so I'm thinking I'll have to default the nulls to some "unknown" value?
Brian

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From: Murphy, Shawn N. Sent: Tuesday, November 08, 2011 6:27 PM To: John Hook; Jack London; i2b2 AUG Members Subject: RE: v1.6.01 release notes?
Thanks John,
Known issues are on the Community Wiki for the Full Releases.
Thanks, Shawn.
From: John Hook [jhook.regenstrief] Sent: Tuesday, November 08, 2011 11:23 AM To: Jack London; i2b2 AUG Members members Cc: Murphy, Shawn N. Subject: RE: v1.6.01 release notes?
The 1.6.01 release notes are available in the upper right corner of the download page.
https://www.i2b2.org/software/#downloadables
John

From: Jack London [jack.london.KimmelCancerCenter] Sent: Tuesday, November 08, 2011 11:08 AM To: i2b2 AUG Members members Cc: Shawn N. Murphy Subject: v1.6.01 release notes?
I just unzipped the i2b2core-doc-16.zip file on the software distribution site
no "Release Notes" or "Known Issues" documents.
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: Patibandla, Nandan [Nandan.Patibandla.childrens.harvard] Sent: Wednesday, November 09, 2011 3:26 PM To: i2b2 AUG Members Subject: SQL Server 2005 SP4
Hi,
We are using i2b2 version 1.5 and also v1.6.
We are planning on applying SQL Server 2005 SP4 patch to the i2b2 database severs. I just want to know whether there are any addressed issues with this patch.
Thank you
Nandan

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From: Russ Waitman [rwaitman.kumc] Sent: Thursday, November 10, 2011 3:55 PM To: Matvey Palchuk Cc: i2b2 AUG Members; schuffr.ohsu Subject: Re: Medications hierarchy?
Matvey, Thank you very much for the reference.
russ

From: Law, James [jlaw.med.umich] Sent: Thursday, November 10, 2011 10:48 AM To: Robert Schuff; i2b2 AUG Members Subject: RE: Medications hierarchy?
Robert-
Our medications are coded to First Data Bank (FDB). FDB provides a unique key for each set of ingredients used in a medication (HICL_SEQNO is what FDB calls this key). We use this as our concept leaf node. This has the effect of making 2 chemically equivalent drugs (for instance wellbutrin and xyban) return the same number of patients, regardless of what the user selects from the ontology tree. This prevents the user from having to find all the chemically equivalent or brand names for a specific formulation. We have found that most of our research data requests are not concerned with brand names vs. generic, so we've modeled our i2b2 meds given this fact.
I've attached a snapshot of our ontology.
As far as the tree, we had a version based on the FDB enhanced therapeutic classification system, but it was decided that it didn't really help people find the drug any faster, so we went with the alphabetic version.
As far as RXNorm... While we do have mapping tables provided by FDB, we don't have a current multi-site project using meds (yet), but when the time comes we will likely use these mappings.
Thanks,
James

Matvey Palchuk <MPalchuk.recomdata> 11/10/2011 9:36 AM
We developed an RxNorm/NDF-RT hierarchy for SHRINE at Harvard Catalyst. It was subsequently refined - see citation below.
We used VA product classes - something the VA folks were not happy about. Apparently they are focusing on things like Mechanism of Action and such for FDA structured labeling, and not maintaining the therapeutic classification.
I am not sure about AHFS - believe the sell a mapping to RxNorm.
Matvey
AMIA Annu Symp Proc. 2010; vol. 2010 pp. 577-81
Enabling Hierarchical View of RxNorm with NDF-RT Drug Classes.
Palchuk MB, Klumpenaar M, Jatkar T, Zottola RJ, Adams WG, Abend AH
NDF-RT is the proposed source of drug classification information. We set out to construct a hierarchy of NDF-RT drug classes and RxNorm medications and evaluate it on medication records data. NDFRT and RxNorm are distributed in different file formats, require different tools to manipulate and linking the two into a hierarchy is a non-trivial exercise. Medication data in RxNorm from two institutions was constrained by the hierarchy. Only 37% of records from one and 65% from another institution were accessible. We subsequently enriched the RxNorm mapping in NDF-RT by exploiting relationships between concepts for branded and generic drugs. Coverage improved dramatically to 93% for both institutions. To improve usability of the resulting hierarchy, we grouped clinical drugs by corresponding clinical drug form.
PMID: 21347044
PMCID: PMC3041416 URL -http://www.ncbi.nlm.nih.gov/pubmed/21347044?dopt=Citation

From: Robert Schuff [schuffr.ohsu] Sent: Thursday, November 10, 2011 2:28 AM To: i2b2 AUG Members Subject: Medications hierarchy?
Hi folks,
I am curious what you all are using for your meds hierarchy and encoding. So far we've just populated using med orders, but we'll also soon be including medication list data. As our first cut we've just used the very basic hierarchy contained within our epic installation which is
Pharm Class
Pharm Subclass
Drug Name
This is a bit sub-optimal so we're investigating other options. Although I haven't validated it fully yet, it appears that there may be a mapping done to UDDF which may get us to a hierarchy through RxNorm. Is there an emerging standard ontology used in i2b2 for meds?
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: Jack London [jack.london.KimmelCancerCenter] Sent: Friday, November 11, 2011 10:48 AM To: i2b2 AUG Members members Subject: oracle and jboss startups
We have noticed that after re-booting our i2b2 VM, we often have queries fail initially. But if we re-start jboss, things work properly.
We wonder whether it's possible that oracle is not completely up and running when jboss re-starts on booting, such that jboss does not properly start up. Anyone have comments on this? Has anyone else observed these problems upon re-booting?
Jack

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From: Murphy, Shawn N. Sent: Friday, November 04, 2011 3:05 PM To: Peter Beninato; Brian Ostasiewski; i2b2 AUG Members Subject: RE: Clarification of CRC apostrophe temporary fix
Yes, sorry if I was confusing about this, and thanks to Brian for clarifying, 1.6.01 gets everything back to "normal".
Thanks,
Shawn.
From: Peter Beninato [beninato.ohsu] Sent: Friday, November 04, 2011 12:41 PM To: Brian Ostasiewski; i2b2 AUG Members Subject: RE: Clarification of CRC apostrophe temporary fix
Ah. Great! Thanks for the clarification.

From: Brian Ostasiewski [bostasie.wakehealth] Sent: Friday, November 04, 2011 9:21 AM To: i2b2 AUG Members Subject: RE: Clarification of CRC apostrophe temporary fix
The fix makes 1.6 behave like all the previous versions behaved. Backward compatibility with existing databases is nice to have when dealing with a warehouse this size.

From: Peter Beninato [beninato.ohsu] Sent: Friday, November 04, 2011 11:21 AM To: Murphy, Shawn N.; Lisa Miao; i2b2 AUG Members Subject: RE: Clarification of CRC apostrophe temporary fix
I have a concern that the fix for this issue, might cause problems for others who understand that in order for a single quote to be represented in a data column it might be necessary to escape the single quotes. In the case of Oracle by including two single quotes in a script, and if this embedded SQL needed to be executed dynamically sometimes it is necessary to add additional escapes.
Might the fix introduce other unintended consequences?
Maybe there shouldn't be a fix, but just a better understanding of how to format the embedded SQL is sufficient?
Peter

From: Murphy, Shawn N. [SNMURPHY.PARTNERS] Sent: Friday, November 04, 2011 7:15 AM To: Lisa Miao; i2b2 AUG Members Subject: RE: Clarification of CRC apostrophe temporary fix
Hi Lisa,
There are some other columns in the ontology table used to construct the sql query such as the c_columnname and c_operator columns although they are less like perhaps to have apostrophes. Other columns that are not used to construct the CRC query are unlikely to be impacted, although some ontology cell (find) queries had a similar problem.
Please note that a fix is out for these issues.
Thanks,
Shawn.

From: Lisa Miao [lmiao.regenstrief] Sent: Monday, October 31, 2011 10:35 AM To: Murphy, Shawn N.; i2b2 AUG Members Subject: RE: Clarification of CRC apostrophe temporary fix
Shawn,
Just double checking here, in addition to i2b2.c_dimcode column, there're a few other columns where apostrophe could show up (and I believe some of them will show up in the SQL query as well), such as i2b2.c_fullname, i2b2.c_dimcode, i2b2.c_tooltip, concept_dimension.concept_path, provider_dimension.provider_path, etc. Should we replace in all these occurrences of apostrophe (with double apostrophe), or is there a list of columns that we should do the replacement?
Thanks,
Lisa.

From: Murphy, Shawn N. [SNMURPHY.PARTNERS] Sent: Friday, October 28, 2011 8:03 PM To: i2b2 AUG Members Subject: Clarification of CRC apostrophe temporary fix
Hi All,
Sorry, the first temporary fix should read (better):
CRC: Need to escape apostrophe in SQL Statements
Temporary fix: Put two single apostrophes in place of one in the c_dimcode column entries where concept_dimension and provider_dimension are the entries in the c_tablename columns in the Ontology Cell table(s).
This is good for getting a few apostrophe entries working if one really needs them before 1.6.01 gets out.
Thanks,
Shawn.

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From: Seth Lenzi [slenzi.gmail] Sent: Monday, November 07, 2011 12:35 PM To: Phillips, Lori C. Cc: Jack London; i2b2 AUG Members Subject: Re: New i2b2 Install, Web Client not connecting...
Looks like things might be working now! I found in the Jboss log file that it was complaining about certain JNDI datasource names not being bound correctly. In the Ontology data source config file (ont-ds.xml) and Workplace data source config file (work-ds.xml) I had the datasource names misspelled. They were "WorkplaceBootStrapDS_Oracle" and "OntologyBootStrapDS_Oracle". I needed to removed the "_Oracle" part from the names. I then was able to successfully log into the web client.
Thanks for all your help!
Seth

From: John Kilian [Jkilian.harthosp] Sent: Monday, November 07, 2011 1:35 PM To: Seth Lenzi; Christopher P Heilala; Phillips, Lori C. Cc: i2b2 AUG Members Subject: RE: New i2b2 Install, Web Client not connecting...
I updated the property files with the dbo suffix, and now I am able to execute against the database. But the next thing I get is a class not found error: (See bolded trace below) (Note: I am still running 1.5) Is a jar missing?
13:07:42,532 DEBUG [DataSourceUtils] Returning JDBC Connection to DataSource 13:07:42,532 DEBUG [JdbcTemplate] Executing SQL query [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, valuetype_cd , c_metadataxml, c_comment from i2b2metadata.dbo.i2b2 where c_fullname like ? and c_hlevel = ? and c_visualattributes not like '_H%' and c_synonym_cd = 'N' order by c_name ] 13:07:42,532 DEBUG [DataSourceUtils] Fetching JDBC Connection from DataSource 13:07:42,533 DEBUG [StatementCreatorUtils] Setting SQL statement parameter value: column index 1, parameter value [\i2b2\Demographics\Gender%], value class [java.lang.String], SQL type unknown 13:07:42,533 DEBUG [StatementCreatorUtils] Setting SQL statement parameter value: column index 2, parameter value [3], value class [java.lang.Integer], SQL type unknown 13:07:42,569 DEBUG [DataSourceUtils] Returning JDBC Connection to DataSource 13:07:42,569 DEBUG [ConceptDao] result size = 3 13:07:50,998 DEBUG [QueryService] Inside setfinder request <ns6:request xmlns:ns2 ="http://www.i2b2.org/xsd/hive/pdo/1.1/" xmlns:ns4="http://www.i2b2.org/xsd/cell/crc/psm/1.1/" xmlns:ns3="http://www.i2b2.org/xsd/cell/crc/pdo/1.1/" xmlns:ns5 ="http://www.i2b2.org/xsd/hive/plugin/" xmlns:ns6="http://www.i2b2.org/xsd/hive/msg/1.1/" xmlns:ns7 ="http://www.i2b2.org/xsd/cell/ont/1.1/" xmlns:ns8 ="http://www.i2b2.org/xsd/cell/crc/psm/querydefinition/1.1/">
<message_header> <proxy> <redirect_url>http://10.16.248.168/i2b2/rest/QueryToolService/request</redirect_url> </proxy>
<sending_application> <application_name>i2b2_QueryTool</application_name>
<application_version>0.2</application_version> </sending_application> <sending_facility>
<facility_name>PHS</facility_name> </sending_facility> <receiving_application>
<application_name>i2b2_DataRepositoryCell</application_name>
<application_version>0.2</application_version> </receiving_application> <receiving_facility>
<facility_name>PHS</facility_name> </receiving_facility> <security>
<domain>i2b2demo</domain> <username>i2b2</username> <password token_ms_timeout="1800000" is_token="true">
SessionKey:5IMbpG7K5cRfo9f2JnL1</password> </security> <message_type>
<message_code>Q04</message_code>
<event_type>EQQ</event_type> </message_type> <message_control_id>
<message_num>9W65Q5Cx987ELm1ZyAIq8</message_num>
<instance_num>0</instance_num> </message_control_id> <processing_id>
<processing_id>P</processing_id>
<processing_mode>I</processing_mode> </processing_id> <accept_acknowledgement_type>messageId</accept_acknowledgement_type> <project_id>Demo</project_id>
</message_header> <request_header>
<result_waittime_ms>180000</result_waittime_ms> </request_header> <message_body>
<ns4:psmheader> <user group="Demo" login="i2b2">i2b2</user> <patient_set_limit>0</patient_set_limit> <estimated_time>0</estimated_time> <request_type>CRC_QRY_runQueryInstance_fromQueryDefinition</request_type>
</ns4:psmheader> <ns4:request xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ns4:query_definition_requestType">
<query_definition> <query_name>Female.18:24:33</query_name> <specificity_scale>0</specificity_scale> <panel>
<panel_number>1</panel_number> <invert>0</invert> <total_item_occurrences>1</total_item_occurrences> <item>
<hlevel>3</hlevel> <item_name>Female</item_name> <item_key>\\i2b2\i2b2\Demographics\Gender\Female\</item_key> <tooltip>Demographic \ Gender \ Female</tooltip> <class>ENC</class> <constrain_by_date> </constrain_by_date> <item_icon>LA</item_icon> <item_is_synonym>false</item_is_synonym>
</item> </panel> </query_definition>
<result_output_list><result_output priority_index="1" name="patient_count_xml" /></result_output_list> </ns4:request>
</message_body> </ns6:request> 13:07:50,999 ERROR [QueryService] Throwable
java.lang.NoClassDefFoundError: edu/harvard/i2b2/crc/datavo/CRCJAXBUtil
at edu.harvard.i2b2.crc.delegate.setfinder.QueryRequestDelegate.handleRequest(QueryRequestDelega te.java:59)
at edu.harvard.i2b2.crc.axis2.QueryService.handleRequest(QueryService.java:129) at edu.harvard.i2b2.crc.axis2.QueryService.request(QueryService.java:67) 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.apache.axis2.receivers.RawXMLINOutMessageReceiver.invokeBusinessLogic(RawXMLINOutMe ssageReceiver.java:88)
at org.apache.axis2.receivers.AbstractInOutSyncMessageReceiver.receive(AbstractInOutSyncMessage Receiver.java:39)
at org.apache.axis2.engine.AxisEngine.receive(AxisEngine.java:493) at org.apache.axis2.transport.http.util.RESTUtil.invokeAxisEngine(RESTUtil.java:153) at org.apache.axis2.transport.http.util.RESTUtil.processPostRequest(RESTUtil.java:102) at org.apache.axis2.transport.http.AxisRESTServlet.doPost(AxisRESTServlet.java:66) at javax.servlet.http.HttpServlet.service(HttpServlet.java:710) at javax.servlet.http.HttpServlet.service(HttpServlet.java:803) at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.jboss.web.tomcat.filters.ReplyHeaderFilter.doFilter(ReplyHeaderFilter.java:96) at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:230) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:175) at
org.jboss.web.tomcat.security.SecurityAssociationValve.invoke(SecurityAssociationValve.java:179) at org.jboss.web.tomcat.security.JaccContextValve.invoke(JaccContextValve.java:84) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102) at
org.jboss.web.tomcat.service.jca.CachedConnectionValve.invoke(CachedConnectionValve.java:157) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:262) at org.apache.coyote.ajp.AjpProcessor.process(AjpProcessor.java:437) at org.apache.coyote.ajp.AjpProtocol$AjpConnectionHandler.process(AjpProtocol.java:366) at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:446) at java.lang.Thread.run(Thread.java:619)
13:07:51,002 ERROR [AxisRESTServlet] java.lang.NullPointerException 13:08:09,393 DEBUG [IdleRemover] run: IdleRemover notifying pools, interval: 30000 13:08:39,911 DEBUG [IdleRemover] run: IdleRemover notifying pools, interval: 30000 13:09:10,431 DEBUG [IdleRemover] run: IdleRemover notifying pools, interval: 30000 13:09:40,893 DEBUG [IdleRemover] run: IdleRemover notifying pools, interval: 30000 13:09:42,620 DEBUG [arjLogger] Periodic recovery - first pass <Mon, 7 Nov 2011 13:09:42> 13:09:42,620 DEBUG [arjLogger] StatusModule: first pass 13:09:42,621 DEBUG [txojLoggerI18N] [com.arjuna.ats.internal.txoj.recovery.TORecoveryModule_3]
TORecoveryModule - first pass 13:09:42,621 DEBUG [loggerI18N] [com.arjuna.ats.internal.jta.recovery.info.firstpass] Local XARecoveryModule - first pass 13:09:52,799 DEBUG [arjLogger] Periodic recovery - second pass <Mon, 7 Nov 2011 13:09:52> 13:09:52,799 DEBUG [arjLogger] AtomicActionRecoveryModule: Second pass 13:09:52,800 DEBUG [txojLoggerI18N] [com.arjuna.ats.internal.txoj.recovery.TORecoveryModule_6]
TORecoveryModule - second pass 13:09:52,800 DEBUG [loggerI18N] [com.arjuna.ats.internal.jta.recovery.info.secondpass] Local XARecoveryModule - second pass 13:10:11,421 DEBUG [IdleRemover] run: IdleRemover notifying pools, interval: 30000 13:10:41,912 DEBUG [IdleRemover] run: IdleRemover notifying pools, interval: 30000
John Kilian, RN, BSCS, BSED
Senior Distributed Applications Programmer/Analyst Hartford Hospital W:(860)545-4213

"Heilala, Christopher P" <HEILALA.CHRISTOPHER.mcrf.mfldclin > 11/7/2011 9:42 AM
Seth,
Sorry, I mislead you to the right spot to add the dbo. prefix for the i2b2hive schema name.
You will want to open the **.properties file (crc, pm, ont, etc.) within the JBOSS_HOME \edu.harvard.i2b2.**\etc\spring directory and add the dbo. Under the 'DataSource Lookup Properties' section. Here's an example from the crc.properties file:

Datasource Lookup properties

queryprocessor.ds.lookup.datasource=CRCDataSourceLookup
queryprocessor.ds.lookup.servertype=SQLSERVER
queryprocessor.ds.lookup.schemaname=i2b2hive.dbo
Sorry for the inconvenience, and I hope this helps. Again, you'll need to rebuild and deploy your solutions.
Chris

On Mon, Nov 7, 2011 at 11:55 AM, Phillips, Lori C. <LCPHILLIPS.partners> wrote:
I think its complaining about your datasource configuration.
Does your ONT_DB_LOOKUP table look correct? Does the C_DB_DATASOURCE column match your ont-ds.xml config file datasource name?

From: Seth Lenzi [slenzi.gmail] Sent: Monday, November 07, 2011 11:40 AM To: Jack London Cc: i2b2 AUG Members members Subject: Re: New i2b2 Install, Web Client not connecting...
Jack,
I edited the values in the tables like you specified and it looks like some progress has been made. I am getting a different error message now from Firebug. Looks like it's related to the GetSchemes call on the OntologyService. It says, "The cell's status message could not be understood."
This might be the problem? I can try redeploying the Ontology Service again...
soapenv:Fault xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/"><faultcode> soapenv:Client</faultcode><faultstring>Servicelocator.getDBDataSource; nested exception is: edu.harvard.i2b2.common.exception.I2B2Exception: Servicelocator.getDBDataSource; nested exception is: org.apache.axis2.AxisFault: Servicelocator.getDBDataSource; nested exception is: edu.harvard.i2b2.common.exception.I2B2Exception: Servicelocator.getDBDataSource</faultstring><detail /></soapenv:Fault>
Seth
[AJAX RESULT i2b2.ONT.ajax.GetSchemes] AJAX Transport SUCCESS i2b2_c...ator.js (line 257)
headerJSON null
readyState 4
request klass { options={...}, transport=XMLHttpRequest, url="index.php", more...}
responseJSON null
responseText "<soapenv:Fault xmlns:so...tail /></soapenv:Fault>"
responseXML Document
status 200
statusText "OK"
transport XMLHttpRequest { responseXML=document, responseText="<soapenv:Fault xmlns:so...tail /></soapenv:Fault>", response="<soapenv:Fault xmlns:so...tail /></soapenv:Fault>", more...}
_getHeaderJSON function()
_getResponseJSON function()
getAllHeaders function()
getAllResponseHeaders function()
getHeader function()
getResponseHeader function()
getStatus function()
getStatusText function()
initialize function()
_proto_ klass { status=0, initialize=function(), statusText="", more...} <soapenv:Fault xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/"><faultcode> soapenv:Client</faultcode><faultstring>Servicelocator.getDBDataSource; nested exception is: edu.harvard.i2b2.common.exception.I2B2Exception: Servicelocator.getDBDataSource; nested exception is: org.apache.axis2.AxisFault: Servicelocator.getDBDataSource; nested exception is: edu.harvard.i2b2.common.exception.I2B2Exception: Servicelocator.getDBDataSource</faultstring><detail /></soapenv:Fault> _defaultCallbackOK()i2b2_c...ator.js (line 295) transport = klass { request=klass, transport=XMLHttpRequest, readyState=4, more...} respondToReadyState()prototype.js (line 1311) readyState = 4 onStateChange()prototype.js (line 1254) bind()prototype.js (line 210) console.error(transport.responseText); i2b2_c...ator.js (line 295) i2b2_c...ator.js (line 256) CALLBACK Processing AJAX i2b2CellMsg
error true
errorMsg "The cell's status message could not be understood."
errorStatus
msgParams Object { proxy_info="<proxy>\n <re..._url>\n </proxy>\n", sec_user="i2b2", sec_pass_node="<password token_ms_time...RSTLYMU5nIoB</password>", more...}
header_msg_datetime "2011-11-07T11:30:49-05:00"
header_msg_id "F6E4QgH18Lz0K57Li2d6U"
proxy_info "<proxy> <redirect_url> http://cancors.dfci.harvard.edu:8181/i2b2/rest/OntologyService/getSchemes</redirect_url> </proxy> "
result_wait_time "180"
sec_domain "i2b2demo"
sec_pass_node "<password token_ms_timeout="1800000" is_token="true"> SessionKey:7OpvPZmzRSTLYMU5nIoB</password>"
sec_project "Demo"
sec_user "i2b2"
msgRequest String { 0="<", 1="?", 2="x", more...}
msgResponse "<soapenv:Fault xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/"><faultcode> soapenv:Client</faultcode><faultstring>Servicelocator.getDBDataSource; nested exception is: edu.harvard.i2b2.common.exception.I2B2Exception: Servicelocator.getDBDataSource; nested exception is: org.apache.axis2.AxisFault: Servicelocator.getDBDataSource; nested exception is: edu.harvard.i2b2.common.exception.I2B2Exception: Servicelocator.getDBDataSource</faultstring><detail /></soapenv:Fault>"
msgUrl "http://cancors.dfci.harvard.edu:8181/i2b2/rest/OntologyService/getSchemes"
proxyUrl "index.php"
refXML Document
timeEnd Date {Mon Nov 07 2011 11:30:50 GMT-0500 (Eastern Standard Time)}
timeStart Date {Mon Nov 07 2011 11:30:49 GMT-0500 (Eastern Standard Time)}
parse function()
I2B2PM.PM_CELL_DATA: "CELL_ID" "PROJECT_PATH" "NAME" "METHOD_CD" "URL" "CAN_OVERRIDE" "CHANGE_DATE" "ENTRY_DATE" "CHANGEBY_CHAR" "STATUS_CD" "CRC" "/" "Data Repository" "REST" "http://cancors.dfci.harvard.edu:8181/i2b2/rest/QueryToolService/" "1" "" "" "" "A" "FRC" "/" "File Repository " "SOAP" "http://cancors.dfci.harvard.edu:8181/i2b2/services/FRService/" "1" "" "" "" "A" "ONT" "/" "Ontology Cell" "REST" "http://cancors.dfci.harvard.edu:8181/i2b2/rest/OntologyService/" "1" "" "" "" "A" "WORK" "/" "Workplace Cell" "REST" "http://cancors.dfci.harvard.edu:8181/i2b2/rest/WorkplaceService/" "1" "" "" "" "A"

From: Heilala, Christopher P [HEILALA.CHRISTOPHER.mcrf.mfldclin] Sent: Monday, November 07, 2011 9:21 AM To: Seth Lenzi Cc: i2b2 AUG Members members Subject: RE: New i2b2 Install, Web Client not connecting...
Also, be cautious when using port 8181...Most Anti-Virus software like to use that port. Try opening an IE browser window from the server and enter in the following URL: http://localhost:8181 and see what you get. If you get an AV log window, then you might want to change the port that you have i2b2 installed to run on.
Chris

From: Jack London [jack.london.KimmelCancerCenter] Sent: Monday, November 07, 2011 8:19 AM To: Seth Lenzi Cc: i2b2 AUG Members members Subject: Re: New i2b2 Install, Web Client not connecting...
Seth,
The "Available Services" page shows your configuration uses port 8181, not 9090. If this is so, you must also edit the entries in the database table I2B2PM.PM_CELL_DATA, changing the port number in the URL column from 9090 to 8181.
Jack

On Nov 7, 2011, at 9:09 AM, Heilala, Christopher P wrote:
Seth,
Are you using SQL Server 2008? If so, within each of the **-ds.xml files (crc, ont, pm, etc.), where you specify the 'schemaname', make sure to add the prefix 'dbo.' In front of the i2b2hive value...You will need to rebuild and deploy your solutions. This resolved the AJAX error for me. I can give you more detail if you need it.
Chris

From: Phillips, Lori C. [LCPHILLIPS.PARTNERS] Sent: Monday, November 07, 2011 8:03 AM To: Seth Lenzi Cc: i2b2 AUG Members Subject: RE: New i2b2 Install, Web Client not connecting...
Seth,
Unfortunately I am not the best person to help with web client errors; I am posting this to members to see if they can help.
You are welcome to try the Workbench however; its the thick client version of the web client and will help you determine if you are having a web client issue or server issue. Just modify the workbench.properties file to point to your instance of the hive.
Lori

From: Seth Lenzi [slenzi.gmail] Sent: Friday, November 04, 2011 4:45 PM To: Phillips, Lori C. Subject: Re: New i2b2 Install, Web Client not connecting...
Hi Lori,
I deployed the project management, ontology, data repository, workplace, and file repository packages. I checked to make sure all the services were up and running by going to /i2b2/services/listServices and it seems they are all there. Still getting the AJAX error, "an error has occurred in the Cell's AJAX library.".
For each of the packages I made sure to update the build.properties files to specify the location of jboss and the axis2.war directory. Before running the ant build files I also updated the /etc/spring property files to specify the paths to the services (updating domain name and port). Also, made sure to update the /etc/jboss/xxx.xml files and specified the connection params to the Oracle database.
I have not been using the i2b2WorkBench yet... Do I have to run this and configure some stuff before using the web client?
It's the same message in Firebug, "The cell's status message could not be understood.". It's trying to go to http://localhost:9090/i2b2/rest/QueryToolService/request and the only place I see this is in the web clients index.php page.
Seth
i2b2_c...ator.js (line 256)
CALLBACK Processing AJAX i2b2CellMsg
error
true
errorMsg
"The cell's status message could not be understood."
errorStatus
msgParams
Object { result_wait_time="180", crc_max_records="20", crc_sort_by="DATE", more...}
crc_max_records
"20" crc_sort_by "DATE" crc_sort_order "DESC" header_msg_datetime "2011-11-04T16:41:44-04:00" header_msg_id "S22SIb6G45Q3hG67c9756" proxy_info "<proxy> <redirect_url>http://localhost:9090/i2b2/rest/QueryToolService/request</redirect_url>
</proxy> " result_wait_time "180" sec_domain "i2b2demo" sec_pass_node "<password token_ms_time...5rHxL15BIwmn</password>" sec_project "Demo" sec_user "i2b2" msgRequest String { 0="<", 1="?", 2="x", more...} msgResponse ""
msgUrl
"http://localhost:9090/i2b2/rest/QueryToolService/request" proxyUrl "index.php" refXML Document timeEnd Date {Fri Nov 04 2011 16:41:44 GMT-0400 (Eastern Daylight Time)} timeStart Date {Fri Nov 04 2011 16:41:44 GMT-0400 (Eastern Daylight Time)} parse function()

Here is the list of services:
http://cancors.dfci.harvard.edu:8181/i2b2/axis2-web/images/asf-logo.gif http://cancors.dfci.harvard.edu:8181/i2b2/axis2-web/images/axis_l.jpg
Available services
OntologyService
Service EPR : http://cancors.dfci.harvard.edu:8181/i2b2/services/OntologyService Service REST epr : http://cancors.dfci.harvard.edu:8181/i2b2/rest/OntologyService
Service Description : OntologyService
Service Status : Active Available Operations
modifyChild
getSchemes
getCategories
deleteChild
getChildren
addChild
updateCRCConcept
getCodeInfo
getDirtyState
getTermInfo
getProcessStatus
getNameInfo

PMService
Service EPR : http://cancors.dfci.harvard.edu:8181/i2b2/services/PMService
Service REST epr : http://cancors.dfci.harvard.edu:8181/i2b2/rest/PMService
Service Description : PMService
Service Status : Active Available Operations
getVersion
getServices

WorkplaceService
Service EPR : http://cancors.dfci.harvard.edu:8181/i2b2/services/WorkplaceService Service REST epr : http://cancors.dfci.harvard.edu:8181/i2b2/rest/WorkplaceService
Service Description : WorkplaceService
Service Status : Active Available Operations
annotateChild
getFoldersByProject
deleteChild
getChildren
addChild
renameChild
moveChild
getFoldersByUserId

Version
Service EPR : http://cancors.dfci.harvard.edu:8181/i2b2/services/Version
Service REST epr : http://cancors.dfci.harvard.edu:8181/i2b2/rest/Version
Service Description : Version
Service Status : Active Available Operations
getVersion

QueryToolService
Service EPR : http://cancors.dfci.harvard.edu:8181/i2b2/services/QueryToolService
Service REST epr : http://cancors.dfci.harvard.edu:8181/i2b2/rest/QueryToolService
Service Description : QueryToolService
Service Status : Active Available Operations
publishDataRequest
request
getLoadDataStatusRequest
pdorequest

FRService
Service EPR : http://cancors.dfci.harvard.edu:8181/i2b2/services/FRService
Service REST epr : http://cancors.dfci.harvard.edu:8181/i2b2/rest/FRService
Service Description : FRService
Service Status : Active Available Operations
recvfileRequest
sendfileRequest
On Fri, Nov 4, 2011 at 3:12 PM, Seth Lenzi <slenzi.gmail> wrote:
OK, thanks again. I'll let you know when/if I succeed or if there are more problems.
Seth

On Fri, Nov 4, 2011 at 2:59 PM, Phillips, Lori C. <LCPHILLIPS.partners> wrote:
PFT is completely optional – you dont really need it.
Start with ontology and see if that comes up. If it works you will see a Navigate terms tree. Then proceed with the others.

From: Seth Lenzi [slenzi.gmail] Sent: Friday, November 04, 2011 2:56 PM
To: Phillips, Lori C. Subject: Re: New i2b2 Install, Web Client not connecting...
No, I haven't installed the Ontology Cell yet. I will do that! I did follow the data installation guide and install all the metadata and demo data in Oracle. All the users have been set up as well.
In addition to the ontology cell, should I also install all the following cells before accessing the web client?
Data Repository cell Workplace cell File repository cell PFT processing cell
Seth

On Fri, Nov 4, 2011 at 2:48 PM, Phillips, Lori C. <LCPHILLIPS.partners> wrote:
I was wondering if you had the wrong axis2 version...
Did you set up the Ontology cell yet? – that is what the url is trying to access.
In your setup the URL should be http://cancors.dfci.harvard.edu:8181/i2b2/rest/OntologyService/....
The URLs of the cells get configured in the PM / admin setup... some also show up in the config files when you set up each cell.
Why dont you try installing ONT, fix the URL and see if you get farther?
I assume your metadata and demodata tables have been set up?
Lori

From: Seth Lenzi [slenzi.gmail] Sent: Friday, November 04, 2011 2:39 PM To: Phillips, Lori C. Subject: Re: New i2b2 Install, Web Client not connecting...
Hi Lori, I made some progress. Looks like I was using axis2 v1.5.5 instead of version 1.1 which is what the docs specify. After installing axis2 v1.1 and redeploying the i2b2.common and i2b2.pm packages I could then see the Service REST epr for the PMService. I fired up the web client and I was able to get in....but...now there appears to be another issue. When I log in I get a javascript error, "an error has occurred in the Cell's AJAX library. Press F12 for more information." I'm using Firefox so when I press F12 I get Firebug. The only thing I see is a reference to and i2b2CellMsg callback. Interestingly the msrUrl is localhost:9090/i2b2/rest/OntologyService/getSchemes.... I suspect this is wrong. The only reference I see to this url is in the web client admin/ directory, in the index.php file. I also included the contents of the i2b2_config_data.js for reference.
Firebug:
CALLBACK Processing AJAX i2b2CellMsg
error true errorMsg "The cell's status message could not be understood." errorStatus
msgParams Object { proxy_info="<proxy>\n <re..._url>\n </proxy>\n", sec_user="i2b2", sec_pass_node="<password token_ms_time...EJIQMXiD163L</password>", more...} msgRequest String { 0="<", 1="?", 2="x", more...} msgResponse "" msgUrl "http://localhost:9090/i2b2/rest/OntologyService/getSchemes" proxyUrl "index.php" refXML Document timeEnd Date {Fri Nov 04 2011 14:32:56 GMT-0400 (Eastern Daylight Time)} timeStart Date {Fri Nov 04 2011 14:32:56 GMT-0400 (Eastern Daylight Time)}
parse function()
i2b2_config_data.js:
{ urlProxy: "index.php", urlFramework: "js-i2b2/", //------------------------------------------------------------------------------------------lstDomains: [
{ name: "cancors.org", domain: "i2b2demo", debug: true, urlCellPM: "http://cancors.dfci.harvard.edu:8181/i2b2/rest/PMService/"
} ] //------------------------------------------------------------------------------------------
}

On Friday, November 4, 2011 12:55:37 PM UTC-4, Lori wrote: Seth,
I think your problem is related to the rest epr not showing up. Do you remember if you did the step where you go to project edu.harvard.i2b2.common and run the jboss_pre_deployment setup ant target? Was the build.properties file set up to point to correct jboss and axis2.war name?
You can try rerunning that step; if that doesnt work you may need to redo the axis.war installation steps.
Once the rest epr is showing up, I am not sure but I think your web client
{ name: "cancors.org",
domain: "i2b2demo",
debug: true,
urlCellPM: "http://cancors.dfci.harvard.edu:8181/i2b2/services/PMService/"
}
should point to "http://cancors.dfci.harvard.edu:8181/i2b2/rest/PMService/"
Lori

From: i2b2-ins....googlegroups [i2b2-ins....googlegroups] On Behalf Of Seth Lenzi Sent: Friday, November 04, 2011 12:40 PM To: i2b2-ins....googlegroups Subject: Re: New i2b2 Install, Web Client not connecting...
Yes, the directory contains the following files and sub directories. The sub directories also contain files.
I should maybe mention that we have a symbolic link setup as well so
that /soft/jboss422/server/default/deploy/i2b2.war/WEB-INF is the same as /misc2/
jboss-4.2.2.GA/server/default/deploy/i2b2.war/WEB-INF
I wouldn't think that matters...

drwxr-x---	2 canprod	users	512 Nov 1 17:31 conf
drwxr-x---	2 canprod	users	512 Nov 1 17:30 services
rw-r----	1 canprod	users	3877 Nov 1 17:26 web.xml
drwxr-x---	2 canprod	users	512 Nov 1 17:26 modules
drwxr-x---	2 canprod	users	3584 Nov 1 17:26 lib
drwxr-x---	4 canprod	users	512 Nov 1 17:26 classes

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