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Questions tagged [i2b2]

For questions involving the i2b2 client/server architectures used for configuring i2b2 (Informatics for Integrating Biology and the Bedside) or developing extensions for i2b2 (ie: database schema build, database data load, ontology setup, hive/cell architectures, JBoss configuration, Apache/IIS setup, Axis configuration, Java setup, extending/customizing i2b2, etc.).

11 questions
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What does this JavaScript mean?

I am working on a legacy application and all JS seems mystrious to me. Here is the few mysterious lines which are loaded before all and I don't have any idea what they are doing. var i2b2 =…
Ajinkya
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1 answer

Java classpath folder missing in project but exists in Windows directory structure for project

I downloaded the application server Java source code from the i2b2.org site and compiling it for deployment. This application runs on top of JBoss. There are 8 project folders in the workspace that I switched to in Eclipse (root directory of where…
JustBeingHelpful
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vote
1 answer

Hive - rlike not returning results meeting multiple conditions

I'm looking to return encounters later than 12-17-2020 for each patient involving any of the antibiotics. I'm expecting many results, as querying by one antibiotic at a time shows me. But when I string them together in rlike, it only returns results…
Nishad Gulvady
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1 answer

Verifying PM Installation Step in i2b2 not working

I have followed all the steps mentioned in the Chapter 5 of the documentation for PM Installation which can be found here.I am at step 5.7 Verify PM Installation Step. And when I run the following URL as mentioned in the documentation…
John
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1 answer

How can I get aggregate counts without repeating first column in group by clause?

This query is forcing me to put f.CONCEPT_CD in the group by clause because I'm using it in the case statements in the select clause. How do I keep the counts in the result set, without repeating records with the same f.PATIENT_NUM? Notice how…
JustBeingHelpful
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2 answers

Run *.sql files in sequence from an XML file using "ant" command (building i2b2 ontology database on SQL Server 2008 Express)?

Below are commands in an i2b2 database setup tutorial to create a bunch of tables and load the data for a particular database. I've only run *.sql commands manually (in a new query window) in SQL Server Management Studio (SSMS) before. Is this…
JustBeingHelpful
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1 answer

Tomcat 7 JSP page: Avoid 500 error when authenticating in Tomcat using Shibboleth authentication session

Tomcat 7 Exception: Apache Tomcat/7.0.63 - HTTP Status 500 - An exception occurred processing JSP page Reference: I integrated this code with our i2b2 application so we could authenticate against our Shibboleth…
JustBeingHelpful
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1 answer

Quicker way of finding duplicates in SQL Server

I'm trying to find a better way of finding duplicates in SQL Server. This took over 20 minutes to run with just over 300 million records before results started showing in the results window within SSMS. Another 22 minutes elapsed before it…
JustBeingHelpful
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Executing Java program (NCBO Extraction Tool) from Windows command prompt not working ... User Guide uses Linux syntax

I'm trying to run a Java command line program from the Windows command prompt to extract and generate an ontology file from the BioPortal (http://bioportal.bioontology.org). It appears that it can't find the class, but perhaps my CLASSPATH…
JustBeingHelpful
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1 answer

Textpad Regular Expression: Replace a group of 3 characters with 5 new lines

I want to beautify the SQL code using this tool. Before this tool will accept it, I want to replace each instance of "<*>" (excluding double quotes) with "\n\n\n\n\n" (5 new lines) in TextPad using the Replace feature and choosing Regular…
JustBeingHelpful
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Two instances of same application on JBoss throws this exception: java.lang.Exception: Port 8083 already in use

On a Windows Server 2008 box, I'm trying to run two instances of the same application. This application (i2b2) is using Apache Axis 2 web services. The JAX-WS web services are running on port 9090, and are calling our application source code in…
JustBeingHelpful
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