Macro for rendering Journal References from Pubmed
What it does
The NCBI macro retrieves the article descriptions from Pubmed and renders them as literature citations (chicago-style).
The abstract is available by clicking on the citation (if available).
Articles retrieved once are stored in the Confluence datasource (table NCBIRecord), thus cached to take the load from NCBI.
Get it: ncbi2.jar
Installation
Install through Administration/Plugins.
Usage
Find your articles using Pubmed and take note of the PMIDS.
In your page write
{cite:list=3213654,5446654}
You should get something like this:
Fornari M, Pluchino F, Solero CL, Giombini S, Luccarelli G, Oliveri G, Lasio G, 1988. "Microsurgical treatment of intramedullary spinal cord tumours." Acta Neurochir Suppl (Wien) 43: 3-8 [PubMed] Baranowska-George T, 1970. "[New method of treatment of aniseikenia by means of localization exercises]" Klin Oczna 40 (2): 191-6 [PubMed]
 | If something is wrong with your id, you will get an error message. However, as the macro currenrly only supports Journal articles you may get an empty output if the record points to book for example. Source code is provided, but you onlay need to adjust the stylesheet to your liking. |
Comments (8)
Aug 15, 2005
Mingyi Liu says:
I got a lengthy system error message when using it on 1.4.2 (JDK 1.5). Does the...I got a lengthy system error message when using it on 1.4.2 (JDK 1.5). Does the macro work on 1.4.2?
Thanks,
Mingyi
Oct 06, 2005
Brendan Pattrson says:
I think the above post is correct. I'm trying to use this with JDK-1.4.2 and I g...I think the above post is correct. I'm trying to use this with JDK-1.4.2 and I get this error:
java.lang.UnsupportedClassVersionError: com/imphar/confluence/ncbiref/NCBIReference (Unsupported major.minor version 49.0)
Meaning it was probably compiled with Java 5. The reason I'm running with JDK-1.4.2 is that its the recommended Confluence configuration (as far as I know). Haven't tried recompiling the source yet.
Oct 22, 2005
Brendan Pattrson says:
I looked at the source code. It uses generics - a Java 5 feature which simply do...I looked at the source code. It uses generics - a Java 5 feature which simply doesn't work under a 1.4 JVM unless someone knows how to get around it in a way that I don't. The notes on the page currently about the jaxp-api don't address this issue.
Correct me if I'm wrong, but basically if you're running with a JVM version 1.4.x (the Atlassian recommended environment) this macro won't work.
Oct 22, 2005
David Peterson [CustomWare] says:
As far as I know, that is the case. That said, I'm running Confluence on my test...As far as I know, that is the case. That said, I'm running Confluence on my test machine in Java 5 without incident, so even though it's not 'officially' supported, it does seem to work fine.
Oct 23, 2005
Daniel Ostermeier says:
There is no reason that Confluence should not run on Java 5. However, we develop...There is no reason that Confluence should not run on Java 5. However, we develop or 1.4 and currently run all of our tests on 1.4, which is why we 'officially' support 1.4.
Mar 16, 2007
Wolfram Richter says:
I fixed it to work with the latest Confluence release (tested with 2.4.2). It s...I fixed it to work with the latest Confluence release (tested with 2.4.2).
It still uses JDK 5 however.
Mar 21, 2007
James Mortimer says:
running conf 2.3.3 and JDK5 I get this error with this test case: {cite:list=3...running conf 2.3.3 and JDK5 I get this error with this test case:
{cite:list=3213654,5446654} OR {cite:list=1}I get a friendly error with this test case
{cite:3213654} OR {cite:id=3213654}Mar 21, 2007
James Mortimer says:
it also takes 60s plus to return. perhaps there is a proxy issue as we are behin...it also takes 60s plus to return. perhaps there is a proxy issue as we are behind a firewall?