MyDas

yesterday I started to look at code for the DAS server MyDAS (http://code.google.com/p/mydas/) that was developed at the EBI. I wanted to use eclipse and the Web/tomcat/WTP setup to develop the mydas server.

Here are some very brief notes on setting up MyDas in eclipse which should at some point be translated into more technical and formal documentation on the biodas site:

mydas notes:

with eclipse use svn exploring then right-click on trunk/mydas/server_core and “check out as maven project”. Also do this again for trunk/mydas/MyDasTemplate

right-click on project and then select maven install from maven menu.
right-click on project again and select Run as server.
if you alter a java class in the MyDasTemplate project src dir then tomcat will auto restart and changes will take effect after 2 seconds. access using url http://localhost:8080/MyDasTemplate/das/sources – a xml document should be displayed, if you see text then use the browser to look at the source.
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How do we modify the mydas.jar which the MyDasTemplate  uses? mydas.jar is put in target dir under web-inf

I changed the mydas.jar that was set by¬† maven to the one from the mydas project (downloaded to eclipse as above project was) do this by right clicking on MyDasTemplate project and “build path”, “configure build path”,”java EE module dependencies”, uncheck the currently selected mydas.jar and “add jars”, select the mydas.jar from the mydas project dir.

To build the mydas project I right-clicked on the pom.xml then “run as” then “maven package” which did indeed build the mydas.jar within the mydas project under target dir. then run as “maven package” in the mydastemplate project pom.xml to make this change in the tomcat server.

system.outs also then appear in the eclipse console.

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ensembl test – test region is wrong in tutorials should be chomosome name and range and coordinate system is wrong it’s not gene-id.

feature by id works http://localhost:8080/MyDasTemplate/das/ensemblTest/features?feature_id=ENSG00000160916

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