There was general support for the idea of communal (Java) libraries for Open chemistry projects and it was suggested that QSAR might be the best place to discuss this.
This is to discuss the tools that we use for building out systems (code, jars, docs, distrib, etc.). These tools are needed for building but not for the final deployment. They often take up a lot of space in the distrib and cause confusion of versions and generic jars (like xerces). For example FOP takes up ca 30% of the JUMBO distrib and we would like to remove it.
There are also advantages in having a central site where people can be educated about these tools and get the latest, running versions
Here are the tools that JUMBO uses for building but not for running:
ant (for building). [we don't distribute this and expect people to install it themselves. We don't use ant custom tasks but you can see that it might be possible.]
saxon for XSLT. We use a lot of XSLT1 and a few XSLT2 functions (mainly result-document). Otherwise we would use the ant/xsl task.
FOP. For documentation. We generate the *.fo using any XSL processor, but need FOP for the final. I think our latest strategy will be to generate the FO but not the PDF.
Doxygen. We don't distribute this but Billy uses it for some of the javadoc.
jtidy. Used for tidying HTML pages (can't even remember where).
junit. I think this is needed if ant runs unit tests?
It would be useful if others can list their requirements and then a list member summarise it and any problems.
As I mailed earlier it's useful to be able to load these jars by ant scripts. Here is what Taverna does (note that they get their jars from ibiblio. Perhaps we should all do the same:
<!-- Fetch .jar files -->
<target name="fetchjars">
<mkdir dir="./netlib"/>
<get src="http://www.ibiblio.org/maven/bsh/jars/bsh-2.0b1.jar"; dest="./netlib/bsh-2.0b1.jar" usetimestamp="yes"/>
<get src="http://www.ibiblio.org/maven/jdom/jars/jdom-b10.jar"; dest="./netlib/jdom-b10.jar" usetimestamp="yes"/>
<get src="http://www.ibiblio.org/maven/axis/jars/axis-1.2-beta-3.jar"; dest="./netlib/axis-1.2-beta-3.jar" usetimestamp="yes"/>
<get src="http://www.ibiblio.org/maven/axis/jars/axis-wsdl4j-1.2-beta-3.jar"; dest="./netlib/axis-wsdl4j-1.2-beta-3.jar" usetimestamp="yes"/>
<get src="http://www.ibiblio.org/maven/axis/jars/axis-jaxrpc-1.2-beta-3.jar"; dest="./netlib/axis-jaxrpc-1.2-beta-3.jar" usetimestamp="yes"/>
<get src="http://www.ibiblio.org/maven/axis/jars/axis-saaj-1.2-beta-3.jar"; dest="./netlib/axis-saaj-1.2-beta-3.jar" usetimestamp="yes"/>
<get src="http://www.ibiblio.org/maven/commons-discovery/jars/commons-discovery-0.2.jar"; dest="./netlib/commons-discovery-0.2.jar" usetimestamp="yes"/>
<get src="http://www.ibiblio.org/maven/commons-logging/jars/commons-logging-1.0.4.jar"; dest="./netlib/commons-logging-1.0.4.jar" usetimestamp="yes"/>
<get src="http://www.ibiblio.org/maven/log4j/jars/log4j-1.2.8.jar"; dest="./netlib/log4j-1.2.8.jar" usetimestamp="yes"/>
<get src="http://www.ibiblio.org/maven/commons-httpclient/jars/commons-httpclient-2.0.jar"; dest="./netlib/commons-httpclient-2.0.jar" usetimestamp="yes"/>
<get src="http://www.ibiblio.org/maven/dom4j/jars/dom4j-1.5.jar"; dest="./netlib/dom4j-1.5.jar" usetimestamp="yes"/>
<get src="http://www.ibiblio.org/maven/xerces/jars/xmlParserAPIs-2.2.1.jar"; dest="./netlib/xmlParserAPIs-2.2.1.jar" usetimestamp="yes"/>
<get src="http://www.ibiblio.org/maven/xerces/jars/xercesImpl-2.6.2.jar"; dest="./netlib/xercesImpl-2.6.2.jar" usetimestamp="yes"/>
<get src="http://www.ibiblio.org/maven/concurrent/jars/concurrent-1.3.4.jar"; dest="./netlib/concurrent-1.3.4.jar" usetimestamp="yes"/>
<get src="http://www.ibiblio.org/maven/servletapi/jars/servlet-api-2.4-20040521.jar"; dest="./netlib/servlet-api-2.4-20040521.jar" usetimestamp="yes"/>
<get src="http://www.ibiblio.org/maven/junit/jars/junit-3.8.jar"; dest="./netlib/junit-3.8.jar" usetimestamp="yes"/>
<get src="http://www.ibiblio.org/maven/poi/jars/poi-2.0-final-20040126.jar"; dest="./netlib/poi-2.0-final-20040126.jar" usetimestamp="yes"/>
Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069
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