From senger at pub.open-bio.org Mon Oct 18 10:35:05 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Mon Oct 18 10:06:33 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200410181435.i9IEZ5Av002428@pub.open-bio.org> senger Mon Oct 18 10:35:05 EDT 2004 Update of /home/repository/moby/moby-live/Java In directory pub.open-bio.org:/tmp/cvs-serv2405 Modified Files: build.properties.template build.xml Log Message: searching data paths and more, see docs/ChangeLog moby-live/Java build.properties.template,1.2,1.3 build.xml,1.7,1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Java/build.properties.template,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/build.properties.template 2003/11/09 01:05:02 1.2 +++ /home/repository/moby/moby-live/Java/build.properties.template 2004/10/18 14:35:05 1.3 @@ -25,3 +25,8 @@ cache.url = http://localhost/jmobycache default.endpoint = http://localhost/cgi-bin/moby default.namespace = http://mobycentral.cbr.nrc.ca/MOBY/Central + +servlet.name.graphs = graphs +servlet.url.graphs = /graphs/* + +registry.cache.dir = /tmp/mobycache =================================================================== RCS file: /home/repository/moby/moby-live/Java/build.xml,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Java/build.xml 2004/09/23 00:18:00 1.7 +++ /home/repository/moby/moby-live/Java/build.xml 2004/10/18 14:35:05 1.8 @@ -46,6 +46,16 @@ + + + + + + + + + + @@ -81,6 +91,7 @@ + @@ -130,6 +141,8 @@ + + @@ -185,6 +198,7 @@ + @@ -250,6 +264,15 @@ + + + + + + + + + @@ -411,7 +434,7 @@ - + @@ -439,60 +462,67 @@ - + description="Deploy jMoby Web Services to local Tomcat."> + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + description="Create a war file with jMoby servlets."> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + @@ -516,5 +546,37 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From senger at pub.open-bio.org Mon Oct 18 10:35:07 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Mon Oct 18 10:06:36 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200410181435.i9IEZ7rb002673@pub.open-bio.org> senger Mon Oct 18 10:35:07 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/webapps In directory pub.open-bio.org:/tmp/cvs-serv2405/src/webapps Modified Files: web.xml.template Log Message: searching data paths and more, see docs/ChangeLog moby-live/Java/src/webapps web.xml.template,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/webapps/web.xml.template,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/webapps/web.xml.template 2003/11/09 01:05:02 1.2 +++ /home/repository/moby/moby-live/Java/src/webapps/web.xml.template 2004/10/18 14:35:07 1.3 @@ -36,9 +36,9 @@ - graphs + @SERVLET_NAME_GRAPHS@ - It produces graphs of data types and service instances + It produces graphs of data and service types and service instances registered by any Biomoby registry. The users can customize both the appeareance and the contents of these graphs. @@ -131,13 +131,24 @@ + + registry_cache_dir + @REGISTRY_CACHE_DIR@ + An absolute path to a directory where the +Moby registry cached objects will be created. By default (when this is +empty) the cache will be created inside the servlet context (in +'webapps/jmoby/cache/'). Note that this is a different cache than the +one defined by 'cache_dir' (that one caches resulting images/graphs). + + + - graphs - /graphs/* + @SERVLET_NAME_GRAPHS@ + @SERVLET_URL_GRAPHS@ From senger at pub.open-bio.org Mon Oct 18 10:35:05 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Mon Oct 18 10:06:36 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200410181435.i9IEZ5ZG002447@pub.open-bio.org> senger Mon Oct 18 10:35:05 EDT 2004 Update of /home/repository/moby/moby-live/Java/docs In directory pub.open-bio.org:/tmp/cvs-serv2405/docs Modified Files: ChangeLog Log Message: searching data paths and more, see docs/ChangeLog moby-live/Java/docs ChangeLog,1.20,1.21 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v retrieving revision 1.20 retrieving revision 1.21 diff -u -r1.20 -r1.21 --- /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/09/24 19:52:55 1.20 +++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/10/18 14:35:05 1.21 @@ -1,3 +1,27 @@ +2004-10-18 Martin Senger + + * New extension of SimpleCache: SimpleFileCache (actually it + existed before but under different name). + + * Add finding paths between selected data types into MobyGraphs + (command-line) client and GraphsServlet (servlet) client. Both + these clients were also significantly changed (hopefully for + better). + + * Added implementations of new interfaces: CentralDigestImpl.java + and CentralDigestCachedImpl.java. Especially the latter one is + useful allowing to cache almost full registry in your file system. + + * Re-implemented the caching mechanism in CentralImpl.java (using + new interface SimpleCache.java). + + * New interface CentralDigest.java allowing to get data from Moby + registry in one go. Also a new interface CentralAll.java + combinaning traditional Central.java and new CentralDigest.java. + + * Added new methods to Central.java allowing to find what registry + we are connected to. + 2004-09-24 Martin Senger * Fixed signatureURL in service response object. From senger at pub.open-bio.org Mon Oct 18 10:35:06 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Mon Oct 18 10:06:37 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200410181435.i9IEZ6HW002548@pub.open-bio.org> senger Mon Oct 18 10:35:06 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/config In directory pub.open-bio.org:/tmp/cvs-serv2405/src/config Modified Files: run-graphs-client Log Message: searching data paths and more, see docs/ChangeLog moby-live/Java/src/config run-graphs-client,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/config/run-graphs-client,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/config/run-graphs-client 2004/09/23 00:18:01 1.1 +++ /home/repository/moby/moby-live/Java/src/config/run-graphs-client 2004/10/18 14:35:06 1.2 @@ -14,4 +14,7 @@ CLASSPATH=${PROJECT_HOME}/build/Clients:$CLASSPATH CLASSPATH=`echo ${PROJECT_HOME}/lib/*.jar | tr ' ' ':'`:$CLASSPATH +# WORK IN PROGRESS!!! +CLASSPATH=`echo echo ${PROJECT_HOME}/lib2/*.jar | tr ' ' ':'`:$CLASSPATH + exec java -cp $CLASSPATH MobyGraphs "$@" From senger at pub.open-bio.org Mon Oct 18 10:35:05 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Mon Oct 18 10:06:46 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200410181435.i9IEZ53U002467@pub.open-bio.org> senger Mon Oct 18 10:35:05 EDT 2004 Update of /home/repository/moby/moby-live/Java/docs/graphs In directory pub.open-bio.org:/tmp/cvs-serv2405/docs/graphs Modified Files: index.html Added Files: Taverna_howto.html Log Message: searching data paths and more, see docs/ChangeLog moby-live/Java/docs/graphs Taverna_howto.html,NONE,1.1 index.html,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/graphs/index.html,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/docs/graphs/index.html 2003/11/25 13:18:10 1.3 +++ /home/repository/moby/moby-live/Java/docs/graphs/index.html 2004/10/18 14:35:05 1.4 @@ -21,14 +21,18 @@ world and perhaps to find new and unexpected pathes, or simply to find unconnected orphans.

+It also creates workflow definitions that can be loaded into Taverna (a workflow engine and a GUI +workbench around it).

+

The BioMoby Graphs are available: