GeWorkbench Web version Dependency Documentation

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This page documents library dependency (in terms of jar files) of the geWorkbench Vaadin version project.

Contents

jar files

(in alphabetical order)

  • anova.jar - why do we need this? anova is a AXIS2 web service, so all wee need should be the AIX2 API supporting jars. This jar is still depended by the ANOVA plug-in, but probably only a small part is really used and that small part may be be completely necessary.
  • appfoundation.jar - vaadin add-on to implement persistence, authentication and authorization. see. https://vaadin.com/directory#addon/appfoundation. dependencies: Eclipselink jar files, javax persistence jar files.
  • aracne-java.jar - used by ARACNe analysis, but similar to ANOVA, it should be smaller only containing the web service API instead of computation itself.
  • axiom-api-1.2.13.jar - (used by AXIS2 ?) [added on 8/9/2012 revision 9897 for web service axis2]
  • axiom-impl-1.2.13.jar - (used by AXIS2 ?) [added on 8/9/2012 revision 9897 for web service axis2]
  • axis2-trnsport-http.jar - one of the 4 axis2-*.jar files [added on 8/9/2012 revision 9897 for web service axis2]
  • axis2-trnsport-local.jar
  • axis2-kernel-1.6.2.jar - verified required by AXIS2 client
  • axis2-adb-1.6.2.jar - verified required by AXIS2 client
  • blackboard-2.2.0.jar - Blackboard is a vaadin add-on which is a centralized event handling system, as per the Observer pattern. For documentation and wiki article see: https://vaadin.com/directory#addon/blackboard Blackboard is not something you have to have to implement an event publication/subscription mechanism; it is mean to tackle the situation of "having a deep component hierarchy" and consequent difficulties.
  • collections-generic-4.0.jar - apache collections. who is using this?
  • commons-codec-1.3.jar - revision 9291
  • commons-collections-3.2.1.jar - revision 9941
  • commons-httpclient-3.1.jar - revision 9291
  • commons-io-2.3.jar - revision 9460
  • commons-lang-2.4.jar - revision 8647
  • commons-logging.jar - revision 8647
  • commons-math-2.2.jar - revision 9873
  • easyuploads-0.5.1.jar - vaadin add-on to support easier implementation of file upload behavior. I am not totally satisfied with this add-on. It is in pre-release status (the latest version is 0.5.1) and does not have documentation of production quality. see http://vaadin.com/addon/easyuploads. I believe Nikhil re-wrote the code when he tried to work on 3267 and probably made this jar file no longer necessary. In such cases, we should document the change in a way that I or any other developers don't need to guess that the change is. Nikhil has removed easy uploads from data upload plugin. It is still used in Marina analysis component. It is also used in SetViewCommand.
  • eclipselink.jar - needed by appfoundation.jar
  • eclipselink-jpa-modelgen_2.3.2.v***.jar
  • Fancylayouts - Vaadin add on that provides fast way to add small amount of transitions to geWorkbench-Web. It's implemented with CSS transitions so transitions work with all modern browsers. For Documentation see: https://vaadin.com/directory#addon/fancylayouts
  • geworkbench-core.jar - all the shared code from geworkbench-core of geWorkbench desktop version, e.g. bison data types.
  • herrarchicalclustering.jar
  • httpcore-4.0.jar [added on 8/9/2012 revision 9897 for web service axis2]
  • icepush, icepush-0.2.1, icepush-gwt : All three jar files are used to implement push mechanism in geWorkbench-web. The basic usage is to update UI from the background thread. see: https://vaadin.com/directory#addon/icepush The latest version is 0.5.5 for vaadin 7; we're using 0.2.1, the last version for vaadin 6. Another reason we should migrate to vaadin 7. See also http://www.icesoft.org/java/projects/ICEpush/overview.jsf for underlying technology.
  • invientcharts - Vaadin addon forcharts. This is a Vaadin wrapper of javascript library highcharts. https://vaadin.com/directory#addon/invient-charts . Why is hightcharts.js in also explicitly included in our project?
  • javax.persistence.jar - we used to have two. keep the newer version and remove the older version. needed by appfoundation.jar.
  • jcommon-1.0.5.jar
  • log4j-1.2.8.jar: to use log4j, log4j.properties must be available on the classpath. This has been fixed.
  • mail-1.4.jar [added on 8/9/2012 revision 9897 for web service axis2]
  • MessageBox - Vaadin addon from effectively displaying notifications. This is quite an improvement over default vaadin notifications. For documentation see:https://vaadin.com/directory#addon/messagebox
  • mysql-connector-java-5.1.18-bin.jar
  • neethi-3.0.2.jar [added on 8/9/2012 revision 9897 for web service axis2]
  • ostermillerutils_1_04_03_for_kahhe.jar - csv parsing?
  • PagedTable-0.6.3.jar - for paged tabular view
  • poi-3.8-20120326.jar - used by TableExport.
  • sessionguard-0.0.5.jar: SessionGuard is a vaadin addon to extend and implement vaadin session. Though we are not using this right now geworkbench-web should not be released without handling user session properly.
  • TableExport-1.3.0.jar - Vaadin addon that is used to export table data to csv and some other file formats. For documentation see: https://vaadin.com/directory#addon/tableexport This is now used by CNKBResultUI, and it depends on poi.
  • ttest.jar
  • vaadin-6.8.1.jar
  • wsdl4j-1.6.2.jar [added on 8/9/2012 revision 9897 for web service axis2]
  • XmlSchema-1.4.7.jar - verified required by AXIS2 client [added on 8/9/2012 revision 9897 for web service axis2]

Mike Su just added a large group of jar files for geneSpace. They need to be documented:

  1. borderlayout-0.3.jar
  2. flexjson-2.1.jar - removed
  3. genspace-common.jar
  4. gwt-dnd-2.6.5.jar - removed
  5. gwt-graphics-1.0.0.jar - removed
  6. jimi.jar
  7. jsonwrapper-0.2.jar - removed
  8. lib-gwt-svg-0.5.2.jar - removed
  9. MultiButton2.0.1.jar
  10. nodegraph-widget-0.1.23.jar - removed
  11. refresher-1.1.1.jar - removed
  12. smack.jar
  13. smackx.jar
  14. vprotovis-0.6.jar

jar files removed

  • analysis.jar - this is newly added. It should be reviewed. If it is to support the web service invocation, it should have been there as early as the first analysis in the form of web service.
  • aracne-main.jar - it seems very likely that it should not be there.
  • colt-1.2.0.jar - numeric library. Added in revision 9407. It seems for aracne.
  • commons-cli.jar - Added in revision 9407. It seems for aracne.
  • mev-*.jar - totally six. Seven jar files (6 mev-* plus SciPartial) were checked in in revision 9855 for anova. I suspect they are used any more.
  • ProtovisGWT-0.4.1.jar - GWT graphics library used to implment SVG graphics in geWorkbench (used in Clustergram/VClustergram and Heatmap/VHeatmap, both of which were removed). For documentation see: http://code.google.com/p/choosel/wiki/ProtovisGWT The last updated date is 2011.
  • JSciCore.jar, JSciPartial.jar: who is using these? Probably anova.
  • javax.persistence-1.0.0.jar - remove the older version of this jar because a later version is also in the project
  • PaginationBar - Vaadin addon to implement pagination for a table. It also provides very good option to implement lazy loading. For documentation see: https://vaadin.com/directory#addon/paginationbar Replaced by PagedTable-0.6.3.jar
  • workbook-0.91.jar: This probably is for ARACNe. If that is true, it should be removed.

The jar files that were added during temporary development activity should be removed.

Vaadin add-ons

(are vaandin add-ons always some jar files or not? we may need to include them in both list.)

  • appfoundation
  • blackboard
  • easyuploads
  • Fancylayouts
  • icepush - three jar files
  • invientcharts
  • PagedTable (PagedTable-0.6.3.jar)
  • MessageBox
  • SessionGuard
  • TableExport

Dependency on other non-java library

  • cytoscape web (javascript)
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