ApiCommonModel

Extends EbrModelCommon.

It includes xml files with basic data types definitions, and their structured searches, for genomic sites. Api stands for ‘Apicomplexan’. These are the first organisms included in our websites when they were first time publicly released as ApiDB BRC (Bioinformatics Resource Center), back in 2002.

Dependencies

• yarn / npm / ant
• WEBAPP_PROP_FILE file (file with one property for the webapp target directory) webappTargetDir=BLAH
• environment variables for GUS_HOME and PROJECT_HOME
• Internal Dependencies
  • WDK, CBIL, ReFlow, EbrcModelCommon

Installation instructions.

• bld ApiCommonModel
• changes to wdk model xml files requires reload of tomcat instance

Operating instructions.

• Installation is successful if you can run “wdkXml -model $MODEL_NAME” without error

Manifest

Model/bin

scripts referenced in tuning manager config and other tuning scripts (portallinker); scripts for creating jbrowse configuration

Model/lib/dst

dataset template files

Model/lib/jbrowse

jbrowse configuration; common and organism specific tracks

Model/lib/perl

utils for datasets and jbrowse

Model/lib/wdk

xml files which define wdk records, searches, params.

Model/lib/xml

tuning manager configuration, jbrowse queries, global dataset presenter xml

Model/src/main/java/org/apidb/apicommon/model/datasetInjector

java code per data class for managing template injection

Model/src/main/java/org/apidb/apicommon/model/report

reporters referenced in wdk xml

Model/src/main/java/org/apidb/apicommon/model/userdataset

Type Handlers for User Datasets