Overview (SeqWare 1.1.2 API)

Packages
Package	Description
io.seqware	Provides new utility classes.
io.seqware.cli	Main class for the simplified CLI.
io.seqware.common.model	Unify status Strings across SeqWare.
io.seqware.metadb.util	Create and manipulate testing databases.
io.seqware.pipeline	Provides utility classes.
io.seqware.pipeline.api	This package will store components of SeqWare that can be programmatically called in order to manage the components of the SeqWare life-cycle.
io.seqware.pipeline.engines	This stores implementations of new workflow engines for prototyping purposes.
io.seqware.pipeline.engines.whitestar	This is a simple reference implementation of a seqware engine used for development and debugging.
io.seqware.pipeline.plugins	Newly written SeqWare plugins
io.seqware.pipeline.plugins.sanity	Base classes for the sanity check tool.
io.seqware.pipeline.plugins.sanity.checks	Various state checks.
io.seqware.webservice.adapter	Hook up custom behaviour for conversion of timestamps.
io.seqware.webservice.client	Customized Java client for admin webservice.
io.seqware.webservice.controller	Classes for customized behaviour for the REST web resources.
io.seqware.webservice.generated.client	Autogenerated Java client class.
io.seqware.webservice.generated.controller	Autogenerated web resources.
io.seqware.webservice.generated.model	Auto-generated model classes.
net.sourceforge.seqware.common	Hooks up Hibernate classes to the metadb.
net.sourceforge.seqware.common.business	Looks like auto-generated classes for Hibernate.
net.sourceforge.seqware.common.business.impl	Looks like auto-generated implementation for Hibernate classes.
net.sourceforge.seqware.common.dao	More hibernate auto-generated.
net.sourceforge.seqware.common.dao.hibernate	More hibernate auto-generated.
net.sourceforge.seqware.common.err	Exceptions.
net.sourceforge.seqware.common.factory	A sad direct database connector and a Hibernate factory.
net.sourceforge.seqware.common.hibernate	Looks like utility classes for navigating the metadb.
net.sourceforge.seqware.common.hibernate.reports	A row of the workflow run report.
net.sourceforge.seqware.common.invitation	Looks like this handles invitations for the portal.
net.sourceforge.seqware.common.metadata	Critical classes that effectively convert API calls into actions against the DB and web service.
net.sourceforge.seqware.common.model	Hibernate model classes for the metadb.
net.sourceforge.seqware.common.model.adapters	Looks like converters from collections to XML.
net.sourceforge.seqware.common.model.comparator	Comparator, used in Hibernate.
net.sourceforge.seqware.common.model.lists	Looks like various container classes for XML serialization.
net.sourceforge.seqware.common.module	Utility classes really.
net.sourceforge.seqware.common.security	Interface that unifies model objects that have the concept of permissions.
net.sourceforge.seqware.common.util	Various utility classes.
net.sourceforge.seqware.common.util.configtools	Handle reading of SeqWare .seqware/settings files.
net.sourceforge.seqware.common.util.exceptiontools	Rather redundant way of printing out exceptions.
net.sourceforge.seqware.common.util.filetools	Tools for dealing with files.
net.sourceforge.seqware.common.util.filetools.lock	Lock files with an old Java API.
net.sourceforge.seqware.common.util.iotools	Buffer outputs.
net.sourceforge.seqware.common.util.jsontools	Tools for json files.
net.sourceforge.seqware.common.util.maptools	Tools for converting ini files to maps.
net.sourceforge.seqware.common.util.processtools	Tools for sleeping processes.
net.sourceforge.seqware.common.util.runtools	Tools for running commands.
net.sourceforge.seqware.common.util.testtools	More tools for creating and manipulating tests databases.
net.sourceforge.seqware.common.util.workflowtools	A strange couple of tools for manipulating workflows.
net.sourceforge.seqware.common.util.xmltools	XML Tools.
net.sourceforge.seqware.pipeline.bundle	Utility classes for interacting with workflow bundles.
net.sourceforge.seqware.pipeline.decider	Interface for deciders.
net.sourceforge.seqware.pipeline.deciders	BasicDecider.
net.sourceforge.seqware.pipeline.module	This package provides the SeqWare module interface and API, including common code and classes.
net.sourceforge.seqware.pipeline.modules	Executables that can be called by workflows and users.
net.sourceforge.seqware.pipeline.modules.utilities	Modules that are used by workflows.
net.sourceforge.seqware.pipeline.plugin	Interface for plugins and the workflow launcher for some reason.
net.sourceforge.seqware.pipeline.plugins	Create and manipulate databases for extended testing.
net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection	PDE's batch metadata injection utility
net.sourceforge.seqware.pipeline.plugins.checkdb	Check the metadb for errors in convention and structure.
net.sourceforge.seqware.pipeline.plugins.checkdb.plugins	Basic checks for all SeqWare databases as well as examples for site specific checks.
net.sourceforge.seqware.pipeline.plugins.deletion	Implementation for the deletion tool that can delete workflow runs.
net.sourceforge.seqware.pipeline.plugins.filelinker	Import files into the metadb.
net.sourceforge.seqware.pipeline.plugins.fileprovenance	Dump out the file provenance report to the user.
net.sourceforge.seqware.pipeline.runner	Runs plugins and modules.
net.sourceforge.seqware.pipeline.tools	Basic utility classes.
net.sourceforge.seqware.pipeline.workflowV2	Back-end for the Java workflow language and Oozie engine.
net.sourceforge.seqware.pipeline.workflowV2.engine.oozie	Implementation of the Oozie workflow engine.
net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object	Implementation of workflow steps for Oozie.
net.sourceforge.seqware.pipeline.workflowV2.model	Classes that implement the tasks within workflows.
net.sourceforge.seqware.queryengine.webservice.controller	Wire up new web resources.
net.sourceforge.seqware.queryengine.webservice.model	Seemingly misplaced model objects for sample hierarchy resource.
net.sourceforge.seqware.queryengine.webservice.security	Hooks up web service authentication.
net.sourceforge.seqware.webservice.resources	Base classes for web resources.
net.sourceforge.seqware.webservice.resources.filters	Restrict web resources results.
net.sourceforge.seqware.webservice.resources.queries	Report various things about the metadb.
net.sourceforge.seqware.webservice.resources.tables	More basic web resources.
net.sourceforge.solexatools	Portal stuff, to be assessed.
net.sourceforge.solexatools.authentication	Portal stuff, to be assessed.
net.sourceforge.solexatools.util	Portal stuff, to be assessed.
net.sourceforge.solexatools.validation	Portal stuff, to be assessed.
net.sourceforge.solexatools.webapp.controller	Portal stuff, to be assessed.
net.sourceforge.solexatools.webapp.metamodel	Portal stuff, to be assessed.