All Classes and Interfaces
Class
Description
An alternative to Spring's
AbstractHtmlElementTag that does not
carry the complexity of form data bindings.Base class for tags that refers to static assets.
Controller for methods involving annotation of experiments (and potentially other things); delegates to
OntologyService and the CharacteristicService.
Note: do not use parametrized collections as parameters for ajax methods in this class! Type information is lost
during proxy creation so DWR can't figure out what type of collection the method should take.
Controller for editing basic information about array designs.
For display of information about array designs that subsume or are subsumed.
A controller to run array design probe mapper either locally or in a space.
A controller to run array design repeat scan either locally or in a space.
Extended value object to carry more data to client.
Used to display table of biomaterials and bioassays.
This is required solely for exposing auditables to remote services would try to marshall the abstract class
Auditable.
For populating "batch" information about experiments.
This controller is responsible for showing a list of all bibliographic references, as well sending the user to the
pubMed.Detail.view when they click on a specific link in that list.
Render meta tags from a bibliographic reference.
Get statistics about and manage caches.
NOTE: Logging messages from this service are important for tracking changes to annotations.
Resolves a ClientAbortException to an empty view.
Deprecated.
An adaptation of the standard Spring CommonsMultipartResolver that uses a MonitoredOutputStream.
Constant values used throughout the application.
This class is designed to put all the public variables in a class to a specified scope - designed for exposing a
Constants class to Tag Libraries.
Implementation of
TagExtraInfo for the constants tag, identifying the scripting object(s) to be
made visible.Created by tesarst on 09/03/17.
Exposes methods for accessing underlying Design Element Data Vectors.
Custom exception resolver for Gemma.
For the display of a summary table about experimental design.
A controller to run differential expression analysis either locally or in a space.
Used to carry information about the experimental design analysis settings to clients.
A controller used to get differential expression analysis and meta analysis results.
A controller to analyze result sets either locally or in a space.
DWR converter for Direction type.
The 8 decimal precision of a double is just a waste of bandwidth in most cases.
Utility class for providing
Path as downloads.Bean to expose for remote access via AJAX, when all that is needed is the ID and a way to know what the class is.
Tag that generates an HTML link for a given
Identifiable entity.Signals that an entity was not found in the system.
Main entry point to editing and viewing experimental designs.
Replaces SimpleExpressionExperimentLoadController
For the download of data files from the browser.
Handle advanced editing of expression experiments.
Handles loading of Expression data into the system when the source is GEO or ArrayExpress, via Spring MVC or AJAX.
For fetching and manipulating ExpressionExperimentSets.
Expression experiment command object that wraps expression experiment visualization preferences.
A lightweight object to hold expression data for a single probe.
An external static asset server that provide assets from a specified base URL.
Represents data for displaying a factor (+ factor values) in a chart.
Used to allow downstream processing to figure out multipart resolution failed without throwing an exception.
Command class to handle uploading of a file
Controller class to upload Files.
Utility methods for uploading files.
Expression data for one probe; designed for conveying small amounts of data to clients.
For 'live searches' from the web interface.
Note: do not use parametrized collections as parameters for ajax methods in this class! Type information is lost
during proxy creation so DWR can't figure out what type of collection the method should take.
Exposes GeneSetServices methods over ajax.
Monitoring of Hibernate status.
Responsible for display of the Gemma 2.0 home page.
Write an
<img/> tag.Performs the standard context preparation from
SpringContextUtils.prepareContext(ApplicationContext)
as well as some more specific Web-related setups.An internal static asset server that uses npm to serve static assets.
Class to handle saving client-side javascript error messages and warnings to a server-side log.
Creates a response that can be consumed by an Ext.data.JsonReader.
Utilities for writing JSON payloads to
HttpServletResponse.A controller to pre-process expression data vectors.
Encapsulates information needed for generic list browsing.
Performs actions required when we wish to indicate that the system is undergoing maintenance and many not behave
normally.
Wrapper for metadata file information for the frontend
Configured the
environment='web' tag to the provided registry.Commons FileItem that uses a MonitoredOutputStream
OutputStream that puts information on how many bytes have been read into a OutputStreamListener.
Provide minimal support for exposing Gemma ontology.
A controller to pre-process expression data (including updating diagnostics)
This class exposes methods for AJAX calls.
Allow users to search for and view PubMed abstracts from NCBI, or from Gemma.
Supports seaching of pubmed references
Write a
<style/> tag.Manages data-level security (ie.
Carries extensive security information about an entity.
Exception raised when a service is unavailable.
Metrics for servlet requests.
Serve static assets from the servlet context.
Controller to signup new users.
Stores information about the validation status of an attempted expression experiment load.
Extends a SimpleExpressionExperimentMetaData with information about the file and provide simplified taxon/platform
information.
Tag for displaying a single-cell sparsity heatmap.
Slight variant of
ContextLoaderListener that logs the time taken to initialize the context.Resolve static assets either froma
InternalStaticAssetServer or from the webapp resources.write a
<style/> tag.Run SVD on a data set.
Provide statistics about the system: hibernate, caches etc.
System statistics
Exposes progress status service check result to the front end.
Simply prints text to the client.
Run misssing value computation via web request.
Resolver used when no other resolver can intervene.
This is created when a multipart request is received (via the CommonsMultipartMonitoredResolver).
Count active sessions
Controller to edit profile of users.
For display and editing of users.
Basic bean to hold number of sessions.
Stores expression profile data from one expression experiment for plotting.
This builder has extras URL-generating capabilities for Web applications.
Controller to provide information on "what's new" in the system