All Classes and Interfaces
Class
Description
Base class for
AnnDataSingleCellDataLoader configurers.Base implementation of
AsyncFactoryBean.An entity which can have an audit trail attached to it.
Base class for bulk expression data matrices.
Partial implementation of
FilteringVoEnabledDao based on the Hibernate Criteria API.Created by tesarst on 07/03/17.
Created by tesarst on 07/03/17.
AbstractDao can find the generic type at runtime and simplify the code implementation of the BaseDao interface
A delegating executor service inspired by
DelegatingSecurityContextExecutorService.The bare minimum to represent a factor value.
Base implementation for
FilteringVoEnabledDao.Meta-information for a filterable property.
Base implementation for
FilteringVoEnabledService.Base class for design element mapper that use gene identifiers.
Base class for identifiable entities.
Base class for ExpressionDataMatrix implementations that can deal with multiple BioAssays per BioMaterial.
Base class to use to pretend to offer filtering, but actually supporting no filterable properties.
Base class for
Persister implementations.Various caches to refer back to not-yet persisted entities (and thus not easily obtainable from the persistence
context).
Partial implementation of
FilteringVoEnabledDao based on the Hibernate Query API.Base for all services handling DAO access.
Handle detection and download of single-cell data from a single file in the supplementary materials of a GEO series.
Created by tesarst on 01/06/17.
Created by tesarst on 01/06/17.
For permissions modification to be triggered, the method name must match certain patterns, which include "create", or
"remove".
Utilities for integrating ACLs with Hibernate
Criteria API.Filter
CompositeSequence based on the permissions of the associated ArrayDesign.Filter collections of
CompositeSequence based on the permissions of the associated ArrayDesign(s).Filter collections of
DataVector and DataVectorValueObjects based on the permissions of the
associated ExpressionExperiment(s).Utilities for integrating ACL into
Query.Extract the chip type from Affymetrix CEL files.
Reads Affymetrix Probe files, including exon arrays.
Extract the scan date from Affymetrix CEL files.
Configuration for aggregating single-cell data.
Exception raised when aggregation fails.
Because agilent makes slides that work with any scanner, the formats are not that predictable.
Signifies a mapping based on sequence alignment performed by the system.
Exception raised when all analyses fail.
Exception raised when all subset analyses failed with an
AnalysisException.Can be thrown when an attempt is made to load data into the system that already exists.
An analysis of one or more Investigations.
Base exception for all differential analysis-related exceptions.
Abstract class representing a single result from an
Analysis and a typical part of an AnalysisResultSet.An abstract class representing a related set of generic analysis results, part of an analysis.
Generic DAO for manipulating
AnalysisResultSet.Interface for services providing
AnalysisResultSet.Exposes an
AnalysisResultSet to the public API.Wraps an
AnalysisResult to expose it on the public API.Provides basic services for dealing with analyses
Used for indication of the suitability, or unsuitability, of an entity for a particular type of analysis.
Defines the different types of analyses our linear modeling framework supports:
GENERICLM - generic linear regression (interactions are omitted, but this could change)
OSTTEST - one sample t-test
OWA - one-way ANOVA
TTEST - two sample t-test
TWO_WAY_ANOVA_WITH_INTERACTION
TWO_WAY_ANOVA_NO_INTERACTION
Utility methods for dealing with analyses.
Detects AnnData in GEO series.
Reads single-cell vectors from the AnnData on-disk HDF5 format.
A configuration for loading single-cell data form AnnData format.
An association between BioSequence and GeneProduct that is provided through an external annotation source, rather
than our own sequence analysis.
To signify the array design was mapped from an external source, not by our own sequence analysis.
Interface implemented by
SingleCellDetector have the capabilities of looking-up archives.Interface defining a class that downloads archives and unpacks them.
Represents an assembly of design elements that are assayed all at once.
An event involving the analysis of an ArrayDesign
Methods to generate annotations for array designs, based on information already in the database.
Created by tesarst on 13/03/17.
The mapping of probes to genes for an ArrayDesign
Supports obtaining detailed information about the sequence analysis of probes on microarrays.
Make new array design based on others
Keep map of relation between new design elements and old ones
Store relationship with mergees
Deprecated.
This class handles persisting array designs.
For an array design, generate gene product mappings for the sequences.
A probe mapper spaces task .
A command object to be used by spaces.
Signifies that the probes were renamed from their original values.
A command object to be used by spaces.
An array design repeat scan spaces task
Aligns sequences from array designs to the genome, using blat, and persists the blat results.
The sequence alignment analysis of an ArrayDesign
Handles collapsing the sequences, attaching sequences to DesignElements, either from provided input or via a fetch.
Used to indicate that all associations that this array design has with BioSequences have been removed.
The updating of the sequences associated with an ArrayDesign
Used to hold information for matching to a new experiment, during persisting.
Value object for quickly displaying varied information about Array Designs.
Async extension of the
FactoryBean interface.Utilities for manipulating async factory beans.
Created by tesarst on 07/03/17.
Manage audit trails on objects.
An event in the life of an object.
Logger for created
AuditEvent.The trail of events (create or update) that occurred in an objects lifetime.
Create and manipulate audit trails.
Deprecated.
this event type was used by the auto-tagger, which has been removed.
Configure the baseCode library from a given property sources.
Exception that wraps a baseCode
OntologySearchException.Interface that supports basic CRUD operations.
Base service class for an immutable entity.
Represents a baseline for a single factor or an interaction of factors.
Utilities for deciding if a factor value is a baseline condition.
Interface for read-only services.
Interface that supports basic CRUD operations.
Created by tesarst on 01/06/17.
Created by tesarst on 01/06/17.
A line parser that produces a Map instead of a Collection.
A simple LineParser implementation that doesn't do anything.
Represents a summary of a batch effect confound.
Test if an experimental design is confounded with batches.
provide some basic information about the properties and strength of a batch effect, if any.
Represents a batch effect.
Task to try to get 'batch' information about an experiment.
Indicate that batch information is missing.
Parse information on batch from raw data files.
Used to indicate a problem with the population of batch information for a given
ExpressionExperiment.Retrieve batch information from the data source, if possible, and populate it into experiments.
Retrieve batch information from the data source, if possible, and populate it into experiments.
Schedule job that populates batch information for all experiments that have been updated since the last run.
Abstract class for events related to batch information.
Indicates that batch information was successfully obtained.
Indicate that batch information has been looked for and was missing.
Event that tracks when batch effects or problems are detected.
Utilities for working with bean factories.
Hook into the bean post-processing lifecycle and record bean initialization time.
Our \@Service etc. annotations in classes end up generating names with "Impl" on the end, unless we explicitly
provide a name.
Implementation of BibliographicReferenceService.
represents a BibliographicReferenceValueObject when this value object is needed in core, the same value object exists
in web
Represents the bringing together of a biomaterial with an assay of some sort (typically an expression assay).
Stores the order of BioAssays referred to in DataVectors.
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
ubic.gemma.model.expression.bioAssayData.BioAssayDimension.
Spring Service base class for
BioAssayDimensionService, provides access to all services and entities
referenced by this service.Strategy used for comparing
BioAssay to sample names from the data.Handle 'flagging' a sample as an outlier.
Represents a set of
BioAssays.Generic service for dealing with all subclasses of
BioAssaySet.Interface for VOs deriving from
BioAssaySet.Parser for BioMart file.
BioMart is a query-oriented data management system.
Class that is responsible for generating a map of BioMartEnsembleNcbiObject value objects which are keyed on ensemble
protein id.
In MAGE, BioMaterial is an abstract class that represents the important substances such as cells, tissues, DNA,
proteins, etc...
Indicates that the biomaterial to bioassay mapping of the expression experiment was modified.
The sequence of a biological polymer such as a protein or DNA.
An association between a BioSequence and a Gene Product.
Spring Service base class for
BioSequenceService, provides access to
all services and entities referenced by this service.Represents a blacklisted entity that should not be loaded into Gemma.
TODO Document Me
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
BlatAssociation.Given a set of BlatAssociations that might be redundant, clean them up and score them.
Spring Service base class for
BlatAssociationService, provides access to all services and entities
referenced by this service.Represents the result of a BLAT search.
Used to convert BlatResult objects into PSL lines that can be displayed in the UCSC Genome Browser.
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
ubic.gemma.model.genome.sequenceAnalysis.BlatResult.Loader to handle results generated by Jim Kent's Blat.
Spring Service base class for
BlatResultService, provides access to all services and entities referenced
by this service.Value object for a
BulkExpressionDataVector containing booleans.A bootstrapped data source that strips the database from the JDBC URL.
Support for paging through the data.
Populate build information in the Log4j
ThreadContext.Slice bulk data vectors.
A bulk expression data matrix that can be efficiently accessed as a primitive int matrix.
Interface for bulk expression data matrices.
Interface for bulk expression data matrices that can be efficiently accessed as a primitive double matrix.
Interface for bulk expression data matrices that can be efficiently accessed as a primitive int matrix.
A data vector storing bulk expression data.
Methods to test business-key-related issues on objects.
Represents a vector of scalars stored as a byte array in a single column.
Utilities for working with byte arrays.
Represents a lock over a cache key.
Represents an acquired lock on a cache key.
Created by tesarst on 04/04/17.
Represents a categorical array.
Enumeration of commonly used categories for referring to in the code.
Represents a category.
Represents a mapping between a Cell Browser metadata column and a Gemma entity.
Write metadata file for the Cell Browser visualization tool.
Generate a tabular matrix format compatible with Cell Browser.
Strategy for mapping sample name to
BioAssay that relies on overlapping cell IDs.Characteristics applicable to individual cells in a
SingleCellDimension.Event emitted when a cell-level characteristics is removed.
Event emitted when a cell-level characteristics is modified (either added or removed).
Utilities for creating, reading and writing mappings of
CellLevelCharacteristics to ExperimentalFactor.Event emitted when a cell-level characteristics is removed.
Represents a cell type assignment where cells from a given dataset are assigned cell types.
Event emitted when a
CellTypeAssignmentEvent is added.Event emitted when a cell type assignment is modified (either added or removed).
Event emitted when a
CellTypeAssignmentEvent is removed.Implementation of a chain of entity mappers.
Determine if a quantitation type (by name) represents background or signal.
Instances of this are used to describe other entities.
This handles characteristic updates from the client: experiment tags, characteristic browser
Value object representation of a
Characteristic.Immutable representation of a chromosome
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
ubic.gemma.model.genome.Chromosome.Some part of a chromosome
Spring Service base class for
ChromosomeService, provides access to all services
and entities referenced by this service.A utility class for
ChromosomeRepresents a BibliographicReference as a citation string (which is really super light value object).
A coexpression analysis of one experiment.
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
ubic.gemma.model.analysis.expression.coexpression.CoexpressionAnalysis.Deals with the Analysis objects for Coexpression - not the coexpression results themselves.
Cache for coexpression results.
Configures the cache for gene2gene coexpression.
Used to cache results; these objects are unmodifiable, and contains the coexpression data for one query gene and one
result gene, in all experiments.
Manages and queries coexpression 'links' between genes.
A key service for working with coexpression at a fairly low level.
Lightweight/convenient object for manipulating coexpression for a pair of genes.
A more heavyweight version of CoexpressionValueObject; has a bit more information about the genes.
An event indicating a comment was added to the auditable.
Persister for ubic.gemma.model.common package classes.
Contains methods to perform 'common' queries that are needed across DAOs.
A search source constituted of multiple other sources.
A "Probe set" (Affymetrix) or a "Probe" (other types of arrays).
This is a convenience object to hold the results of CompositeSequence mapping results.
Parse the "old" array description format.
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
ubic.gemma.model.expression.biomaterial.Compound.
Spring Service base class for
CompoundService, provides access to all services and entities referenced
by this service.Constants used across Gemma.
Representing a person or organization that can be contacted about, or is the source of, data in the system.
Represents a contrast.
Represents a contrast between "conditions".
Represents a contrast result.
Stores selected details of the contrasts for a single DifferentialExpressionResult
Helper object, not for general use.
Defines a class that can convert objects from one type to another.
Create a new database and drop an existing one if desired.
Created by tesarst on 06/03/17.
Created by tesarst on 13/03/17.
Class encapsulating all the curation information for Curatable objects.
Event types that can change
CurationDetails of Curatable objects.
Indicates that previous validation is being invalidated
Indicates that a data type (for a specific QuantitationType, possibly new) was added.
A reference to a record in a database.
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
DatabaseEntry.Spring Service base class for
DatabaseEntryService, provides access to all services and entities
referenced by this service.ValueObject for database entry
Populates the database schema.
Search source for direct database results.
Generates textual views of the database so other people can use the data.
A high-level service for deleting data and their associated files.
ArrayExpress stores files in an FTP site as tarred-gzipped archives.
Represents an AnnData dataframe.
Base interface for loading expression data in Gemma.
Configures a
DataLoader from a DataLoaderConfig.Indicates that a data type (for a specific QuantitationType, possibly new) was removed.
Signifies that the data for the experiment was replaced (or filled in) after the experiment was loaded into the
system.
Class to handle cases where there are multiple GEO dataset for a single actual experiment.
Retrieve GEO GDS files from the NCBI FTP server.
Update or fill in the data associated with an experiment.
An abstract class representing a one-dimensional vector of data about some aspect of an
ExpressionExperiment.Compute descriptive statistics for
DataVector.Base class for value objects of
BulkExpressionDataVector.An interface for
ExecutorService that delegate to another ExecutorService.Represents a dense AnnData matrix.
Interface for objects that have a human-readable name and description.
Data vector associated to a
CompositeSequence.Maps gene identifiers to
CompositeSequence.An analysis of changes in expression levels across experimental conditions
Holds the settings used for differential expression analysis, and defines some defaults.
Indicates the experiment was the subject of a differential expression analysis.
Service methods to do database-related work for differential expression analysis
Transactional methods for dealing with differential expression analyses.
Specialized command object for removing analysis results.
Result of an analysis of differences in expression levels -- a single test (e.g., for one gene or one probe), for one
factor.
File service for arbitrary list of
DifferentialExpressionAnalysisResult.Wraps an
ExpressionAnalysisResultSet and expose it to the public API.This class contains data for a column in metaheatmap visualization.
Unlike
DiffExResultSetSummaryValueObject, this value object is meant for the public API.A command object to be used by spaces.
A differential expression analysis spaces task
A helper class for the differential expression analyzers.
Summary of a differential expression analysis
Differential expression service to run the differential expression analysis (and persist the results using the
appropriate data access objects).
Represents a complete set of data for a differential expression query over a set of genes x conditions (resultSets x
contrasts).
A value object with meta analysis results.
Cache for differential expression results.
Cache for data from differential expression result queries.
This is a key class for queries to retrieve differential expression results (as well as standard CRUD aspects of
working with DifferentialExpressionResults).
Main entry point to retrieve differential expression data.
Created with IntelliJ IDEA.
Created with IntelliJ IDEA.
Encapsulates the search for differential expression results, for a set of genes and experiments (which can be
grouped)
Used to indicate the suitability status of an ExpressionExperiment for differential expression analysis.
Represents the results for one probe.
Writer for
DifferentialExpressionAnalysis.Used to perform meta-analyses of complete data sets (actually result sets), select the top genes, and potentially
store the results.
A command object to be used by spaces.
A differential expression meta-analysis space task
A command object with a selected factor and associated experiment.
Value object for differential expression result for one result - corresponds to the
DifferentialExpressionAnalysisResults for one gene in one ResultSet (combined for multiple probes), but represents
only the "selected" analysisResult.
Summary of a result set.
Represents the direction of a change e.g. in expression.
An event that occurs when a curator has validated the entity and indicated that it is "approved".
Value object for a
BulkExpressionDataVector containing doubles.Mock mail sender for testing.
Occurs when empirical bayes estimation fails.
This class provides a fast-path to
AclQueryUtils that uses the denormalized mask for anonymous users.Metrics for Ehcache 2.4 series.
A right singular vector (a.k.a. eigengenes)
author: anton date: 10/02/13
An empty bulk expression data matrix.
Used to make a 'dummy matrix' that has the column information populated.
Value object that represents a file record line from BioMart as configured with query parameters.
Match design elements using Ensembl IDs.
Map external identifiers to Gemma entities.
Mapping statistics computed from a given set of entities and identifiers.
A stateful entity mapper keeps an internal state for a set of candidates to optimize the mapping process.
A simple task command that contains an entity ID and class.
This builder allows for generating URLs for entities in Gemma Web and REST.
Exception raised when an Entrez reply contains an
ERROR tag.Represents an Entrez search query.
Possible values for the Entrez
retmode parameter.Low-level utilities for generating Entrez URLs.
Utilities for manipulating Entrez XML responses.
Environment profiles used in the Spring context.
High-level API for interacting with NCBI Entrez utilities.
Extends
Executors to ensure that security context logging works as expected.
Parse a description of ExperimentalFactors from a file, and associate it with a given ExpressionExperiment.
See interface for docs.
Spring Service base class for
ubic.gemma.model.expression.experiment.ExperimentalDesignService, provides
access to all services and entities referenced by this service.Describes an event that involved a change of assignment of factor value to bio material, or other changes in the
experimental design.
Tools for visualizing experimental designs.
Output compatible with
ExperimentalDesignImporterImpl.ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).
Represents coexpression at the level of experiment, referinng to links stored as Gene2GeneCoexpression.
Use to finish final transactional step in updating platform
An analysis of one or more ExpressionExperiments
A group of results for an ExpressionExperiment.
Matrix of booleans mapped from an ExpressionExperiment.
A data structure that holds a reference to the data for a given expression experiment.
Supports the creation and location of 'flat file' versions of data in the system, for download by users.
Generate filenames for various types of data files.
Expression data heatmap for experiments and subsets.
Warning, not fully tested.
Represents a matrix of data from an
ExpressionExperiment.Methods to organize ExpressionDataMatrices by column (or at least provide the ordering).
Encapsulates information about the row 'label' for a ExpressionDataMatrix.
Tools for easily getting data matrices for analysis in a consistent way.
Tools for easily getting data matrices for analysis in a consistent way.
Base interface for writing
ExpressionDataMatrix.Interface for matrices that can provide unboxed doubles.
Perform SVD on an expression data matrix, E = U S V'.
An event involving an ExpressionExperiment
Methods for correcting batch effects.
Provides status of batch information for datasets.
Created by tesarst on 13/03/17.
Methods to handle filtering expression experiments for analysis.
Types of metadata files that can be attached to an
ExpressionExperiment.
The event that this experiment has had its array design switched (typically to a 'merged' one.
Switch an expression experiment from one array design to another.
Sets up the array designs before saving an experiment.
Sets up the array designs, put the designelements in the data vectors.
Methods for reading and creating reports on ExpressinExperiments.
Handles creation, serialization and/or marshaling of reports about expression experiments.
Handles delegation of report generation (to the space, or run locally)
Handles searching for experiments and experiment sets
A grouping of expression studies.
Spring Service base class for
ubic.gemma.model.analysis.expression.ExpressionExperimentSetService,
provides access to all services and entities referenced by this service.This class will handle population of ExpressionExperimentSetValueObjects.
A subset of samples from an ExpressionExperiment
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet.Indicates that we have updated an expression experiment's information from GEO, after it was already loaded in Gemma.
Indicates that the "Vector merging" has been done on the associated experiment.
Service for reading and appending to changelog files.
Enumerates various globally available
ExternalDatabase by name.Provides convenience methods to provide ExternalDatabases and DatabaseEntries for common cases, such as Genbank.
Class to provide functionality to load genes from a tab delimited file.
The value for a ExperimentalFactor, representing a specific instance of the factor, such as "10 ug/kg" or "mutant"
Each factorvalue can be associated with multiple characteristics (or with a measurement).
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
ubic.gemma.model.expression.experiment.FactorValue.This interface needed to be extracted for factor value deletions in
order to be able to make the methods transactional
Handles deletions of a factor values.
Keep track of the first failed migration when multiple migrations are performed in a single transaction.
Deprecated.
Indicates that a factor value needs attention.
Ontology service for factor values and their annotations.
Represents an ontology statement.
Spring Service base class for
FactorValueService, provides access
to all services and entities referenced by this service.Deprecated.
aim towards using the
FactorValueBasicValueObject.Indicates that the attempt to get batch information failed due to an error.
Deprecated.
Represents a failed data replace.
Interface representing a class that can retrieve sequences from Blast databases.
FASTA sequence file parser.
Indicates that FASTQ headers were present, but were not in a format that yields usable information on batches.
Interface for classes that can fetch files from a remote location and copy them to a specified location.
Search source that can retrieve results matching specific fields.
Use to indicate a file format error.
Metadata about a file lock.
Process-level information about the file lock.
Create shared and exclusive locks for files.
Holds the necessary information to filter an entity with a property, operator and right-hand side value.
Holds settings for filtering.
Interface for filtering-capable DAO.
Interface for filtering-capable services.
Interface for VO-enabled DAO with filtering capabilities.
Interface VO-enabled service with filtering capabilities.
Represents a conjunction of disjunctions of
Filter.*
Fetcher that can fetch archives (e.g., tar.gz) and unpack them.
Factory and pool for
FTPClient.This implementation maintains one pool of FTP clients per URL authority (i.e
URL.getAuthority()).Download files by FTP.
Represents quality information about a data set.
Represents administrative geeq information.
Modes for filling GEEQ scores.
Represents publicly available geeq information
Ontology created for Gemma.
A minimalist client for accessing Gemma's RESTful API.
For endpoints that return no data (i.e. a 201 No Content reply code).
For endpoints that may return an error.
A response from the API, which is either a
GemmaRestApiClient.DataResponse or GemmaRestApiClient.ErrorResponse.Indicate that a property or type is only visible not visible outside of Gemma REST.
Indicate that a property is exclusively used for Gemma Web.
Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).
Used to store information about what happened when the GENE2CS table was updated.
Entity representing a relationship between two genes.
Represents coexpression of a pair of genes.
Entity representing a relationship between two genes identified by ID, rather than by the Gene entity (for efficiency
reasons).
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
ubic.gemma.model.genome.gene.GeneAlias.Important: this is slightly misnamed, since it potentially includes links that have support of zero.
Represents the coexpression node degree for a gene summarized across experiments, at each level of support.
Represents a GeneCoexpressionNodeDegree
Provides access to Gene2Gene links.
Tracks the datasets in which coexpression for a gene has been tested.
core service for Gene
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
Gene.Represents an analysis that combines the results of other analyses of differential expression.
Provides access to
DifferentialExpressionAnalysisResults and meta-analysis results.* @author frances
This is a convenience value object to hold a BlatResult and its associated gene products and genes.
Populate/update the gene multifunctionality information in the system.
Compute gene multifunctionality and store it in the database.
GO-based search source.
Generic cell-level characteristics.
Service that simplifies operation with curatable entities of unknown types.
A meter binder that delegates to the appropriate
Executor implementation.A generic loader that can be used to load single cell with a tabular metadata file.
Attach all the given
MeterBinder to the registry.Looks through text file looking for a date near the top of the file in a reasonable format.
A meter binder that delegates to the appropriate
TaskExecutor implementation.Service for searching genes (and gene sets)
Service for searching genes (and gene sets)
A grouping of genes that share a common relationship
The interface for managing groupings of genes.
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
ubic.gemma.model.genome.gene.GeneSet.Service for managing gene sets
Service for managing gene sets
Represents a Gene group gene set
* @author tvrossum
This class will handle population of GeneSetValueObjects.
Cache of the 'tested-in' information for genes.
Strategy to match a
BioAssay against a sample name provided by GEO.Gets records from GEO and compares them to Gemma.
This is marked as
Lazy since we don't use it outside Gemma Web, so it won't be loaded unless it's needed.Represents data for one channel on a microarray in GEO.
Constants used to help decipher GEO data files.
Convert GEO domain objects into Gemma objects.
Abstract class from which other GEO objects are descended.
A GEO-curated dataset.
Handle fetching and parsing GEO files.
GEO object generator that works on local files.
Class for parsing GSE and GDS files from NCBI GEO.
This simply holds the results obtained from parsing.
Bean describing a microarray platform in GEO
Represents a GEO query.
Used to contain GEO summary information from the 'Browse' views.
Type of records that can be browsed in GEO.
Represents a group of samples that were replicated.
Permitted types of replication.
Configuration to use to retrieve GEO records from a
GeoQuery.Represents a sample (GSM) in GEO.
Holds information about GEO samples that "go together" across datasets (GDS), because they came from the same sample
(or so we infer)
Enumeration of possible fields for searching GEO records.
Represents a set of GEO samples that were submitted together.
Non-interactive fetching, processing and persisting of GEO data.
This is the main single-cell data detector that delegates to other more specific detectors.
Represents a subset of samples.
Class to store the expression data prior to conversion.
A GeoVariable represents variables which were investigated.
Permitted descriptions of terms.
This enumeration was originally based on GO, but is used for all entities that have evidenciary aspects; Thus it has
been expanded to include: Terms from RGD (rat genome database)
IED = Inferred from experimental data
IAGP = Inferred from association of genotype and phenotype
IPM = Inferred from phenotype manipulation
QTM = Quantitative Trait Measurement
And our own custom code IIA which means Inferred from Imported Annotation to distinguish IEAs that we ourselves have
computed
See https://geneontology.org/docs/guide-go-evidence-codes/ for documentation of GO evidence codes.
Perform useful queries against GoldenPath (UCSC) databases.
Using the Goldenpath databases for comparing sequence alignments to gene locations.
Authority for groups (kind of like a "user role", but for group-based authorization)
Represents an HDF5 attribute.
Represents an HDF5 dataset.
Represents all the fundamental H5 types from which all other types are derived.
Minimal interface for a labelled heatmap.
Metrics for Hibernate 4.
Query metrics for Hibernate 4.
Search source based on Hibernate Search.
The sole purpose of this class is to limit usages of
org.springframework.orm to this package.Custom highlighter for search results.
Interface for mappers that can provide hints of identifier candidates.
The number of probes meeting a given q-value threshold in the result set.
Grabs urls like ftp:///ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data
Factory for
HomologeneService.Reads in the homologene list as specified in the Gemmea.properties file.
A generic class for fetching files via HTTP and writing them to a local file system.
Represents a set of IDs for entities (e.g., genes or experiments), stored in a bitSet.
Interface for objects that have a numerical id.
Utilities for
Identifiable.Base implementations for value objects representing persistent objects
Mark a DAO method as ignored for auditing.
Parse an Illumina "manifest.txt" file (tab-delimited).
Indexer service.
Created with IntelliJ IDEA.
Exception raised when the quantitation of an
ExpressionDataMatrix does not agree with the one inferred.Populate some initial data for tests.
Used to indicate that analysis was skipped, not necessarily an error.
Exception raised when an
encoding-type attribute has an unexpected value.Exception raised when a log2 conversion fails.
An abstract concept of a scientific study
Represents a layer.
Mark beans as lazy-init by default.
Handles fitting linear models with continuous or fixed-level covariates.
The difference between this class and BasicLineMapParser is more flexibility in how keys are provided.
A Parser that processes its input line-by-line.
Handles the actual coexpression analysis, once handed data that has been prepared.
Holds parameters needed for LinkAnalysis.
Configures whether only one of the two thresholds should be used.
Computing coexpression links for an expression experiment
Handles the persistence phase of a Link analysis.
Handles moving gene coexpression links from memory into the database; updates related meta-data.
Running link analyses through the spring context; will persist the results if the configuration says so.
Command object for Link analysis
Helper class to use for generating the link objects for persistence.
Utilities and algorithms for
List.Used for testing, but might have other uses, to fetch GEO data from local files instead of the GEO website.
A fetcher that only looks locally for "family" files (GPLXXX_family, GSEXXX_family).
Reimplementation of
LocalSessionFactoryBean that supports resolving XSD
schemas in the classpath.The sole purpose of this class is to limit usages of
org.springframework.orm to this package.A locked path.
Detects Loom files in series and samples.
Highlighter with additional capabilities for Lucene.
Utilities for parsing search queries using Lucene.
Indicate that an entity has been made private.
Indicate that an entity has been made public.
Creates a security context using manual authentication.
A simple implementation of
EntityMapper that uses a Map to store association between identifiers and
entities.Represents an AnnData mapping.
A wrapper for an
ExpressionDataMatrix that applies a mask to the data, allowing selective access to the
underlying matrix.Represents an AnnData matrix.
A quasi-universal matrix mask.
Writes
BulkExpressionDataMatrix to various tabular formats.Indicate that a collection may be intentionally uninitialized.
Responsible for returning the coordinates of the experiment's Mean-Variance relationship.
Manage the mean-variance relationship.
Utilities for
Measurement.Add metrics from each available
Ehcache in the given CacheManager to the supplied meter registry.Detects 10X MEX data from GEO series and samples.
Bundles a directory containing MEX files into a TAR archive.
Writes
SingleCellExpressionDataMatrix to the 10x MEX format.Load single cell data from 10X Genomics MEX format.
Configure a
MexSingleCellDataLoader for a given directory and collection of BioAssays.Exception raised when a HDF5 file/group/dataset is lacking a
encoding-type and/or encoding-version
attribute.Represents a gene that was not tested.
Computing missing values for an expression experiment
Utilities for working with Gemma models.
An interface for bulk matrices that supports multiple
BioAssay per BioMaterial.
See ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/README
Class to parse the NCBI gene2accession files.
This parses GO annotations from NCBI.
Convert NCBIGene2Accession objects into Gemma Gene objects with associated GeneProducts.
Simple helper data structure that stores an NcbiGeneInfo and its associated
NcbiGene2Accession elements.
Combines information from the gene2accession and gene_info files from NCBI Gene.
Class to download files for NCBI gene.
Represents the information from the "gene_history" file from NCBI (for one gene's history).
Parse the NCBI "gene_history" file.
See ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/README
See http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn unknown (0)
, 36
Class to parse the gene_info file from NCBI Gene.
Load or update information about genes from the NCBI Gene database.
Match design elements using the NCBI ID.
Base class for events altering
CurationDetails.getNeedsAttention().Indicates that previous validation is being invalidated
Helper methods to get FTP connection.
Exception raised when suitable factor is left for analysis.
Wrapper object used to track and eliminate duplicates.
Represents a gene that was tested, but the result wasn't significant.
Exception raised when retrieving a non-unique QT by name.
This is a special kind of preprocessing exception that occurs when filtering the expression data matrix result in no
rows left.
Exception raised when no sample is left for analysis.
This event type resets the trouble flag of curation details of a curatable object.
Single-cell data loader used when no data is available.
Match design elements using the official symbol of a gene.
Highlighter specialized for ontology terms.
Factory bean for baseCode's
OntologyService.Has a static method for finding out which ontologies are loaded into the system and a general purpose find method
that delegates to the many ontology services.
Utilities for working with ontologies.
Container for details about a proposed outlier
Methods to (attempt to) detect outliers in data sets.
Service for removing sample(s) from an expression experiment.
Interface for classes that allow parsing of files and streams.
Utilities to be used by parsers and loaders.
An exception that indicate that the search query could not be parsed.
A correlation analysis for a given data set, designed for selection of values based on criteria set by the user.
Represents a change in permissions of an
Auditable entity.Interface defining the ability to create domain objects in bulk or singly.
This interface contains a few extensions to the base
Persister interface to handle special cases with
ExpressionExperiment.A service that knows how to persist Gemma-domain objects.
Deprecated.
not needed
Deprecated.
as Person is deprecated
Deprecated.
as Person is deprecated
A very simple value object to represent a physical location
Fetch GEO "GPLXXX_family.soft.gz" files
General-purpose pointcuts to recognize CRUD operations etc.
Helper class for sample coexpression analysis.
A "processed expression data vector create" task
Allows us to catch preprocessing errors and handle them correctly.
Encapsulates steps that are done to expression data sets after they are loaded and experimental design curated.
Command object for processing data vectors.
Primitive storage types for data vectors.
Only stored for some of the probes (e.g. the top ones)
Holds parameters for how mapping should be done.
Provides methods for mapping sequences to genes and gene products.
Parse probes from a tabular file.
Represents the processed data that is used for actual analyses.
Computation of the "processed" expression data with the ranking (by 'expression level') information filled in, for an
Expression Experiment
Report progress.
This appender is used by remote tasks to send progress notifications to the webapp.
Represents a context under which progress update logs are intercepted the
ProgressUpdateCallback is
invoked.Callback used to emit progress updates.
Represents a mapping between a query/criteria property and some original property space.
Utilities for dealing with
PropertyMapping.Deprecated.
This has been replaced with Spring-based configuration
SettingsConfig and usage of Value
to inject configurations.Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
Protocol.Search PubMed for terms, retrieve document records.
Manage the loading of large numbers of pubmed entries into the database.
Simple class to parse XML in the format defined by
ncbi.
Interface implemented by single-cell data transformation that require Python.
Perform quantile normalization on a matrix, as described in:
Exception raised when an
ExpressionDataMatrix does not meet the expectations set by a given
QuantitationType.Base class for representing problematic
QuantitationType conversion.Perform various computations on ExpressionDataMatrices (usually in-place).
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
QuantitationType.An exception that wraps a
QuantitationTypeDetectionException.Has the unpleasant task of figuring out what the quantitation type should look like, given a description and name
string.
Value object for the
QuantitationType.Utilities for
Query.Defines a class that produces object that can be consumed by other classes.
Deprecated.
Retrieve and unpack the raw data files for GEO series.
Data for one design element, across one or more bioassays, for a single quantitation type.
Provides methods that can be applied to both RawExpressionDataVector and ProcessedExpressionDataVector
Abstract record-based parser.
An association between a BioSequence and a GeneProduct based on external database identifiers.
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
ReferenceAssociation.Persist objects like Gene2GOAssociation.
Event triggered when the release details of a
Versioned entity are
updated.A BioAssay-to-sample-name matcher that renames samples before matching them.
Parses a file that contains a mapping between old and new bioassay names.
Scan sequences for repeats using RepeatMasker.
A "probe" (Affymetrix); for other types of arrays, there is no practical distinction between compositesequences and
reporters, and all analysis would take place at the level of CompositeSequences.
Convert
DataVector to different PrimitiveType.Used to indicate that the suitability status of an experiment is the default.
Indicate that the method should be retried on failure.
Provide logging when an operation has failed and is being retried.
Filter out rows that have "too many" missing values.
Remove rows that have no BioSequence associated with the row.
The 'analysis' in the name is a bit of a stretch here, as this object servers purely as an aggregator
of all the sample coexpression matrices.
Manage the "sample correlation/coexpression" matrices.
Holds the data of the sample coexpression matrix
Exception raised in preprocessing when there is a problem with sample coexpression analysis.
Event used when a sample is removed from an experiment (typically due to QC concerns or when marked as an outlier).
Indicates that samples that were previously removed have been "put back", e.g. un-marked as an outlier.
Convert
DataVector to different ScaleType.Generic interface for classes that extract scan dates from raw data files.
Fetch the SRDF file
Exception raised by the
SearchService when the search could not be performed.Represents an individual search result.
Object to store search results of different classes in a similar way for displaying to user (ex: enables genes and
gene sets to be entries in the same combo box) object types handled are: Gene, GeneSet, GeneSetValueObject,
ExpressionExperiment and ExpressionExperimentSet SearchObject is also handled if the object it holds is of any of
those types for a gene or experiment, the memberIds field is a collection just containing the object's id. memberIds
is just for convenience on the client.
This is a special kind of set designed for holding
SearchResult.This service is used for performing searches using free text or exact matches to items in the database.
Configuration options for searching.
author: anton date: 18/03/13
Search source that provides
SearchResult from a search engine.Indicate that the search failed due to a
TimeoutException.A base service for securable entities.
A base service for securable entities with filtering and VO capabilities.
Specialization of Spring task-running support so task threads have secure context (without using MODE_GLOBAL!).
A secure Quartz job bean that executes with a given security context.
Used to assign a bin to a chromosome location, identify bins for a range, or to generate SQL to add to a query on a
GoldenPath database.
Convenient methods for manipulating BioSequences and PhysicalLocations
Tools for writing biosequences to files so they can be analyzed by external tools, and then read back into Gemma.
An interface for data loaders that can load sequencing data.
Configuration for loading sequencing data.
Represents sequencing metadata for a
BioAssay.Load sequencing metadata from a TSV file.
Adapt a
SequencingMetadataFileDataLoader so that it can be used as a SingleCellDataLoader.Interface implemented by single-cell detector that can contextualize a sample within a series.
Performs conversion by identifier and collection of identifier for a
BaseReadOnlyService.Perform conversion to value object by entity, ID and collections of entities and IDs and also to entity by ID and
collection of IDs.
Deprecated.
This has been replaced with Spring-based configuration
SettingsConfig and usage of Value
to inject configurations.Beans declaration for making the settings available via the Spring Environment and placeholder substitution.
Class to manage the gfServer and run BLAT searches.
A simple strategy for matching BioAssay to sample name.
A simple design element mapper that simply uses the name as identifier.
A simple downloader for FTP and HTTP(s) URLs.
Load experiment from a flat file.
Convert a simple matrix and some meta-data into an ExpressionExperiment.
Represents the basic data to enter about an expression experiment when starting from a delimited file of data
Simple implementation of methods for fetching sequences from blast-formatted databases, using blastdbcmd (aka
fastacmd)
A safer substitute for
SimpleHTMLFormatter that escape existing HTML tags
and use lowercase <b> tags.A simple retry implementation with exponential backoff.
An interface for work that can be retried.
Holds the state of a retry attempt.
A simple thread factory based on a preferably unique thread name prefix.
Indicates that we got batch information, but there was (as far as we can tell) just one batch.
Represents a boxplot(s) of single-cell data.
Common interface for all single cell data loaders.
Basic configuration for loading single-cell data.
Interface for configuring a single-cell data loader.
High-level service for loading single-cell data.
Pack an AnnData object by removing unnecessary zeroes.
Represents a single-cell data transformation.
Transpose a single-cell dataset.
Supported single-cell data types.
Utilities for aggregating single-cell data vectors.
Descriptive statistics for single cell data.
Interface for single-cell data detectors from GEO.
Represents a single-cell dimension, holding shared information for a set of
SingleCellExpressionDataVector.Value object for a single-cell dimension.
In a single-cell expression data matrix, each column represents a cell.
An expression data vector that contains data at the resolution of individual cells.
Utilities for working with
SingleCellExpressionDataVector.Aggregate single-cell vectors.
Aggregates single-cell expression data.
Methods for aggregating single-cell expression data.
High-level service for splitting and aggregating single-cell expression experiments.
Split a single-cell expression experiment into sub-experiments by cell type.
Simple transformation with input and output files.
Utility class for handling masks in single-cell analysis.
Utilities for slicing single cell data.
Heatmap that displays the sparsity of single-cell data.
Compute sparsity metrics for single cell data.
Emitted when a collection of
ExpressionExperimentSubSet for holding aggregated single-cell data is created.An analysis of a single experiment or subset.
Interface for analysis service manipulating single experiments.
Indicates that batches with only a single sample were found, which means we don't form batches at all.
Indiates that there was at least one batch with only one sample.
Log4j2 appender that report log events to a Slack channel.
Represents a slice of
List.Represents a directed sort by a property.
Direction of the sort.
A sparse array backed by an
ArrayList.A subclass of
List for sparsely stored lists.Utilities for dealing with sparse
ListRepresents a sparse AnnData matrix.
A sparse range array is a data structure that efficiently stores arrays of repeated elements by encoding their
starting offsets.
Subclass that computes correlations using ranks.
Configuration for splitting single-cell expression data in pseudo-bulks.
TODO Document Me
Split an experiment into multiple experiments.
Methods to create Spring contexts for Gemma manually.
Parses SRA runinfo format.
Parses SRA XML format.
A special kind of characteristic that act as a statement.
Represents a VO for a
Statement, typically part of a FactorValueBasicValueObject.Implementation of the
CacheKeyLock interface that uses a static week map to store locks by key.Utilities for working with
StopWatch.Various utilities for manipulating strings.
Obtained from the TaskRunningService, can be used to monitor status.
Represents a subquery right-hand side of a
Filter.Mode to use when filtering with a subquery.
Represents the datasets in which a link was found in ("supported").
Exception raised when suspicious values are detected in an
ExpressionDataMatrix.Exception raised when the SVD of a given expression data matrix cannot be computed.
Exception raised if a SVD cannot be computed.
Store information about SVD of expression data and comparisons to factors/batch information.
Performs Singular value decomposition on experiment data to get eigengenes, and does comparison of those PCs to
factors recorded in the experimental design.
Perform SVD on expression data and store the results.
This does a very minimal parse of Swissprot records, just to get mRNAs associated with a single protein.
Functions for maintaining the database.
Write a set of single-cell vectors to a simple tabular format.
This command class is used to allow communication of parameters for a task between a client and task running service,
which might be on a different computer.
Post-processor that wraps
TaskExecutor, AsyncTaskExecutor and SchedulingTaskExecutor with a
DelegatingSecurityContextTaskExecutor.Post-process
TaskExecutor, AsyncTaskExecutor and SchedulingTaskExecutor such that they
inherit the ThreadContext of their callers.author: anton
date: 10/02/13
author: anton date: 10/02/13
This class describes the result of long-running task.
Handles the execution of tasks in threads that can be checked by clients later.
Taxon information from NCBI comes as a tar.gz archive; only the names.dmp file is of interest.
Load taxa into the system.
Parse the "names.dmp" file from NCBI, ftp://ftp.ncbi.nih.gov/pub/taxonomy/.
A utility class for taxon.
This will exclude the component or configuration from component scanning.
Converts a text resource into a set of lines.
Vocabulary for The Gemma Factor Value Ontology (TGFVO).
Consistent initialization logic for the entity graph.
Interface for populating the Log4j
ThreadContext with custom information.Utilities for creating
Thread objects.Indicates that the data set had too few samples or probes to be analyzed (after filtering), and was skipped
Base class for events that alter the
CurationDetails.getTroubled() flag.Sets the trouble flag of curation details of any Curatable object.
Bunch of utilities for writing data to TSV.
Utility methods for taking an ExpressionExperiment and returning various types of ExpressionDataMatrices, such as the
processed data, preferred data, background, etc.
Computes a missing value matrix for ratiometric data sets.
Space task for computing two channel missing values.
Overrides Hibernate
ResultTransformer interface to include type safety.Indicates that FASTQ headers were present, but they were not usable for determining batches, typically because of
invalid formatting or lack of information.
A collection that is intentionally not initialized.
Exception raised when an operation is performed on an intentionally uninitialized collection.
A list that is intentionally not initialized.
A set that is intentionally not initialized.
Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
ubic.gemma.model.common.measurement.Unit.*
Indicates that the associated Experiment is NOT suitable for differential expression analysis.
Exception raised when data in a given representation cannot be converted to another representation.
Exception raised when data from a given scale cannot be converted to another scale.
Exception raised when data from a given quantitation type cannot be converted to another quantitation type.
Used to indicate failure was due to the format being unusable, but the files are available.
A user of the software system, who is authenticated.
DAO Class: is able to create, update, remove, load, and find objects of type
ubic.gemma.model.common.auditAndSecurity.User.An organized group of researchers with an identifiable leader and group members.
Overrides gsec's UserManager to provide Gemma-specific types.
Implementation for Spring Security, plus some other handy methods.
Simple username/password authenticator.
Override a few definition from gsec so that we can use Gemma-specific implementations safely.
Annotate class representing value objects.
Attempt to identify a preset value (ontology term) for certain strings found in GEO data sets and other places.
Tackles the problem of concatenating DesignElementDataVectors for a single experiment.
Interface implemented by entities that are externally versioned.
Base class for events relating to a
Versioned entity.A value object to hold onto the 'new' objects.
Creates reports that can be shown on the web pages or in social media feeds.
Service to collect data on object that are new in the system.
Handy methods for dealing with XML.
Resolves Hibernate XSD schemas from the classpath.