Constant Field Values

Contents

• ca.corefacility.*

ca.corefacility.*

ca.corefacility.bioinformatics.irida.config.analysis.AnalysisExecutionServiceConfig

Modifier and Type	Constant Field	Value
public static final int	ASYNC_ORDER	998

ca.corefacility.bioinformatics.irida.config.environment.IridaEnvironmentPostProcessor

Modifier and Type	Constant Field	Value
public static final int	ORDER	-2147483637

ca.corefacility.bioinformatics.irida.config.repository.IridaApiRepositoriesConfig

Modifier and Type	Constant Field	Value
public static final int	TRANSACTION_MANAGEMENT_ORDER	1000

ca.corefacility.bioinformatics.irida.config.security.IridaApiSecurityConfig

Modifier and Type	Constant Field	Value
public static final int	METHOD_SECURITY_ORDER	2147483647

ca.corefacility.bioinformatics.irida.config.web.IridaRestApiWebConfig

Modifier and Type	Constant Field	Value
public static final int	MAX_IN_MEMORY_SIZE	1048576

ca.corefacility.bioinformatics.irida.model.IridaClientDetails

Modifier and Type	Constant Field	Value
public static final java.lang.String	CLIENT_ID_CONSTRAINT_NAME	"UK_CLIENT_DETAILS_CLIENT_ID"

ca.corefacility.bioinformatics.irida.model.RemoteAPI

Modifier and Type	Constant Field	Value
public static final java.lang.String	SERVICE_URI_CONSTRAINT_NAME	"UK_REMOTE_API_SERVICEURI"

ca.corefacility.bioinformatics.irida.model.user.User

Modifier and Type	Constant Field	Value
public static final java.lang.String	USER_EMAIL_CONSTRAINT_NAME	"user_email_constraint"
public static final java.lang.String	USER_USERNAME_CONSTRAINT_NAME	"user_username_constraint"

ca.corefacility.bioinformatics.irida.model.workflow.description.IridaToolParameter

Modifier and Type	Constant Field	Value
public static final char	PARAMETER_NAME_SEPARATOR	46

ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowParameter

Modifier and Type	Constant Field	Value
public static final java.lang.String	IGNORE_DEFAULT_VALUE	""

ca.corefacility.bioinformatics.irida.plugins.IridaPlugin

Modifier and Type	Constant Field	Value
public static final java.lang.String	PLUGIN_API_VERSION	"1.1.0"

ca.corefacility.bioinformatics.irida.repositories.ProjectEventRepository

Modifier and Type	Constant Field	Value
public static final java.lang.String	GET_EVENTS_FOR_USER	"SELECT e FROM ProjectEvent e INNER JOIN e.project as p WHERE ((p in (select puj.project from ProjectUserJoin puj where puj.user = :forUser)) or (p in (select ugpj.project from UserGroupJoin ugj, UserGroupProjectJoin ugpj where ugj.group = ugpj.userGroup and ugj.user = :forUser)))"

ca.corefacility.bioinformatics.irida.repositories.ProjectRepository

Modifier and Type	Constant Field	Value
public static final java.lang.String	EXCLUDE_PROJECT	"p != :exclude"
public static final java.lang.String	MANAGER_IN_GROUP	"(p in (select ugpj.project from UserGroupJoin ugj, UserGroupProjectJoin ugpj where ugj.group = ugpj.userGroup and ugj.user = :forUser and ugpj.projectRole = ca.corefacility.bioinformatics.irida.model.enums.ProjectRole.PROJECT_OWNER))"
public static final java.lang.String	MANAGER_ON_PROJECT	"(p in (select puj.project from ProjectUserJoin puj where puj.user = :forUser and puj.projectRole = ca.corefacility.bioinformatics.irida.model.enums.ProjectRole.PROJECT_OWNER))"
public static final java.lang.String	PROJECT_MANAGER_PERMISSION	"((p in (select puj.project from ProjectUserJoin puj where puj.user = :forUser and puj.projectRole = ca.corefacility.bioinformatics.irida.model.enums.ProjectRole.PROJECT_OWNER)) or (p in (select ugpj.project from UserGroupJoin ugj, UserGroupProjectJoin ugpj where ugj.group = ugpj.userGroup and ugj.user = :forUser and ugpj.projectRole = ca.corefacility.bioinformatics.irida.model.enums.ProjectRole.PROJECT_OWNER)))"
public static final java.lang.String	PROJECT_NAME_LIKE	"(p.name like CONCAT(\'%\', :projectName,\'%\'))"
public static final java.lang.String	PROJECT_PERMISSIONS	"((p in (select puj.project from ProjectUserJoin puj where puj.user = :forUser)) or (p in (select ugpj.project from UserGroupJoin ugj, UserGroupProjectJoin ugpj where ugj.group = ugpj.userGroup and ugj.user = :forUser)))"
public static final java.lang.String	USER_IN_GROUP	"(p in (select ugpj.project from UserGroupJoin ugj, UserGroupProjectJoin ugpj where ugj.group = ugpj.userGroup and ugj.user = :forUser))"
public static final java.lang.String	USER_ON_PROJECT	"(p in (select puj.project from ProjectUserJoin puj where puj.user = :forUser))"

ca.corefacility.bioinformatics.irida.ria.config.GalaxySessionInterceptor

Modifier and Type	Constant Field	Value
public static final java.lang.String	GALAXY_CALLBACK_URL	"galaxyCallbackUrl"
public static final java.lang.String	GALAXY_CLIENT_ID	"galaxyClientID"

ca.corefacility.bioinformatics.irida.ria.config.UserSecurityInterceptor

Modifier and Type	Constant Field	Value
public static final java.lang.String	CURRENT_USER_DETAILS	"CURRENT_USER_DETAILS"

ca.corefacility.bioinformatics.irida.ria.config.thymeleaf.webpacker.WebpackerDialect

Modifier and Type	Constant Field	Value
public static final java.lang.String	ENTRY_ATTR	"entry"

ca.corefacility.bioinformatics.irida.ria.utilities.FileUtilities

Modifier and Type	Constant Field	Value
public static final java.lang.String	ATTACHMENT_FILENAME	"attachment;filename="
public static final java.lang.String	CONTENT_DISPOSITION	"Content-Disposition"
public static final java.lang.String	CONTENT_TYPE_APPLICATION_ZIP	"application/zip"
public static final java.lang.String	CONTENT_TYPE_TEXT	"text/plain"
public static final java.lang.String	EXTENSION_HTML_ZIP	".html.zip"
public static final java.lang.String	EXTENSION_ZIP	".zip"

ca.corefacility.bioinformatics.irida.ria.utilities.components.DataTable

Modifier and Type	Constant Field	Value
public static final java.lang.String	REQUEST_PARAM_DRAW	"draw"
public static final java.lang.String	REQUEST_PARAM_LENGTH	"length"
public static final java.lang.String	REQUEST_PARAM_SEARCH_VALUE	"search[value]"
public static final java.lang.String	REQUEST_PARAM_SORT_COLUMN	"order[0][column]"
public static final java.lang.String	REQUEST_PARAM_SORT_DIRECTION	"order[0][dir]"
public static final java.lang.String	REQUEST_PARAM_START	"start"
public static final java.lang.String	RESPONSE_PARAM_DATA	"data"
public static final java.lang.String	RESPONSE_PARAM_DRAW	"draw"
public static final java.lang.String	RESPONSE_PARAM_RECORDS_FILTERED	"recordsFiltered"
public static final java.lang.String	RESPONSE_PARAM_RECORDS_TOTAL	"recordsTotal"
public static final java.lang.String	RESPONSE_PARAM_SORT_COLUMN	"order[0][column]"
public static final java.lang.String	RESPONSE_PARAM_SORT_DIRECTION	"order[0][dir]"

ca.corefacility.bioinformatics.irida.ria.utilities.converters.FileSizeConverter

Modifier and Type	Constant Field	Value
public static final int	BYTES_PER_GB	1073741824
public static final int	BYTES_PER_KB	1024
public static final int	BYTES_PER_MB	1048576

ca.corefacility.bioinformatics.irida.ria.web.BaseController

Modifier and Type	Constant Field	Value
protected static final java.lang.String	MODEL_ERROR_ATTR	"errors"

ca.corefacility.bioinformatics.irida.ria.web.analysis.AnalysisController

Modifier and Type	Constant Field	Value
public static final java.lang.String	ANALYSIS_PAGE	"analysis"
public static final java.lang.String	PAGE_ANALYSIS_LIST	"analyses/analyses"
public static final java.lang.String	PAGE_USER_ANALYSIS_OUPUTS	"analyses/user-analysis-outputs"

ca.corefacility.bioinformatics.irida.ria.web.components.datatables.models.DataTablesResponseModel

Modifier and Type	Constant Field	Value
public static final java.lang.String	ROW_ID_PREFIX	"row_"

ca.corefacility.bioinformatics.irida.ria.web.linelist.dto.UISampleMetadata

Modifier and Type	Constant Field	Value
public static final java.lang.String	OWNER	"owner"

ca.corefacility.bioinformatics.irida.ria.web.login.PasswordResetController

Modifier and Type	Constant Field	Value
public static final java.lang.String	PASSWORD_RESET_PAGE	"password/password_reset"

ca.corefacility.bioinformatics.irida.ria.web.oauth.OltuAuthorizationController

Modifier and Type	Constant Field	Value
public static final java.lang.String	TOKEN_ENDPOINT	"/api/oauth/authorization/token"

ca.corefacility.bioinformatics.irida.ria.web.oauth.RemoteAPIController

Modifier and Type	Constant Field	Value
public static final java.lang.String	CLIENTS_PAGE	"remote_apis/list"
public static final java.lang.String	PARENT_FRAME_RELOAD_PAGE	"remote_apis/parent_reload"

ca.corefacility.bioinformatics.irida.ria.web.pipelines.PipelineController

Modifier and Type	Constant Field	Value
public static final java.lang.String	BASE_URL	"/pipelines"

ca.corefacility.bioinformatics.irida.ria.web.projects.ProjectsController

Modifier and Type	Constant Field	Value
public static final java.lang.String	LIST_PROJECTS_PAGE	"projects/projects"
public static final java.lang.String	PROJECTS_DIR	"projects/"
public static final java.lang.String	SYNC_NEW_PROJECT_PAGE	"projects/project_sync"

ca.corefacility.bioinformatics.irida.ria.web.services.UISequenceFileService

Modifier and Type	Constant Field	Value
public static final java.lang.String	IMG_DUPLICATION_LEVEL	"duplicationlevel"
public static final java.lang.String	IMG_PERBASE	"perbase"
public static final java.lang.String	IMG_PERSEQUENCE	"persequence"

ca.corefacility.bioinformatics.irida.security.permissions.files.ReadReferenceFilePermission

Modifier and Type	Constant Field	Value
public static final java.lang.String	PERMISSION_PROVIDED	"canReadReferenceFile"

ca.corefacility.bioinformatics.irida.security.permissions.files.UpdateReferenceFilePermission

Modifier and Type	Constant Field	Value
public static final java.lang.String	PERMISSION_PROVIDED	"canUpdateReferenceFile"

ca.corefacility.bioinformatics.irida.security.permissions.metadata.ReadMetadataEntryPermission

Modifier and Type	Constant Field	Value
public static final java.lang.String	PERMISSION_PROVIDED	"canReadMetadataEntry"

ca.corefacility.bioinformatics.irida.security.permissions.metadata.ReadMetadataTemplatePermission

Modifier and Type	Constant Field	Value
public static final java.lang.String	PERMISSION_PROVIDED	"canReadMetadataTemplate"

ca.corefacility.bioinformatics.irida.security.permissions.metadata.ReadProjectMetadataResponsePermission

Modifier and Type	Constant Field	Value
public static final java.lang.String	PERMISSION_PROVIDED	"readProjectMetadataResponse"

ca.corefacility.bioinformatics.irida.security.permissions.metadata.UpdateMetadataTemplatePermission

Modifier and Type	Constant Field	Value
public static final java.lang.String	PERMISSION_PROVIDED	"canUpdateMetadataTemplate"

ca.corefacility.bioinformatics.irida.security.permissions.project.ReadProjectPermission

Modifier and Type	Constant Field	Value
public static final java.lang.String	PERMISSION_PROVIDED	"canReadProject"

ca.corefacility.bioinformatics.irida.service.analysis.annotations.RunAsUserAspect

Modifier and Type	Constant Field	Value
public static final int	RUN_AS_USER_ORDER	999

ca.corefacility.bioinformatics.irida.service.analysis.execution.AnalysisExecutionServiceAspect

Modifier and Type	Constant Field	Value
public static final int	ANALYSIS_EXECUTION_ASPECT_ORDER	999

ca.corefacility.bioinformatics.irida.service.export.ExportUploadService

Modifier and Type	Constant Field	Value
public static final java.lang.String	NCBI_ACCESSION_METADATA_LABEL	"NCBI SRA Accession"

ca.corefacility.bioinformatics.irida.service.impl.CRUDServiceImpl<KeyType extends java.io.Serializable,ValueType extends Timestamped<KeyType>>

Modifier and Type	Constant Field	Value
protected static final java.lang.String	CREATED_DATE_SORT_PROPERTY	"createdDate"

ca.corefacility.bioinformatics.irida.service.impl.EmailControllerImpl

Modifier and Type	Constant Field	Value
public static final java.lang.String	PIPELINE_STATUS_TEMPLATE	"pipeline-status-email"
public static final java.lang.String	RESET_TEMPLATE	"password-reset-link"
public static final java.lang.String	SUBSCRIPTION_TEMPLATE	"subscription-email"
public static final java.lang.String	SYNC_EXPIRED_TEMPLATE	"sync-expired"
public static final java.lang.String	WELCOME_TEMPLATE	"welcome-email"

ca.corefacility.bioinformatics.irida.service.remote.impl.Fast5ObjectRemoteServiceImpl

Modifier and Type	Constant Field	Value
public static final java.lang.String	REL_SAMPLE_SEQUENCE_FILE_FAST5	"sample/sequenceFiles/fast5"

ca.corefacility.bioinformatics.irida.service.remote.impl.GenomeAssemblyRemoteServiceImpl

Modifier and Type	Constant Field	Value
public static final java.lang.String	SAMPLE_ASSEMBLY_REL	"sample/assemblies"

ca.corefacility.bioinformatics.irida.service.remote.impl.ProjectRemoteServiceImpl

Modifier and Type	Constant Field	Value
public static final java.lang.String	PROJECTS_BOOKMARK	"/projects"

ca.corefacility.bioinformatics.irida.service.remote.impl.SampleRemoteServiceImpl

Modifier and Type	Constant Field	Value
public static final java.lang.String	FILE_SAMPLE_REL	"sample"
public static final java.lang.String	PROJECT_SAMPLES_REL	"project/samples"
public static final java.lang.String	SAMPLES_CACHE_NAME	"samplesForProject"

ca.corefacility.bioinformatics.irida.service.remote.impl.SequenceFilePairRemoteServiceImpl

Modifier and Type	Constant Field	Value
public static final java.lang.String	SAMPLE_SEQENCE_FILE_PAIRS_REL	"sample/sequenceFiles/pairs"

ca.corefacility.bioinformatics.irida.service.remote.impl.SingleEndSequenceFileRemoteServiceImpl

Modifier and Type	Constant Field	Value
public static final java.lang.String	SAMPLE_SEQENCE_FILE_UNPAIRED_REL	"sample/sequenceFiles/unpaired"

ca.corefacility.bioinformatics.irida.web.controller.api.RESTAnalysisSubmissionController

Modifier and Type	Constant Field	Value
public static final java.lang.String	ANALYSIS_REL	"analysis"
public static final java.lang.String	FILE_REL	"outputFile"
public static final java.lang.String	INPUT_FILES_PAIRED_REL	"input/paired"
public static final java.lang.String	INPUT_FILES_UNPAIRED_REL	"input/unpaired"
public static final java.lang.String	SUBMISSIONS_REL	"analysisSubmissions"

ca.corefacility.bioinformatics.irida.web.controller.api.RESTGenericController<Type extends IridaRepresentationModel & IridaThing & java.lang.Comparable<Type>>

Modifier and Type	Constant Field	Value
public static final java.lang.String	REL_COLLECTION	"collection"
public static final java.lang.String	REL_RELATIONSHIP	"relationship"
public static final java.lang.String	RELATED_RESOURCES_NAME	"relatedResources"
public static final java.lang.String	RESOURCE_NAME	"responseResource"

ca.corefacility.bioinformatics.irida.web.controller.api.RESTUsersController

Modifier and Type	Constant Field	Value
public static final java.lang.String	REL_USER_PROJECTS	"user/projects"
public static final java.lang.String	USER_PROJECTS_MAP_LABEL	"projects"

ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectSamplesController

Modifier and Type	Constant Field	Value
public static final java.lang.String	REL_PROJECT	"sample/project"
public static final java.lang.String	REL_PROJECT_SAMPLE	"project/sample"
public static final java.lang.String	REL_PROJECT_SAMPLES	"project/samples"

ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectsController

Modifier and Type	Constant Field	Value
public static final java.lang.String	PROJECT_HASH_REL	"project/hash"
public static final java.lang.String	REL_PROJECT	"project"

ca.corefacility.bioinformatics.irida.web.controller.api.projects.RESTProjectUsersController

Modifier and Type	Constant Field	Value
public static final java.lang.String	METADATA_ROLE_KEY	"metadataRole"
public static final java.lang.String	REL_PROJECT_USERS	"project/users"
public static final java.lang.String	USER_ID_KEY	"userId"
public static final java.lang.String	USER_ROLE_KEY	"role"

ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleAssemblyController

Modifier and Type	Constant Field	Value
public static final java.lang.String	REL_ASSEMBLY_ANALYSIS	"assembly/analysis"
public static final java.lang.String	REL_SAMPLE	"sample"
public static final java.lang.String	REL_SAMPLE_ASSEMBLIES	"sample/assemblies"

ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleMetadataController

Modifier and Type	Constant Field	Value
public static final java.lang.String	ALL_METADATA_REL	"project/samples/metadata"
public static final java.lang.String	METADATA_REL	"sample/metadata"
public static final java.lang.String	SAMPLE_REL	"sample"

ca.corefacility.bioinformatics.irida.web.controller.api.samples.RESTSampleSequenceFilesController

Modifier and Type	Constant Field	Value
public static final java.lang.String	REL_AUTOMATED_ASSEMBLY	"analysis/assembly"
public static final java.lang.String	REL_PAIR	"pair"
public static final java.lang.String	REL_PAIR_FORWARD	"pair/forward"
public static final java.lang.String	REL_PAIR_REVERSE	"pair/reverse"
public static final java.lang.String	REL_PAIR_SAMPLE	"sequenceFilePair/sample"
public static final java.lang.String	REL_QC_SEQFILE	"qc/sequencefile"
public static final java.lang.String	REL_SAMPLE	"sample"
public static final java.lang.String	REL_SAMPLE_SEQUENCE_FILE_FAST5	"sample/sequenceFiles/fast5"
public static final java.lang.String	REL_SAMPLE_SEQUENCE_FILE_PAIRS	"sample/sequenceFiles/pairs"
public static final java.lang.String	REL_SAMPLE_SEQUENCE_FILE_UNPAIRED	"sample/sequenceFiles/unpaired"
public static final java.lang.String	REL_SAMPLE_SEQUENCE_FILES	"sample/sequenceFiles"
public static final java.lang.String	REL_SEQ_OBJECT	"sequenceFile/sequencingObject"
public static final java.lang.String	REL_SEQ_QC	"sequencefile/qc"
public static final java.lang.String	REL_SEQUENCEFILE_SAMPLE	"sequenceFile/sample"
public static final java.lang.String	REL_SISTR_TYPING	"analysis/sistr"
public static final java.lang.String	SEQUENCE_FILE_ID_KEY	"sequenceFileId"

ca.corefacility.bioinformatics.irida.web.controller.api.sequencingrun.RESTSequencingRunController

Modifier and Type	Constant Field	Value
public static final java.lang.String	MISEQ_REL	"sequencingRun/miseq"

ca.corefacility.bioinformatics.irida.web.controller.api.sequencingrun.RESTSequencingRunSequenceFilesController

Modifier and Type	Constant Field	Value
public static final java.lang.String	SEQUENCEFILE_ID_KEY	"sequenceFileId"

ca.corefacility.bioinformatics.irida.web.spring.view.CSVView

Modifier and Type	Constant Field	Value
public static final java.lang.String	DEFAULT_CONTENT_TYPE	"text/csv"

ca.corefacility.bioinformatics.irida.web.spring.view.FastaView

Modifier and Type	Constant Field	Value
public static final java.lang.String	DEFAULT_CONTENT_TYPE	"application/fasta"

ca.corefacility.bioinformatics.irida.web.spring.view.FastqView

Modifier and Type	Constant Field	Value
public static final java.lang.String	DEFAULT_CONTENT_TYPE	"application/fastq"

ca.corefacility.bioinformatics.irida.web.spring.view.GenbankView

Modifier and Type	Constant Field	Value
public static final java.lang.String	DEFAULT_CONTENT_TYPE	"application/genbank"

ca.corefacility.bioinformatics.irida.web.spring.view.NewickFileView

Modifier and Type	Constant Field	Value
public static final java.lang.String	DEFAULT_CONTENT_TYPE	"application/newick"