Constant Field Values

io.seqware.*

• io.seqware.pipeline.engines.whitestar.Persistence 

  Modifier and Type	Constant Field	Value
  public static final String	PERSISTENT_DIR	"whitestar"
  public static final String	STATE_FILENAME	"state.json"
  public static final String	WORKFLOW_FILENAME	"workflow.json"
  public static final String	WORKFLOW_RUN_FILENAME	"workflowRun.json"

• io.seqware.pipeline.plugins.WorkflowLauncher 

  Modifier and Type	Constant Field	Value
  public static final String	LAUNCH_SCHEDULED	"launch-scheduled"

• io.seqware.pipeline.plugins.WorkflowRescheduler 

  Modifier and Type	Constant Field	Value
  public static final String	INPUT_FILES	"input-files"

• io.seqware.pipeline.plugins.WorkflowScheduler 

  Modifier and Type	Constant Field	Value
  public static final String	INPUT_FILES	"input-files"
  public static final String	OVERRIDE_INI_DESC	"Override ini options on the command after the separator \"--\" with pairs of \"--<key> <value>\""

• io.seqware.pipeline.plugins.WorkflowWatcher 

  Modifier and Type	Constant Field	Value
  public static final String	OVERRIDE_INI_DESC	"Override ini options on the command after the separator \"--\" with pairs of \"--<key> <value>\""

• io.seqware.pipeline.plugins.sanity.ProvidedBundleUserPhase5 

  Modifier and Type	Constant Field	Value
  public static final String	WORKFLOW	"Workflow"

• io.seqware.pipeline.plugins.sanity.SanityCheck 

  Modifier and Type	Constant Field	Value
  public static final int	NUMBER_TO_OUTPUT	100

net.sourceforge.*

• net.sourceforge.seqware.common.business.ExperimentLibraryDesignService 

  Modifier and Type	Constant Field	Value
  public static final String	NAME	"ExperimentLibraryDesignService"

• net.sourceforge.seqware.common.business.ExperimentService 

  Modifier and Type	Constant Field	Value
  public static final String	NAME	"ExperimentService"

• net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService 

  Modifier and Type	Constant Field	Value
  public static final String	NAME	"ExperimentSpotDesignReadSpecService"

• net.sourceforge.seqware.common.business.ExperimentSpotDesignService 

  Modifier and Type	Constant Field	Value
  public static final String	NAME	"ExperimentSpotDesignService"

• net.sourceforge.seqware.common.business.FileService 

  Modifier and Type	Constant Field	Value
  public static final String	NAME	"fileService"

• net.sourceforge.seqware.common.business.FileTypeService 

  Modifier and Type	Constant Field	Value
  public static final String	NAME	"FileTypeService"

• net.sourceforge.seqware.common.business.FileUploadService 

  Modifier and Type	Constant Field	Value
  public static final String	NAME	"FileUploadService"

• net.sourceforge.seqware.common.business.InvoiceService 

  Modifier and Type	Constant Field	Value
  public static final String	NAME	"invoiceService"

• net.sourceforge.seqware.common.business.IUSService 

  Modifier and Type	Constant Field	Value
  public static final String	NAME	"IUSService"

• net.sourceforge.seqware.common.business.LaneService 

  Modifier and Type	Constant Field	Value
  public static final String	NAME	"laneService"

• net.sourceforge.seqware.common.business.LibrarySelectionService 

  Modifier and Type	Constant Field	Value
  public static final String	NAME	"LibrarySelectionService"

• net.sourceforge.seqware.common.business.LibrarySourceService 

  Modifier and Type	Constant Field	Value
  public static final String	NAME	"LibrarySourceService"

• net.sourceforge.seqware.common.business.LibraryStrategyService 

  Modifier and Type	Constant Field	Value
  public static final String	NAME	"LibraryStrategyService"

• net.sourceforge.seqware.common.business.OrganismService 

  Modifier and Type	Constant Field	Value
  public static final String	NAME	"OrganismService"

• net.sourceforge.seqware.common.business.PlatformService 

  Modifier and Type	Constant Field	Value
  public static final String	NAME	"PlatformService"

• net.sourceforge.seqware.common.business.ProcessingService 

  Modifier and Type	Constant Field	Value
  public static final String	NAME	"processingService"

• net.sourceforge.seqware.common.business.RegistrationService 

  Modifier and Type	Constant Field	Value
  public static final String	NAME	"registrationService"

• net.sourceforge.seqware.common.business.SampleService 

  Modifier and Type	Constant Field	Value
  public static final String	NAME	"sampleService"

• net.sourceforge.seqware.common.business.SequencerRunService 

  Modifier and Type	Constant Field	Value
  public static final String	NAME	"SequencerRunService"

• net.sourceforge.seqware.common.business.ShareStudyService 

  Modifier and Type	Constant Field	Value
  public static final String	NAME	"shareStudyService"

• net.sourceforge.seqware.common.business.ShareWorkflowRunService 

  Modifier and Type	Constant Field	Value
  public static final String	NAME	"shareWorkflowRunService"

• net.sourceforge.seqware.common.business.StudyService 

  Modifier and Type	Constant Field	Value
  public static final String	NAME	"StudyService"

• net.sourceforge.seqware.common.business.StudyTypeService 

  Modifier and Type	Constant Field	Value
  public static final String	NAME	"StudyTypeService"

• net.sourceforge.seqware.common.business.WorkflowParamService 

  Modifier and Type	Constant Field	Value
  public static final String	NAME	"workflowParamService"

• net.sourceforge.seqware.common.business.WorkflowParamValueService 

  Modifier and Type	Constant Field	Value
  public static final String	NAME	"WorkflowParamValueService"

• net.sourceforge.seqware.common.business.WorkflowRunParamService 

  Modifier and Type	Constant Field	Value
  public static final String	NAME	"WorkflowRunParamService"

• net.sourceforge.seqware.common.business.WorkflowRunService 

  Modifier and Type	Constant Field	Value
  public static final String	NAME	"WorkflowRunService"

• net.sourceforge.seqware.common.business.WorkflowService 

  Modifier and Type	Constant Field	Value
  public static final String	NAME	"WorkflowService"

• net.sourceforge.seqware.common.model.Sample 

  Modifier and Type	Constant Field	Value
  public static final String	GEO_REACTION_ID_ATTR_TAG	"geo_reaction_id"

• net.sourceforge.seqware.common.module.ReturnValue 

  Modifier and Type	Constant Field	Value
  public static final int	DBCOULDNOTDISCONNECT	81
  public static final int	DBCOULDNOTINITIALIZE	80
  public static final int	DIRECTORYNOTREADABLE	3
  public static final int	DIRECTORYNOTWRITABLE	11
  public static final int	ENVVARNOTFOUND	14
  public static final int	FAILURE	15
  public static final int	FILEEMPTY	12
  public static final int	FILENOTEXECUTABLE	10
  public static final int	FILENOTREADABLE	4
  public static final int	FILENOTWRITABLE	5
  public static final int	FREEMARKEREXCEPTION	70
  public static final int	INVALIDARGUMENT	9
  public static final int	INVALIDFILE	7
  public static final int	INVALIDPARAMETERS	2
  public static final int	INVALIDPLUGIN	120
  public static final int	METADATAINVALIDIDCHAIN	8
  public static final int	NOTIMPLEMENTED	-1
  public static final int	NULL	-99
  public static final int	PROCESSING	100
  public static final int	PROGRAMFAILED	1
  public static final int	QUEUED	101
  public static final int	RETURNEDHELPMSG	110
  public static final int	RUNNERERR	91
  public static final int	RUNTIMEEXCEPTION	6
  public static final int	SETTINGSFILENOTFOUND	13
  public static final int	SQLQUERYFAILED	82
  public static final int	STDOUTERR	90
  public static final int	SUCCESS	0
  public static final int	UNKNOWN	130

• net.sourceforge.seqware.common.util.configtools.ConfigTools 

  Modifier and Type	Constant Field	Value
  public static final String	SEQWARE_SETTINGS_PROPERTY	"SEQWARE_SETTINGS"

• net.sourceforge.seqware.common.util.filetools.FileTools 

  Modifier and Type	Constant Field	Value
  public static final String	FORCE_HOST	"force-host"

• net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil 

  Modifier and Type	Constant Field	Value
  protected final int	READ_ATTEMPTS	1000

• net.sourceforge.seqware.common.util.maptools.MapTools 

  Modifier and Type	Constant Field	Value
  public static final String	LEGACY_VAR_BUNDLE_DIR	"workflow_bundle_dir"
  public static final String	LEGACY_VAR_DATE	"date"
  public static final String	LEGACY_VAR_RANDOM	"random"
  public static final String	VAR_BUNDLE_DIR	"sqw.bundle-dir"
  public static final String	VAR_DATE	"sqw.date"
  public static final String	VAR_DATETIME	"sqw.datetime"
  public static final String	VAR_RANDOM	"sqw.random"
  public static final String	VAR_TIMESTAMP	"sqw.timestamp"
  public static final String	VAR_UUID	"sqw.uuid"
  public static final String	VAR_WORKFLOW_VERSION	"sqw.bundle-seqware-version"

• net.sourceforge.seqware.pipeline.module.Module 

  Modifier and Type	Constant Field	Value
  public static final String	VERSION	"0.7.0"

• net.sourceforge.seqware.pipeline.modules.GenericCommandRunner 

  Modifier and Type	Constant Field	Value
  public static final int	DEFAULT_QUEUE_LENGTH	10
  public static final String	GCR_STDERR	"gcr-stderr"
  public static final String	GCR_STDERR_BUFFERSIZE	"gcr-stderr-buffer-size"
  public static final String	GCR_STDOUT	"gcr-stdout"
  public static final String	GCR_STDOUT_BUFFERSIZE	"gcr-stdout-buffer-size"

• net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker 

  Modifier and Type	Constant Field	Value
  public static final String	WORKFLOW_RUN_ACCESSION	"workflow-run-accession"

• net.sourceforge.seqware.pipeline.plugins.checkdb.CheckDB 

  Modifier and Type	Constant Field	Value
  public static final int	NUMBER_TO_OUTPUT	100

• net.sourceforge.seqware.pipeline.plugins.fileprovenance.ProvenanceUtility 

  Modifier and Type	Constant Field	Value
  public static final String	ALL	"all"

• net.sourceforge.seqware.pipeline.workflowV2.WorkflowV2Utility 

  Modifier and Type	Constant Field	Value
  public static final String	WORKFLOW_CLASS	"workflow_class"
  public static final String	WORKFLOW_ENGINE	"workflow_engine"
  public static final String	WORKFLOW_TYPE	"workflow_type"

• net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob 

  Modifier and Type	Constant Field	Value
  public static final String	SCRIPTS_SUBDIR	"generated-scripts"
  public static final String	SGE_MAX_MEMORY_PARAM_VARIABLE	"${maxMemory}"
  public static final String	SGE_THREADS_PARAM_VARIABLE	"${threads}"

• net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.StringTruncator 

  Modifier and Type	Constant Field	Value
  public static final int	DUPLICATION_LIMIT	9999
  public static final int	ROOT_CHAR_COUNT	45

• net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.WorkflowApp 

  Modifier and Type	Constant Field	Value
  public static final String	JOB_PREFIX	"s"
  public static final String	URIOOZIEWORKFLOW	"uri:oozie:workflow:0.4"

• net.sourceforge.seqware.webservice.resources.tables.FileChildWorkflowRunsResource 

  Modifier and Type	Constant Field	Value
  public static final String	DIRECT_SEARCH	"DIRECT_SEARCH"

• net.sourceforge.solexatools.util.Constant 

  Modifier and Type	Constant Field	Value
  public static final String	ANALYSIS_VIEW	"redirect:/myAnalisysList.htm"
  public static final String	EXPERIMENT_PREFIX	"exp_"
  public static final String	FILE_PREFIX	"fl_"
  public static final String	IUS_PREFIX	"ius_"
  public static final String	LANE_PREFIX	"seq_"
  public static final String	PROCESSING_PREFIX	"ae_"
  public static final String	SAMPLE_PREFIX	"sam_"
  public static final String	SEQUENCER_VIEW	"redirect:/sequencerRunList.htm"
  public static final String	STUDY_PREFIX	"study_"
  public static final String	STUDY_VIEW	"redirect:/myStudyList.htm"
  public static final String	WORKFLOW_RUN_PREFIX	"wfr_"

• net.sourceforge.solexatools.util.LaunchWorkflowUtil 

  Modifier and Type	Constant Field	Value
  public static final String	SELECTED_FILES	"selectedLaunchFiles"
  public static final String	SELECTED_NODES	"launchSelectedNodes"
  public static final String	SELECTED_VALUES	"selectedWorkflowParamValueId"

• net.sourceforge.solexatools.util.PaginationUtil 

  Modifier and Type	Constant Field	Value
  public static final int	SIZE_COUNT_FILE	5
  public static final int	SIZE_COUNT_TREE	20

• net.sourceforge.solexatools.util.SequencerRunHtmlUtil 

  Modifier and Type	Constant Field	Value
  public static final String	TYPE_TREE	"sr"

• net.sourceforge.solexatools.util.StudyHtmlUtil 

  Modifier and Type	Constant Field	Value
  public static final String	TYPE_TREE	"st"

• net.sourceforge.solexatools.util.WorkflowRunHtmlUtil 

  Modifier and Type	Constant Field	Value
  public static final String	TYPE_TREE_COMPLETED	"wfr"
  public static final String	TYPE_TREE_RUNNNING	"wfrr"

• net.sourceforge.solexatools.validation.LoginValidator 

  Modifier and Type	Constant Field	Value
  protected static final String	CONST_AT_SIGN	"@"

• net.sourceforge.solexatools.webapp.controller.BulkDownloaderController 

  Modifier and Type	Constant Field	Value
  public static final int	BUFFERSIZE	512000

• net.sourceforge.solexatools.webapp.controller.SampleWorkflowRunsController 

  Modifier and Type	Constant Field	Value
  public static final String	SAMPLE_SWID	"sw"

• net.sourceforge.solexatools.webapp.controller.SearchController 

  Modifier and Type	Constant Field	Value
  public static final String	SEARCH_CASE_SENSITIVE	"search.checked"

• net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController 

  Modifier and Type	Constant Field	Value
  public static final String	CHECK	"check"
  public static final String	CSV_TYPE	"csvtype"
  public static final String	FILE_EXPERIMENT_NAME	"f_exp_name"
  public static final String	FILE_EXPERIMENT_SWID	"f_exp_swid"
  public static final String	FILE_FILE	"f_file"
  public static final String	FILE_IUS	"f_ius"
  public static final String	FILE_IUS_NAME	"f_ius_name"
  public static final String	FILE_IUS_SWID	"f_ius_swid"
  public static final String	FILE_IUS_TAG	"f_ius_tag"
  public static final String	FILE_LANE	"f_lane"
  public static final String	FILE_LANE_NAME	"f_lane_name"
  public static final String	FILE_LANE_NUMBER	"f_lane_num"
  public static final String	FILE_LANE_SWID	"f_lane_swid"
  public static final String	FILE_LIBRARY	"f_library"
  public static final String	FILE_META_TYPE	"f_file_meta"
  public static final String	FILE_PARENT_SAMPLE_NAME	"f_sample_name"
  public static final String	FILE_PARENT_SAMPLE_SWID	"f_sample_swid"
  public static final String	FILE_PATH	"f_file_path"
  public static final String	FILE_PROCESSING_ALG	"f_processing_alg"
  public static final String	FILE_PROCESSING_SWID	"f_processing_swid"
  public static final String	FILE_RUN_NAME	"f_run_name"
  public static final String	FILE_RUN_SWID	"f_run_swid"
  public static final String	FILE_SAMPLE	"f_sample"
  public static final String	FILE_SAMPLE_NAME	"f_child_sample_name"
  public static final String	FILE_SAMPLE_SWID	"f_child_sample_swid"
  public static final String	FILE_SEQUENCER_NAME	"f_seqrun_name"
  public static final String	FILE_SEQUENCER_SWID	"f_seqrun_swid"
  public static final String	FILE_STUDY_SWID	"f_study_swid"
  public static final String	FILE_STUDY_TITLE	"f_study_title"
  public static final String	FILE_SWID	"f_file_swid"
  public static final String	FILE_TEMPLATE	"f_template"
  public static final String	FILE_TISSUE	"f_tissue"
  public static final String	FILE_WF_NAME	"f_wf_name"
  public static final String	FILE_WF_SWID	"f_wf_swid"
  public static final String	FILE_WF_VERSION	"f_wf_version"
  public static final String	PAGE_NUM	"page"
  public static final String	ROWS_PER_PAGE	"rp"
  public static final String	SEQ_RUN_ID	"seq_run_id"
  public static final String	SORT_NAME	"sortname"
  public static final String	SORT_ORDER	"sortorder"
  public static final String	SORT_ORDER_ASC	"asc"
  public static final String	SORT_ORDER_DESC	"desc"
  public static final String	TABLE_MODEL	"tablemodel"
  public static final String	TABLE_SEL	"tablesel"

• net.sourceforge.solexatools.webapp.controller.StudyReportBoxController 

  Modifier and Type	Constant Field	Value
  public static final String	CHECK	"check"
  public static final String	CSV_TYPE	"csvtype"
  public static final String	JSON	"json"
  public static final String	SORT_NAME	"sortname"
  public static final String	SORT_ORDER	"sortorder"
  public static final String	STUDY_ID	"study_id"

• net.sourceforge.solexatools.webapp.controller.StudyReportTableController 

  Modifier and Type	Constant Field	Value
  public static final String	FILE_EXPERIMENT_NAME	"f_exp_name"
  public static final String	FILE_EXPERIMENT_SWID	"f_exp_swid"
  public static final String	FILE_FILE	"f_file"
  public static final String	FILE_IUS	"f_ius"
  public static final String	FILE_IUS_SWID	"f_ius_swid"
  public static final String	FILE_IUS_TAG	"f_ius_tag"
  public static final String	FILE_LANE	"f_lane"
  public static final String	FILE_LANE_NAME	"f_lane_name"
  public static final String	FILE_LANE_NUMBER	"f_lane_num"
  public static final String	FILE_LANE_SWID	"f_lane_swid"
  public static final String	FILE_LIBRARY	"f_library"
  public static final String	FILE_META_TYPE	"f_file_meta"
  public static final String	FILE_PARENT_SAMPLE_NAME	"f_sample_name"
  public static final String	FILE_PARENT_SAMPLE_SWID	"f_sample_swid"
  public static final String	FILE_PATH	"f_file_path"
  public static final String	FILE_PROCESSING_ALG	"f_processing_alg"
  public static final String	FILE_PROCESSING_SWID	"f_processing_swid"
  public static final String	FILE_RUN_NAME	"f_run_name"
  public static final String	FILE_RUN_SWID	"f_run_swid"
  public static final String	FILE_SAMPLE	"f_sample"
  public static final String	FILE_SAMPLE_NAME	"f_child_sample_name"
  public static final String	FILE_SAMPLE_SWID	"f_child_sample_swid"
  public static final String	FILE_SEQUENCER_NAME	"f_seqrun_name"
  public static final String	FILE_SEQUENCER_SWID	"f_seqrun_swid"
  public static final String	FILE_STUDY_SWID	"f_study_swid"
  public static final String	FILE_STUDY_TITLE	"f_study_title"
  public static final String	FILE_SWID	"f_file_swid"
  public static final String	FILE_TEMPLATE	"f_template"
  public static final String	FILE_TISSUE	"f_tissue"
  public static final String	FILE_WF_NAME	"f_wf_name"
  public static final String	FILE_WF_SWID	"f_wf_swid"
  public static final String	FILE_WF_VERSION	"f_wf_version"
  public static final String	JSON	"json"
  public static final String	PAGE_NUM	"page"
  public static final String	ROWS_PER_PAGE	"rp"
  public static final String	SAMPLE_CHILD	"s_child"
  public static final String	SAMPLE_SAMPLE	"s_sample"
  public static final String	SORT_NAME	"sortname"
  public static final String	SORT_ORDER	"sortorder"
  public static final String	SORT_ORDER_ASC	"asc"
  public static final String	SORT_ORDER_DESC	"desc"
  public static final String	STUDY_ID	"study_id"
  public static final String	TABLE_MODEL	"tablemodel"
  public static final String	TABLE_SEL	"tablesel"