Constant Field Values

Contents

• <Unnamed>
• gov.nih.*
• org.quartz.*

<Unnamed>.*

BAMCommandLineLoader

Modifier and Type	Constant Field	Value
public static final String	APP_CONTEXT	"appContext-BAMLoader.xml"

gov.nih.*

gov.nih.nci.ncicb.tcga.dcc.ConstantValues

Modifier and Type	Constant Field	Value
public static final String	ACCESS_TYPE	"access_type"
public static final int	ALIQUOT_BARCODE_LENGTH	29
public static final String	APP_NAME_ANNOTATIONS	"annotations"
public static final String	APP_NAME_COMMON	"common"
public static final String	APP_NAME_DAM	"dam"
public static final String	APP_NAME_DATA_BROWSER	"databrowser"
public static final String	APP_NAME_DATA_REPORTS_WEB	"datareports-web"
public static final String	APP_NAME_METADATA_BROWSER	"uuid"
public static final String	APP_NAME_QCLIVE	"qclive-core"
public static final String	APP_NAME_UUID	"uuid"
public static final String	ARCHIVE_AVAILABLE	"Available"
public static final String	ARCHIVE_DEPLOYED_TO	"Archive deployed to: "
public static final String	ARCHIVE_EXTENSION	".tar.gz"
public static final String	ARCHIVE_IN_REVIEW	"In Review"
public static final String	ARCHIVE_PRIVATE	"Private"
public static final String	AVAILABILITY	"availability"
public static final String	AVAILABILITY_AVAILABLE	"A"
public static final String	AVAILABILITY_NOTAPPLICABLE	"NA"
public static final String	AVAILABILITY_NOTAVAILABLE	"N"
public static final String	AVAILABILITY_PENDING	"P"
public static final String	BARCODE	"barcode"
public static final int	BATCH_SIZE	500
public static final String	BCR_BATCH	"bcr_batch"
public static final String	BIOTAB_GENERATOR_DELAY	"biotabGeneratorDelay"
public static final String	BIOTAB_GENERATOR_JOB	"biotabGeneratorJob"
public static final String	BIOTAB_GENERATOR_TRIGGER	"biotabGeneratorTrigger"
public static final String	BIOTAB_SCHEDULER	"qcliveCronJobScheduler"
public static final String	BUILT_BARCODE	"built_barcode"
public static final String	CENTER	"center"
public static final String	CENTER_ID	"center_id"
public static final String	CENTER_QUERIES_SPRING_BEAN_NAME	"centerQueries"
public static final String	CHARACTERISTICS_GENOTYPE	"Characteristics [Genotype]"
public static final String	CHARACTERISTICS_ORGANISM	"Characteristics [Organism]"
public static final String	CHECKING_SDRF_FILE	"-- Checking SDRF File --"
public static final String	CLINICAL_CACHE_GENERATOR_SPRING_BEAN_NAME	"clinicalCacheFileGenerator"
public static final String	CLINICAL_NOTPROTECTED_CENTER	"-777"
public static final String	CLINICAL_PLATFORMTYPE	"-999"
public static final String	CLINICAL_PROTECTED_CENTER	"-888"
public static final String	COMMAND_ADD	"Add"
public static final String	COMMAND_DELETE	"Delete"
public static final String	COMMAND_UPDATE	"Update"
public static final String	COMMON_ARCHIVE_QUERIES_SPRING_BEAN_NAME	"archiveQueries"
public static final String	COMPRESSED_ARCHIVE_EXTENSION	".tar.gz"
public static final String	CONTROL_DISEASE	"CNTL"
public static final String	DAM_HELPER_SPRING_BEAN_NAME	"damHelper"
public static final String	DATA_BEAN	"DataBean"
public static final int	DATA_LEVEL_2	2
public static final String	DATA_LEVEL_2_STR	"level2"
public static final int	DATALEVEL_UNKNOWN	0
public static final String	DEFAULT_DISEASETYPE	"GBM"
public static final String	DEPLOYING_ARCHIVE	"Deploying archive..."
public static final String	DEPRECATED_SDRF_HEADER_FILE_PATH	"gov/DeprecatedSDRFHeaders.txt"
public static final String	DIR_UNKNOWN	"unknown"
public static final String	DISEASE_ARCHIVE_QUERIES_SPRING_BEAN_NAME	"diseaseArchiveQueries"
public static final String	DISEASE_ROUTING_DS	"diseaseDataSource"
public static final String	DOMAIN_NAME_DOES_NOT_MATCH	"FAILURE: The Domain Name of the archive does not match the Domain Name in the Protocol Name column in the IDF file."
public static final String	EMAIL_SEPARATOR	","
public static final String	EXON_QUANTIFICATION_SOURCE_FILE_TYPE	"expression_exon"
public static final String	EXPERIMENT_DAO_OBJECT_SPRING_BEAN_NAME	"experimentDAO"
public static final String	FAILED_MD5_CHECK	"FAILED! The MD5 Check Failed, we are stopping the process."
public static final String	FAILURE_CHARACTERISTICS_GENOTYPE_COLUMN	"FAILURE: The Characteristics [Genotype] column in the SDRF file does not contain any valid data."
public static final String	FAILURE_CHARACTERISTICS_ORGANISM_COLUMN	"FAILURE: The Characteristics[Organism] column in the SDRF file does not contain any valid data."
public static final String	FAILURE_MISSING	"FAILURE: Missing: "
public static final String	FAILURE_ORPHANED_VALUE	"FAILURE The Value "
public static final String	FAILURE_SAMPLE_NAME_COLUMN	"FAILURE: The Sample Name column in the SDRF file does not contain any valid data."
public static final String	FAILURE_TERM_SOURCE_REF_VALUES	"FAILURE: The Term Source REF values don\'t match those in the IDF file."
public static final String	FAILURE_THE_MATERIAL_TYPE	"FAILURE: The Material Type column in the SDRF file does not contain any valid data."
public static final String	FAILURE_THE_PROVIDER_COLUMN	"FAILURE: The Provider column in the SDRF file does not contain any valid data."
public static final String	FAILURE_THE_SDRF_FILE	"FAILURE: The SDRF File "
public static final String	FAILURE_THE_SOURCE_NAME_COLUMN	"FAILURE: The Source Name column in the SDRF file does not contain any valid data."
public static final String	FAILURE_TOO_MANY_PROTOCOL_TYPES	"FAILURE: You have too many \"Protocol Types\"(s) in your IDF."
public static final String	FILE_EXTENSION_XML	"xml"
public static final String	FILES_LISTED_IN_MAGE_SDRF_ERROR	"Files listed in MAGE SDRF are missing from your manifest. The Files are:"
public static final String	FROM_IDF_TERM_SOURCE_NAME	" from IDF Term Source Name"
public static final String	GENE_QUANTIFICATION_RSEM_GENE_NORMALIZED_SOURCE_FILE_TYPE	"expression_rsem_gene_normalized"
public static final String	GENE_QUANTIFICATION_RSEM_GENE_SOURCE_FILE_TYPE	"expression_rsem_gene"
public static final String	GENE_QUANTIFICATION_RSEM_ISOFORMS_NORMALIZED_SOURCE_FILE_TYPE	"expression_rsem_isoforms_normalized"
public static final String	GENE_QUANTIFICATION_RSEM_ISOFORMS_SOURCE_FILE_TYPE	"expression_rsem_isoforms"
public static final String	GENE_QUANTIFICATION_SOURCE_FILE_TYPE	"expression_gene"
public static final String	IDF_ORPHANED_TERM_SOURCE_NAME	" in the IDF file is orphaned, and does not exist in the values listed in Term Source Name."
public static final String	IDF_VALUES_NOT_ALLOWED	"FAILURE: The IDF File contains -> values which are not allowed. Please review those columns with the -> and enter an appropriate value."
public static final int	IN_CLAUSE_SIZE	300
public static final String	INCORRECT_NUMBER_OF_ELEMENTS_PROTOCL_NAME	"FAILURE: The Protocol Name Validator is reporting an incorrect number of elements in your Protocol Name value. Errors will follow below."
public static final String	INVALID_PATTERN_DETECTED	"FAILURE: An invalid pattern was detected for the Array Design REF value in the SDRF file."
public static final String	ISOFORM_QUANTIFICATION_SOURCE_FILE_TYPE	"isoform_quantification"
public static final String	JOB_BEAN_NAME	"JobBeanName"
public static final String	JUNCTION_QUANTIFICATION_SOURCE_FILE_TYPE	"expression_junction"
public static final int	LATEST_ARCHIVE	1
public static final String	LEVEL_2_CACHE_GROUP_NAME	"Level_2_Cache"
public static final String	LEVEL_2_LOADER_GROUP_NAME	"Level_2_Loader"
public static final String	LEVEL2_CACHE_ENQUEUER_SPRING_BEAN_NAME	"level2DataCacheEnqueuer"
public static final String	LEVEL2_CACHE_GENERATOR_SPRING_BEAN_NAME	"level2DataCacheGenerator"
public static final String	LEVEL23_SAMPLE_PHRASE	"selected_samples"
public static final String	LISTED_IN_THE_MAGE_FILE_IS_INVALID_OR_MISSING	" listed in the MAGE file is INVALID OR MISSING!"
public static final String	LIVE_OBJECT_SPRING_BEAN_NAME	"qcLive"
public static final String	LIVE_SCHEDULER	"liveScheduler"
public static final String	MAIL_ERROR_HELPER_SPRING_BEAN_NAME	"mailErrorHelper"
public static final String	MAIL_SENDER_SPRING_BEAN_NAME	"mailSender"
public static final String	MANIFEST_NAME	"MANIFEST.txt"
public static final String	MATERIAL_TYPE	"Material Type"
public static final String	MD5_EXTENSION	".md5"
public static final String	MD5_HASH_FAIL	"The Archive\'s MD5 hash check failed for Archive: "
public static final String	MD5_HASH_PASS	"The Archive\'s MD5 hash check passed for Archive: "
public static final String	MIRNA_QUANTIFICATION_SOURCE_FILE_TYPE	"mirna_quantification"
public static final String	MISSING_FILE_REFERENCED_IN_SDRF	"Missing file referenced in SDRF: "
public static final int	NOT_ASSIGNED	-1
public static final String	PIPE_SYMBOL	"|"
public static final String	PLATFORM	"platform"
public static final String	PLATFORM_DOES_NOT_MATCH	"FAILURE: The Platform of the archive does not match the Platform in the Protocol Name column in the IDF file."
public static final String	PLATFORM_ID	"platform_id"
public static final String	PLATFORM_QUERIES_SPRING_BEAN_NAME	"platformQueries"
public static final String	PLATFORM_TYPE	"platformType"
public static final String	PLATFORM_TYPE_ID	"platform_type_id"
public static final String	PROT_REF_NOT_FOUND	" was not found in the IDF Protocol Name."
public static final String	PROTECTED_DIR	"tcga4yeo"
public static final String	PROTECTEDSTATUS	"protectedStatus"
public static final String	PROTECTEDSTATUS_PROTECTED	"Protected"
public static final String	PROTECTEDSTATUS_PROTECTED_VALUE	"P"
public static final String	PROTECTEDSTATUS_PUBLIC	"Public"
public static final String	PROTECTEDSTATUS_PUBLIC_VALUE	"N"
public static final String	PROTEIN_ARRAY_PLATFORM	"MDA_RPPA_Core"
public static final String	PROTEIN_EXPRESSION_SOURCE_FILE_TYPE	"protein_expression"
public static final String	PROTOCOL_DESCRIPTION	"Protocol Description"
public static final String	PROTOCOL_DESCRIPTION_FOR_PROTOCOL_NAME	"FAILURE: The Protocol Description for Protocol Name: "
public static final String	PROTOCOL_DESCRIPTION_FROM_IDF	" \"Protocol Description\"(s) from your IDF."
public static final String	PROTOCOL_NAME	"Protocol Name"
public static final String	PROTOCOL_NAME_CANNOT_BE_EMPTY	" cannot be empty. It needs to contain an informative value (e.g. a URL to the protocol or an actual description of the protocol. The value -> is not valid."
public static final String	PROTOCOL_NAME_DOESNT_MATCH	"FAILURE: The Protocol Name in the IDF doesn\'t match the Protocol REF in the SDRF!"
public static final String	PROTOCOL_TERM_SOURCE_REF	"Protocol Term Source REF"
public static final String	PROTOCOL_TYPE	"Protocol Type"
public static final String	PROTOCOL_TYPE_FROM_IDF	" \"Protocol Type\"(s) from your IDF."
public static final String	PROTOCOL_TYPE_IS_INVALID	"FAILURE: The Protocol Type is invalid in the Protocol Name column in the IDF file."
public static final String	PROVIDER	"Provider"
public static final String	PUBLIC_DIR	"anonymous"
public static final String	QCLIVE_SHUTDOWN_MESSAGE	"The QCLive application is being restarted or shutdown."
public static final String	REVISION	"revision"
public static final String	SAMPLE	"sample"
public static final String	SAMPLE_NAME	"Sample Name"
public static final String	SDRF_HEADER_FILE_PATH	"gov/SDRFHeaders.txt"
public static final String	SERIAL_INDEX	"serial_index"
public static final String	SOURCE_NAME	"Source Name"
public static final String	SRDF_PROTOCOL_REF	"The SRDF Protocol REF: "
public static final String	STARTUP_ERROR	"You did not pass the archive name as part of the process.\n\nThe correct usage is:\n\n ./validator.sh archiveName\n\nAlternately if you already have the exploded archive, you may pass in a second argument to bypass MD5 checking and untar\'ing.\n\n ./validator.sh archiveName bypass\n\nThe above is ONLY recommended to quickly test the contents of your archive, and the archive must exist in the same location as the already exploded directory.\nPlease always check the full archive processing before submitting to the DCC.\n\n[Stopping Processing.]\n\n"
public static final String	TERM_SOURCE_FILE	"Term Source File"
public static final String	TERM_SOURCE_NAME	"Term Source Name"
public static final String	TERM_SOURCE_REF	"Term Source REF"
public static final String	TERM_SOURCE_VERSION	"Term Source Version"
public static final String	TOO_MANY_PROTOCOL_DESCRIPTION	"FAILURE: You have too many \"Protocol Description\" in your IDF."
public static final String	TOO_MANY_PROTOCOL_TERM_SOURCE_REFS	"FAILURE: You have too many \"Protocol Term Source REF\"(s) in your IDF."
public static final String	UNCLASSIFIED_BATCH	"Unclassified"
public static final String	UNCOMPRESSED_ARCHIVE_EXTENSION	".tar"
public static final String	UUID	"uuid"
public static final String	UUID_HIERARCHY_QUERIES	"uuidHierarchyQueriesImpl"
public static final String	VERSION_NUMBER_IS_INVALID	"FAILURE: The Version number is invalid in the Protocol Name column in the IDF file."
public static final String	WS_BARCODE_DELIMITER	","
public static final String	WS_BATCH_DELIMITER	","
public static final char	WS_QUERY_PARAMETERS_DELIMITER	44

gov.nih.nci.ncicb.tcga.dcc.annotations.web.AnnotationControllerImpl

Modifier and Type	Constant Field	Value
public static final String	ATTRIBUTE_LAST_SEARCH_RESULTS	"lastSearchResults"
protected static final String	ERROR_MESSAGE_KEY	"errorMessage"

gov.nih.nci.ncicb.tcga.dcc.bamloader.BAMLoaderConstants

Modifier and Type	Constant Field	Value
public static final String	ALIQUOT_QUERY	"select SHIPPED_BIOSPECIMEN_ID, BUILT_BARCODE from SHIPPED_BIOSPECIMEN order by BUILT_BARCODE"
public static final String	BAM_DELETE	"delete from BAM_FILE"
public static final String	BAM_INSERT	"insert into BAM_FILE (BAM_FILE_ID, BAM_FILE_NAME, DISEASE_ID, CENTER_ID, BAM_FILE_SIZE, DATE_RECEIVED, BAM_DATATYPE_ID) values (?, ?, ?, ?, ?, ?, ?)"
public static final String	BAM_TO_ALIQUOT_DELETE	"delete from SHIPPED_BIOSPECIMEN_BAMFILE"
public static final String	BAM_TO_ALIQUOT_INSERT	"insert into SHIPPED_BIOSPECIMEN_BAMFILE (SHIPPED_BIOSPECIMEN_ID, BAM_FILE_ID) values (?, ?)"
public static final int	BATCH_SIZE	1000
public static final String	CENTER_QUERY	"select CENTER_ID, SHORT_NAME, CENTER_TYPE_CODE from CENTER order by SHORT_NAME"
public static final String	DATATYPE_BAM_QUERY	"select BAM_DATATYPE_ID, BAM_DATATYPE, GENERAL_DATATYPE from BAM_FILE_DATATYPE order by BAM_DATATYPE"
public static final String	DISEASE_QUERY	"select DISEASE_ID, DISEASE_ABBREVIATION, DISEASE_NAME from DISEASE where ACTIVE=1 order by DISEASE_NAME"
public static final String	EXTENDED_BAM_INSERT	"insert into BAM_FILE (ANALYSIS_ID, BAM_FILE_ID, BAM_FILE_NAME, DISEASE_ID, CENTER_ID, BAM_FILE_SIZE, DATE_RECEIVED, BAM_DATATYPE_ID, ANALYTE_CODE,DCC_RECEIVED_DATE) values (?,?, ?, ?, ?, ?, ?, ?,?,?)"

gov.nih.nci.ncicb.tcga.dcc.common.bean.Archive

Modifier and Type	Constant Field	Value
public static final String	STATUS_AVAILABLE	"Available"
public static final String	STATUS_DEPLOYED	"Deployed"
public static final String	STATUS_IN_REVIEW	"In Review"
public static final String	STATUS_INTERRUPTED	"Interrupted"
public static final String	STATUS_INVALID	"Invalid"
public static final String	STATUS_UPLOADED	"Uploaded"
public static final String	STATUS_VALIDATED	"Validated"
public static final String	TYPE_AUX	"aux"
public static final String	TYPE_CLASSIC	"classic"
public static final String	TYPE_LEVEL_1	"Level_1"
public static final String	TYPE_LEVEL_2	"Level_2"
public static final String	TYPE_LEVEL_3	"Level_3"
public static final String	TYPE_LEVEL_4	"Level_4"
public static final String	TYPE_MAGE_TAB	"mage-tab"

gov.nih.nci.ncicb.tcga.dcc.common.bean.DccAnnotation

Modifier and Type	Constant Field	Value
public static final String	STATUS_APPROVED	"Approved"
public static final String	STATUS_PENDING	"Pending"
public static final String	STATUS_RESCINDED	"Rescinded"

gov.nih.nci.ncicb.tcga.dcc.common.bean.MetaDataBean

Modifier and Type	Constant Field	Value
public static final String	DASH	"-"

gov.nih.nci.ncicb.tcga.dcc.common.bean.ShippedBiospecimen

Modifier and Type	Constant Field	Value
public static final int	PARTICIPANT_CODE_INDEX	4
public static final int	PLATE_INDEX	9
public static final int	PORTION_SEQUENCE_INDEX	8
public static final int	PROJECT_CODE_INDEX	2
public static final int	RECEIVING_CENTER_INDEX	10
public static final int	SAMPLE_SEQUENCE_INDEX	7
public static final int	SAMPLE_TYPE_CODE_INDEX	6
public static final String	SHIPPED_ITEM_NAME_ALIQUOT	"Aliquot"
public static final String	SHIPPED_ITEM_NAME_PORTION	"Shipping Portion"
public static final int	TSS_CODE_INDEX	3

gov.nih.nci.ncicb.tcga.dcc.common.bean.ShippedBiospecimenElement

Modifier and Type	Constant Field	Value
public static final String	SHIPPED_ELEMENT_TYPE_ANALYTE_TYPE_CODE	"analyte_code"
public static final String	SHIPPED_ELEMENT_TYPE_NAME_PLATE_ID	"plate_id"
public static final String	SHIPPED_ELEMENT_TYPE_NAME_PORTION_SEQUENCE	"portion_sequence"
public static final String	SHIPPED_ELEMENT_TYPE_NAME_SAMPLE_SEQUENCE	"sample_sequence"
public static final String	SHIPPED_ELEMENT_TYPE_NAME_SAMPLE_TYPE_CODE	"sample_type_code"

gov.nih.nci.ncicb.tcga.dcc.common.dao.ClinicalMetaQueries

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_CONTEXT	"dam"

gov.nih.nci.ncicb.tcga.dcc.common.dao.UUIDDAOImpl

Modifier and Type	Constant Field	Value
public static final String	BARCODES_FROM_UUIDS_MAPPING_QUERY	"with v as (REPLACE_UUID) select bh.barcode, v.uuid from v left outer join uuid u on v.uuid = u.uuid left outer join barcode_history bh on bh.barcode_id = u.latest_barcode_id order by v.uuid"
public static final String	MERGE_PATIENT_UUID_FILE_ID	" merge into participant_uuid_file using dual on (UUID=lower(?) and FILE_ID=?) when not matched then insert (UUID, FILE_ID) values(lower(?), ?)"
public static final String	QUERY_EXISTING_BARCODES	"select barcode from barcode_history where barcode in (REPLACE_BARCODE)"
public static final String	QUERY_EXISTING_UUIDS	"select uuid from uuid where uuid in (REPLACE_UUID)"
public static final String	REPLACE_BARCODE	"REPLACE_BARCODE"
public static final String	REPLACE_UUID	"REPLACE_UUID"
public static final String	UUIDS_FROM_BARCODES_MAPPING_QUERY	"with v as (REPLACE_BARCODE) select distinct bh.uuid, v.barcode from v left outer join barcode_history bh on v.barcode = bh.barcode order by v.barcode"

gov.nih.nci.ncicb.tcga.dcc.common.dao.annotations.AnnotationQueriesJDBCImpl

Modifier and Type	Constant Field	Value
public static final String	UPDATE_CURATED_QUERY	"update annotation set curated=? where annotation_id=?"
public static final String	UPDATE_RESCINDED_QUERY	"update annotation set rescinded=? where annotation_id=?"

gov.nih.nci.ncicb.tcga.dcc.common.dao.annotations.AnnotationSearchCriteria

Modifier and Type	Constant Field	Value
public static final String	ANNOTATION_ITEM_SEPARATOR	","

gov.nih.nci.ncicb.tcga.dcc.common.dao.jdbc.ArchiveQueriesJDBCImpl

Modifier and Type	Constant Field	Value
public static final String	RETRIEVE_MAGE_TAB_LOCATION	"select deploy_location from archive_info a, archive_type t, center c, platform p, disease d where a.is_latest = 1 and a.center_id = c.center_id and c.domain_name = ? and a.platform_id = p.platform_id and p.platform_name = ? and a.archive_type_id = t.archive_type_id and t.archive_type = \'mage-tab\' and a.disease_id = d.disease_id and d.disease_abbreviation = ? and a.series = ? "

gov.nih.nci.ncicb.tcga.dcc.common.dao.jdbc.BatchNumberQueriesJDBCImpl

Modifier and Type	Constant Field	Value
public static final String	GET_BATCH_NUMBER_ASSIGNMENT_QUERY	" select batch_number_assignment.batch_id,disease.disease_abbreviation, center.domain_name from batch_number_assignment, disease,center where batch_number_assignment.center_id = center.center_id and batch_number_assignment.disease_id = disease.disease_id and batch_number_assignment.batch_id= ? order by center.domain_name"
public static final String	IS_VALID_BATCH_ASSIGNMENT_QUERY	"select count(*) from batch_number_assignment bna, center c, disease d where c.center_id= bna.center_id and d.disease_id= bna.disease_id and bna.batch_id=? and c.domain_name=? and d.disease_abbreviation=?"

gov.nih.nci.ncicb.tcga.dcc.common.dao.jdbc.CenterQueriesJDBCImpl

Modifier and Type	Constant Field	Value
public static final String	GET_UUID_CENTER_QUERY	"select center_id from center where is_uuid_converted > 0 and domain_name=? and center_type_code=?"

gov.nih.nci.ncicb.tcga.dcc.common.dao.jdbc.Level2DataQueriesJDBCImpl

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_FETCHSIZE	1000
public static final String	REPLACE_IN_CLAUSE	"REPLACE_IN_CLAUSE"

gov.nih.nci.ncicb.tcga.dcc.common.dao.jdbc.PortionAnalyteQueriesJDBCImpl

Modifier and Type	Constant Field	Value
public static final String	QUERY_PORTION_ANALYTE	"select portion_analyte_code, definition from portion_analyte order by definition"

gov.nih.nci.ncicb.tcga.dcc.common.dao.jdbc.ShippedBiospecimenQueriesJDBCImpl

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_FETCHSIZE	1000
public static final String	SQL_DISEASE_UUID	"SELECT disease_abbreviation FROM uuid u, barcode_history bh, disease d WHERE u.latest_barcode_id = bh.barcode_id AND u.UUID = ? AND bh.disease_id = d.disease_id"

gov.nih.nci.ncicb.tcga.dcc.common.dao.jdbc.TissueSourceSiteQueriesJDBCImpl

Modifier and Type	Constant Field	Value
public static final String	QUERY_AGGREGATE_TISSUE_SOURCE_SITE	"select RTRIM(XMLAGG(XMLELEMENT(e,tss_code || \',\') order by tss_code).EXTRACT(\'//text()\'),\',\') tss_code, tss_definition from tissue_source_site group by tss_definition order by tss_definition, tss_code"
public static final String	QUERY_DISEASE_FOR_TISSUE_SOURCE_SITE	"select distinct disease.disease_abbreviation from tissue_source_site tss, tss_to_disease, disease where tss.tss_code = tss_to_disease.tss_code and tss_to_disease.disease_id = disease.disease_id and tss.tss_code = ? order by disease.disease_abbreviation"
public static final String	QUERY_TISSUE_SOURCE_SITE	"select tss_code, tss_definition from tissue_source_site order by tss_definition, tss_code"

gov.nih.nci.ncicb.tcga.dcc.common.dao.jdbc.UUIDTypeQueriesJDBCImpl

Modifier and Type	Constant Field	Value
public static final String	QUERY_UUID_ITEM_TYPE	"select item_type_id, item_type, sort_order from uuid_item_type order by sort_order"
public static final String	QUERY_UUID_ITEM_TYPE_ID	"Select item_type_id from uuid_item_type where upper(item_type)=? "

gov.nih.nci.ncicb.tcga.dcc.common.generation.BioTabDataProcessorUtil

Modifier and Type	Constant Field	Value
public static final String	DATE_OF	"date_of_"
public static final String	DAY_OF	"day_of_"
public static final String	MONTH_OF	"month_of_"
public static final String	YEAR_OF	"year_of_"

gov.nih.nci.ncicb.tcga.dcc.common.generation.BioTabFileGenerator

Modifier and Type	Constant Field	Value
public static final String	BIOTAB	"biotab"
public static final String	BIOTAB_GENERATOR_SPRING_BEAN_NAME	"bioTabFileGenerator"

gov.nih.nci.ncicb.tcga.dcc.common.security.impl.SecurityFilter

Modifier and Type	Constant Field	Value
public static final String	ALLOWABLE_RESOURCES_ROOT_INIT_PARAM_NAME	"allowableResourcesRoot"
public static final String	BYPASS_DEFAULT_RESPONSE_STATUS_CODE_INIT_PARAM_NAME	"bypassDefaultResponseStatusCode"
public static final String	IGNORE_CANONICALIZATION_FOR_URI_PATHS_INIT_PARAM_NAME	"ignoreCanonicalizationForURIPaths"
public static final String	IGNORE_PARAM_VALIDATION_FOR_NAMES_INIT_PARAM_NAME	"ignoreParamValidationForNames"
public static final String	PARAM_VALUE_MAX_LENGTH_INIT_PARAM_NAME	"paramValueMaxLength"
public static final String	QUERY_STRING_MAX_LENGTH_INIT_PARAM_NAME	"queryStringMaxLength"
public static final String	RETAIN_EMPTY_QUERY_PARAM_VALUES_INIT_PARAM_NAME	"retainEmptyQueryParamValues"
public static final String	URI_STRING_MAX_LENGTH_INIT_PARAM_NAME	"uriStringMaxLength"
public static final String	URL_STRING_MAX_LENGTH_INIT_PARAM_NAME	"urlStringMaxLength"
public static final String	USE_STRICT_VALIDATION_FOR_URI_PATHS_INIT_PARAM_NAME	"useStrictValidationForURIPaths"

gov.nih.nci.ncicb.tcga.dcc.common.security.impl.SecurityFilterRequestWrapper

Modifier and Type	Constant Field	Value
public static final String	IF_NONE_MATCH_HEADER_NAME	"If-None-Match"

gov.nih.nci.ncicb.tcga.dcc.common.security.impl.SecurityFilterResponseWrapper

Modifier and Type	Constant Field	Value
public static final String	ETAG_HEADER_NAME	"ETag"

gov.nih.nci.ncicb.tcga.dcc.common.security.impl.SecurityUtilImpl

Modifier and Type	Constant Field	Value
public static final String	NOT_AUTHENTICATED	"not_authenticated"

gov.nih.nci.ncicb.tcga.dcc.common.service.Level2DataService

Modifier and Type	Constant Field	Value
public static final String	FILE_EXTENSION	".txt"

gov.nih.nci.ncicb.tcga.dcc.common.service.annotations.AnnotationServiceImpl

Modifier and Type	Constant Field	Value
public static final String	APPROVED	"approved"
public static final String	PENDING	"pending"
public static final String	REDACTION	"redaction"

gov.nih.nci.ncicb.tcga.dcc.common.util.CommonBarcodeAndUUIDValidatorImpl

Modifier and Type	Constant Field	Value
public static final String	ALIQUOT_BARCODE_REGEXP	"((TCGA)-([A-Z0-9]{2})-([A-Z0-9]{4})-((\\d{2})([A-Z]{1}))-((\\d{2})([A-Z]{1}))-([A-Z0-9]{4})-(\\d{2}))"
protected static final String	BCR_CENTER	"bcrCenter"
public static final String	PATIENT_BARCODE_REGEXP	"((TCGA)-([A-Z0-9]{2})-([A-Z0-9]{4}))"
protected static final String	PORTION_ANALYTE	"portionAnalyte"
protected static final String	PROJECT	"project"
protected static final String	SAMPLE_TYPE	"sampleType"
public static final String	SHIPMENT_PORTION_BARCODE_REGEXP	"((TCGA)-([A-Z0-9]{2})-([A-Z0-9]{4})-((\\d{2})([A-Z]{1}))-(\\d{2})-([A-Z0-9]{4})-(\\d{2}))"
protected static final String	TSS	"tss"

gov.nih.nci.ncicb.tcga.dcc.common.util.ExportUtils

Modifier and Type	Constant Field	Value
public static final String	ATTRIBUTE_COLUMN_HEADERS	"cols"
public static final String	ATTRIBUTE_DATA	"data"
public static final String	ATTRIBUTE_DATE_FORMAT	"dateFormat"
public static final String	ATTRIBUTE_EXPORT_TYPE	"exportType"
public static final String	ATTRIBUTE_FILE_NAME	"fileName"
public static final String	ATTRIBUTE_TITLE	"title"

gov.nih.nci.ncicb.tcga.dcc.common.util.FileUtil

Modifier and Type	Constant Field	Value
public static final String	MD5	".md5"
public static final String	TAR	".tar"
public static final String	TAR_GZ	".tar.gz"

gov.nih.nci.ncicb.tcga.dcc.common.util.LoggingJobHistoryPlugin

Modifier and Type	Constant Field	Value
protected static final String	DATE_FORMAT	"yyyy/MM/dd HH:mm:ss S"

gov.nih.nci.ncicb.tcga.dcc.common.util.UUIDConstants

Modifier and Type	Constant Field	Value
public static final String	ABBREVIATION	"abbreviation"
public static final String	ALIQUOT	"aliquot"
public static final String	ANALYTE	"analyte"
public static final String	ANALYTE_COMBO	"analyteCombo"
public static final String	ANALYTE_TYPE	"analyteType"
public static final String	ASC	"ASC"
public static final String	BARCODE	"barcode"
public static final String	BARCODE_FIELD	"barcodeField"
public static final String	BARCODE_SEARCH_RADIO	"barcodeSearchRadio"
public static final String	BATCH	"batch"
public static final String	BCR	"bcr"
public static final String	BCR_COMBO	"bcrCombo"
public static final String	BOTTOM	"bottom"
public static final String	CELL_LINE	"cellLine"
public static final String	CELL_LINE_CONTROL	"Cell Line Control"
public static final String	CENTER	"center"
public static final String	CENTER_COMBO	"centerCombo"
public static final String	CENTER_TYPE	"centerType"
public static final String	CENTER_TYPE_COMBO	"centerTypeCombo"
public static final String	CENTER_USER	"center_user"
public static final String	CODE	"code"
public static final String	COLS	"cols"
public static final String	COLUMN	"column"
public static final String	COLUMN_CENTER_NAME	"center"
public static final String	COLUMN_CREATED_BY	"createdBy"
public static final String	COLUMN_CREATION_DATE	"creationDate"
public static final String	COLUMN_DISEASE	"diseaseAbbrev"
public static final String	COLUMN_GENERATION_METHOD	"generationMethod"
public static final String	COLUMN_LATEST_BARCODE	"latestBarcode"
public static final String	COLUMN_UUID	"uuid"
public static final String	CREATE_DATE	"createDate"
public static final String	CSV	"csv"
public static final String	DATA	"data"
public static final String	DATE_FORMAT	"MM/dd/yyyy"
public static final String	DATE_FORMAT_US_STRING	"MM/dd/yyyy"
public static final int	DEFAULT_LIMIT	25
public static final int	DEFAULT_START	0
public static final String	DESC	"DESC"
public static final String	DIR	"dir"
public static final String	DISEASE	"disease"
public static final String	DISEASE_COMBO	"diseaseCombo"
public static final String	DOMAIN	"domain"
public static final String	DRUG	"drug"
public static final String	ELEMENT_TYPE	"elementType"
public static final String	EMPTY_SEARCH_PARAMS_FILTER	""
public static final String	ERROR_MESSAGE	"errorMessage"
public static final String	EXAMINATION	"examination"
public static final String	EXCEL	"xl"
public static final String	EXPORT_DATA	"exportData"
public static final String	EXPORT_DATE_FORMAT	"dateFormat"
public static final String	EXPORT_FILENAME	"fileName"
public static final String	EXPORT_TITLE	"title"
public static final String	EXPORT_TYPE	"exportType"
public static final String	EXPORT_UUID	"uuidExport"
public static final String	FALSE	"false"
public static final String	FILE	"file"
public static final String	FILE_SEARCH_RADIO	"fileSearchRadio"
public static final String	FILTER	"filter"
public static final String	JSON	"/json"
public static final String	LIMIT	"limit"
public static final String	MASTER_USER	"DCC"
public static final String	MIDDLE	"middle"
public static final String	NAME	"name"
public static final String	NORMAL	"normal"
public static final String	PARTICIPANT	"participant"
public static final String	PARTICIPANT_ID	"participantId"
public static final String	PLATE	"plate"
public static final String	PLATE_ID	"plateId"
public static final String	PLATFORM	"platform"
public static final String	PLATFORM_COMBO	"platformCombo"
public static final String	PORTION	"portion"
public static final String	PORTION_ID	"portionId"
public static final String	RADIATION	"radiation"
public static final String	RECEIVING_CENTER	"receivingCenter"
public static final String	REPORT_RESULTS	"reportResults"
public static final String	REPORT_TYPE_MISSING_UUID	"missingUUID"
public static final String	REPORT_TYPE_NEW_UUID	"newUUID"
public static final String	REPORT_TYPE_SUBMITTED_UUID	"submittedUUID"
public static final String	SAMPLE	"sample"
public static final String	SAMPLE_COMBO	"sampleCombo"
public static final String	SAMPLE_TYPE	"sampleType"
public static final String	SEARCH_CRITERIA	"searchCriteria"
public static final String	SEARCH_PARAMS	"searchParams"
public static final String	SEARCH_RESULTS	"searchResults"
public static final String	SEPARATOR	","
public static final String	SHIPPED_PORTION	"shippedPortion"
public static final String	SHORT_LETTER_CODE	"short Letter Code"
public static final String	SLIDE	"slide"
public static final String	SLIDE_LAYER	"slideLayer"
public static final String	SORT	"sort"
public static final String	START	"start"
public static final String	STUDY_NAME	"study Name"
public static final String	SUBMITTED_AFTER	"submittedAfter"
public static final String	SUBMITTED_BEFORE	"submittedBefore"
public static final String	SUCCESS	"success"
public static final String	SURGERY	"surgery"
public static final String	TAB	"tab"
public static final String	TISSUE_SOURCE_SITE	"tissueSourceSite"
public static final String	TOP	"top"
public static final String	TOTAL_COUNT	"totalCount"
public static final String	TRUE	"true"
public static final String	TSS	"tss"
public static final String	TUMOR	"tumor"
public static final String	TYPE	"type"
public static final String	UPDATE_AFTER	"updateAfter"
public static final String	UPDATE_BEFORE	"updateBefore"
public static final String	UPDATE_DATE	"updateDate"
public static final String	UPDATED_AFTER	"updatedAfter"
public static final String	UPDATED_BEFORE	"updatedBefore"
public static final String	UUID	"uuid"
public static final String	UUID_BROWSER_DATA	"uuidBrowserData"
public static final String	UUID_BROWSER_EXPORT_URL	"/uuidBrowserExport.htm"
public static final String	UUID_BROWSER_FILTER_DATA_URL	"/uuidBrowserFilterData.json"
public static final String	UUID_BROWSER_JSON_URL	"/uuidBrowser.json"
public static final String	UUID_BROWSER_UPLOAD_URL	"/uuidUploadStatus.htm"
public static final String	UUID_BROWSER_UPLOAD_VIEW	"uuidUploadStatus"
public static final String	UUID_BROWSER_URL	"/uuidBrowser.htm"
public static final String	UUID_BROWSER_VIEW	"uuidBrowser"
public static final String	UUID_FIELD	"uuidField"
public static final String	UUID_LIST	"uuidList"
public static final String	UUID_PARENT_DATA	"uuidParentData"
public static final String	UUID_PARENT_JSON_URL	"/uuidParent.json"
public static final String	UUID_SEARCH_RADIO	"uuidSearchRadio"
public static final String	UUID_TYPE	"uuidType"
public static final String	UUID_TYPE_COMBO	"uuidTypeCombo"
public static final String	VIAL	"vial"
public static final String	VIAL_ID	"vialId"
public static final String	XML	"/xml"

gov.nih.nci.ncicb.tcga.dcc.common.webservice.HttpStatusCode

Modifier and Type	Constant Field	Value
public static final int	ACCEPTED	202
public static final int	CREATED	201
public static final int	I_M_A_TEAPOT	418
public static final int	INTERNAL_SERVER_ERROR	500
public static final int	NO_CONTENT	204
public static final int	NOT_FOUND	404
public static final int	OK	200
public static final int	PRECONDITION_FAILED	412
public static final int	REQUEST_ENTITY_TOO_LARGE	413
public static final int	UNPROCESSABLE_ENTITY	422
public static final int	UNSUPPORTED_MEDIA_TYPE	415

gov.nih.nci.ncicb.tcga.dcc.dam.Messages

Modifier and Type	Constant Field	Value
public static final String	CACHE_ERROR	"Cache Error: "
public static final String	CACHE_FILE_NOT_FOUND	"Cache file {0} not found"

gov.nih.nci.ncicb.tcga.dcc.dam.bean.DataFile

Modifier and Type	Constant Field	Value
public static final String	LEVEL_2	"2"
public static final String	LEVEL_3	"3"

gov.nih.nci.ncicb.tcga.dcc.dam.bean.QuartzJobHistory

Modifier and Type	Constant Field	Value
public static final String	ESTIMATED_UNCOMPRESSED_SIZE	"estimatedUncompressedSize"
public static final String	JOB_DATA	"jobData"
public static final String	JOB_WS_SUBMISSION_DATE	"jobWSSubmissionDate"
public static final String	LINK_TEXT	"linkText"

gov.nih.nci.ncicb.tcga.dcc.dam.dao.DAMQueriesCGCCLevel1

Modifier and Type	Constant Field	Value
public static final String	EXCLUDE_CENTER_TYPE_CODE	"BCR"

gov.nih.nci.ncicb.tcga.dcc.dam.dao.DAMQueriesCGCCLevelTwoAndThree

Modifier and Type	Constant Field	Value
protected static final String	GET_DATASETS_QUERY	"select distinct e.experiment_id, hr.bestbarcode from hybrid_ref_data_set hr_ds, data_set ds, hybridization_ref hr, experiment e where e.base_name=? and e.data_deposit_batch=? and e.data_revision=? and e.experiment_id=ds.experiment_id and hr_ds.hybridization_ref_id=hr.hybridization_ref_id and ds.data_set_id=hr_ds.data_set_id and data_level=? and use_in_dam=1 and load_complete=1"
protected static final String	GET_FILE_INFO_QUERY	" select distinct h.hybridization_ref_id, h.bestbarcode, ds.data_set_id, ds.source_file_type, ds.access_level, f.file_size, ds.experiment_id\n from data_set ds, data_Set_file df, hybrid_ref_data_set hd, hybridization_Ref h, file_info f, shipped_biospecimen_file bf, shipped_biospecimen b where ds.load_complete = 1 and ds.use_in_DAM = 1 and ds.experiment_id in (EXPERIMENT_ID_PLACEHOLDER) and ds.data_set_id = hd.data_Set_id and hd.hybridization_ref_id=h.hybridization_ref_id and h.bestbarcode in (BESTBARCODE_PLACEHOLDER) and ds.data_set_id = df.data_set_id and df.file_id=f.file_id and f.file_id=bf.file_id and h.bestbarcode = b.built_barcode and bf.shipped_biospecimen_id=b.shipped_biospecimen_id and b.built_barcode in (BESTBARCODE_PLACEHOLDER)"
protected static final int	SIXTY_FOUR_MEGS	65536

gov.nih.nci.ncicb.tcga.dcc.dam.dao.DAMQueriesLevel2

Modifier and Type	Constant Field	Value
protected static final String	HYBRIDIZATION_VALUE_QUERY_HINT	"/*+ FULL(hv) PARALLEL(hv, 4) */"

gov.nih.nci.ncicb.tcga.dcc.dam.dao.DAMQueriesLevel3CNA_SNP

Modifier and Type	Constant Field	Value
public static final String	CNA_VALUE	"cna_value"

gov.nih.nci.ncicb.tcga.dcc.dam.dao.DAMQueriesLevel3ExpGene

Modifier and Type	Constant Field	Value
public static final String	EXPGENE_VALUE	"expgene_value"

gov.nih.nci.ncicb.tcga.dcc.dam.dao.DAMQueriesLevel3Methylation

Modifier and Type	Constant Field	Value
public static final String	METHYLATION_VALUE	"methylation_value"

gov.nih.nci.ncicb.tcga.dcc.dam.dao.DAMQueriesMetadata

Modifier and Type	Constant Field	Value
public static final String	SAMPLE_ANNOTATION_FILENAME	"sampleAnnotation.txt"

gov.nih.nci.ncicb.tcga.dcc.dam.dao.DAMUtils

Modifier and Type	Constant Field	Value
public static final String	CNA	"CNV (CN Array)"
public static final String	CNA_SNP	"CNA_SNP"
public static final String	DATA_TYPE_ID	"data_type_id"
public static final String	EXON	"exon"
public static final String	EXPGENE	"ExpGene"
public static final String	FTP_DISPLAY	"ftp_display"
public static final String	LOW_PASS	"CNV (Low Pass DNASeq)"
public static final String	METHYLATION	"methylation"
public static final String	MIRNA	"mirna"
public static final String	MIRNA_SEQ_TYPE	"miRNASeq"
public static final String	MIRNASEQ	"miRNASeq"
public static final String	MIRNASEQ_ISOFORM	"Quantification-miRNA Isoform"
public static final String	MIRNASEQ_QUANTIFICATION	"Quantification-miRNA"
public static final String	NAME	"name"
public static final String	PROTEIN_EXP	"Expression-Protein"
public static final String	RNA_SEQ	"rnaseq"
public static final String	RNA_SEQ_EXON	"Quantification-Exon"
public static final String	RNA_SEQ_GENE	"Quantification-Gene"
public static final String	RNA_SEQ_JUNCTION	"Quantification-Junction"
public static final String	RNA_SEQ_TYPE	"RNASeq"
public static final String	RNA_SEQ_V2	"RNASeqV2"
public static final String	SNP	"snp"
public static final String	TOTAL_RNA_SEQ_V2	"TotalRNASeqV2"
public static final String	TRANSCRIPTOME	"transcriptome"

gov.nih.nci.ncicb.tcga.dcc.dam.dao.DataAccessMatrixQueries

Modifier and Type	Constant Field	Value
public static final String	AVAILABILITY_AVAILABLE	"A"
public static final String	AVAILABILITY_NOTAPPLICABLE	"NA"
public static final String	AVAILABILITY_NOTAVAILABLE	"N"
public static final String	AVAILABILITY_PENDING	"P"
public static final String	CLINICAL_BIOTAB_CENTER	"-777"
public static final String	CLINICAL_PLATFORMTYPE	"-999"
public static final String	CLINICAL_XML_CENTER	"-666"
public static final String	DEFAULT_DISEASETYPE	"GBM"
public static final String	GENERIC_BCR_CENTER	"BCR"
public static final String	LEVEL_CLINICAL	"C"
public static final String	LEVEL_METADATA	"M"
public static final String	SHOW_COMPLETE_ROWS_ONLY	"SCRO"
public static final String	TUMORNORMAL_CELL_LINE_CONTROL	"C"
public static final String	TUMORNORMAL_HEALTHY_TISSUE_CONTROL	"N"
public static final String	TUMORNORMAL_NORMAL_WITH_MATCHED_TUMOR	"NT"
public static final String	TUMORNORMAL_TUMOR_WITH_MATCHED_NORMAL	"TN"
public static final String	TUMORNORMAL_TUMOR_WITHOUT_MATCHED_NORMAL	"T"

gov.nih.nci.ncicb.tcga.dcc.dam.dao.jdbc.QuartzJobHistoryQueriesImpl

Modifier and Type	Constant Field	Value
public static final String	FIRE_TIME	"fire_time"
public static final String	IS_COMPLETE	"is_complete"
public static final String	JOB_DATA	"job_data"
public static final String	JOB_GROUP	"job_group"
public static final String	JOB_NAME	"job_name"
public static final String	LAST_UPDATED	"last_updated"
public static final String	QRTZ_JOB_HISTORY	"qrtz_job_history"
public static final String	QUEUE_NAME	"queue_name"
public static final String	STATUS	"status"
public static final String	TIME_ENQUEUED	"time_enqueued"

gov.nih.nci.ncicb.tcga.dcc.dam.dao.usage.AbstractUsageLogger

Modifier and Type	Constant Field	Value
protected static final String	DATE_FORMAT_STRING	"dd-MMM-yyyy HH:mm:ss"

gov.nih.nci.ncicb.tcga.dcc.dam.dao.usage.UsageLoggerFileImpl

Modifier and Type	Constant Field	Value
protected static final String	DATE_FORMAT_STRING	"MM/dd/yyyy HH:mm:ss zzz"

gov.nih.nci.ncicb.tcga.dcc.dam.service.FilePackagerEnqueuer

Modifier and Type	Constant Field	Value
public static final String	JOB_GROUP_ARCHIVE_DELETION	"archiveDeletionGroup"
public static final String	JOB_GROUP_FILE_PACKAGER	"filePackagerGroup"
public static final String	JOB_GROUP_QUARTZ_JOB_HISTORY_DELETION	"quartzJobHistoryDeletionGroup"
public static final int	PRIORITY_DELETION	150
public static final String	QUEUE_NAME_BIG_JOB	"big"
public static final String	QUEUE_NAME_SMALL_JOB	"small"
public static final String	SPRING_BEAN_NAME_FOR_ARCHIVE_DELETION_JOB	"archiveDeletionJob"
public static final String	SPRING_BEAN_NAME_FOR_FILEPACKAGER_JOB	"filePackagerJob"
public static final String	SPRING_BEAN_NAME_FOR_QUARTZ_JOB_HISTORY_DELETION_JOB	"quartzJobHistoryDeletionJob"

gov.nih.nci.ncicb.tcga.dcc.dam.service.JobDelegate

Modifier and Type	Constant Field	Value
public static final String	DATA_BEAN	"DataBean"
public static final String	JOB_BEAN_NAME	"JobBeanName"

gov.nih.nci.ncicb.tcga.dcc.dam.util.DataAccessMatrixJSPUtil

Modifier and Type	Constant Field	Value
public static final String	ATTRIBUTE_KEY_CENTERS	"centers"
public static final String	ATTRIBUTE_KEY_DATATYPES	"datatypes"
public static final String	ATTRIBUTE_KEY_PLATFORMS	"platforms"
public static final int	DAFP_POLLING_INTERVAL	30000
public static final String	FIELD_CENTER_DISPLAY_NAME	"display_name"
public static final String	FIELD_CENTER_ID	"center_id"
public static final String	FIELD_CENTER_SHORT_NAME	"short_name"
public static final String	FIELD_DATA_TYPE_ID	"data_type_id"
public static final String	FIELD_DATA_TYPE_NAME	"name"
public static final String	FIELD_DATA_TYPE_SORT_ORDER	"sort_order"
public static final String	FIELD_PLATFORM_ID	"platform_id"
public static final String	FIELD_PLATFORM_NAME	"platform_name"
public static final String	PSEUDO_CENTER_BIOTAB	"Biotab"
public static final String	PSEUDO_CENTER_XML	"XML"
public static final String	PSEUDO_DATATYPE_CLINICAL	"Clinical"

gov.nih.nci.ncicb.tcga.dcc.dam.view.DAMColorScheme

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_COLOR_SCHEME	"Availability"

gov.nih.nci.ncicb.tcga.dcc.dam.view.DAMDefaultColorScheme

Modifier and Type	Constant Field	Value
public static final String	COLORSCHEMENAME	"Availability"

gov.nih.nci.ncicb.tcga.dcc.dam.view.DAMFacade

Modifier and Type	Constant Field	Value
public static final String	AVAILABILITY_AVAILABILE	"A"
public static final String	AVAILABILITY_NOTAPPLICABLE	"NA"
public static final String	FACADE_KEY_NAME	"damFacade"

gov.nih.nci.ncicb.tcga.dcc.dam.view.DAMHelper

Modifier and Type	Constant Field	Value
public static final String	CACHE_CENTERS	"centers"
public static final String	CACHE_DATA_TYPES	"datatypes"
public static final String	CACHE_PLATFORMS	"platforms"
public static final String	CACHE_TUMORS	"tumors"

gov.nih.nci.ncicb.tcga.dcc.dam.view.DataAccessDownloadModel

Modifier and Type	Constant Field	Value
public static final String	COLOR_PROTECTED	"red"

gov.nih.nci.ncicb.tcga.dcc.dam.view.request.DAFPSecondaryRequest

Modifier and Type	Constant Field	Value
public static final String	URL_ARGUMENT	"fileInfo"

gov.nih.nci.ncicb.tcga.dcc.dam.view.request.FilterRequestI

Modifier and Type	Constant Field	Value
public static final String	DATE_FORMAT	"MM/dd/yyyy"
public static final String	GOTO_FILETREE	"filetree"
public static final String	GOTO_MATRIX	"matrix"
public static final String	GOTO_PARAM	"goto"

gov.nih.nci.ncicb.tcga.dcc.dam.view.request.SelectionRequest

Modifier and Type	Constant Field	Value
public static final String	MODE_CELLS	"cells"
public static final String	MODE_HEADER	"header"
public static final String	MODE_NOOP	"noop"
public static final String	MODE_SELECTALL	"selectall"
public static final String	MODE_UNSELECTALL	"unselectall"

gov.nih.nci.ncicb.tcga.dcc.dam.web.ArchiveListerController

Modifier and Type	Constant Field	Value
public static final String	PAGE_NAME	"list.htm"
public static final String	PARAM_NAME_ACCESS_LEVEL	"accessLevel"
public static final String	PARAM_NAME_ARCHIVE	"archive"
public static final String	PARAM_NAME_CENTER	"center"
public static final String	PARAM_NAME_CENTER_TYPE	"centerType"
public static final String	PARAM_NAME_DISEASE	"disease"
public static final String	PARAM_NAME_PLATFORM	"platform"

gov.nih.nci.ncicb.tcga.dcc.dam.web.DataMatrixStatusRequestController

Modifier and Type	Constant Field	Value
public static final String	PARAM_NAME_JOB	"job"
public static final String	REQUEST_MAPPING	"/jobStatus.htm"

gov.nih.nci.ncicb.tcga.dcc.dam.web.WebController

Modifier and Type	Constant Field	Value
protected static final String	SESSION_KEY_NAME	"damSessionKey"

gov.nih.nci.ncicb.tcga.dcc.data.datastore.FileDataStoreImpl

Modifier and Type	Constant Field	Value
public static final long	MAX_FILE_SIZE	10485760L

gov.nih.nci.ncicb.tcga.dcc.datareports.constants.AliquotIdBreakdownReportConstants

Modifier and Type	Constant Field	Value
public static final String	ALIQUOT_ID_BREAKDOWN_DATA	"aliquotIdBreakdownData"
public static final String	ALIQUOT_ID_BREAKDOWN_EXPORT_URL	"/aliquotIdBreakdownExport.htm"
public static final String	ALIQUOT_ID_BREAKDOWN_FILTER_MODEL	"aliquotIdBreakdownFilterModel"
public static final String	ALIQUOT_ID_BREAKDOWN_REPORT_JSON_URL	"/aliquotIdBreakdownReport.json"
public static final String	ALIQUOT_ID_BREAKDOWN_REPORT_URL	"/aliquotIdBreakdownReport.htm"
public static final String	ALIQUOT_ID_BREAKDOWN_REPORT_VIEW	"aliquotIdBreakdownReport"
public static final String	EMPTY_ALIQUOT_ID_BREAKDOWN_FILTER	"{\"aliquotId\":\"\",\"analyteId\":\"\",\"sampleId\":\"\",\"participantId\":\"\"}"
public static final String	QUERY_ALIQUOT_ID_BREAKDOWN	"select barcode, biospecimen, sample, specific_patient, project_code, tss_code, patient, sample_type_code, sample_sequence, portion_sequence, portion_analyte_code, plate_id, bcr_center_id from shipped_biospecimen_aliquot where is_viewable = 1 order by barcode"

gov.nih.nci.ncicb.tcga.dcc.datareports.constants.AliquotReportConstants

Modifier and Type	Constant Field	Value
public static final String	ALIQUOT_ARCHIVE_JSON_URL	"/aliquotArchive.json"
public static final String	ALIQUOT_ARCHIVE_VIEW	"aliquotArchive"
public static final String	ALIQUOT_DATA	"aliquotData"
public static final String	ALIQUOT_EXPORT_URL	"/aliquotExport.htm"
public static final String	ALIQUOT_FILTER_DATA_URL	"/aliquotFilterData.json"
public static final String	ALIQUOT_FILTER_MODEL	"aliquotFilterModel"
public static final String	ALIQUOT_REPORT_JSON_URL	"/aliquotReport.json"
public static final String	ALIQUOT_REPORT_URL	"/aliquotReport.htm"
public static final String	ALIQUOT_REPORT_VIEW	"aliquotReport"
public static final String	EMPTY_ALIQUOT_FILTER	"{\"disease\":\"\",\"levelOne\":\"\",\"aliquotId\":\"\",\"center\":\"\",\"levelTwo\":\"\",\"bcrBatch\":\"\",\"platform\":\"\",\"levelThree\":\"\"}"
public static final String	LEVEL_ONE	"levelOne"
public static final String	LEVEL_THREE	"levelThree"
public static final String	LEVEL_TWO	"levelTwo"
public static final String	QUERY_ALIQUOT_ARCHIVES_FILES	"SELECT DISTINCT a.archive_id, a.archive_name, f.file_id, f.file_name, fa.file_location_url FROM shipped_biospecimen bb , shipped_biospecimen_file bf, file_info f, file_to_archive fa, archive_info a WHERE bb.built_barcode = ? AND bb.shipped_biospecimen_id = bf.shipped_biospecimen_id AND bf.file_id = f.file_id AND f.level_number = ? AND f.file_id = fa.file_id AND fa.archive_id = a.archive_id AND a.is_latest=1 ORDER BY a.archive_id"
public static final String	QUERY_ALIQUOT_LIST	"SELECT centers.disease_abbreviation,centers.barcode,bcr.batch_number,centers.center,centers.platform as platform_alias,centers.level1,centers.level2,centers.level3 FROM (SELECT biospecimen_id,disease_abbreviation, barcode, center_name||chr(32)||\'(\'||center_type_code||\')\' as center, platform, DECODE(submit_level1,\'Y\',\'Submitted\',\'Not Submitted\') level1,DECODE(submit_level2,\'Y\',\'Submitted\',\'Not Submitted\') level2,DECODE (submit_level3,\'Y\',\'Submitted\',\'Not Submitted\') level3 FROM latest_samples_received_by_dcc) centers LEFT OUTER JOIN (SELECT biospecimen_id, disease_abbreviation, barcode, batch_number,center_name||chr(32)||\'(\'||center_type_code||\')\' as center FROM samples_sent_by_bcr) bcr ON centers.biospecimen_id = bcr.biospecimen_id UNION SELECT nvl(centers.disease_abbreviation,bcr.disease_abbreviation) as disease_abbreviation,nvl(centers.barcode,bcr.barcode) as barcode,bcr.batch_number,nvl(centers.center,bcr.center) as center,nvl(centers.platform,\'bio\') as platform_alias,nvl(centers.level1,\'Not Submitted\') as level1,nvl(centers.level2,\'Not Submitted\') as level2,nvl(centers.level3,\'Not Submitted\') as level3 FROM (SELECT biospecimen_id,disease_abbreviation, barcode, center_name||chr(32)||\'(\'||center_type_code||\')\' as center, platform, DECODE(submit_level1,\'Y\',\'Submitted\',\'Not Submitted\') level1,DECODE(submit_level2,\'Y\',\'Submitted\',\'Not Submitted\') level2,DECODE(submit_level3,\'Y\',\'Submitted\',\'Not Submitted\') level3 FROM latest_samples_received_by_dcc) centers RIGHT OUTER JOIN (SELECT biospecimen_id, disease_abbreviation, barcode, batch_number,center_name||chr(32)||\'(\'||center_type_code||\')\' as center FROM samples_sent_by_bcr) bcr ON centers.biospecimen_id = bcr.biospecimen_id"

gov.nih.nci.ncicb.tcga.dcc.datareports.constants.BCRPipelineReportConstants

Modifier and Type	Constant Field	Value
public static final String	BCR_PREP_HOME_URL	"/BCRPipelineReport.htm"
public static final String	BCR_PREP_HOME_VIEW	"BCRPipelineReport"

gov.nih.nci.ncicb.tcga.dcc.datareports.constants.CodeTablesReportConstants

Modifier and Type	Constant Field	Value
public static final String	BCR_BATCH_CODE	"bcrBatchCode"
public static final String	CELL_LINE_CONTROL_DISPLAY	"Cell Line Control"
public static final String	CENTER_CODE	"centerCode"
public static final String	CENTER_TYPE	"centerType"
public static final String	CODE	"code"
public static final String	CODE_TABLES_EXPORT_URL	"/codeTablesExport.htm"
public static final String	CODE_TABLES_REPORT	"codeTablesReport"
public static final String	CODE_TABLES_REPORT_JSON_URL	"/codeTablesReport.json"
public static final String	CODE_TABLES_REPORT_URL	"/codeTablesReport.htm"
public static final String	CODE_TABLES_REPORT_VIEW	"codeTablesReport"
public static final String	DEFINITION	"definition"
public static final String	DISEASE_STUDY	"diseaseStudy"
public static final String	PLATFORM_CODE	"platformCode"
public static final String	QUERY_BCR_BATCH	"select b.batch_id,d.disease_abbreviation, d.disease_name as study_name,c.short_name as bcr from batch_number_assignment b, disease d, center c where b.disease_id=d.disease_id and b.center_id=c.center_id order by batch_id"
public static final String	QUERY_CENTER	"select bcr_center_id,domain_name,ctbc.center_type_code,ctbc.display_name,short_name from center c, center_to_bcr_center ctbc where c.center_id = ctbc.center_id order by bcr_center_id"
public static final String	QUERY_DATA_LEVEL	"select level_number,level_definition from data_level"
public static final String	QUERY_DATA_TYPE	"select center_type_code,name,ftp_display,available from data_type order by sort_order"
public static final String	QUERY_DISEASE	"select disease_abbreviation,disease_name from disease order by disease_name"
public static final String	QUERY_DISEASE_ACTIVE	"select disease_abbreviation,disease_name from disease where active = 1 order by disease_name"
public static final String	QUERY_PLATFORM	"select platform_name,platform_alias,platform_display_name,available from platform order by sort_order"
public static final String	QUERY_PORTION_ANALYTE	"select portion_analyte_code,definition from portion_analyte order by portion_analyte_code"
public static final String	QUERY_SAMPLE_TYPE	"select sample_type_code,definition,short_letter_code from sample_type order by sample_type_code"
public static final String	QUERY_TISSUE	"select tissue from tissue order by tissue_id"
public static final String	QUERY_TISSUE_SOURCE_SITE	"SELECT tss.tss_code as tss_no, tss.tss_definition as site, d.disease_name as study_name, c.short_name as BCR FROM tissue_source_site tss, tss_to_disease td, disease d, center c WHERE tss.tss_code = td.tss_code AND td.disease_id=d.disease_id AND tss.receiving_center_id = c.center_id ORDER BY tss.tss_code"
public static final String	STUDY_CODE	"studyCode"
public static final String	STUDY_NAME	"studyName"
public static final String	TISSUE_SOURCE_SITE	"tissueSourceSite"

gov.nih.nci.ncicb.tcga.dcc.datareports.constants.DatareportsCommonConstants

Modifier and Type	Constant Field	Value
public static final String	ALIQUOT_ID	"aliquotId"
public static final String	ALIQUOT_UUID	"aliquotUUID"
public static final String	ALL	"all"
public static final String	ANALYTE_ID	"analyteId"
public static final String	ASC	"ASC"
public static final String	BATCH	"batch"
public static final String	BCR	"bcr"
public static final String	BCR_BATCH	"bcrBatch"
public static final String	BR	"<br />"
public static final String	CENTER	"center"
public static final String	CENTER_ID	"centerId"
public static final String	CGCC	"CGCC"
public static final String	COLS	"cols"
public static final String	CSV	"csv"
public static final String	DATA_LEVEL	"dataLevel"
public static final String	DATA_TYPE	"dataType"
public static final String	DATAREPORTS_HOME_URL	"/dataReportsHome.htm"
public static final String	DATAREPORTS_HOME_VIEW	"dataReportsHome"
public static final String	DATE	"date"
public static final String	DATE_FORMAT_US_STRING	"MM/dd/yyyy"
public static final String	DATE_FROM	"dateFrom"
public static final String	DATE_TIME_FORMAT_US_STRING	"MM/dd/yyyy HH:mm"
public static final String	DATE_TO	"dateTo"
public static final String	DESC	"DESC"
public static final String	DIR	"dir"
public static final String	DISEASE	"disease"
public static final String	EXPORT_DATA	"data"
public static final String	EXPORT_DATE_FORMAT	"dateFormat"
public static final String	EXPORT_FILENAME	"fileName"
public static final String	EXPORT_TITLE	"title"
public static final String	EXPORT_TYPE	"exportType"
public static final String	FILE_SIZE	"fileSize"
public static final String	FILTER	"filter"
public static final String	FILTER_REQ	"filterReq"
public static final String	FORM_FILTER	"formFilter"
public static final String	GBM	"GBM"
public static final String	GSC	"GSC"
public static final String	IGC	"igc"
public static final String	LEVEL	"level"
public static final String	LIMIT	"limit"
public static final String	MODE	"mode"
public static final String	NA	"N/A"
public static final String	NOT_AVAILABLE	"N/A"
public static final String	OV	"OV"
public static final String	PAGE_SIZE	"pageSize"
public static final String	PARTICIPANT	"participant"
public static final String	PARTICIPANT_ID	"participantId"
public static final String	PLATE_ID	"plateId"
public static final String	PLATFORM	"platform"
public static final String	PORTION_ID	"portionId"
public static final String	PROJECT	"project"
public static final String	SAMPLE_ID	"sampleId"
public static final String	SAMPLE_TYPE	"sampleType"
public static final String	SELECTION	"selection"
public static final String	SEPARATOR	","
public static final String	SERVER_URL	"serverUrl"
public static final String	SHOW_FILTER_BOX	"showFilterBox"
public static final String	SORT	"sort"
public static final String	START	"start"
public static final String	TAB	"tab"
public static final String	TISSUE	"tissue"
public static final String	TOTAL_COUNT	"totalCount"
public static final String	TYPE	"type"
public static final String	VALID	"valid"
public static final String	VIAL_ID	"vialId"
public static final String	XL	"xl"
public static final String	YES	"yes"

gov.nih.nci.ncicb.tcga.dcc.datareports.constants.LatestGenericReportConstants

Modifier and Type	Constant Field	Value
public static final String	ARCHIVE_NAME	"archiveName"
public static final String	ARCHIVE_TYPE	"archiveType"
public static final String	ARCHIVE_URL	"deployLocation"
public static final String	DATE_ADDED	"dateAdded"
public static final String	EMPTY_LATEST_ARCHIVE_FILTER	"{\"archiveType\":\"\",\"dateFrom\":\"\",\"dateTo\":\"\"}"
public static final String	LATEST_ARCHIVE_DATA	"latestArchiveData"
public static final String	LATEST_ARCHIVE_EXPORT_URL	"/latestArchiveExport.htm"
public static final String	LATEST_ARCHIVE_FILTER_DATA_URL	"/latestArchiveFilterData.json"
public static final String	LATEST_ARCHIVE_FILTER_MODEL	"latestArchiveFilterModel"
public static final String	LATEST_ARCHIVE_REPORT_JSON_URL	"/latestArchiveReport.json"
public static final String	LATEST_ARCHIVE_REPORT_URL	"/latestArchiveReport.htm"
public static final String	LATEST_ARCHIVE_REPORT_VIEW	"latestArchiveReport"
public static final String	MAF_NAME	"mafName"
public static final String	MAF_URL	"mafUrl"
public static final String	QUERY_ARCHIVE_TYPE	"select type from archive_type order by type"
public static final String	QUERY_LATEST_ARCHIVE	"select a.archive_name, a.date_added, a.deploy_location from archive_info a where a.is_latest = 1 and a.deploy_status = \'Available\' order by a.archive_name, a.date_added"
public static final String	QUERY_LATEST_ARCHIVE_BY_TYPE	"select a.archive_name,a.date_added, a.deploy_location from archive_info a, archive_type t where a.is_latest = 1 and a.deploy_status = \'Available\' and a.archive_type_id = t.ARCHIVE_TYPE_ID and t.archive_type = ? order by a.archive_name,a.date_added"
public static final String	QUERY_LATEST_COMBINED	"select distinct a.archive_name,a.date_added, a.deploy_location, t.archive_type, COALESCE(sdrf2.file_name,sdrf1.file_name) as sdrf_file_name, COALESCE(sdrf2.file_location_url, sdrf1.file_location_url) as sdrf_file_location_url, maf.file_name as maf_file_name, maf.file_location_url as maf_file_location_url FROM archive_type t, archive_info a LEFT OUTER JOIN( select a.archive_name,a.date_added,f.file_name,fa.file_location_url , a.center_id, a.platform_id, a.disease_id from archive_info a, file_info f, File_to_Archive fa where a.is_latest = 1 and a.archive_id = fa.archive_id and f.file_name like \'%.maf\' and f.file_id = fa.file_id order by 1,2) maf ON a.center_id = maf.center_id and a.platform_id=maf.platform_id and a.disease_id = maf.disease_id LEFT OUTER JOIN(select a.archive_name,a.date_added,f.file_name,fa.file_location_url , a.center_id, a.platform_id, a.disease_id from archive_info a, archive_type t, file_info f, File_to_Archive fa where a.is_latest = 1 and a.archive_type_id = t.archive_type_id and a.archive_id = fa.archive_id and f.file_name like \'%sdrf%\' and f.file_id = fa.file_id and t.archive_type = \'mage-tab\' order by 1,2) sdrf2 ON a.center_id = sdrf2.center_id and a.platform_id=sdrf2.platform_id and a.disease_id=sdrf2.disease_id LEFT OUTER JOIN (select a.archive_name,a.date_added,a.deploy_location,f.file_name,fa.file_location_url , a.center_id, a.platform_id, a.disease_id from archive_info a, file_info f, File_to_Archive fa where a.is_latest = 1 and a.archive_name not like \'%mage-tab%\' and a.archive_id = fa.archive_id and f.file_name like \'%sdrf%\' and f.file_id = fa.file_id order by 1,2 ) sdrf1 ON a.center_id = sdrf1.center_id and a.platform_id=sdrf1.platform_id and a.disease_id=sdrf1.disease_id and a.archive_name=sdrf1.archive_name where a.is_latest = 1 and a.deploy_status = \'Available\' and a.archive_type_id = t.archive_type_id order by a.archive_name"
public static final String	QUERY_LATEST_MAF	"select a.archive_name,a.date_added, fa.file_location_url from archive_info a, archive_type t, file_info f, File_to_Archive fa where a.is_latest = 1 and a.deploy_status = \'Available\' and a.archive_type_id = t.ARCHIVE_TYPE_ID and a.archive_id = fa.archive_id and f.file_name like \'%maf%\' and f.file_id = fa.file_id order by a.archive_name,a.date_added"
public static final String	QUERY_LATEST_SDRF	"select a.archive_name,a.date_added, fa.file_location_url from archive_info a, archive_type t, file_info f, File_to_Archive fa where a.is_latest = 1 and a.deploy_status = \'Available\' and a.archive_type_id = t.archive_type_id and a.archive_id = fa.archive_id and f.file_name like \'%sdrf%\' and f.file_id = fa.file_id and t.archive_type = \'mage-tab\' order by a.archive_name, a.date_added"
public static final String	REAL_NAME	"realName"
public static final String	SDRF_NAME	"sdrfName"
public static final String	SDRF_URL	"sdrfUrl"

gov.nih.nci.ncicb.tcga.dcc.datareports.constants.PendingUUIDReportConstants

Modifier and Type	Constant Field	Value
public static final String	EMPTY_PENDING_UUID_REPORT_FILTER	"{\"bcr\":\"\",\"batch\":\"\",\"center\":\"\",\"plateId\":\"\"}"
public static final String	PENDING_UUID_REPORT_DATA	"pendingUUIDData"
public static final String	PENDING_UUID_REPORT_EXPORT_URL	"/pendingUUIDExport.htm"
public static final String	PENDING_UUID_REPORT_FILTER_DATA_URL	"/pendingUUIDFilterData.json"
public static final String	PENDING_UUID_REPORT_FILTER_MODEL	"pendingUUIDFilterModel"
public static final String	PENDING_UUID_REPORT_JSON_URL	"/pendingUUIDReport.json"
public static final String	PENDING_UUID_REPORT_URL	"/shipped-items-pending-bcr-data-submission.htm"
public static final String	PENDING_UUID_REPORT_VIEW	"shipped-items-pending-bcr-data-submission"

gov.nih.nci.ncicb.tcga.dcc.datareports.constants.ProjectCaseDashboardConstants

Modifier and Type	Constant Field	Value
public static final String	EMPTY_PROJECT_CASE_DASHBOARD_FILTER	"{\"disease\":\"\"}"
public static final String	PROJECT_CASE_DASHBOARD_DATA	"projectCaseDashboardData"
public static final String	PROJECT_CASE_DASHBOARD_EXPORT_URL	"/projectCaseDashboardExport.htm"
public static final String	PROJECT_CASE_DASHBOARD_FILTER_DATA_URL	"/projectCaseDashboardFilterData.json"
public static final String	PROJECT_CASE_DASHBOARD_FILTER_MODEL	"projectCaseDashboardFilterModel"
public static final String	PROJECT_CASE_DASHBOARD_JSON_URL	"/projectCaseDashboard.json"
public static final String	PROJECT_CASE_DASHBOARD_URL	"/projectCaseDashboard.htm"
public static final String	PROJECT_CASE_DASHBOARD_VIEW	"projectCaseDashboard"
public static final String	QUERY_COMPLETE_CASE_BY_DISEASE	"select count(distinct participant_barcode) as complete_cases from pcod_normal_tumor_stats where cn_TumorCount = 1 and cn_NormalCount = 1 and (expArray_TumorCount = 1 or expRnaSeq_TumorCount = 1) and mirna_TumorCount = 1 and methylation_TumorCount = 1 and gsc_exome_TumorCount = 1 and gsc_exome_NormalCount = 1 and mutation_TumorCount= 1 and mutation_normalCount = 1 and disease_abbreviation = ?"
public static final String	QUERY_PROJECT_CASE_COUNTS	"select disease_abbreviation, metholated_data_cases, microrna_data_cases, exparray_data_cases, exprnaseq_data_cases, copynumber_data_cases, gsc_mutation_data_cases, gsc_microrna_cases, gsc_rnaseq_cases, gsc_exome_cases, gsc_genome_cases, gcc_lowpass_cases, gsc_lowpass_cases from projectoverview_case_counts order by disease_abbreviation"
public static final String	QUERY_REFRESH_PROJECT_CASE_DASHBOARD_PROC	"call pcod_report.build_projectOverview_counts()"
public static final String	TARGET_CASE_JSON_FILE	"targetCase.json"
public static final String	TOTALS	"TOTALS"

gov.nih.nci.ncicb.tcga.dcc.datareports.constants.SampleSummaryReportConstants

Modifier and Type	Constant Field	Value
public static final String	BCR_SENT	"totalBCRSent"
public static final String	BCR_UNKNOWN	"totalBCRUnaccountedFor"
public static final String	CENTER_EMAIL	"centerEmail"
public static final String	CENTER_SENT	"totalCenterSent"
public static final String	CENTER_UNKNOWN	"totalCenterUnaccountedFor"
public static final String	EMAIL_NOTE1	"<div align=\'left\'><span>A value of <quote>Undetermined</quote> for Platform indicates that the DCC has not received data for the indicated sample-analytes<br/><span style=\'color: red;\'>* = Although not in the latest current archive, level 4 data has been submitted</span><br/></span><br /></div>"
public static final String	EMAIL_NOTE2	"<div align=\'left\'><span>The most up-to-date information is always available as a dynamic web report."
public static final String	EMPTY_SAMPLE_SUMMARY_FILTER	"\t{\"disease\":\"\",\"center\":\"\",\"portionAnalyte\":\"\",\"platform\":\"\",\"levelFourSubmitted\":\"\"}"
public static final String	LAST_REFRESH	"last_refresh"
public static final String	LEVEL1_SS	"totalLevelOne"
public static final String	LEVEL2_SS	"totalLevelTwo"
public static final String	LEVEL3_SS	"totalLevelThree"
public static final String	LEVEL4_SS	"levelFourSubmitted"
public static final String	PORTION_ANALYTE	"portionAnalyte"
public static final String	QUERY_CENTER_EMAIL_INFO	"select c.domain_name, c.center_type_code, ce.email_address, c.display_name from center c, center_email ce where c.center_id = ce.center_id and center_type_code <> \'BCR\';"
public static final String	QUERY_REFRESH_SAMPLE_SUMMARY_TABLE	"call build_sample_summary_report()"
public static final String	QUERY_SAMPLE_IDS_BCR_REPORTED_SENDING_TO_CENTER_QUERY	"SELECT sample, LISTAGG(to_char(ship_Date, \'YYYY/MM/DD\'), (\', \')) WITHIN GROUP (ORDER BY ship_Date DESC) as ship_Date FROM samples_sent_by_bcr WHERE disease_abbreviation = ? AND center_name = ? AND center_type_code = ? AND portion_analyte_code = ? GROUP BY sample"
public static final String	QUERY_SAMPLE_IDS_DCC_RECEIVED_FROM_CENTER	"SELECT sample, LISTAGG(to_char(date_received, \'YYYY/MM/DD\'), \', \') WITHIN GROUP (ORDER BY date_received DESC) as date_received FROM latest_samples_received_by_dcc WHERE disease_abbreviation = ? AND center_name = ? AND center_type_code = ? AND portion_analyte_code = ? AND platform = ? GROUP BY sample"
public static final String	QUERY_SAMPLE_IDS_WITH_LEVEL_X_DATA	"SELECT bb.sample, LISTAGG(to_char(a.date_added, \'YYYY/MM/DD\'), \', \') WITHIN GROUP (ORDER BY a.date_Added DESC) as date_added FROM center c, archive_info a, platform p, file_info f, center_to_bcr_center cb, shipped_biospecimen_file bf, shipped_biospecimen_aliquot bb, disease d, file_to_archive fa WHERE c.center_id = a.center_id AND c.center_id = cb.center_id AND d.disease_abbreviation = ? AND c.domain_name = ? AND cb.center_type_code = ? AND bb.portion_analyte_code = ? AND bb.is_viewable = 1 AND p.platform_alias = ? AND f.level_number = ? AND a.platform_id = p.platform_id AND f.file_id = fa.file_id AND a.archive_id = fa.archive_id AND f.file_id = bf.file_id AND a.disease_id = d.disease_id AND bf.shipped_biospecimen_id = bb.shipped_biospecimen_id AND a.is_latest = 1 AND a.deploy_status = \'Available\' GROUP BY bb.sample"
public static final String	QUERY_SAMPLE_SUMMARY	"select * from sample_summary_report_detail order by disease_abbreviation, center_name, center_type_code, portion_analyte_code"
public static final String	QUERY_SAMPLE_SUMMARY_FOR_DISEASE_ABBR	"select * from sample_summary_report_detail where disease_abbreviation = ? order by center_name, center_type_code, portion_analyte_code"
public static final String	QUERY_TOTAL_SAMPLES_BCR_SENT	"SELECT count(distinct bb.sample) as samples, d.disease_abbreviation, c.center_id, c.domain_name as center_name, cb.center_type_code as center_type, bb.portion_analyte_code as portion_analyte FROM shipped_biospecimen_aliquot bb, shipped_biospec_bcr_archive ba, Archive_info a, disease d, center c, center_to_bcr_center cb WHERE c.center_id = cb.center_id AND cb.bcr_center_id = bb.bcr_center_id AND bb.shipped_biospecimen_id = ba.shipped_biospecimen_id AND ba.archive_id = a.archive_id AND a.disease_id = d.disease_id AND a.is_latest = 1 AND bb.is_viewable = 1 AND a.deploy_status = \'Available\' GROUP BY d.disease_abbreviation,c.center_id ,c.domain_name,cb.center_type_code,bb.portion_analyte_code order by domain_name"
public static final String	QUERY_TOTAL_SAMPLES_CGCC_SENT	"SELECT count(distinct bb.sample) as samples, d.disease_abbreviation, c.center_id, c.domain_name as center_name, cb.center_type_code as center_type, p.platform_alias as platform, bb.portion_analyte_code as portion_analyte FROM archive_info a, center c, platform p, disease d, file_info f, file_to_archive fa, center_to_bcr_center cb, shipped_biospecimen_file bf, shipped_biospecimen_aliquot bb WHERE a.is_latest = 1 AND a.deploy_status = \'Available\' AND a.center_id = c.center_id AND a.platform_id = p.platform_id AND a.disease_id = d.disease_id AND f.file_id = fa.file_id AND a.archive_id = fa.archive_id AND f.file_id = bf.file_id AND bf.shipped_biospecimen_id = bb.shipped_biospecimen_id AND bb.is_viewable = 1 AND bb.bcr_center_id = cb.bcr_center_id GROUP BY d.disease_abbreviation, c.center_id , c.domain_name, cb.center_type_code, p.platform_alias , bb.portion_analyte_code order by domain_name"
public static final String	QUERY_TOTAL_SAMPLES_GSC_SENT	"SELECT count(distinct bb.sample) as samples, d.disease_abbreviation, c.center_id, c.domain_name as center_name, cb.center_type_code as center_type, p.platform_alias as platform, bb.portion_analyte_code as portion_analyte FROM archive_info a, center c, platform p, disease d, file_info f, file_to_archive fa, center_to_bcr_center cb, shipped_biospecimen_file bf, shipped_biospecimen_aliquot bb WHERE a.is_latest = 1 AND a.deploy_status = \'Available\' AND a.center_id = c.center_id AND a.platform_id = p.platform_id AND a.disease_id = d.disease_id AND f.file_id = fa.file_id AND a.archive_id = fa.archive_id AND f.file_id = bf.file_id AND bf.shipped_biospecimen_id = bb.shipped_biospecimen_id AND bb.is_viewable = 1 AND bb.bcr_center_id = cb.bcr_center_id GROUP BY d.disease_abbreviation, c.center_id, c.domain_name, cb.center_type_code, p.platform_alias, bb.portion_analyte_code order by domain_name"
public static final String	QUERY_UNACCOUNTED_FOR_BCR_SAMPLE_IDS_THAT_CENTER_REPORTED	"SELECT sample, LISTAGG(to_char(date_received, \'YYYY/MM/DD\'), \', \') WITHIN GROUP (ORDER BY date_received DESC) as date_received FROM latest_samples_received_by_dcc WHERE disease_abbreviation = ? AND center_name = ? AND center_type_code = ? AND portion_analyte_code = ? AND platform = ? and sample not in ( SELECT sample FROM samples_sent_by_bcr WHERE disease_abbreviation = ? AND center_name = ? AND center_type_code = ? AND portion_analyte_code = ? ) GROUP BY sample"
public static final String	QUERY_UNACCOUNTED_FOR_CENTER_SAMPLE_IDS_THAT_BCR_REPORTED	"SELECT sample, LISTAGG(to_char(ship_Date, \'YYYY/MM/DD\'), \', \') WITHIN GROUP (ORDER BY ship_Date DESC) as ship_Date from samples_sent_by_bcr WHERE disease_abbreviation = ? AND center_name = ? AND center_type_code = ? AND portion_analyte_code = ? AND sample not in( SELECT sample FROM latest_samples_received_by_dcc WHERE disease_abbreviation = ? AND center_name = ? AND center_type_code = ? AND portion_analyte_code = ? AND platform = ? ) GROUP BY sample"
public static final String	QUESTIONS_COMMENTS	"If you have any questions or comments about this email or the reports listed here, please contact the DCC via the contact listed below.</span></div>"
public static final String	REPORT_DISCLAIMER	"Disclaimer: The above table(s) reflect as accurately as possible the sample IDs and ID annotations submitted to the DCC to date. At the present time, the intended platform for a given aliquot can only be inferred from the disease and the identity of the GSC/CGCC that is encoded in the aliquot ID. If a given GSC/CGCC is using only one platform for a given disease, then this inference will be accurate. If the GSC/CGCC is using more than one platform for a disease, the DCC cannot accurately report ID counts per platform per disease. Of course, once a GSC/CGCC submits molecular data for an aliquot to the DCC, then the platform is known. In Phase 2 of the TCGA project there will be a standard operating procedure for a GSC/CGCC to report the intended platform for a given aliquot before submitting the molecular data."
public static final String	SAMPLE_DETAILED_EXPORT_URL	"/sampleDetailedExport.htm"
public static final String	SAMPLE_DETAILED_JSON_URL	"/sampleDetailedReport.json"
public static final String	SAMPLE_DETAILED_REPORT_VIEW	"sampleDetailedReport"
public static final String	SAMPLE_SUMMARY_DATA	"sampleSummaryData"
public static final String	SAMPLE_SUMMARY_DB_FILE	"SampleSummary_TestDB.xml"
public static final String	SAMPLE_SUMMARY_EXPORT_URL	"/sampleSummaryExport.htm"
public static final String	SAMPLE_SUMMARY_FILTER_DATA_URL	"/sampleSummaryFilterData.json"
public static final String	SAMPLE_SUMMARY_FILTER_MODEL	"sampleSummaryFilterModel"
public static final String	SAMPLE_SUMMARY_REPORT_JSON_URL	"/sampleSummaryReport.json"
public static final String	SAMPLE_SUMMARY_REPORT_URL	"/sampleSummaryReport.htm"
public static final String	SAMPLE_SUMMARY_REPORT_VIEW	"sampleSummaryReport"
public static final String	SS_URL	"/datareports/sampleSummaryReport.htm"
public static final String	TOTAL_BCR_SENT	"total_bcr_sent"
public static final String	TOTAL_BCR_UNACCOUNTED	"total_bcr_unaccounted"
public static final String	TOTAL_CENTER_UNACCOUNTED	"total_center_unaccounted"
public static final String	TOTAL_CENTERS_SENT	"total_centers_sent"
public static final String	TOTAL_WITH_LEVEL1	"total_with_level1"
public static final String	TOTAL_WITH_LEVEL2	"total_with_level2"
public static final String	TOTAL_WITH_LEVEL3	"total_with_level3"

gov.nih.nci.ncicb.tcga.dcc.datareports.constants.StatsDashboardConstants

Modifier and Type	Constant Field	Value
public static final String	QUERY_ABS_TOTAL_NUMBER_ARCHIVE_DOWNLOAD	"select sum(action_total) from portal_action_summary where action_type_id=34"
public static final String	QUERY_ABS_TOTAL_NUMBER_ARCHIVE_RECEIVED	"select count(*) from archive_info"
public static final String	QUERY_ABS_TOTAL_SIZE_ARCHIVE_DOWNLOAD	"select sum(action_total) from portal_action_summary where action_type_id=36"
public static final String	QUERY_ABS_TOTAL_SIZE_ARCHIVE_RECEIVED	"select sum(final_size_kb) from archive_info"
public static final String	QUERY_CUMULATIVE_NUMBER_ARCHIVE_DOWNLOAD_PER_MONTHYEAR	"SELECT TO_CHAR(TO_DATE(NVL(monthyear,0),\'MM/YYYY\'),\'MON-YYYY\') as monthyear, sum(downloads) over (ORDER BY TO_DATE(NVL(monthyear,0),\'MM/YYYY\') rows between unbounded preceding and current row) as cumulative FROM (SELECT monthyear, sum(action_total) as downloads FROM portal_action_summary WHERE action_type_id=34 AND disease_abbreviation =? GROUP BY monthyear) ORDER BY TO_DATE(NVL(monthyear,0),\'MM/YYYY\')"
public static final String	QUERY_CUMULATIVE_NUMBER_ARCHIVE_RECEIVED_PER_MONTHYEAR	"select to_char(trunc(date_added,\'MONTH\'),\'MON/YYYY\') as monthyr, sum(count(*)) over (order by trunc(date_added,\'MONTH\') rows between unbounded preceding and current row) as cumulative from archive_info a, disease d where a.disease_id=d.disease_id and disease_abbreviation = ? group by trunc(date_added,\'MONTH\') order by trunc(date_added,\'MONTH\')"
public static final String	QUERY_CUMULATIVE_SIZE_ARCHIVE_DOWNLOAD_PER_MONTHYEAR	"SELECT TO_CHAR(TO_DATE(NVL(monthyear,0),\'MM/YYYY\'),\'MON-YYYY\') as monthyear, sum(downloads) over (ORDER BY TO_DATE(NVL(monthyear,0),\'MM/YYYY\') rows between unbounded preceding and current row) as cumulative FROM (SELECT monthyear, sum(action_total) as downloads FROM portal_action_summary WHERE action_type_id=36 AND disease_abbreviation = ? GROUP BY monthyear) ORDER BY TO_DATE(NVL(monthyear,0),\'MM/YYYY\')"
public static final String	QUERY_CUMULATIVE_SIZE_ARCHIVE_RECEIVED_PER_MONTHYEAR	"select to_char(trunc(date_added,\'MONTH\'),\'MON/YYYY\') as monthyr, sum(sum(final_size_kb)) over (order by trunc(date_added,\'MONTH\') rows between unbounded preceding and current row) as cumulative from archive_info a, disease d where a.disease_id=d.disease_id and disease_abbreviation = ? group by trunc(date_added,\'MONTH\') order by trunc(date_added,\'MONTH\')"
public static final String	QUERY_FILTER_BATCH	"select selection, sum(action_total) from portal_action_summary where action_type_id=? group by selection order by to_number(regexp_substr(selection,\'[0-9]+\'))"
public static final String	QUERY_FILTER_PIE_CHART	"select selection, sum(action_total) from portal_action_summary where action_type_id=? group by selection order by selection"
public static final String	QUERY_FILTER_PIE_CHART_PER_DISEASE	"select disease_abbreviation, sum(action_total) from portal_action_summary where action_type_id=? and selection = ? group by disease_abbreviation order by disease_abbreviation"
public static final String	QUERY_NUMBER_ARCHIVE_DOWNLOAD_PER_MONTHYEAR	"SELECT TO_CHAR(TO_DATE(NVL(monthyear,0),\'MM/YYYY\'),\'MON-YYYY\') as monthyear, NVL(downloads,0) as downloads FROM (SELECT monthyear, sum(action_total) as downloads FROM portal_action_summary WHERE action_type_id=34 AND disease_abbreviation = ? GROUP BY monthyear) ORDER BY TO_DATE(NVL(monthyear,0),\'MM/YYYY\')"
public static final String	QUERY_NUMBER_ARCHIVE_DOWNLOAD_TOTAL_PER_DISEASE	"select disease_abbreviation, sum(action_total) from portal_action_summary where action_type_id=34 group by disease_abbreviation order by disease_abbreviation"
public static final String	QUERY_NUMBER_ARCHIVE_RECEIVED_PER_MONTHYEAR	"select to_char(trunc(date_added,\'MONTH\'),\'MON/YYYY\') as monthyr, count(*) from archive_info a, disease d where a.disease_id=d.disease_id and disease_abbreviation = ? group by trunc(date_added,\'MONTH\') order by trunc(date_added,\'MONTH\')"
public static final String	QUERY_NUMBER_ARCHIVE_RECEIVED_TOTAL_PER_DISEASE	"select disease_abbreviation,count(*) from archive_info a, disease d where a.disease_id=d.disease_id group by disease_abbreviation order by disease_abbreviation"
public static final String	QUERY_REFRESH_STATS_DASHBOARD_PROC	"call build_portal_action_summary.get_summary_details()"
public static final String	QUERY_SIZE_ARCHIVE_DOWNLOAD_PER_MONTHYEAR	"SELECT TO_CHAR(TO_DATE(NVL(monthyear,0),\'MM/YYYY\'),\'MON-YYYY\') as monthyear, NVL(downloads,0) as downloads FROM (SELECT monthyear, sum(action_total) as downloads FROM portal_action_summary WHERE action_type_id=36 AND disease_abbreviation = ? GROUP BY monthyear) ORDER BY TO_DATE(NVL(monthyear,0),\'MM/YYYY\')"
public static final String	QUERY_SIZE_ARCHIVE_DOWNLOAD_TOTAL_PER_DISEASE	"select disease_abbreviation, sum(action_total) from portal_action_summary where action_type_id=36 group by disease_abbreviation order by disease_abbreviation"
public static final String	QUERY_SIZE_ARCHIVE_RECEIVED_PER_MONTHYEAR	"select to_char(trunc(date_added,\'MONTH\'),\'MON/YYYY\') as monthyr, sum(final_size_kb) from archive_info a, disease d where a.disease_id=d.disease_id and disease_abbreviation = ? group by trunc(date_added,\'MONTH\') order by trunc(date_added,\'MONTH\')"
public static final String	QUERY_SIZE_ARCHIVE_RECEIVED_TOTAL_PER_DISEASE	"select disease_abbreviation,sum(final_size_kb) as total_size_kb from archive_info a, disease d where a.disease_id=d.disease_id group by disease_abbreviation order by disease_abbreviation"
public static final String	STATS_DASHBOARD_HOME_URL	"/statsDashboard.htm"
public static final String	STATS_DASHBOARD_HOME_VIEW	"statsDashboard"

gov.nih.nci.ncicb.tcga.dcc.datareports.constants.SubmissionReportConstants

Modifier and Type	Constant Field	Value
public static final String	SUBMISSION_REPORT_URL	"/submissionReport.htm"
public static final String	SUBMISSION_REPORT_VIEW	"submissionReport"

gov.nih.nci.ncicb.tcga.dcc.datareports.service.PendingUUIDProcessor

Modifier and Type	Constant Field	Value
protected static final String	ALIQUOT	"Aliquot"
protected static final String	ANALYTE_TYPE_KEY	"analyte_type"
protected static final String	BATCH_NUMBER_KEY	"batch_number"
protected static final String	BCR_ALIQUOT_BARCODE_KEY	"bcr_aliquot_barcode"
protected static final String	BCR_ALIQUOT_UUID_KEY	"bcr_aliquot_uuid"
protected static final String	BCR_KEY	"bcr"
protected static final String	BCR_SHIPPED_PORTION_BARCODE_KEY	"bcr_shipment_portion_barcode"
protected static final String	BCR_SHIPPED_PORTION_UUID_KEY	"bcr_shipment_portion_uuid"
protected static final String	BCR_VALUE_IGC	"IGC"
protected static final String	BCR_VALUE_NCH	"NCH"
protected static final String	CENTER	"center"
protected static final String	DATE_FORMAT_US_DASHES	"MM-dd-yyyy"
protected static final String	NULL_VALUE	"null"
protected static final String	PLATE	"plate"
protected static final String	PLATE_ID	"plate_id"
protected static final String	PORTION_NUMBER_KEY	"portion_number"
protected static final String	SAMPLE_TYPE_KEY	"sample_type"
protected static final String	SHIPPED_DATE_KEY	"ship_date"
protected static final String	SHIPPED_PORTION	"Shipped Portion"
protected static final String	VIAL_NUMBER_KEY	"vial_number"

gov.nih.nci.ncicb.tcga.dcc.io.api.codec.kryo.Kryo01FrameDecoder

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_MAX_FRAME_LENGTH	65536
public static final int	LENGTH_FIELD_LENGTH	4

gov.nih.nci.ncicb.tcga.dcc.io.api.config.IoApiConfigProfileType

Modifier and Type	Constant Field	Value
public static final String	DEVELOPMENT_PNAME	"dev"
public static final String	EMBEDDED_PNAME	"embed"
public static final String	LOCAL_PNAME	"local"
public static final String	METRICS_PNAME	"metrics"
public static final String	PRODUCTION_PNAME	"prod"
public static final String	QA_PNAME	"qa"
public static final String	STAGE_PNAME	"stage"
public static final String	TEST_PNAME	"test"
public static final String	TLS_PNAME	"tls"

gov.nih.nci.ncicb.tcga.dcc.io.api.domain.message.MessageHeaders

Modifier and Type	Constant Field	Value
public static final String	BATCH_SIZE	"batchSize"
public static final String	CONTENT_ENCODING	"contentEncoding"
public static final String	CONTENT_TYPE	"contentType"
public static final String	ERROR_CHANNEL	"errorChannel"
public static final String	ID	"id"
public static final String	PRIORITY	"priority"
public static final String	REPLY_CHANNEL	"replyChannel"
public static final String	SEQUENCE_NUMBER	"sequenceNumber"
public static final String	SEQUENCE_SIZE	"sequenceSize"
public static final String	TIMESTAMP	"timestamp"

gov.nih.nci.ncicb.tcga.dcc.io.api.util.NetUtils

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_PORT	8080
public static final int	DEFAULT_PORT_SECURE	8443

gov.nih.nci.ncicb.tcga.dcc.io.api.util.concurrent.GzipDeflateFilesTask

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_THRESHOLD	2

gov.nih.nci.ncicb.tcga.dcc.io.api.util.nio.FileUtil

Modifier and Type	Constant Field	Value
public static final String	WILDCARD_GLOB_PATTERN	"*"

gov.nih.nci.ncicb.tcga.dcc.io.client.analytics.TelemetryClient

Modifier and Type	Constant Field	Value
public static final String	SERVICE_URI	"service/telemetry"

gov.nih.nci.ncicb.tcga.dcc.io.client.config.ClientMetricsConfig

Modifier and Type	Constant Field	Value
public static final String	CLIENT_METRICS_LOGGING_CTX	"io.client.metrics"

gov.nih.nci.ncicb.tcga.dcc.io.client.config.HttpClientConfig

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_SERVER_PORT	9888

gov.nih.nci.ncicb.tcga.dcc.io.client.deltaencode.DeltaEncodeClient

Modifier and Type	Constant Field	Value
public static final String	SERVICE_URI	"service/deltaEncode"

gov.nih.nci.ncicb.tcga.dcc.io.server.api.AbstractServer

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_SERVER_NAME	"I/O Server"

gov.nih.nci.ncicb.tcga.dcc.io.server.api.ApplicationContainer

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_WEBAPP_BASE_DIR	"src/main/webapp"
public static final String	DEFAULT_WEBAPP_DESCRIPTOR	"/WEB-INF/web.xml"

gov.nih.nci.ncicb.tcga.dcc.io.server.http.config.WebApplicationInitializer

Modifier and Type	Constant Field	Value
public static final String	CHARACTER_ENCODING	"UTF-8"

gov.nih.nci.ncicb.tcga.dcc.qclive.Messages

Modifier and Type	Constant Field	Value
public static final String	ARCHIVE_NAME_DUPLICATE_SERIAL_INDEX_MSG	"Duplicate serial index. Serial index {0} already exists in {1} center {2} disease"
public static final String	ARCHIVE_NAME_INVALID_SERIAL_INDEX_MSG	"Invalid serial index. Serial index {0} is already assigned to {1} center {2} disease"
public static final String	FILE_COMPRESS_ERR_MSG	"Unexpected error while compressing cache file {0}. Error details: {1}\n"
public static final String	LEVEL2_DATA_GENERATION_ERR	"Level2 Data Generation Error"
public static final String	LEVEL2_DATA_GENERATION_ERR_MSG	"Unexpected error while generating Level2 data cache files for {0}-{1}-{2}-{3}, Error details: {4}\n"

gov.nih.nci.ncicb.tcga.dcc.qclive.bean.DataFile

Modifier and Type	Constant Field	Value
public static final String	FILETYPE_UNKNOWN	"--unknown--"

gov.nih.nci.ncicb.tcga.dcc.qclive.bean.Experiment

Modifier and Type	Constant Field	Value
public static final String	BIOSPECIMEN_CORE_RESOURCE	"Biospecimen Core Resource"
public static final String	CANCER_GENOMIC_CHARACTERIZATION_CENTER	"Cancer Genomic Characterization Center"
public static final String	GENOME_SEQUENCING_CENTER	"Genome Sequencing Center"
public static final String	STATUS_CHECKED	"Checked"
public static final String	STATUS_DEPLOYED	"Deployed"
public static final String	STATUS_FAILED	"Failed"
public static final String	STATUS_PENDING	"Pending"
public static final String	STATUS_UP_TO_DATE	"Up to date"
public static final String	STATUS_VALID	"Valid"
public static final String	TYPE_BCR	"BCR"
public static final String	TYPE_CGCC	"CGCC"
public static final String	TYPE_GDAC	"GDAC"
public static final String	TYPE_GSC	"GSC"

gov.nih.nci.ncicb.tcga.dcc.qclive.bean.VcfFile

Modifier and Type	Constant Field	Value
public static final String	HEADER_TYPE_ALT	"ALT"
public static final String	HEADER_TYPE_CHROM	"CHROM"
public static final String	HEADER_TYPE_FILEFORMAT	"fileformat"
public static final String	HEADER_TYPE_FILTER	"FILTER"
public static final String	HEADER_TYPE_FORMAT	"FORMAT"
public static final String	HEADER_TYPE_ID	"ID"
public static final String	HEADER_TYPE_INFO	"INFO"
public static final String	HEADER_TYPE_POS	"POS"
public static final String	HEADER_TYPE_QUAL	"QUAL"
public static final String	HEADER_TYPE_REF	"REF"
public static final String	HEADER_TYPE_SAMPLE	"SAMPLE"
public static final String	HEADER_TYPE_TCGA_VERSION	"tcgaversion"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.QcContext

Modifier and Type	Constant Field	Value
public static final String	WARNING_MSG	"Too many warnings. New warning messages will not be recorded"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.AbstractMafFileHandler<O>

Modifier and Type	Constant Field	Value
public static final String	COMMENT_LINE_TOKEN	"#"
protected static final String	FIELD_BAM_FILE	"BAM_File"
public static final String	FIELD_CENTER	"GSC_Center"
public static final String	FIELD_CENTER_NAME	"Center"
public static final String	FIELD_CHROMOSOME	"Chromosome"
public static final String	FIELD_DBSNP_RS	"dbSNP_RS"
public static final String	FIELD_DBSNP_VAL_STATUS	"dbSNP_Val_Status"
public static final String	FIELD_END_POSITION	"End_position"
public static final String	FIELD_ENTREZ_GENE_ID	"Entrez_Gene_Id"
public static final String	FIELD_HUGO_SYMBOL	"Hugo_Symbol"
public static final String	FIELD_MAF2_END_POSITION	"End_Position"
public static final String	FIELD_MAF2_START_POSITION	"Start_Position"
public static final String	FIELD_MATCH_NORM_SEQ_ALLELE1	"Match_Norm_Seq_Allele1"
public static final String	FIELD_MATCH_NORM_SEQ_ALLELE2	"Match_Norm_Seq_Allele2"
public static final String	FIELD_MATCH_NORM_VALIDATION_ALLELE1	"Match_Norm_Validation_Allele1"
public static final String	FIELD_MATCH_NORM_VALIDATION_ALLELE2	"Match_Norm_Validation_Allele2"
public static final String	FIELD_MATCHED_NORM_SAMPLE_BARCODE	"Matched_Norm_Sample_Barcode"
public static final String	FIELD_MATCHED_NORM_SAMPLE_UUID	"Matched_Norm_Sample_UUID"
public static final String	FIELD_MUTATION_STATUS	"Mutation_Status"
public static final String	FIELD_NCBI_BUILD	"NCBI_Build"
public static final String	FIELD_REFERENCE_ALLELE	"Reference_Allele"
protected static final String	FIELD_SCORE	"Score"
protected static final String	FIELD_SEQUENCE_SOURCE	"Sequence_Source"
protected static final String	FIELD_SEQUENCER	"Sequencer"
public static final String	FIELD_SEQUENCING_PHASE	"Sequencing_Phase"
public static final String	FIELD_START_POSITION	"Start_position"
public static final String	FIELD_STRAND	"Strand"
public static final String	FIELD_TUMOR_SAMPLE_BARCODE	"Tumor_Sample_Barcode"
public static final String	FIELD_TUMOR_SAMPLE_UUID	"Tumor_Sample_UUID"
public static final String	FIELD_TUMOR_SEQ_ALLELE1	"Tumor_Seq_Allele1"
public static final String	FIELD_TUMOR_SEQ_ALLELE2	"Tumor_Seq_Allele2"
public static final String	FIELD_TUMOR_VALIDATION_ALLELE1	"Tumor_Validation_Allele1"
public static final String	FIELD_TUMOR_VALIDATION_ALLELE2	"Tumor_Validation_Allele2"
public static final String	FIELD_VALIDATION_METHOD	"Validation_Method"
public static final String	FIELD_VALIDATION_STATUS	"Validation_Status"
public static final String	FIELD_VARIANT_CLASSIFICATION	"Variant_Classification"
public static final String	FIELD_VARIANT_TYPE	"Variant_Type"
public static final String	FIELD_VERIFICATION_STATUS	"Verification_Status"
public static final String	MAF_EXTENSION	".maf"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.AbstractSdrfHandler<I,O>

Modifier and Type	Constant Field	Value
public static final String	ALIQUOT_HEADER	"Hybridization Name"
public static final String	COMMENT_ARCHIVE_NAME	"Comment [TCGA Archive Name]"
public static final String	COMMENT_DATA_LEVEL	"Comment [TCGA Data Level]"
public static final String	COMMENT_DATA_TYPE	"Comment [TCGA Data Type]"
public static final String	COMMENT_INCLUDE_FOR_ANALYSIS	"Comment [TCGA Include for Analysis]"
public static final String	EXTRACT_NAME	"Extract Name"
public static final String	FILE_COLUMN_END	"File"
public static final String	FILE_COLUMN_SUFFIX	"File"
protected static final String	IMAGE_FILE	"Image File"
public static final String	PROTOCOL_REF	"Protocol REF"
public static final String	SDRF_EXTENSION	".sdrf.txt"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.AlteredFileListCreator

Modifier and Type	Constant Field	Value
public static final String	DCC_ALTERED_FILES_NAME	"DCC_ALTERED_FILES.txt"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.ArchiveDeployer

Modifier and Type	Constant Field	Value
protected static final String	LOCATION_PUBLIC	"Public"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.ArchiveReadmeCreator

Modifier and Type	Constant Field	Value
public static final String	DATE_FORMAT_FOR_README	"MM/dd/yyyy"
public static final int	LINE_WIDTH	100

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.ChangeLogCreator

Modifier and Type	Constant Field	Value
public static final String	CHANGE_FILE_NAME	"CHANGES_DCC.txt"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.ClinicalDateObscurer

Modifier and Type	Constant Field	Value
public static final String	README_FILENAME	"README_HIPAA_AGES.txt"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.Maf2FileProcessor

Modifier and Type	Constant Field	Value
public static final String	FIELD_BAM_FILE	"BAM_File"
public static final String	FIELD_SCORE	"Score"
public static final String	FIELD_SEQUENCE_SOURCE	"Sequence_Source"
public static final String	FIELD_SEQUENCER	"Sequencer"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.SdrfProcessor

Modifier and Type	Constant Field	Value
public static final String	PROTEIN_SDRF_PLATFORM_CODE	"MDA_RPPA_Core"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.validation.AbstractIdfValidator

Modifier and Type	Constant Field	Value
protected static final String	PROTOCOL_PARAMETERS	"Protocol Parameters"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.validation.AbstractSdrfValidator

Modifier and Type	Constant Field	Value
protected static final String	BARCODE_COMMENT_COLUMN_NAME	"Comment [TCGA Barcode]"
protected static final String	BLANK	""
protected static final String	EXTRACT_NAME_COLUMN_NAME	"Extract Name"
protected static final int	NUM_HEADERS	1
protected static final String	SDRF_NULL	"->"
protected static final int	ZERO_INDEX_OFFSET	1

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.validation.ArchiveNameValidator

Modifier and Type	Constant Field	Value
public static final int	INDEX_IN_ARCHIVE_NAME_ARCHIVE_TYPE	4
public static final int	INDEX_IN_ARCHIVE_NAME_DOMAIN	1
public static final int	INDEX_IN_ARCHIVE_NAME_PLATFORM	3
public static final int	INDEX_IN_ARCHIVE_NAME_REVISION	6
public static final int	INDEX_IN_ARCHIVE_NAME_SERIAL	5
public static final int	INDEX_IN_ARCHIVE_NAME_SERIES	7
public static final int	INDEX_IN_ARCHIVE_NAME_TUMOR_TYPE	2
public static final String	TCGA_PROJECT	"TCGA"
public static final String	TCGA_SERIES_VALUE	"0"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.validation.DNASeqSdrfValidator

Modifier and Type	Constant Field	Value
public static final String	PROPRIETARY	"Proprietary"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.validation.GscIdfValidator

Modifier and Type	Constant Field	Value
public static final String	PROTOCOL_PARAMETERS_VALUES_SEPARATOR	";"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.validation.MafFileValidator

Modifier and Type	Constant Field	Value
public static final String	MULTI_VALUE_SEPARATOR	";"
protected static final String	MUTATION_STATUS_GERMLINE	"Germline"
protected static final String	MUTATION_STATUS_LOH	"LOH"
protected static final String	MUTATION_STATUS_SOMATIC	"Somatic"
protected static final String	VALIDATION_STATUS_UNKNOWN	"Unknown"
protected static final String	VALIDATION_STATUS_VALID	"Valid"
protected static final String	VALIDATION_STATUS_WILDTYPE	"Wildtype"
protected static final String	VERIFICATION_STATUS_VERIFIED	"Verified"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.validation.MafFileValidatorV2_4

Modifier and Type	Constant Field	Value
protected static final String	VALIDATION_METHOD_NONE	"none"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.validation.MageTabExperimentValidator

Modifier and Type	Constant Field	Value
public static final String	MATRIX_FILE_COLUMN_DESIGNATOR	"Data Matrix File"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.validation.ManifestValidator

Modifier and Type	Constant Field	Value
public static final String	MANIFEST_FILE	"MANIFEST.txt"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.validation.MD5Validator

Modifier and Type	Constant Field	Value
public static final String	STATUS_PENDING	"Pending"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.validation.MiRNASeqDataFileValidator

Modifier and Type	Constant Field	Value
protected static final String	CROSS_MAPPED	"cross-mapped"
protected static final String	MIRNA_ID	"miRNA_ID"
public static final String	MIRNASEQ	"miRNASeq"
protected static final String	READ_COUNT	"read_count"
protected static final String	READS_PER_MILLION_MIRNA_MAPPED	"reads_per_million_miRNA_mapped"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.validation.MiRNASeqFileValidator

Modifier and Type	Constant Field	Value
public static final String	MIRNA_FILE_EXTENSION	"mirna.quantification.txt"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.validation.MiRNASeqIsoformFileValidator

Modifier and Type	Constant Field	Value
protected static final String	ISOFORM_COORDS	"isoform_coords"
public static final String	ISOFORM_FILE_EXTENSION	"isoform.quantification.txt"
protected static final String	MIRNA_REGION	"miRNA_region"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.validation.MiRnaSeqSdrfValidator

Modifier and Type	Constant Field	Value
public static final String	WIG_FILE_EXTENSION	".wig"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.validation.ProteinArrayLevelThreeDataFileValidator

Modifier and Type	Constant Field	Value
public static final String	archiveFileExtension	".txt"
public static final String	ignoreList	"MANIFEST.txt;README.txt;DESCRIPTION.txt"
public static final String	PROTEIN_ARRAY_PLATFORM	"MDA_RPPA_Core"
public static final String	PROTEIN_ARRAY_PLATFORM_DATA_TYPE	"protein_expression"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.validation.ProteinArraySdrfValidator

Modifier and Type	Constant Field	Value
public static final String	ARRAY_NAME	"Array Name"
public static final String	COMMENT_ANTIBODY_TYPE	"Comment [TCGA Antibody Name]"
public static final String	COMMENT_BIOSPECIMEN_TYPE	"Comment [TCGA Biospecimen Type]"
public static final String	COMMENT_DATA_TYPE	"Comment [TCGA Data Type]"
public static final String	COMMENT_FILE_TYPE	"Comment [TCGA File Type]"
public static final String	COMMENT_MD5	"Comment [TCGA MD5]"
public static final String	DATA_TRANSFORMATION_NAME	"Data Transformation Name"
public static final String	HYBRIDIZATION_NAME	"Hybridization Name"
public static final String	NORMALIZATION_NAME	"Normalization Name"
public static final String	PROTEIN_ARRAY_PLATFORM	"MDA_RPPA_Core"
public static final String	SCAN_NAME	"Scan Name"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.validation.RNASeqDataFileValidator

Modifier and Type	Constant Field	Value
protected static final String	MEDIAN_LENGTH_NORMALIZED_HEADER	"median_length_normalized"
protected static final String	RAW_COUNTS_HEADER	"raw_counts"
public static final String	RNASEQ	"RNASeq"
protected static final String	RPKM_HEADER	"RPKM"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.validation.RNASeqExonFileValidator

Modifier and Type	Constant Field	Value
public static final String	EXON_FILE_EXTENSION	"*.exon.quantification.txt,*.exon_quantification.txt"
protected static final String	EXON_HEADER	"exon"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.validation.RNASeqGeneFileValidator

Modifier and Type	Constant Field	Value
public static final String	GENE_FILE_EXTENSION	"gene.quantification.txt"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.validation.RNASeqJunctionFileValidator

Modifier and Type	Constant Field	Value
public static final String	JUNCTION_FILE_EXTENSION	"*.spljxn.quantification.txt,*.junction_quantification.txt"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.validation.RNASeqRSEMGeneNormalizedFileValidator

Modifier and Type	Constant Field	Value
public static final String	RSEM_GENE_NORMAL_FILE_EXTENSION	"rsem.genes.normalized_results"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.validation.RNASeqRSEMGeneResultsFileValidator

Modifier and Type	Constant Field	Value
public static final String	RSEM_GENES_RESULTS_FILE_EXTENSION	"rsem.genes.results"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.validation.RNASeqRSEMIsoformFileValidator

Modifier and Type	Constant Field	Value
public static final String	RSEM_ISOFORM_RESULTS_FILE_EXTENSION	"rsem.isoforms.results"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.validation.RNASeqRSEMIsoformNormalizedFileValidator

Modifier and Type	Constant Field	Value
public static final String	RSEM_ISOFORM_NORMAL_FILE_EXTENSION	"rsem.isoforms.normalized_results"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.validation.RNASeqRSEMValidator

Modifier and Type	Constant Field	Value
public static final String	GENE_ID	"gene_id"
public static final String	ISOFORM_ID	"isoform_id"
public static final String	NORMALIZED_COUNT	"normalized_count"
public static final String	RAW_COUNT	"raw_count"
public static final String	SCALED_ESTIMATE	"scaled_estimate"
public static final String	TRANSCRIPT_ID	"transcript_id"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.validation.RnaSeqSdrfValidator

Modifier and Type	Constant Field	Value
public static final String	V1_EXON_FILE_EXTENSION	"*.exon.quantification.txt"
public static final String	V1_JUNCTION_FILE_EXTENSION	"*.spljxn.quantification.txt"
public static final String	V2_EXON_FILE_EXTENSION	"*.exon_quantification.txt"
public static final String	V2_JUNCTION_FILE_EXTENSION	"*.junction_quantification.txt"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.validation.TraceFileValidator

Modifier and Type	Constant Field	Value
public static final String	TR_EXTENSION	".tr"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.validation.xml.BiospecimenXmlValidator

Modifier and Type	Constant Field	Value
public static final String	ANALYTE_TYPE_ID	"analyte_type_id"
public static final String	BIOSPECIMEN_XML_VALIDATOR_NAME	"biospecimen XML file validation"
public static final String	CENTER_ID	"center_id"
public static final String	PATIENT_ID	"patient_id"
public static final String	PLATE_ID	"plate_id"
public static final String	PORTION_NUMBER	"portion_number"
public static final String	SAMPLE_TYPE_ID	"sample_type_id"
public static final String	TISSUE_SOURCE_SITE	"tissue_source_site"
public static final String	VIAL_NUMBER	"vial_number"
public static final String	XML_EXTENSION	".xml"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.validation.xml.ClinicalXmlValidator

Modifier and Type	Constant Field	Value
public static final String	PATIENT_BARCODE_XPATH_EXPRESSION	"//patient/bcr_patient_barcode"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.action.validation.xml.XmlValidator

Modifier and Type	Constant Field	Value
public static final String	XML_EXTENSION	".xml"
public static final String	XML_FILE_GLOB_PATTERN	"*.{xml}"
public static final String	XSD_EXTENSION	".xsd"
public static final String	XSD_FILE_GLOB_PATTERN	"*.{xsd}"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.util.ArchiveCompressorTarGzImpl

Modifier and Type	Constant Field	Value
public static final String	GZIP_EXTENSION	".gz"
public static final String	TAR_EXTENSION	".tar"
public static final String	TAR_GZIP_EXTENSION	".tar.gz"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.util.ArchiveCompressorZipImpl

Modifier and Type	Constant Field	Value
public static final String	ZIP_EXTENSION	".zip"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.util.BCRUtilsImpl

Modifier and Type	Constant Field	Value
public static final String	AUXILIARY	"auxiliary"
public static final String	BIOSPECIMEN	"biospecimen"
public static final String	CONTROL	"control"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.util.DateComparator

Modifier and Type	Constant Field	Value
public static final String	PRECISION_DAY	"day"
public static final String	PRECISION_MONTH	"month"
public static final String	PRECISION_YEAR	"year"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.util.PatientBarcodeValidator

Modifier and Type	Constant Field	Value
public static final String	PATIENT_BARCODE_PATTERN_STRING	"((TCGA)-([A-Z0-9]{2})-([A-Z0-9]{4}))"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.util.TcgaVcfFileDataLineValidatorImpl

Modifier and Type	Constant Field	Value
public static final String	FORMAT_VALUE_AD	"AD"
public static final String	FORMAT_VALUE_BQ	"BQ"
public static final String	FORMAT_VALUE_DP	"DP"
public static final String	FORMAT_VALUE_DP4	"DP4"
public static final String	FORMAT_VALUE_SS	"SS"
public static final String	INFO_KEY_EVENT	"EVENT"

gov.nih.nci.ncicb.tcga.dcc.qclive.common.util.TcgaVcfFileHeaderValidator

Modifier and Type	Constant Field	Value
public static final String	FILEDATE_FORMAT	"yyyyMMdd"
public static final String	HEADER_TYPE_ASSEMBLY	"assembly"
public static final String	HEADER_TYPE_CENTER	"center"
public static final String	HEADER_TYPE_FILEDATE	"fileDate"
public static final String	HEADER_TYPE_GENE_ANNO	"geneAnno"
public static final String	HEADER_TYPE_INDIVIDUAL	"INDIVIDUAL"
public static final String	HEADER_TYPE_PEDIGREE	"PEDIGREE"
public static final String	HEADER_TYPE_PHASING	"phasing"
public static final String	HEADER_TYPE_REFERENCE	"reference"
public static final String	HEADER_TYPE_SAMPLE	"SAMPLE"
public static final String	HEADER_TYPE_VCFPROCESSLOG	"vcfProcessLog"
public static final String	SAMPLE_KEY_ACCESSION	"Accession"
public static final String	SAMPLE_KEY_FILE	"File"
public static final String	SAMPLE_KEY_GENOME_DESCRIPTION	"Genome_Description"
public static final String	SAMPLE_KEY_GENOMES	"Genomes"
public static final String	SAMPLE_KEY_ID	"ID"
public static final String	SAMPLE_KEY_INDIVIDUAL	"Individual"
public static final String	SAMPLE_KEY_MIXTURE	"Mixture"
public static final String	SAMPLE_KEY_PLATFORM	"Platform"
public static final String	SAMPLE_KEY_SAMPLE_NAME	"SampleName"
public static final String	SAMPLE_KEY_SAMPLE_TCGA_BARCODE	"SampleTCGABarcode"
public static final String	SAMPLE_KEY_SAMPLE_UUID	"SampleUUID"
public static final String	SAMPLE_KEY_SOURCE	"Source"
public static final String	UUID_REGEXP	"[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}"
public static final String	VCF_PROCESS_LOG_HEADER_TAG_VALUES_DEFAULT_SEPARATOR	","
public static final String	VCF_PROCESS_LOG_HEADER_TAG_VALUES_SPECIAL_SEPARATOR	";"
public static final String	VCF_PROCESS_LOG_INPUTVCF_TAG	"InputVCF"
public static final String	VCF_PROCESS_LOG_MERGE_TAG_PREFIX	"Merge"
public static final String	VCF_PROCESS_LOG_MISSING_IDENTIFIER	"."

gov.nih.nci.ncicb.tcga.dcc.qclive.common.util.VcfFileDataLineValidatorImpl

Modifier and Type	Constant Field	Value
public static final String	DATA_VALUE_SEPARATOR	";"
public static final String	KEY_VALUE_SEPARATOR	"="
protected static final String	SAMPLE_DATA_FIELD_VALUES_SEPARATOR	","
public static final String	SAMPLE_DATA_SEPARATOR	":"

gov.nih.nci.ncicb.tcga.dcc.qclive.dao.jdbc.LevelThreeQueriesImpl

Modifier and Type	Constant Field	Value
public static final String	ADD_CNA_VALUE	"INSERT INTO cna_value(cna_value_id, data_set_id, hybridization_ref_id, chromosome, chr_start, chr_stop, num_mark, seg_mean, tumor_count, normal_count) VALUES (CNA_VALUE_SEQ.nextval, ?,?,?,?,?,?,?,?,?)"
public static final String	ADD_DATA_SET	"INSERT INTO data_set (data_set_id, experiment_id, source_file_name, source_file_type, access_level, load_complete, use_in_dam , dam_comments , data_level , center_id, platform_id, archive_id ) VALUES (?, ?, ?, ?, ?, ?, NULL,NULL, ?, ?, ?, ?)"
public static final String	ADD_DATA_SET_FILE	"INSERT INTO data_set_file(data_set_file_id, data_set_id, file_name, load_start_date, file_id) VALUES(data_set_file_seq.nextval, ?, ?, sysdate, ?)"
public static final String	ADD_EXPERIMENT	"insert into experiment (experiment_id, center_id, platform_id, base_name, data_deposit_batch, data_revision) values (experiment_experiment_id_seq.NEXTVAL,?,?,?,?,?)"
public static final String	ADD_EXPGENE	"INSERT INTO expgene_value(expgene_value_id, data_set_id, hybridization_ref_id, entrez_gene_symbol, expression_value) VALUES(EXPGENE_VALUE_SEQ.nextval, ?,?,?,?)"
public static final String	ADD_HYBREF_DATASET	"INSERT INTO hybrid_ref_data_set (hybref_dataset_id, hybridization_ref_id, data_set_id, hybridization_ref_name) VALUES (hybref_dataset_seq.NEXTVAL,?,?,?)"
public static final String	ADD_HYBRIDIZATION_REF	"INSERT INTO hybridization_ref (hybridization_ref_id, bestBarcode, sample_name, uuid) VALUES (?,?,?,?)"
public static final String	ADD_METHYLATION_VALUE	"INSERT INTO methylation_value(methylation_value_id,probe_name,data_set_id, hybridization_ref_id, beta_value, entrez_gene_symbol, chromosome, chr_position) VALUES(METHYLATION_VALUE_SEQ.nextval, ?, ?, ?, ?, ?, ?, ?)"
public static final String	GET_DATA_SET	"SELECT data_set_id FROM data_set WHERE experiment_id = ? AND source_file_name = ? AND source_file_type = ? AND access_level = ?"
public static final String	GET_EXPERIMENT_ID_QUERY	"SELECT experiment_id FROM experiment WHERE base_name = ? AND data_deposit_batch = ? AND data_revision = ?"
public static final String	GET_FILE_FOR_ARCHIVE	"SELECT f.file_name,f.file_id FROM file_info f, file_to_archive fa WHERE fa.archive_id = ? AND fa.file_id=f.file_id"
public static final String	GET_HYBREDIZATION_REF	"SELECT hybridization_ref_id FROM hybridization_ref WHERE bestBarcode=?"
public static final String	GET_HYBREF_DATASET	"SELECT hybref_dataset_id FROM hybrid_ref_data_set WHERE hybridization_ref_id=? AND data_set_id = ?"
public static final String	GET_HYBRIDIZATION_REF_ID	" SELECT hybref_hybridization_seq.nextval FROM dual"
public static final String	GET_TUMOR_BARCODES_FOR_FILE	"SELECT built_barcode FROM shipped_biospecimen_breakdown sb, sample_type s, shipped_biospecimen_file sbf WHERE sbf.FILE_ID = ? AND sbf.SHIPPED_BIOSPECIMEN_ID = sb.SHIPPED_BIOSPECIMEN_ID AND sb.sample_type_code=s.sample_type_code AND s.is_tumor=1"
public static final String	RETRIEVE_DEPLOY_LOCATION	"SELECT deploy_location, is_latest,disease_abbreviation FROM archive_info a, disease d WHERE a.disease_id = d.disease_id AND archive_name=? "
public static final String	SET_LOAD_STATUS_QUERY	"UPDATE data_set SET load_complete=1, use_in_dam=1 WHERE data_set_id = ?"
public static final String	UPDATE_ARCHIVE_INFO	"UPDATE archive_info SET DATA_LOADED_DATE=SYSDATE WHERE archive_id=?"
public static final String	UPDATE_DATA_SET_FILE	"UPDATE data_set_file SET is_loaded=1, load_end_date=sysdate WHERE data_set_id=? AND file_name=? AND file_id = ?"

gov.nih.nci.ncicb.tcga.dcc.qclive.live.Live

Modifier and Type	Constant Field	Value
public static final String	QUARTZ_JOB_GROUP	"QCLive"

gov.nih.nci.ncicb.tcga.dcc.qclive.live.service.ArchiveCleanupJob

Modifier and Type	Constant Field	Value
public static final String	ARCHIVE	"archive"
public static final String	ARCHIVE_FAILED	"archiveFailed"

gov.nih.nci.ncicb.tcga.dcc.qclive.live.service.ClinicalLoaderJob

Modifier and Type	Constant Field	Value
public static final String	CLINICAL_ARCHIVES	"clinicalArchives"
public static final String	CLINICAL_PROCESSED_ARCHIVES	"clinicalProcessedArchives"

gov.nih.nci.ncicb.tcga.dcc.qclive.live.service.LiveScheduler

Modifier and Type	Constant Field	Value
public static final String	ARCHIVE_NAME	"archiveName"
public static final String	EXPERIMENT_NAME	"experimentName"
public static final String	EXPERIMENT_TYPE	"experimentType"
public static final String	STATE_CONTEXT	"stateContext"

gov.nih.nci.ncicb.tcga.dcc.qclive.loader.bamloader.BAMLoader

Modifier and Type	Constant Field	Value
public static final String	LIVE	"live"

gov.nih.nci.ncicb.tcga.dcc.qclive.loader.levelthree.record.file.segment.BroadMitEduSegmentRecord

Modifier and Type	Constant Field	Value
public static final String	CENTER_NAME	"broad.mit.edu"

gov.nih.nci.ncicb.tcga.dcc.qclive.loader.levelthree.record.file.segment.GenomeWustlEduSegmentRecord

Modifier and Type	Constant Field	Value
public static final String	CENTER_NAME	"genome.wustl.edu"

gov.nih.nci.ncicb.tcga.dcc.qclive.loader.levelthree.record.file.segment.HmsHarvardEduSegmentRecord

Modifier and Type	Constant Field	Value
public static final String	CENTER_NAME	"hms.harvard.edu"

gov.nih.nci.ncicb.tcga.dcc.qclive.loader.levelthree.record.file.segment.HudsonAlphaOrgSegmentRecord

Modifier and Type	Constant Field	Value
public static final String	CENTER_NAME	"hudson.alpha.org"

gov.nih.nci.ncicb.tcga.dcc.qclive.loader.levelthree.record.file.segment.MskccOrgSegmentRecord

Modifier and Type	Constant Field	Value
public static final String	CENTER_NAME	"mskcc.org"

gov.nih.nci.ncicb.tcga.dcc.qclive.loader.levelthreedata.LevelThreeDataLoader

Modifier and Type	Constant Field	Value
public static final String	ACCESS_LEVEL_PUBLIC	"PUBLIC"

gov.nih.nci.ncicb.tcga.dcc.qclive.service.LoaderEnqueuer

Modifier and Type	Constant Field	Value
protected static final String	JOBRUNNER_MAPNAME	"loaderRunner"

gov.nih.nci.ncicb.tcga.dcc.qclive.soundcheck.Soundcheck

Modifier and Type	Constant Field	Value
public static final String	FILE_PARAMETER_KEY	"archiveFile"
public static final String	VALIDATOR_URL_AND_MESSAGE	"The latest version of the validator can be found here: https://wiki.nci.nih.gov/display/TCGA/Download+TCGA+Archive+Validator"

gov.nih.nci.ncicb.tcga.dcc.qclive.standalone.StandaloneValidator

Modifier and Type	Constant Field	Value
public static final String	VALIDATOR_URL_AND_MESSAGE	"The latest version of the validator can be found here: "
public static final String	VERSION_FORMAT	"Client-side Validator %s%n"

gov.nih.nci.ncicb.tcga.dcc.qclive.util.QCliveXMLSchemaValidator

Modifier and Type	Constant Field	Value
public static final String	W3C_XML_SCHEMA_NS_URI	"http://www.w3.org/2001/XMLSchema"
public static final String	XSD_EXTENSION	".xsd"

gov.nih.nci.ncicb.tcga.dcc.uuid.constants.UUIDBrowserConstants

Modifier and Type	Constant Field	Value
public static final String	QUERY_EXISTING_BARCODES	"select barcode from barcode_history where barcode in(REPLACE_BARCODE)"
public static final String	QUERY_UUID_BROWSER	"select disease_abbreviation, uuid, parent_uuid, is_redacted, platforms, item_type_id, tss_code, center_id_bcr, batch_number, barcode, participant_number, sample_type_code, sample_sequence, portion_sequence, portion_analyte_code, plate_id, receiving_center_id, slide, slide_layer, create_date, update_date, is_shipped, shipped_date, center_code from uuid_hierarchy order by disease_abbreviation"
public static final String	QUERY_UUID_BROWSER_BY_BARCODE	"select disease_abbreviation, uuid, parent_uuid, is_redacted, platforms, item_type_id, tss_code, center_id_bcr, batch_number, barcode, participant_number, sample_type_code, sample_sequence, portion_sequence, portion_analyte_code, plate_id, receiving_center_id, slide, slide_layer, create_date, update_date, is_shipped, shipped_date, center_code from uuid_hierarchy where barcode = ? order by disease_abbreviation"
public static final String	QUERY_UUID_BROWSER_BY_BARCODES	"select disease_abbreviation, uuid, parent_uuid, is_redacted, platforms, item_type_id, tss_code, center_id_bcr, batch_number, barcode, participant_number, sample_type_code, sample_sequence, portion_sequence, portion_analyte_code, plate_id, receiving_center_id, slide, slide_layer, create_date, update_date, is_shipped, shipped_date, center_code from uuid_hierarchy where barcode in (REPLACE_BARCODE) order by disease_abbreviation"
public static final String	QUERY_UUID_BROWSER_BY_UUID	"select disease_abbreviation, uuid, parent_uuid, is_redacted, platforms, item_type_id, tss_code, center_id_bcr, batch_number, barcode, participant_number, sample_type_code, sample_sequence, portion_sequence, portion_analyte_code, plate_id, receiving_center_id, slide, slide_layer, create_date, update_date, is_shipped, shipped_date, center_code from uuid_hierarchy where uuid = ? order by disease_abbreviation"
public static final String	QUERY_UUID_BROWSER_BY_UUIDS	"select disease_abbreviation, uuid, parent_uuid, is_redacted, platforms, item_type_id, tss_code, center_id_bcr, batch_number, barcode, participant_number, sample_type_code, sample_sequence, portion_sequence, portion_analyte_code, plate_id, receiving_center_id, slide, slide_layer, create_date, update_date, is_shipped, shipped_date, center_code from uuid_hierarchy where uuid in (REPLACE_UUID) order by disease_abbreviation"
public static final String	REPLACE_BARCODE	"REPLACE_BARCODE"
public static final String	REPLACE_UUID	"REPLACE_UUID"

org.quartz.*

org.quartz.impl.jdbcjobstore.QueueJobStore

Modifier and Type	Constant Field	Value
public static final String	RECOVERED_INTERRUPTED_JOB	"recovered_incomplete_job"