/
validation_logs.txt
570 lines (566 loc) · 280 KB
/
validation_logs.txt
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. ____ _ __ _ _
/\\ / ___'_ __ _ _(_)_ __ __ _ \ \ \ \
( ( )\___ | '_ | '_| | '_ \/ _` | \ \ \ \
\\/ ___)| |_)| | | | | || (_| | ) ) ) )
' |____| .__|_| |_|_| |_\__, | / / / /
=========|_|==============|___/=/_/_/_/
:: Spring Boot :: (v2.3.3.RELEASE)
13:10:22::218 INFO g.springframework.boot.StartupInfoLogger : Starting Loader on coffeelake with PID 45728 (/home/afollette/IdeaProjects/pdxfinder/indexer/target/classes started by afollette in /home/afollette/IdeaProjects/pdxfinder)
13:10:22::220 INFO g.springframework.boot.SpringApplication : No active profile set, falling back to default profiles: default
13:10:22::245 INFO springframework.boot.logging.DeferredLog : Devtools property defaults active! Set 'spring.devtools.add-properties' to 'false' to disable
13:10:22::563 INFO y.config.RepositoryConfigurationDelegate : Multiple Spring Data modules found, entering strict repository configuration mode!
13:10:22::564 INFO y.config.RepositoryConfigurationDelegate : Bootstrapping Spring Data JPA repositories in DEFAULT mode.
13:10:22::603 INFO y.config.RepositoryConfigurationDelegate : Finished Spring Data repository scanning in 34ms. Found 7 JPA repository interfaces.
13:10:22::605 INFO y.config.RepositoryConfigurationDelegate : Multiple Spring Data modules found, entering strict repository configuration mode!
13:10:22::605 INFO y.config.RepositoryConfigurationDelegate : Bootstrapping Spring Data Neo4j repositories in DEFAULT mode.
13:10:22::638 INFO y.config.RepositoryConfigurationDelegate : Finished Spring Data repository scanning in 31ms. Found 27 Neo4j repository interfaces.
13:10:22::800 INFO trationDelegate$BeanPostProcessorChecker : Bean 'h2Configuration' of type [org.pdxfinder.configuration.H2Configuration$$EnhancerBySpringCGLIB$$4f116242] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)
13:10:22::954 INFO rg.hibernate.jpa.internal.util.LogHelper : HHH000204: Processing PersistenceUnitInfo [name: default]
13:10:22::976 INFO org.hibernate.Version : HHH000412: Hibernate ORM core version 5.4.20.Final
13:10:23::035 INFO on.reflection.java.JavaReflectionManager : HCANN000001: Hibernate Commons Annotations {5.1.0.Final}
13:10:23::082 INFO com.zaxxer.hikari.HikariDataSource : HikariPool-1 - Starting...
13:10:33::209 INFO com.zaxxer.hikari.HikariDataSource : HikariPool-1 - Start completed.
13:10:33::219 INFO org.hibernate.dialect.Dialect : HHH000400: Using dialect: org.hibernate.dialect.H2Dialect
13:10:33::699 INFO a.platform.internal.JtaPlatformInitiator : HHH000490: Using JtaPlatform implementation: [org.hibernate.engine.transaction.jta.platform.internal.NoJtaPlatform]
13:10:33::704 INFO orm.jpa.AbstractEntityManagerFactoryBean : Initialized JPA EntityManagerFactory for persistence unit 'default'
13:10:33::725 INFO s.autoconfigure.OptionalLiveReloadServer : LiveReload server is running on port 35729
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.eclipse.collections.impl.utility.ArrayListIterate (file:/home/afollette/.m2/repository/org/eclipse/collections/eclipse-collections/9.2.0/eclipse-collections-9.2.0.jar) to field java.util.ArrayList.elementData
WARNING: Please consider reporting this to the maintainers of org.eclipse.collections.impl.utility.ArrayListIterate
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
13:10:41::630 INFO org.pdxfinder.CreateBaseCommand : Setting up CreateBaseCommand option
13:10:42::328 INFO g.springframework.boot.StartupInfoLogger : Started Loader in 20.287 seconds (JVM running for 30.834)
13:10:42::334 INFO org.pdxfinder.LoadDiseaseOntology : LoadDiseaseOntology finished after 0 minute(s) and 0 second(s)
13:10:42::334 INFO org.pdxfinder.utils.CreateLocalFeeds : CreateLocalFeeds finished after 0 minute(s) and 0 second(s)
13:10:42::334 INFO rg.pdxfinder.reportmanager.ReportManager : There are no message entries in the Report Manager.
13:10:42::376 INFO inder.commandline.FinderCommandLine$Load : Loading using supplied parameters:
Load[dataDirectory=/home/afollette/Finder_Data_Repositories/pdxfinder-data, initializeMappingDB=false, validateOnlyRequested=true, postLoadRequested=false, springDataNeo4jUri='null', debReload='null', springDatasourceUrl='null']
13:10:42::376 INFO org.pdxfinder.commandline.FinderLoader : Loading cache ...
13:10:42::622 INFO org.pdxfinder.commandline.FinderLoader : Running requested PDX dataset loaders [Test-Minimal, HCI-BCM, IRCC-CRC, JAX, MDAnderson, PDMR, Wistar-MDAnderson-Penn, WUSTL, CRL, Curie-BC, Curie-LC, Curie-OC, IRCC-GC, PMLB, TRACE, UOC-BC, UOM-BC, VHIO-BC, VHIO-CRC, DFCI-CPDM, NKI, JAX-XDOG, SJCRH, UMCG, VHIO-PC, LIH, PPTC]...
13:10:42::623 INFO org.pdxfinder.dataloaders.updog.Updog : Using UPDOG to import HCI-BCM PDX data from [/home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/HCI-BCM]
Reading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/HCI-BCM/HCI-BCM_metadata-sharing.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/HCI-BCM/HCI-BCM_metadata-model.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/HCI-BCM/HCI-BCM_metadata-patient.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/HCI-BCM/HCI-BCM_metadata-checklist.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/HCI-BCM/HCI-BCM_metadata-loader.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/HCI-BCM/HCI-BCM_metadata-model_validation.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/HCI-BCM/HCI-BCM_sampleplatform-data.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/HCI-BCM/HCI-BCM_metadata-sample.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/HCI-BCM/drug/HCI-BCM_drugdosing-Sheet1.tsv13:10:43::029 INFO ders.updog.tablevalidation.ErrorReporter : Limiting output to the first 50 errors:
13:10:43::029 ERROR ders.updog.tablevalidation.ErrorReporter : 9 validation errors found:
13:10:43::029 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [HCI-BCM]: Missing value(s) in required column [name]
13:10:43::029 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-loader.tsv] for provider [HCI-BCM]: Missing value(s) in required column [internal_url]
13:10:43::029 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [HCI-BCM]: Missing value(s) in required column [accessibility]
13:10:43::029 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model.tsv] for provider [HCI-BCM]: Missing value(s) in required column [passage_number]
13:10:43::030 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [HCI-BCM]: Missing value(s) in required column [provider_type]
13:10:43::030 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model_validation.tsv] for provider [HCI-BCM]: Missing value(s) in required column [validation_host_strain_full]
13:10:43::030 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [HCI-BCM]: in column [tumour_type] found 1 values not in a required category. Required Categories: [primary,metastatic,recurrent,refactory,not collected,not provided] Value found : [not specified]
13:10:43::030 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [HCI-BCM]: in column [age_in_years_at_collection] found 33 values have characters not contains in US ASCII numbers and pP-., : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:10:43::030 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model_validation.tsv] for provider [HCI-BCM]: in column [passages_tested] found 18 values have characters not contains in US ASCII numbers and pP-., : [multiple, multiple, multiple, multiple, multiple, multiple, multiple, multiple, multiple, multiple, multiple, multiple, multiple, multiple, multiple, multiple, multiple, multiple]
13:10:43::030 INFO org.pdxfinder.dataloaders.updog.Updog : Using UPDOG to import IRCC-CRC PDX data from [/home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/IRCC-CRC]
Reading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/IRCC-CRC/IRCC-CRC_metadata-checklist.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/IRCC-CRC/IRCC-CRC_metadata-model.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/IRCC-CRC/IRCC-CRC_metadata-sample.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/IRCC-CRC/IRCC-CRC_metadata-model_validation.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/IRCC-CRC/IRCC-CRC_sampleplatform-data.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/IRCC-CRC/IRCC-CRC_metadata-loader.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/IRCC-CRC/IRCC-CRC_metadata-patient.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/IRCC-CRC/IRCC-CRC_metadata-sharing.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/IRCC-CRC/drug/IRCC-CRC_drugdosing-Sheet1.tsv13:10:52::051 INFO ders.updog.tablevalidation.ErrorReporter : Limiting output to the first 50 errors:
13:10:52::051 ERROR ders.updog.tablevalidation.ErrorReporter : 9 validation errors found:
13:10:52::051 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [IRCC-CRC]: Missing value(s) in required column [name]
13:10:52::051 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [IRCC-CRC]: Missing value(s) in required column [accessibility]
13:10:52::051 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [IRCC-CRC]: Missing value(s) in required column [provider_type]
13:10:52::051 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model_validation.tsv] for provider [IRCC-CRC]: Missing value(s) in required column [validation_host_strain_full]
13:10:52::052 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [IRCC-CRC]: in column [sex] found 3 values not in a required category. Required Categories: [male,female,other,not collected,not provided] Value found : [not specified, not specified, not specified]
13:10:52::052 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [IRCC-CRC]: in column [age_in_years_at_collection] found 17 values have characters not contains in US ASCII numbers and pP-., : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:10:52::052 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model_validation.tsv] for provider [IRCC-CRC]: in column [passages_tested] found 531 values have characters not contains in US ASCII numbers and pP-., : [0, 1, 2, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 2, 0, 1, 2, 0, 1, 2, 0, 1, 2, 0, 1, 2, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 2, 4, 1, 2, 0, 1, 2, 3, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 2, 0, 1, 2, 0, 1, 2, 3, 4, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 0, 1, 2, 4, 0, 1, 2, 3, 4, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 2, 0, 1, 2, 0, 1, 2, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 4, 5, 6, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 2, 0, 1, 2, 0, 1, 2, 0, 1, 2, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 4, 5, 0, 1, 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13:10:52::052 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [IRCC-CRC]: Broken one_to_one relation [(metadata-sample.tsv) sample_id -> model_id (metadata-sample.tsv)]: in [metadata-sample.tsv] one-to-one found 3 relationships with conflicts [(CRC0691LM,CRC0691LM), (CRC0691LM,CRC0691LM), (CRC0691LM,CRC0691LM)]
13:10:52::052 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [IRCC-CRC]: Broken one_to_many relation [(metadata-sample.tsv) sample_id -> patient_id (metadata-sample.tsv)]: in [metadata-sample.tsv] one-to-many found 3 relationships with conflicts [(11000206,CRC0691LM), (11000206,CRC0691LM), (11000206,CRC0691LM)]
13:10:52::052 INFO org.pdxfinder.dataloaders.updog.Updog : Using UPDOG to import MDAnderson PDX data from [/home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/MDAnderson]
Reading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/MDAnderson/MDAnderson_metadata-sample.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/MDAnderson/MDAnderson_metadata-sharing.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/MDAnderson/MDAnderson_metadata-patient.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/MDAnderson/MDAnderson_metadata-loader.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/MDAnderson/MDAnderson_metadata-model.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/MDAnderson/MDAnderson_metadata-model_validation.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/MDAnderson/MDAnderson_metadata-checklist.tsv13:10:52::120 INFO ders.updog.tablevalidation.ErrorReporter : Limiting output to the first 50 errors:
13:10:52::120 ERROR ders.updog.tablevalidation.ErrorReporter : 17 validation errors found:
13:10:52::120 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [MDAnderson]: Missing value(s) in required column [name]
13:10:52::120 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-loader.tsv] for provider [MDAnderson]: Missing value(s) in required column [internal_url]
13:10:52::120 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [MDAnderson]: Missing value(s) in required column [accessibility]
13:10:52::120 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model_validation.tsv] for provider [MDAnderson]: Missing value(s) in required column [passages_tested]
13:10:52::120 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [MDAnderson]: Missing value(s) in required column [provider_type]
13:10:52::120 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model_validation.tsv] for provider [MDAnderson]: Missing value(s) in required column [validation_host_strain_full]
13:10:52::120 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [MDAnderson]: in column [model_id] found 1 values have characters not contained in US ASCII Alphanumeric and ._~- : [MDA B1002 / C0997]
13:10:52::120 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [MDAnderson]: in column [patient_id] found 1 values have characters not contained in US ASCII Alphanumeric and ._~- : [MDA B1002 / C0997]
13:10:52::121 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [MDAnderson]: in column [sample_id] found 1 values have characters not contained in US ASCII Alphanumeric and ._~- : [MDA B1002 / C0997]
13:10:52::121 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [MDAnderson]: in column [patient_id] found 1 values have characters not contained in US ASCII Alphanumeric and ._~- : [MDA B1002 / C0997]
13:10:52::121 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [MDAnderson]: in column [model_id] found 1 values have characters not contained in US ASCII Alphanumeric and ._~- : [MDA B1002 / C0997]
13:10:52::121 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model.tsv] for provider [MDAnderson]: in column [model_id] found 1 values have characters not contained in US ASCII Alphanumeric and ._~- : [MDA B1002 / C0997]
13:10:52::121 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model.tsv] for provider [MDAnderson]: in column [publications] found 43 values not of type: PMID: [8 digit id] (comma separated) : [29093017, 29093017, 29093017, 29093017, 29093017, 29093017, 29093017, 29093017, 29093017, 29093017, 29093017, 29093017, 29093017, 29093017, 29093017, 29093017, 29093017, 29093017, 29093017, 29093017, 29093017, 29093017, 29093017, 29093017, 29093017, 29093017, 25444907, 25444907, 25444907, 25444907, 25444907, 25444907, 25444907, 25444907, 25444907, 25444907, 25444907, 25444907, 25444907, 25444907, 25444907, 25444907, 25444907]
13:10:52::121 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [MDAnderson]: in column [tumour_type] found 3 values not in a required category. Required Categories: [primary,metastatic,recurrent,refactory,not collected,not provided] Value found : [not specified, not specified, not specified]
13:10:52::121 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [MDAnderson]: in column [age_in_years_at_collection] found 2 values have characters not contains in US ASCII numbers and pP-., : [not specified, not specified]
13:10:52::121 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model_validation.tsv] for provider [MDAnderson]: in column [passages_tested] found 26 values have characters not contains in US ASCII numbers and pP-., : [p1 (and >p1), p1 (and >p1), p1 (and >p1), p1 (and >p1), p1 (and >p1), p1 (and >p1), p1 (and >p1), p1 (and >p1), p1 (and >p1), p1 (and >p1), p1 (and >p1), p1 (and >p1), p1 (and >p1), p1 (and >p1), p1 (and >p1), p1 (and >p1), p1 (and >p1), p1 (and >p1), p1 (and >p1), p1 (and >p1), p1 (and >p1), p1 (and >p1), p1 (and >p1), p1 (and >p1), p1 (and >p1), p1 (and >p1)]
13:10:52::121 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [MDAnderson]: in column [collection_site] found 4 values have characters not contained in US ASCII Alphanumeric and ().',:;-/ : [primary colon & liver, liver & lung, peritoneal & ascites, pancreatic net & liver]
13:10:52::121 INFO org.pdxfinder.dataloaders.updog.Updog : Using UPDOG to import PDMR PDX data from [/home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/PDMR]
Reading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/PDMR/PDMR_metadata-checklist.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/PDMR/PDMR_metadata-patient.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/PDMR/PDMR_metadata-sample.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/PDMR/PDMR_metadata-loader.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/PDMR/PDMR_sampleplatform-data.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/PDMR/PDMR_metadata-sharing.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/PDMR/PDMR_metadata-model_validation.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/PDMR/PDMR_metadata-model.tsv13:10:52::249 INFO ders.updog.tablevalidation.ErrorReporter : Limiting output to the first 50 errors:
13:10:52::249 ERROR ders.updog.tablevalidation.ErrorReporter : 12 validation errors found:
13:10:52::249 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [PDMR]: Missing value(s) in required column [email]
13:10:52::250 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [PDMR]: Missing value(s) in required column [provider_name]
13:10:52::250 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [PDMR]: Missing value(s) in required column [name]
13:10:52::250 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [PDMR]: Missing value(s) in required column [project]
13:10:52::250 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [PDMR]: Missing value(s) in required column [provider_abbreviation]
13:10:52::250 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [PDMR]: Missing value(s) in required column [accessibility]
13:10:52::250 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [PDMR]: Missing value(s) in required column [provider_type]
13:10:52::250 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model_validation.tsv] for provider [PDMR]: Missing value(s) in required column [validation_host_strain_full]
13:10:52::250 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [PDMR]: in column [tumour_type] found 26 values not in a required category. Required Categories: [primary,metastatic,recurrent,refactory,not collected,not provided] Value found : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:10:52::250 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [PDMR]: in column [age_in_years_at_collection] found 4 values have characters not contains in US ASCII numbers and pP-., : [not specified, not specified, not specified, not specified]
13:10:52::250 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model_validation.tsv] for provider [PDMR]: in column [passages_tested] found 1134 values have characters not contains in US ASCII numbers and pP-., : [all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, all, 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13:10:52::250 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [PDMR]: in column [diagnosis] found 20 values have characters not contained in US ASCII Alphanumeric and ().',:;-/ : [pharyngeal squam cell carcinoma moderate to poorly differentiated final pathology dx confirmed p16+ extensive lymphovascular invasion identified 4 of 30 lymph nodes positive at levels 2a and 3ho adenocarcinoma of the distal esophagus - t4n1m1a stage iv a in 2007 location of known metastases lymph nodes, vaginal cancer nos invasive poorly differentiated non-keratinizing squamous cell carcinoma final path dx confirmed + lymphovascular invasion at primary and metastatic locations prior ho endometrioid endometrial adenocarcinoma surgery only metastatic location suburethral lymph nodes, adenocarcinoma - colon final surgical pathology dx confirmed invasive into pericolic fat with intravascular tumor present +118 lymph nodes tumor stagegrade moderately differentiated, adenocarcinoma - colon moderately to poorly differentiated final pathology dx confirmed with focal tumor budding tumor invades through muscularis propria into percolic fat lymphovascular perineural and extramural large vein invasion present 521 lymph nodes + location of known metastases lymph nodestumor gradestage pt3n2a, invasive breast carcinoma ductal tnbc final pathology dx confirmed with high grade ductal carcinoma in situ with comedo necrosis +lymphovascular invasion tumor gradestage elston-ellis grade 3 pt2, adenocarcinoma - pancreas wmucinous features final pathology dx confirmed with 5-10 of liver involved by metastasis tumor stagegrade grade iv moderately differentiatedlocation of known metastases lung multifocal liver carcinomatosis abdominal lymph nodes diaphragmconcurrent dx papillary rcc pax8+ ck7+ cd117- grade 1 and clear cell rcc pax8+ ck7- cd117-prior ho basel cell carcinoma and bladder cancer, adenocarcinoma - pancreas invasive moderately differentiated final pathology dx confirmed tumor invades peripancreatic soft tissues 1023 lymph nodes +, neuroendocrine cancer nos large cell carcinoma of the cecum final pathology dx confirmed invasive into the sigmoid colon and bladder 621 lymph nodes + mitotic rate 2910 hpf ki67 proliferation index 40-50 tumor stagegrade pt4b pn2blocation of known metastases lymph nodes, liporal cavity squam cell car final pathology dx confirmed +432 lymph nodes tumor gradestage pt2n2b moderately differentiated, urothelialbladder cancer nos invasive urothelial carcinoma of the bladder patient ebv+ tumor gradestage high-gradelocation of known metastases kidney, adenocarcinoma - pancreas ductal final pathology dx confirmed with peripancreatic soft tissue invasion and lymphovascular and perinueral invasion 422 lymph nodes + location of known metastases lymph nodestumor gradestage pt3pn1 stage iib ajcc, squamous cell lung carcinoma +perineural invasion 211 hilar ln positive tumor stagegrade moderately differentiated, adenocarcinoma - colon mucinous and signet-ring features final pathology dx confirmed high-grade with mucinous and signet-ring features and prominent tumor budding tumor arises in ascending colon and invades the subserosa and lympho-vascular space extramural venous and perineural invasion identified 1+ lymph node mesenteric msi-hightumor gradestage high-grade pt3n1am1blocation of known metastasis lymph nodes, adenocarcinoma - colon final pathology dx confirmed invasive into the subserosa perineural invasion + tumor gradestage pt3pn0 low grade, adenocarcinoma - colon per site notes patient diagnosed in 2011 with synchronous colon + rectal cancer recurrent disease, adenocarcinoma - colon poorly differentiated with mucinous features final pathology dx confirmed invasive through muscularis propria into pericolic fat lymphovascular space invasion present 118 lymph nodes+ho prostate cancer treated with radiation tumor gradestage pt3 pn1a, h n squamous cell car nos invasive moderately differentiated final pathology dx confirmed with direct extension into auditory canal skin parotid gland and temporal bone +lymphovascular and perineural invasion with positive margins 2 level 2b of 62 lymph nodes examined + for metastatic carcinoma +extranodal extensionprior malignancy rcc treated surgically only with no known recurrence to date tumor gradestage pt3 pn2blocation of metastases lymph nodes, melanoma melanoma treated surgically only at diagnosisprior malignancy brca+ breast cancer stage 3b papillary thyroid carcinoma treated surgically only location of known metastases liver diaphragm omentum small bowel sacral ala, melanoma melanoma treated surgically only at diagnosisprior malignancy brca+ breast cancer stage 3b papillary thyroid carcinoma treated surgically only location of known metastases liver diaphragm omentum small bowel sacral ala, liporal cavity squam cell car final pathology 635 lymph nodes + for lymph-vascular and perineural invasion tumor gradestage pt4an2b]
13:10:52::250 INFO org.pdxfinder.dataloaders.updog.Updog : Using UPDOG to import Wistar-MDAnderson-Penn PDX data from [/home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/Wistar-MDAnderson-Penn]
Reading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/Wistar-MDAnderson-Penn/Wistar-MDAnderson-Penn_metadata-sample.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/Wistar-MDAnderson-Penn/Wistar-MDAnderson-Penn_metadata-model_validation.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/Wistar-MDAnderson-Penn/Wistar-MDAnderson-Penn_metadata-loader.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/Wistar-MDAnderson-Penn/Wistar-MDAnderson-Penn_metadata-sharing.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/Wistar-MDAnderson-Penn/Wistar-MDAnderson-Penn_metadata-model.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/Wistar-MDAnderson-Penn/Wistar-MDAnderson-Penn_metadata-patient.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/Wistar-MDAnderson-Penn/Wistar-MDAnderson-Penn_metadata-checklist.tsv13:10:52::310 INFO ders.updog.tablevalidation.ErrorReporter : Limiting output to the first 50 errors:
13:10:52::310 ERROR ders.updog.tablevalidation.ErrorReporter : 12 validation errors found:
13:10:52::310 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [Wistar-MDAnderson-Penn]: Missing value(s) in required column [name]
13:10:52::310 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [Wistar-MDAnderson-Penn]: Missing value(s) in required column [diagnosis]
13:10:52::310 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-loader.tsv] for provider [Wistar-MDAnderson-Penn]: Missing value(s) in required column [internal_url]
13:10:52::311 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [Wistar-MDAnderson-Penn]: Missing value(s) in required column [accessibility]
13:10:52::311 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [Wistar-MDAnderson-Penn]: Missing value(s) in required column [provider_type]
13:10:52::311 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model_validation.tsv] for provider [Wistar-MDAnderson-Penn]: Missing value(s) in required column [validation_host_strain_full]
13:10:52::311 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [Wistar-MDAnderson-Penn]: in column [patient_id] found 19 values have characters not contained in US ASCII Alphanumeric and ._~- : [WISTAR ID#115, WISTAR ID#67, WISTAR ID#78C, WISTAR ID#97, WISTAR ID#98, WISTAR MP#11_14, WISTAR MP#12_238 EG, WISTAR MP#12_238 EG, WISTAR MP#13_495, WISTAR MP#13_674, WISTAR MP#13_674, WISTAR MP#14_1173, WISTAR MP#14_1202, WISTAR MP#14_749, WISTAR MP#14_771, WISTAR MP#15_1496, WISTAR MP#15_1532, WISTAR MP#608, WISTAR Pt PPP; fem]
13:10:52::311 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [Wistar-MDAnderson-Penn]: in column [patient_id] found 17 values have characters not contained in US ASCII Alphanumeric and ._~- : [WISTAR ID#115, WISTAR ID#67, WISTAR ID#78C, WISTAR ID#97, WISTAR ID#98, WISTAR MP#11_14, WISTAR MP#12_238 EG, WISTAR MP#13_495, WISTAR MP#13_674, WISTAR MP#14_1173, WISTAR MP#14_1202, WISTAR MP#14_749, WISTAR MP#14_771, WISTAR MP#15_1496, WISTAR MP#15_1532, WISTAR MP#608, WISTAR Pt PPP; fem]
13:10:52::311 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [Wistar-MDAnderson-Penn]: in column [sex] found 7 values not in a required category. Required Categories: [male,female,other,not collected,not provided] Value found : [not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:10:52::311 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [Wistar-MDAnderson-Penn]: in column [tumour_type] found 1 values not in a required category. Required Categories: [primary,metastatic,recurrent,refactory,not collected,not provided] Value found : [not specified]
13:10:52::311 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [Wistar-MDAnderson-Penn]: in column [age_in_years_at_collection] found 9 values have characters not contains in US ASCII numbers and pP-., : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:10:52::311 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model_validation.tsv] for provider [Wistar-MDAnderson-Penn]: in column [passages_tested] found 82 values have characters not contains in US ASCII numbers and pP-., : [mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6, mp1-mp6]
13:10:52::311 INFO org.pdxfinder.dataloaders.updog.Updog : Using UPDOG to import WUSTL PDX data from [/home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/WUSTL]
Reading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/WUSTL/WUSTL_metadata-model.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/WUSTL/WUSTL_metadata-checklist.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/WUSTL/WUSTL_metadata-sharing.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/WUSTL/WUSTL_metadata-model_validation.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/WUSTL/WUSTL_metadata-loader.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/WUSTL/WUSTL_metadata-patient.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/WUSTL/WUSTL_metadata-sample.tsv13:10:52::358 INFO ders.updog.tablevalidation.ErrorReporter : Limiting output to the first 50 errors:
13:10:52::358 ERROR ders.updog.tablevalidation.ErrorReporter : 14 validation errors found:
13:10:52::358 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [WUSTL]: Missing value(s) in required column [name]
13:10:52::358 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-loader.tsv] for provider [WUSTL]: Missing value(s) in required column [internal_url]
13:10:52::358 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [WUSTL]: Missing value(s) in required column [accessibility]
13:10:52::358 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [WUSTL]: Missing value(s) in required column [provider_type]
13:10:52::358 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [WUSTL]: in column [model_id] found 2 values have characters not contained in US ASCII Alphanumeric and ._~- : [WUSTL 292 [2]-07, WUSTL 356 [2]-07]
13:10:52::358 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [WUSTL]: in column [patient_id] found 2 values have characters not contained in US ASCII Alphanumeric and ._~- : [WUSTL 292 [2], WUSTL 356 [2]]
13:10:52::358 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [WUSTL]: in column [sample_id] found 2 values have characters not contained in US ASCII Alphanumeric and ._~- : [WUSTL 292 [2]-07, WUSTL 356 [2]-07]
13:10:52::358 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [WUSTL]: in column [patient_id] found 2 values have characters not contained in US ASCII Alphanumeric and ._~- : [WUSTL 292 [2], WUSTL 356 [2]]
13:10:52::358 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [WUSTL]: in column [model_id] found 2 values have characters not contained in US ASCII Alphanumeric and ._~- : [WUSTL 292 [2]-07, WUSTL 356 [2]-07]
13:10:52::359 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model.tsv] for provider [WUSTL]: in column [model_id] found 2 values have characters not contained in US ASCII Alphanumeric and ._~- : [WUSTL 292 [2]-07, WUSTL 356 [2]-07]
13:10:52::359 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [WUSTL]: in column [sex] found 11 values not in a required category. Required Categories: [male,female,other,not collected,not provided] Value found : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:10:52::359 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [WUSTL]: in column [tumour_type] found 9 values not in a required category. Required Categories: [primary,metastatic,recurrent,refactory,not collected,not provided] Value found : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:10:52::359 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [WUSTL]: in column [age_in_years_at_collection] found 11 values have characters not contains in US ASCII numbers and pP-., : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:10:52::359 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [WUSTL]: in column [prior_treatment] found 82 values not in a required category. Required Categories: [yes,no,not provided,not collected] Value found : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:10:52::359 INFO org.pdxfinder.dataloaders.updog.Updog : Using UPDOG to import CRL PDX data from [/home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/CRL]
Reading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/CRL/CRL_sampleplatform-data.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/CRL/CRL_metadata-model_validation.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/CRL/CRL_metadata-sample.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/CRL/CRL_metadata-sharing.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/CRL/CRL_metadata-checklist.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/CRL/CRL_metadata-loader.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/CRL/CRL_metadata-model.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/CRL/CRL_metadata-patient.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/CRL/treatment/CRL_patienttreatment-Sheet1.tsv13:10:52::568 INFO ders.updog.tablevalidation.ErrorReporter : Limiting output to the first 50 errors:
13:10:52::568 ERROR ders.updog.tablevalidation.ErrorReporter : 14 validation errors found:
13:10:52::568 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [CRL]: in column [sex] found 66 values not in a required category. Required Categories: [male,female,other,not collected,not provided] Value found : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:10:52::568 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [CRL]: in column [ethnicity_assessment_method] found 539 values genetic : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not 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specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:10:52::568 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [CRL]: in column [treatment_naive_at_collection] found 271 values not in a required category. Required Categories: [treatment naive,not treatment naive,not collected,not provided] Value found : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:10:52::568 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model.tsv] for provider [CRL]: in column [publications] found 541 values not of type: PMID: [8 digit id] (comma separated) : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:10:52::568 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [CRL]: in column [tumour_type] found 156 values not in a required category. Required Categories: [primary,metastatic,recurrent,refactory,not collected,not provided] Value found : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:10:52::569 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [CRL]: in column [age_in_years_at_collection] found 63 values have characters not contains in US ASCII numbers and pP-., : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:10:52::569 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model_validation.tsv] for provider [CRL]: in column [passages_tested] found 541 values have characters not contains in US ASCII numbers and pP-., : [<5,9,14, <5,1,4, <5,14,20, <5,12,33, <5,13,21, <5,0,19, <5,9,22, <5,5,5, <5,6,8, <5,1,3, <5,0,2, <5,12,15, <5,5,14, <5,1,2, <5,1,3, <5,13,20, <5,1,5, <5,5,7, <5,3,6, <5,4,6, <5,4,8, <5,3,6, <5,4,6, <5,6,9, <5,8,12, <5,13,17, <5, <5, <5,7,11, <5,5,6, <5,2,6, <5,3,7, <5,30,26, <5,20,31, <5,20,15, <5,24,10, <5,23,10, <5,9,12,0,7, <5,18,12, <5,19,20, <5,15,11, <5,17,13, <5,14,17, <5,11,18, <5,18,12, <5,15,14, <5,6,12, <5,11,16,14, <5,22,11, <5,10,14, <5,17,18, <5,27,9, <5,22,18, <5,13,18, <5,8,20, <5,5,7, <5,5,7,8, <5,3,8, <5,4,8, <5,6,17, <5,4,13, <5,13,4, <5,12,14, <5,3,4, <5,3,9, <5,6,16, <5,5,8, <5,7,11, <5,4,13, <5,6,11, <5,5,6, <5,4,5, <5,10,6, <5,5,6,14, <5,5,4, <5,6,14, <5,8,12, <5,7,12, <5,5,14, <5,10,11,0,2,4, <5,3,13, <5,3,5, <5,8,16, <5,3,5, <5,3,10, <5,2,4, <5,7,10, <5,7,9, <5,7,14, <5,3,8, <5,2,5, <5,0,3, <5,2,6, <5,1,5, <5, <5,1,4, <5,3,3, <5, <5,4,7, <5,1,9, <5,6,17, <5,6,15, <5,10,23, <5,3,13, <5,3,14, <5,8,17, <5,3,11, <5,2,15, <5,3,14, <5,2,14, <5,3,7, <5,4,12, <5,3,18, <5,4,15, <5,2,17, <5,3,11, <5,2,11, <5,2,9, <5,3,6, <5,2,11, <5,3,11, <5, <5,2,10, <5, <5, <5, <5, <5,3,7, <5,0,4, <5, <5,20,34, <5,7,17, <5,8,25, <5,11,14, <5,11,16, <5,6,22, <5,7,10, <5,9,22, <5,7,12, <5,12,21, <5,8,15, <5,10,20, <5,10,12, <5,1,6, <5,4,17, <5,5,8, <5,2,16, <5,3,8, <5, <5,4,8, <5, <5,3,7, <5, <5, <5, <5, <5, <5, <5,9,27, <5,3,12, <5,1,10, <5,3,4, <5,4,5, <5,3,4, <5, <5,6,10, <5, <5,5,6, <5,5,13, <5,6,11, <5,6,14, <5,6,7, <5,5,10, <5,4,9, <5,6,18, <5,13,20, <5,12,19, <5,7,18, <5,15,18, <5,8,19, <5,11,12, <5,9,19, <5,5,12, <5,8,18, <5,12,19, <5,8,17, <5,7,25, <5,11,19, <5,8,14, <5,12,21, <5,11,13, <5,17,28, <5,8,17, <5,6,17, <5,7,13, <5,1,5, <5,4,7, <5,3,8, <5,1,6, <5,4,10, <5,6,9, <5,5,12, <5,3,9, <5,2,9, <5,3,11, <5,3,6, <5,2,7, <5,6,8, <5, <5,3,6, <5,4,7, <5,0,5, <5, <5,4,6, <5,3,6, <5,16,29, <5,12,12, <5,11,26, <5,8,19, <5,16,23, <5,6,12, <5,13,15, <5,4,15, <5,6,15, <5,7,16, <5,4,15, <5,5,15, <5,9,20, <5,4,14, <5,2,8, <5,4,8, <5,2,10, <5,2,6, <5,1,12, <5,1,11, <5,2,12, <5,1,10, <5,9,10, <5,2,6, <5,1,6, <5,0,4, <5,2,9, <5, <5, <5, <5,8,21, <5,13,26, <5,8,14, <5,11,21, <5,10,23, <5,9,32, <5,11,26, <5,2,8, <5,4,12, <5,2,14, <5,11,19, <5,10,24, <5,19,20, <5,16,21, <5,12,24, <5,10,14, <5,5,14, <5,2,12, <5, <5,3,9, <5, <5, <5, <5, <5, <5,3,4, <5,5,10, <5,12,20, <5,2,8, <5,2,na, <5, <5, <5,3,7, <5,4,10, <5,2,5, <5,10,26, <5,21,26, <5,11,33, <5,13,15, <5,17,26, <5,11,17, <5,7,9, <5,10,23, <5, <5,9,19, <5,10,17, <5,11,20, <5,11,26, <5,16,26, <5,5,9, <5,17,26, <5,3,7, <5,11,23, <5,13,22, <5,8,17, <5,11,25, <5,9,17, <5,10,13, <5,4,13, <5,9,16, <5,17,18, <5,6,15, <5,5,11, <5, <5,4,10, <5,3,12, <5,2,14, <5,2,9, <5,4,13, <5,6,14, <5,3,3, <5, <5, <5,5,8, <5,16,27, <5,32,39, <5,4,9, <5,5,9, <5,16,25, <5,14,18, <5,4,7, <5,2,6, <5, <5, <5, <5, <5, <5,3,6, <5,3,5, <5,4,7, <5,9,23,-1, <5,5,21,-1, <5,8,22, <5,6,13, <5,10,13,13,14, <5,7,19, <5,4,12, <5,3,23, <5,2,14, <5,5,10, <5,6,20, <5,2,12,16,3,11, <5,4,16, <5,2,19, <5,7,15,-1, <5,4,13, <5,5,15, <5,5,9, <5,3,9, <5,1,5, <5,4,11, <5,5,9, <5,8,15, <5,4,6,2,4, <5,6,7,9,3, <5,3,6,14,1, <5,3,10, <5,4,12, <5,4,11, <5,5,14, <5,4,12, <5,5,15, <5,3,6, <5,4,7, <5,4,11, <5,5,11,2,15, <5,5,8, <5,3,17, <5,5,6, <5,3,5,4,9, <5,4,10, <5,5,10, <5,4,13, <5,4,14, <5,5,13, <5, <5,2,12, <5, <5,4,12, <5,18,27, <5,7,16, <5,9,8, <5,6,8, <5,5,26, <5,10,16, <5,4,8, <5,6,7, <5, <5,4,6, <5,2,4, <5,18,25, <5,13,17, <5,20,36, <5,6,9, <5,11,15, <5,14,36, <5,15,19, <5,10,13, <5,9,19, <5,4,21, <5,12,17, <5,10,15, <5,4,10, <5,2,12, <5,2,7, <5,1,5, <5,3,7, <5,4,9, <5,5,10, <5,0,5, <5,0,6, <5,3,4, <5,1,4, <5, <5,0,6, <5,0,3, <5,0,6, <5,4,6, <5,0,4, <5,4,7, <5,5,7, <5,3,4, <5,0,6, <5,1,4, <5, <5, <5, <5, <5,2,3, <5,7,11, <5,4,8, <5,11,18, <5,14,21, <5,11,17, <5,8,12, <5,27,39, <5,11,12, <5,15,22, <5,5,20, <5,10,29, <5,13,12, <5,7,11, <5,3,7, <5,4,8, <5,7,11, <5,0,3, <5, <5,3,4, <5,6,7, <5,4,5, <5,12,13, <5,16,24, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5, <5]
13:10:52::569 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [CRL]: in column [age_at_initial_diagnosis] found 539 values have characters not contains in US ASCII numbers and pP-., : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:10:52::569 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model.tsv] for provider [CRL]: in column [passage_number] found 10 values have characters not contains in US ASCII numbers and pP-., : [0, 4,8, 0, 4,6, 5,0, 3, 0, 4,8, 0, 4,20, 0, 8,19, 0, 6,10, 5,0, 4, 0, 8,13, 0, 4,10]
13:10:52::569 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [CRL]: in column [prior_treatment] found 541 values not in a required category. Required Categories: [yes,no,not provided,not collected] Value found : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:10:52::569 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [CRL]: in column [collection_date] found 130 values not of type: [MMM YYYY] three letter month and 4 digit year : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:10:52::569 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [CRL]: Duplicates found in column [model_id]: [CRL-2533-subrenal]
13:10:52::569 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [CRL]: Broken one_to_one relation [(metadata-sample.tsv) sample_id -> model_id (metadata-sample.tsv)]: in [metadata-sample.tsv] one-to-one found 2 relationships with conflicts [(PS_2533-subrenal,CRL-2533-subrenal), (PS_2533-subrenal,CRL-2533-subrenal)]
13:10:52::569 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [CRL]: Broken one_to_many relation [(metadata-sample.tsv) sample_id -> patient_id (metadata-sample.tsv)]: in [metadata-sample.tsv] one-to-many found 4 relationships with conflicts [(patient_0271,PS_2533-subrenal), (patient_0506,PS_2533-subrenal), (patient_0271,PS_2533-subrenal), (patient_0506,PS_2533-subrenal)]
13:10:52::569 INFO org.pdxfinder.dataloaders.updog.Updog : Using UPDOG to import Curie-BC PDX data from [/home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/Curie-BC]
Reading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/Curie-BC/Curie-BC_metadata-sharing.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/Curie-BC/Curie-BC_metadata-model.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/Curie-BC/Curie-BC_metadata-loader.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/Curie-BC/Curie-BC_metadata-model_validation.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/Curie-BC/Curie-BC_metadata-checklist.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/Curie-BC/Curie-BC_metadata-sample.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/Curie-BC/Curie-BC_metadata-patient.tsv13:10:59::413 INFO ders.updog.tablevalidation.ErrorReporter : Limiting output to the first 50 errors:
13:10:59::414 ERROR ders.updog.tablevalidation.ErrorReporter : 5 validation errors found:
13:10:59::414 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [Curie-BC]: in column [ethnicity_assessment_method] found 5 values genetic : [not specified, not specified, not specified, not specified, not specified]
13:10:59::414 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model.tsv] for provider [Curie-BC]: in column [publications] found 1 values not of type: PMID: [8 digit id] (comma separated) : [pmid:17606733; pmid:29463559; pmid:27374081]
13:10:59::414 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model_validation.tsv] for provider [Curie-BC]: in column [passages_tested] found 1 values have characters not contains in US ASCII numbers and pP-., : [3, 15, 27]
13:10:59::414 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model.tsv] for provider [Curie-BC]: in column [passage_number] found 1 values have characters not contains in US ASCII numbers and pP-., : [1,3, 12, 15, 27]
13:10:59::414 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [Curie-BC]: in column [collection_date] found 3 values not of type: [MMM YYYY] three letter month and 4 digit year : [2002-12-01, 2003-02-01, 2006-03-01]
13:10:59::414 INFO org.pdxfinder.dataloaders.updog.Updog : Using UPDOG to import Curie-LC PDX data from [/home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/Curie-LC]
Reading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/Curie-LC/Curie-LC_metadata-model.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/Curie-LC/Curie-LC_metadata-model_validation.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/Curie-LC/Curie-LC_sampleplatform-data.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/Curie-LC/Curie-LC_metadata-loader.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/Curie-LC/Curie-LC_metadata-sample.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/Curie-LC/Curie-LC_metadata-sharing.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/Curie-LC/Curie-LC_metadata-patient.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/Curie-LC/Curie-LC_metadata-checklist.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/Curie-LC/drug/Curie-LC_drugdosing-Sheet1.tsv13:10:59::519 INFO ders.updog.tablevalidation.ErrorReporter : Limiting output to the first 50 errors:
13:10:59::519 ERROR ders.updog.tablevalidation.ErrorReporter : 6 validation errors found:
13:10:59::519 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [Curie-LC]: in column [ethnicity_assessment_method] found 6 values genetic : [not specified, not specified, not specified, not specified, not specified, not specified]
13:10:59::519 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [Curie-LC]: in column [collection_event] found 6 values Not of type: collection event [0-9] : [not specified, not specified, not specified, not specified, not specified, not specified]
13:10:59::519 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [Curie-LC]: in column [sharable] found 6 values not in a required category. Required Categories: [yes,no,not provided] Value found : [not specified, not specified, not specified, not specified, not specified, not specified]
13:10:59::519 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model_validation.tsv] for provider [Curie-LC]: in column [passages_tested] found 3 values have characters not contains in US ASCII numbers and pP-., : [3, 30, 4, 2, 1, 1, 16]
13:10:59::519 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model.tsv] for provider [Curie-LC]: in column [passage_number] found 1 values have characters not contains in US ASCII numbers and pP-., : [4, 2, 1]
13:10:59::519 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [Curie-LC]: in column [collection_date] found 2 values not of type: [MMM YYYY] three letter month and 4 digit year : [2008-06-01, 2008-08-01]
13:10:59::519 INFO org.pdxfinder.dataloaders.updog.Updog : Using UPDOG to import Curie-OC PDX data from [/home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/Curie-OC]
Reading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/Curie-OC/Curie-OC_metadata-patient.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/Curie-OC/Curie-OC_metadata-checklist.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/Curie-OC/Curie-OC_metadata-loader.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/Curie-OC/Curie-OC_metadata-sharing.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/Curie-OC/Curie-OC_metadata-model_validation.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/Curie-OC/Curie-OC_metadata-sample.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/Curie-OC/Curie-OC_metadata-model.tsv13:10:59::608 INFO ders.updog.tablevalidation.ErrorReporter : Limiting output to the first 50 errors:
13:10:59::608 ERROR ders.updog.tablevalidation.ErrorReporter : 5 validation errors found:
13:10:59::608 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [Curie-OC]: in column [ethnicity_assessment_method] found 5 values genetic : [not specified, not specified, not specified, not specified, not specified]
13:10:59::608 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [Curie-OC]: in column [collection_event] found 5 values Not of type: collection event [0-9] : [not specified, not specified, not specified, not specified, not specified]
13:10:59::608 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [Curie-OC]: in column [sharable] found 5 values not in a required category. Required Categories: [yes,no,not provided] Value found : [not specified, not specified, not specified, not specified, not specified]
13:10:59::608 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model.tsv] for provider [Curie-OC]: in column [publications] found 1 values not of type: PMID: [8 digit id] (comma separated) : [pmid: 29245952; pmid: 30244973]
13:10:59::608 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [Curie-OC]: in column [history] found 1 values have characters not contained in US ASCII Alphanumeric and ().',:;-/ : [previous breast cancer( er+, her2+)]
13:10:59::608 INFO org.pdxfinder.dataloaders.updog.Updog : Using UPDOG to import IRCC-GC PDX data from [/home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/IRCC-GC]
Reading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/IRCC-GC/IRCC-GC_metadata-loader.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/IRCC-GC/IRCC-GC_metadata-model_validation.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/IRCC-GC/IRCC-GC_metadata-checklist.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/IRCC-GC/IRCC-GC_sampleplatform-data.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/IRCC-GC/IRCC-GC_metadata-sample.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/IRCC-GC/IRCC-GC_metadata-model.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/IRCC-GC/IRCC-GC_metadata-patient.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/IRCC-GC/IRCC-GC_metadata-sharing.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/IRCC-GC/treatment/patienttreatment-Sheet1.tsv13:11:03::370 INFO ders.updog.tablevalidation.ErrorReporter : Limiting output to the first 50 errors:
13:11:03::370 ERROR ders.updog.tablevalidation.ErrorReporter : 5 validation errors found:
13:11:03::370 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [IRCC-GC]: Missing value(s) in required column [accessibility]
13:11:03::370 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [IRCC-GC]: in column [ethnicity_assessment_method] found 76 values genetic : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:11:03::370 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [IRCC-GC]: in column [treatment_naive_at_collection] found 15 values not in a required category. Required Categories: [treatment naive,not treatment naive,not collected,not provided] Value found : [not treatment naïve, not treatment naïve, not treatment naïve, not treatment naïve, not treatment naïve, not treatment naïve, not treatment naïve, not treatment naïve, not treatment naïve, not treatment naïve, not treatment naïve, not treatment naïve, not treatment naïve, not treatment naïve, not treatment naïve]
13:11:03::370 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model.tsv] for provider [IRCC-GC]: in column [publications] found 79 values not of type: PMID: [8 digit id] (comma separated) : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:11:03::370 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [IRCC-GC]: in column [age_in_years_at_collection] found 1 values have characters not contains in US ASCII numbers and pP-., : [not specified]
13:11:03::370 INFO org.pdxfinder.dataloaders.updog.Updog : Using UPDOG to import PMLB PDX data from [/home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/PMLB]
Reading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/PMLB/PMLB_metadata-model_validation.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/PMLB/PMLB_sampleplatform-data.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/PMLB/PMLB_metadata-checklist.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/PMLB/PMLB_metadata-model.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/PMLB/PMLB_metadata-sharing.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/PMLB/PMLB_metadata-loader.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/PMLB/PMLB_metadata-patient.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/PMLB/PMLB_metadata-sample.tsv13:11:10::927 INFO ders.updog.tablevalidation.ErrorReporter : Limiting output to the first 50 errors:
13:11:10::927 ERROR ders.updog.tablevalidation.ErrorReporter : 7 validation errors found:
13:11:10::928 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [PMLB]: Missing value(s) in required column [project]
13:11:10::928 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [PMLB]: in column [collection_event] found 3 values Not of type: collection event [0-9] : [collection 1, collection 2, collection 1]
13:11:10::928 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [PMLB]: in column [tumour_type] found 3 values not in a required category. Required Categories: [primary,metastatic,recurrent,refactory,not collected,not provided] Value found : [not specified, not specified, not specified]
13:11:10::928 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [PMLB]: in column [age_in_years_at_collection] found 3 values have characters not contains in US ASCII numbers and pP-., : [not specified, not specified, not specified]
13:11:10::928 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [PMLB]: in column [primary_site] found 3 values have characters not contained in US ASCII Alphanumeric and ().',:;-/ : [lower alveolus & gingiva, lower alveolus & gingiva, lower alveolus & gingiva]
13:11:10::928 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [PMLB]: in column [collection_site] found 3 values have characters not contained in US ASCII Alphanumeric and ().',:;-/ : [lower alveolus & gingiva, lower alveolus & gingiva, lower alveolus & gingiva]
13:11:10::928 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [PMLB]: in column [collection_date] found 7 values not of type: [MMM YYYY] three letter month and 4 digit year : [not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:11:10::928 INFO org.pdxfinder.dataloaders.updog.Updog : Using UPDOG to import TRACE PDX data from [/home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/TRACE]
Reading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/TRACE/TRACE_metadata-patient.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/TRACE/TRACE_metadata-checklist.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/TRACE/TRACE_metadata-sharing.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/TRACE/TRACE_metadata-loader.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/TRACE/TRACE_metadata-model.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/TRACE/TRACE_sampleplatform-data.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/TRACE/TRACE_metadata-model_validation.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/TRACE/TRACE_metadata-sample.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/TRACE/treatment/TRACE_patienttreatment-Sheet1.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/TRACE/drug/TRACE_drugdosing-Sheet1.tsv13:11:17::554 INFO ders.updog.tablevalidation.ErrorReporter : Limiting output to the first 50 errors:
13:11:17::554 ERROR ders.updog.tablevalidation.ErrorReporter : 8 validation errors found:
13:11:17::554 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [TRACE]: in column [ethnicity_assessment_method] found 20 values genetic : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:11:17::554 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [TRACE]: in column [treatment_naive_at_collection] found 8 values not in a required category. Required Categories: [treatment naive,not treatment naive,not collected,not provided] Value found : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:11:17::554 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model.tsv] for provider [TRACE]: in column [publications] found 26 values not of type: PMID: [8 digit id] (comma separated) : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, 27626319, 27626319, 27626319, 27626319, 27626319, 27626319, 27626319, 27626319, 27626319, 27626319, pmid: 28232476 , pmid: 28232476 , pmid: 28232476 , pmid: 28232476 , pmid: 28232476 , pmid: 28232476 , pmid: 28232476 , pmid: 28232476 , pmid: 28232476 ]
13:11:17::554 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [TRACE]: in column [tumour_type] found 1 values not in a required category. Required Categories: [primary,metastatic,recurrent,refactory,not collected,not provided] Value found : [relapse]
13:11:17::554 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [TRACE]: in column [provider_type] found 8 values not in a required category. Required Categories: [academia,industry,academia and industry,CRO,pharma] Value found : [academia , academia , academia , academia , academia , academia , academia , academia ]
13:11:17::554 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [TRACE]: in column [age_at_initial_diagnosis] found 1 values have characters not contains in US ASCII numbers and pP-., : [not specified]
13:11:17::555 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [TRACE]: in column [collection_date] found 31 values not of type: [MMM YYYY] three letter month and 4 digit year : [2013-04-01, 2013-09-01, 2013-09-01, 2015-02-01, oct/15, jan 13, feb13, mar 13, may 13, jun 13, jun 13, jul 13, sep 13, oct 13, mar 14, 2013-04-01, 2013-12-01, 2011-01-01, 2012-06-01, 2013-09-01, 2013-10-01, 2012-03-01, 2013-03-01, 2013-03-01, 2013-10-01, 2013-03-01, 2013-05-01, 2013-06-01, 2013-06-01, 2014-03-01, 2014-06-01]
13:11:17::555 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [TRACE]: Duplicates found in column [model_id]: [PAC0016PR]
13:11:17::555 INFO org.pdxfinder.dataloaders.updog.Updog : Using UPDOG to import UOC-BC PDX data from [/home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/UOC-BC]
Reading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/UOC-BC/UOC-BC_sampleplatform-data.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/UOC-BC/UOC-BC_metadata-model_validation.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/UOC-BC/UOC-BC_metadata-sharing.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/UOC-BC/UOC-BC_metadata-loader.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/UOC-BC/UOC-BC_metadata-patient.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/UOC-BC/UOC-BC_metadata-model.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/UOC-BC/UOC-BC_metadata-checklist.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/UOC-BC/UOC-BC_metadata-sample.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/UOC-BC/treatment/patienttreatment-Sheet1.tsv13:11:25::016 INFO ders.updog.tablevalidation.ErrorReporter : Limiting output to the first 50 errors:
13:11:25::016 ERROR ders.updog.tablevalidation.ErrorReporter : 7 validation errors found:
13:11:25::017 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [UOC-BC]: in column [ethnicity_assessment_method] found 50 values genetic : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:11:25::017 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [UOC-BC]: in column [treatment_naive_at_collection] found 59 values not in a required category. Required Categories: [treatment naive,not treatment naive,not collected,not provided] Value found : [not treatment naïve, not treatment naïve, not treatment naïve, not treatment naïve, not treatment naïve, not treatment naïve, not treatment naïve, treatment naïve, not treatment naïve, treatment naïve, treatment naïve, treatment naïve, not specified, not treatment naïve, not treatment naïve, treatment naïve, treatment naïve, not specified, treatment naïve, treatment naïve, yes, treatment naïve, not treatment naïve, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:11:25::017 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [UOC-BC]: in column [sharable] found 36 values not in a required category. Required Categories: [yes,no,not provided] Value found : [available, but not able to be shared at this stage, available, but not able to be shared at this stage, available, but not able to be shared at this stage, available, but not able to be shared at this stage, available, but not able to be shared at this stage, available, but not able to be shared at this stage, available, but not able to be shared at this stage, available, but not able to be shared at this stage, available, but not able to be shared at this stage, available, but not able to be shared at this stage, available, but not able to be shared at this stage, available, but not able to be shared at this stage, available, but not able to be shared at this stage, available, but not able to be shared at this stage, available, but not able to be shared at this stage, available, but not able to be shared at this stage, available, but not able to be shared at this stage, available, but not able to be shared at this stage, available, but not able to be shared at this stage, available, but not able to be shared at this stage, available, but not able to be shared at this stage, available, but not able to be shared at this stage, available, but not able to be shared at this stage, available, but not able to be shared at this stage, available, but not able to be shared at this stage, available, but not able to be shared at this stage, available, but not able to be shared at this stage, available, but not able to be shared at this stage, available, but not able to be shared at this stage, available, but not able to be shared at this stage, not available, available, but not able to be shared at this stage, available, but not able to be shared at this stage, available, but not able to be shared at this stage, available, but not able to be shared at this stage, available, but not able to be shared at this stage]
13:11:25::017 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [UOC-BC]: in column [tumour_type] found 25 values not in a required category. Required Categories: [primary,metastatic,recurrent,refactory,not collected,not provided] Value found : [metastastic, metastastic, metastastic, metastastic, metastastic, metastastic, metastastic, metastastic, metastastic, metastastic, metastastic, metastastic, metastastic, metastastic, metastastic, metastastic, metastastic, metastastic, metastastic, metastastic, metastastic, metastastic, metastastic, metastastic, metastastic]
13:11:25::017 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [UOC-BC]: in column [age_at_initial_diagnosis] found 50 values have characters not contains in US ASCII numbers and pP-., : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:11:25::017 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [UOC-BC]: in column [prior_treatment] found 38 values not in a required category. Required Categories: [yes,no,not provided,not collected] Value found : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:11:25::017 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [UOC-BC]: in column [collection_date] found 59 values not of type: [MMM YYYY] three letter month and 4 digit year : [jul 15, nov 14, mar 14, oct 13, oct 13, oct 13, oct 13, nov 13, jan 14, jan 14, feb 14, feb 14, apr 14, may 14, may 14, apr 15, may 15, jan 16, feb 16, aug 16, sep 16, oct 16, mar 17, jun 17, mar 15, apr 17, nov 16, dec 16, feb 17, apr 17, may 17, may 17, jun 17, jun 17, jul 17, jul 17, dec 17, jul 18, oct 18, jul 17, may 17, jun 17, may 11, may 12, jun 11, feb 12, mar 12, mar 13, aug 13, jan 14, jan 14, jan 14, may 14, dec 14, aug 15, apr 18, mar 18, aug 18, mar 14]
13:11:25::017 INFO org.pdxfinder.dataloaders.updog.Updog : Using UPDOG to import UOM-BC PDX data from [/home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/UOM-BC]
Reading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/UOM-BC/UOM-BC_metadata-loader.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/UOM-BC/UOM-BC_metadata-sample.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/UOM-BC/UOM-BC_metadata-model_validation.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/UOM-BC/UOM-BC_metadata-patient.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/UOM-BC/UOM-BC_metadata-sharing.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/UOM-BC/UOM-BC_metadata-checklist.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/UOM-BC/UOM-BC_sampleplatform-data.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/UOM-BC/UOM-BC_metadata-model.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/UOM-BC/treatment/UOM-BC_patienttreatment-Sheet1.tsv13:11:25::100 INFO ders.updog.tablevalidation.ErrorReporter : Limiting output to the first 50 errors:
13:11:25::100 ERROR ders.updog.tablevalidation.ErrorReporter : 6 validation errors found:
13:11:25::100 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [UOM-BC]: in column [ethnicity_assessment_method] found 12 values genetic : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:11:25::100 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [UOM-BC]: in column [collection_event] found 1 values Not of type: collection event [0-9] : [collection event 1]
13:11:25::100 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [UOM-BC]: in column [age_in_years_at_collection] found 1 values have characters not contains in US ASCII numbers and pP-., : [not specified]
13:11:25::101 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model_validation.tsv] for provider [UOM-BC]: in column [passages_tested] found 2 values have characters not contains in US ASCII numbers and pP-., : [not specified, not specified]
13:11:25::101 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [UOM-BC]: in column [age_at_initial_diagnosis] found 1 values have characters not contains in US ASCII numbers and pP-., : [not specified]
13:11:25::101 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [UOM-BC]: in column [collection_date] found 12 values not of type: [MMM YYYY] three letter month and 4 digit year : [nd, nd, nd, nd, nd, nd, nd, nd, nd, nd, nd, nd]
13:11:25::101 INFO org.pdxfinder.dataloaders.updog.Updog : Using UPDOG to import VHIO-BC PDX data from [/home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/VHIO-BC]
Reading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/VHIO-BC/VHIO-BC_metadata-sharing.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/VHIO-BC/VHIO-BC_metadata-model_validation.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/VHIO-BC/VHIO-BC_sampleplatform-data.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/VHIO-BC/VHIO-BC_metadata-model.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/VHIO-BC/VHIO-BC_metadata-sample.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/VHIO-BC/VHIO-BC_metadata-checklist.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/VHIO-BC/VHIO-BC_metadata-patient.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/VHIO-BC/VHIO-BC_metadata-loader.tsv13:11:25::189 INFO ders.updog.tablevalidation.ErrorReporter : Limiting output to the first 50 errors:
13:11:25::189 ERROR ders.updog.tablevalidation.ErrorReporter : 6 validation errors found:
13:11:25::190 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [VHIO-BC]: in column [ethnicity_assessment_method] found 5 values genetic : [not specified, not specified, not specified, not specified, not specified]
13:11:25::190 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [VHIO-BC]: in column [treatment_naive_at_collection] found 1 values not in a required category. Required Categories: [treatment naive,not treatment naive,not collected,not provided] Value found : [not specified]
13:11:25::190 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model.tsv] for provider [VHIO-BC]: in column [publications] found 1 values not of type: PMID: [8 digit id] (comma separated) : [not specified]
13:11:25::190 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [VHIO-BC]: in column [age_in_years_at_collection] found 5 values have characters not contains in US ASCII numbers and pP-., : [not specified, not specified, not specified, not specified, not specified]
13:11:25::190 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [VHIO-BC]: in column [age_at_initial_diagnosis] found 5 values have characters not contains in US ASCII numbers and pP-., : [not specified, not specified, not specified, not specified, not specified]
13:11:25::190 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [VHIO-BC]: in column [prior_treatment] found 2 values not in a required category. Required Categories: [yes,no,not provided,not collected] Value found : [not specified, not specified]
13:11:25::190 INFO org.pdxfinder.dataloaders.updog.Updog : Using UPDOG to import VHIO-CRC PDX data from [/home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/VHIO-CRC]
Reading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/VHIO-CRC/VHIO-CRC_metadata-loader.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/VHIO-CRC/VHIO-CRC_metadata-sample.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/VHIO-CRC/VHIO-CRC_metadata-checklist.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/VHIO-CRC/VHIO-CRC_metadata-model_validation.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/VHIO-CRC/VHIO-CRC_metadata-model.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/VHIO-CRC/VHIO-CRC_sampleplatform-data.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/VHIO-CRC/VHIO-CRC_metadata-sharing.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/VHIO-CRC/VHIO-CRC_metadata-patient.tsv13:11:25::250 INFO ders.updog.tablevalidation.ErrorReporter : Limiting output to the first 50 errors:
13:11:25::250 ERROR ders.updog.tablevalidation.ErrorReporter : 8 validation errors found:
13:11:25::250 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [VHIO-CRC]: in column [sex] found 2 values not in a required category. Required Categories: [male,female,other,not collected,not provided] Value found : [not specified, not specified]
13:11:25::250 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [VHIO-CRC]: in column [ethnicity_assessment_method] found 68 values genetic : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:11:25::250 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [VHIO-CRC]: in column [treatment_naive_at_collection] found 24 values not in a required category. Required Categories: [treatment naive,not treatment naive,not collected,not provided] Value found : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:11:25::251 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model.tsv] for provider [VHIO-CRC]: in column [publications] found 1 values not of type: PMID: [8 digit id] (comma separated) : [pmid:24170545, pmid:26224873, pmid:9944140]
13:11:25::251 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [VHIO-CRC]: in column [age_in_years_at_collection] found 3 values have characters not contains in US ASCII numbers and pP-., : [not specified, not specified, not specified]
13:11:25::251 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model_validation.tsv] for provider [VHIO-CRC]: in column [passages_tested] found 73 values have characters not contains in US ASCII numbers and pP-., : [4 ,5, 7, 8, 9, 10, 11, 12, 16, 17, 0, 1, 2, 3, 0, 1, 2, 0, 1, 2, 0, 1, 2, 0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 0, 1, 2, 0, 1, 2, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 0, 1, 2, 3, 4, 0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 0, 1, 0, 1, 2, 3, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 0, 1, 2, 3, 0, 1, 2, 0, 1, 0, 1 ,2, 0, 1 ,2, 0, 1 ,2, 0, 1 ,2, 0, 1 ,2, 0, 1, 0, 1 ,2, 0, 1, 0, 1, 0, 1, 2, 3, 4, 6, 7, 8, 9, 14, 15, 0, 1, 2, 3, 4, 6, 7, 9, 10, 12, 14, 15, 16, 17, 19, 20, 21, 22, 23, 0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 0, 1, 2, 3, 4, 5, 6, 0, 1, 4, 5, 6, 7, 0, 1, 2, 3, 4, 0, 1, 2, 3, 0, 1, 0, 1, 0, 1, 2, 0, 1, 0, 1, 2, 0, 1, 0, 1, 0, 1, 2, 0, 1, 2, 0, 1, 0, 1, 0, 1, 2, 0, 1, 0, 1, 0, 1, 0, 1, 2, 0, 1, 2, 0, 1, 0, 1, 0, 1, 0, 1, 2, 3, 0, 1, 0, 1, 2, 0, 1, 2, 0, 1, 2, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 2, 0, 1, 2, 3, 0, 1, 2, 0, 1, 0, 1]
13:11:25::251 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [VHIO-CRC]: in column [age_at_initial_diagnosis] found 3 values have characters not contains in US ASCII numbers and pP-., : [not specified, not specified, not specified]
13:11:25::251 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [VHIO-CRC]: in column [prior_treatment] found 74 values not in a required category. Required Categories: [yes,no,not provided,not collected] Value found : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:11:25::251 INFO org.pdxfinder.dataloaders.updog.Updog : Using UPDOG to import DFCI-CPDM PDX data from [/home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/DFCI-CPDM]
Reading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/DFCI-CPDM/DFCI-CPDM_metadata-model_validation.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/DFCI-CPDM/DFCI-CPDM_metadata-sample.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/DFCI-CPDM/DFCI-CPDM_metadata-checklist.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/DFCI-CPDM/DFCI-CPDM_metadata-model.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/DFCI-CPDM/DFCI-CPDM_metadata-patient.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/DFCI-CPDM/DFCI-CPDM_metadata-loader.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/DFCI-CPDM/DFCI-CPDM_metadata-sharing.tsv13:11:25::377 INFO ders.updog.tablevalidation.ErrorReporter : Limiting output to the first 50 errors:
13:11:25::377 ERROR ders.updog.tablevalidation.ErrorReporter : 18 validation errors found:
13:11:25::377 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [DFCI-CPDM]: Missing value(s) in required column [project]
13:11:25::378 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model.tsv] for provider [DFCI-CPDM]: Missing value(s) in required column [engraftment_type]
13:11:25::378 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model.tsv] for provider [DFCI-CPDM]: Missing value(s) in required column [sample_type]
13:11:25::378 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model.tsv] for provider [DFCI-CPDM]: Missing value(s) in required column [passage_number]
13:11:25::378 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [DFCI-CPDM]: in column [sex] found 67 values not in a required category. Required Categories: [male,female,other,not collected,not provided] Value found : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:11:25::378 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [DFCI-CPDM]: in column [ethnicity_assessment_method] found 678 values genetic : [self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, not specified, self assessed, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, self assessed, not specified, not specified, not specified, not specified, not specified, self assessed, not specified, not specified, not specified, not specified, self assessed, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, self assessed, not specified, not specified, self assessed, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, self assessed, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, self assessed, not specified, not specified, not specified, not specified, not specified, not specified, self assessed, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, self assessed, not specified, not specified, self assessed, not specified, not specified, not specified, self assessed, not specified, not specified, self assessed, not specified, not specified, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, not specified, self assessed, not specified, self assessed, self assessed, self assessed, not specified, self assessed, not specified, self assessed, self assessed, not specified, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, not specified, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, not specified, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, not specified, not specified, self assessed, not specified, self assessed, self assessed, self assessed, self assessed, self assessed, not specified, self assessed, not specified, self assessed, self assessed, not specified, not specified, self assessed, not specified, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, not specified, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, not specified, self assessed, self assessed, self assessed, self assessed, self assessed, not specified, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, not specified, self assessed, self assessed, not specified, self assessed, not specified, self assessed, self assessed, self assessed, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, not specified, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, not specified, self assessed, self assessed, self assessed, self assessed, self assessed, not specified, self assessed, self assessed, not specified, self assessed, self assessed, self assessed, self assessed, not specified, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, not specified, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, not specified, self assessed, not specified, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, not specified, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self 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self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, not specified, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, not specified, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, not specified, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed, self assessed]
13:11:25::378 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [DFCI-CPDM]: in column [treatment_naive_at_collection] found 563 values not in a required category. Required Categories: [treatment naive,not treatment naive,not collected,not provided] Value found : [not specified, previously received treatment, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, previously received treatment, not specified, not specified, not specified, not specified, not specified, previously received treatment, not specified, not specified, not specified, not specified, previously received treatment, not specified, previously received treatment, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, previously received treatment, not specified, not specified, not specified, not specified, not specified, not specified, previously received treatment, not specified, not specified, previously received treatment, previously received treatment, previously received treatment, not specified, previously received treatment, not specified, not specified, not specified, not specified, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, not specified, not specified, previously received treatment, not specified, previously received treatment, not specified, not specified, previously received treatment, not specified, previously received treatment, previously received treatment, not specified, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, not specified, previously received treatment, previously received treatment, not specified, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, not specified, not specified, not specified, previously received treatment, previously received treatment, previously received treatment, not specified, not specified, previously received treatment, not specified, not specified, not specified, not specified, not specified, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, not specified, not specified, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, not specified, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, not specified, previously received treatment, previously received treatment, previously received treatment, previously received treatment, previously received treatment, not specified, previously received treatment, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, previously received treatment, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, previously received treatment]
13:11:25::378 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [DFCI-CPDM]: in column [collection_event] found 33 values Not of type: collection event [0-9] : [collection1, collection2, collection1, collection2, collection1, collection2, collection3, collection1, collection2, collection3, collection1, collection2, collection3, collection1, collection2, collection3, collection1, collection2, collection3, collection1, collection2, collection1, collection2, collection3, collection1, collection2, collection3, collection1, collection2, collection3, collection1, collection2, collection3]
13:11:25::378 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [DFCI-CPDM]: in column [sharable] found 110 values not in a required category. Required Categories: [yes,no,not provided] Value found : [to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced, to be announced]
13:11:25::378 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [DFCI-CPDM]: in column [tumour_type] found 575 values not in a required category. Required Categories: [primary,metastatic,recurrent,refactory,not collected,not provided] Value found : [recurrent secondary, recurrent primary, recurrent primary, recurrent primary, recurrent primary, recurrent primary, recurrent primary, recurrent secondary, recurrent primary, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, relapse, not specified, relapse, not specified, not specified, not specified, relapse, not specified, not specified, not specified, relapse, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, relapse, not specified, not specified, not specified, not specified, not specified, not specified, not specified, relapse, not specified, relapse, not specified, not specified, not specified, not specified, not specified, not specified, relapse, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, relapse, relapse, relapse, not specified, not specified, relapse, not specified, not specified, not specified, not specified, not specified, not specified, relapse, not specified, recurrent primary, recurrent primary, recurrent primary, recurrent primary, recurrent primary, recurrent primary, recurrent primary, relapse, not specified, not specified, not specified, relapse, not specified, relapse, relapse, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, relapse, not specified, not specified, not specified, not specified, not specified, relapse, relapse, relapse, not specified, not specified, not specified, relapse, not specified, not specified, relapse, not specified, relapse, not specified, relapse, relapse, relapse, relapse, secondary, relapse, relapse, not specified, not specified, relapse, not specified, relapse, relapse, relapse, relapse, secondary, not specified, secondary, relapse, relapse, not specified, secondary, relapse, secondary, not specified, not specified, not specified, not specified, not specified, relapse, not specified, relapse, relapse, not specified, not specified, not specified, relapse, not specified, not specified, not specified, not specified, relapse, relapse, relapse, relapse, not specified, relapse, relapse, not specified, not specified, not specified, relapse, relapse, relapse, relapse, relapse, not specified, not specified, not specified, not specified, not specified, not specified, not specified, relapse, relapse, relapse, relapse, not specified, not specified, relapse, relapse, relapse, not specified, not specified, not specified, not specified, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, not specified, not specified, not specified, relapse, relapse, not specified, not specified, not specified, relapse, relapse, relapse, relapse, relapse, not specified, not specified, not specified, not specified, not specified, not specified, not specified, relapse, relapse, relapse, not specified, relapse, relapse, relapse, relapse, relapse, not specified, not specified, relapse, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, relapse, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, recurrent primary, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, recurrent primary]
13:11:25::378 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [DFCI-CPDM]: in column [provider_type] found 679 values not in a required category. Required Categories: [academia,industry,academia and industry,CRO,pharma] Value found : [academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic, academic]
13:11:25::378 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [DFCI-CPDM]: in column [age_in_years_at_collection] found 73 values have characters not contains in US ASCII numbers and pP-., : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:11:25::378 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model_validation.tsv] for provider [DFCI-CPDM]: in column [passages_tested] found 678 values have characters not contains in US ASCII numbers and pP-., : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:11:25::378 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [DFCI-CPDM]: in column [age_at_initial_diagnosis] found 616 values have characters not contains in US ASCII numbers and pP-., : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:11:25::379 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [DFCI-CPDM]: in column [history] found 10 values have characters not contained in US ASCII Alphanumeric and ().',:;-/ : [br grade 3/3, er negative, pr negative, her-2 "focally positive in 5% tumor cells (2+)", grade iii ductal carcinoa, er+(rare), pr+(rare), her-, t2nmx, grade iii ductal carcinoa, er+(rare), pr+(rare), her-, t2nmx, metastasis_breast; er+, pr+, her2-, grade iii invasive ductal carcinoma; er+, pr-, her2-, p53 mutant, t2n0mx, high grade metastatic serous carcinoma positive for moc31, ck7, ca126, wt1 and er+, negative for calretinin and ck20, high grade ductal carcinoma, t3n3am1, er-, pr-, her2+, metastasis_breast;er+ pr- her2- invasive ductal carcinoma, mets to left breast (mammary carcinoma), metastasis_breast, pt2n1amn/a. er- pr- her2-", er- pr- her2+; invasive mammary carcinoma ductal type; giia, t2n0mn/a]
13:11:25::379 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [DFCI-CPDM]: Broken one_to_one relation [(metadata-sample.tsv) sample_id -> model_id (metadata-sample.tsv)]: in [metadata-sample.tsv] one-to-one found 42 relationships with conflicts [(DFBL-78399,DFBL-78399-R0), (DFBL-86381,DFBL-86381-R1), (DFBL-86381,DFBL-86381-R0), (DFBL-86381,DFBL-86381-V2), (DFTL-22685,DFTL-22685-V4), (DFTL-22685,DFTL-22685-Q1), (DFTL-22685,DFTL-22685-V0), (DFTL-51398,DFTL-51398-V2), (DFTL-51398,DFTL-51398-R0), (DFTL-51398,DFTL-51398-R1), (DFTL-78024,DFTL-78024-V4), (DFBL-13727,DFBL-13727-V2), (DFTL-78024,DFTL-78024-R0), (DFBL-13727,DFBL-13727-R0), (DFTL-78024,DFTL-78024-V1), (DFBL-13796,DFBL-13796-V1), (DFBL-13796,DFBL-13796-R0), (DFTL-85005,DFTL-85005-V4), (DFTL-85005,DFTL-85005-R0), (DFTL-85005,DFTL-85005-V1), (DFBL-28030,DFBL-28030-V2), (DFBL-28030,DFBL-28030-R0), (DFBL-28030,DFBL-28030-V1), (DFBL-31357,DFBL-31357-V1), (DFBL-31357,DFBL-31357-R0), (DFBL-45974,DFBL-45974-R1), (DFBL-45974,DFBL-45974-R0), (DFBL-45974,DFBL-45974-V2), (DFBL-47933,DFBL-47933-V1), (DFBL-47933,DFBL-47933-R0), (DFBL-49659,DFBL-49659-R0), (DFAM-14043,DFAM-14043-Q2), (DFBL-49659,DFBL-49659-V1), (DFAM-14043,DFAM-14043-R0), (DFBL-49659,DFBL-49659-V2), (DFBL-72516,DFBL-72516-R2), (DFBL-72516,DFBL-72516-R0), (DFBL-72516,DFBL-72516-V2), (DFBL-75549,DFBL-75549-R2), (DFBL-75549,DFBL-75549-R0), (DFBL-75549,DFBL-75549-V2), (DFBL-78399,DFBL-78399-V1)]
13:11:25::379 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [DFCI-CPDM]: Broken table_key relation [(metadata-model.tsv) model_id -> model_id (metadata-sharing.tsv)]: 26 orphan row(s) found in [metadata-model.tsv]
13:11:25::379 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [DFCI-CPDM]: Broken one_to_many relation [(metadata-sample.tsv) sample_id -> patient_id (metadata-sample.tsv)]: in [metadata-sample.tsv] one-to-many found 42 relationships with conflicts [(DFAM-14043,DFAM-14043), (DFAM-14043,DFAM-14043), (DFBL-13727,DFBL-13727), (DFBL-13727,DFBL-13727), (DFBL-13796,DFBL-13796), (DFBL-13796,DFBL-13796), (DFBL-28030,DFBL-28030), (DFBL-28030,DFBL-28030), (DFBL-28030,DFBL-28030), (DFBL-31357,DFBL-31357), (DFBL-31357,DFBL-31357), (DFBL-45974,DFBL-45974), (DFBL-45974,DFBL-45974), (DFBL-45974,DFBL-45974), (DFBL-47933,DFBL-47933), (DFBL-47933,DFBL-47933), (DFBL-49659,DFBL-49659), (DFBL-49659,DFBL-49659), (DFBL-49659,DFBL-49659), (DFBL-72516,DFBL-72516), (DFBL-72516,DFBL-72516), (DFBL-72516,DFBL-72516), (DFBL-75549,DFBL-75549), (DFBL-75549,DFBL-75549), (DFBL-75549,DFBL-75549), (DFBL-78399,DFBL-78399), (DFBL-78399,DFBL-78399), (DFBL-86381,DFBL-86381), (DFBL-86381,DFBL-86381), (DFBL-86381,DFBL-86381), (DFTL-22685,DFTL-22685), (DFTL-22685,DFTL-22685), (DFTL-22685,DFTL-22685), (DFTL-51398,DFTL-51398), (DFTL-51398,DFTL-51398), (DFTL-51398,DFTL-51398), (DFTL-78024,DFTL-78024), (DFTL-78024,DFTL-78024), (DFTL-78024,DFTL-78024), (DFTL-85005,DFTL-85005), (DFTL-85005,DFTL-85005), (DFTL-85005,DFTL-85005)]
13:11:25::379 INFO org.pdxfinder.dataloaders.updog.Updog : Using UPDOG to import NKI PDX data from [/home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/NKI]
Reading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/NKI/NKI_metadata-checklist.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/NKI/NKI_metadata-sample.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/NKI/NKI_metadata-sharing.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/NKI/NKI_sampleplatform-data.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/NKI/NKI_metadata-loader.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/NKI/NKI_metadata-model_validation.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/NKI/NKI_metadata-model.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/NKI/NKI_metadata-patient.tsv13:11:35::661 INFO ders.updog.tablevalidation.ErrorReporter : Limiting output to the first 50 errors:
13:11:35::661 ERROR ders.updog.tablevalidation.ErrorReporter : 2 validation errors found:
13:11:35::662 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model.tsv] for provider [NKI]: in column [publications] found 2 values not of type: PMID: [8 digit id] (comma separated) : [not specified, not specified]
13:11:35::662 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [NKI]: in column [collection_date] found 7 values not of type: [MMM YYYY] three letter month and 4 digit year : [43839, 43930, 43840, 43871, 44053, 43901, 43933]
13:11:35::662 INFO org.pdxfinder.dataloaders.updog.Updog : Using UPDOG to import JAX-XDOG PDX data from [/home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/JAX-XDOG]
13:11:35::663 ERROR org.pdxfinder.dataloaders.updog.Reader : There was an error reading the files
java.nio.file.NoSuchFileException: /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/JAX-XDOG
at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:92)
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:116)
at java.base/sun.nio.fs.UnixFileSystemProvider.newDirectoryStream(UnixFileSystemProvider.java:432)
at java.base/java.nio.file.Files.newDirectoryStream(Files.java:471)
at java.base/java.nio.file.Files.list(Files.java:3698)
at org.pdxfinder.dataloaders.updog.Reader.readAllTsvFilesIn(Reader.java:26)
at org.pdxfinder.dataloaders.updog.Updog.readPdxTablesFromPath(Updog.java:71)
at org.pdxfinder.dataloaders.updog.Updog.run(Updog.java:51)
at org.pdxfinder.commandline.FinderLoader.callRelevantLoader(FinderLoader.java:174)
at org.pdxfinder.commandline.FinderLoader.loadRequestedPdxData(FinderLoader.java:153)
at org.pdxfinder.commandline.FinderLoader.run(FinderLoader.java:99)
at org.pdxfinder.commandline.FinderCommandLine$Load.call(FinderCommandLine.java:122)
at org.pdxfinder.commandline.FinderCommandLine$Load.call(FinderCommandLine.java:44)
at picocli.CommandLine.executeUserObject(CommandLine.java:1743)
at picocli.CommandLine.access$900(CommandLine.java:145)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2101)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2068)
at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:1935)
at picocli.CommandLine.execute(CommandLine.java:1864)
at org.pdxfinder.commandline.ApplicationRunner.run(ApplicationRunner.java:23)
at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:795)
at org.springframework.boot.SpringApplication.callRunners(SpringApplication.java:779)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:322)
at org.springframework.boot.builder.SpringApplicationBuilder.run(SpringApplicationBuilder.java:140)
at org.pdxfinder.Loader.main(Loader.java:13)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.boot.devtools.restart.RestartLauncher.run(RestartLauncher.java:49)
13:11:35::665 ERROR aloaders.updog.tablevalidation.Validator : Not all required tables where present for JAX-XDOG. Aborting further validation
13:11:35::665 INFO ders.updog.tablevalidation.ErrorReporter : Limiting output to the first 50 errors:
13:11:35::665 ERROR ders.updog.tablevalidation.ErrorReporter : 6 validation errors found:
13:11:35::665 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-loader.tsv] for provider [JAX-XDOG]: Missing required table
13:11:35::665 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [JAX-XDOG]: Missing required table
13:11:35::665 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model_validation.tsv] for provider [JAX-XDOG]: Missing required table
13:11:35::665 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [JAX-XDOG]: Missing required table
13:11:35::665 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model.tsv] for provider [JAX-XDOG]: Missing required table
13:11:35::665 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [JAX-XDOG]: Missing required table
13:11:35::665 INFO org.pdxfinder.dataloaders.updog.Updog : Using UPDOG to import SJCRH PDX data from [/home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/SJCRH]
Reading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/SJCRH/SJCRH_metadata-checklist.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/SJCRH/SJCRH_metadata-loader.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/SJCRH/SJCRH_metadata-model.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/SJCRH/SJCRH_metadata-patient .tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/SJCRH/SJCRH_metadata-model_validation.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/SJCRH/SJCRH_metadata-patient.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/SJCRH/SJCRH_metadata-sharing.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/SJCRH/SJCRH_metadata-sample.tsv13:11:42::898 INFO ders.updog.tablevalidation.ErrorReporter : Limiting output to the first 50 errors:
13:11:42::898 ERROR ders.updog.tablevalidation.ErrorReporter : 12 validation errors found:
13:11:42::906 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [SJCRH]: Missing value(s) in required column [email]
13:11:42::906 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [SJCRH]: Missing value(s) in required column [project]
13:11:42::906 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [SJCRH]: in column [ethnicity_assessment_method] found 164 values genetic : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:11:42::906 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [SJCRH]: in column [treatment_naive_at_collection] found 13 values not in a required category. Required Categories: [treatment naive,not treatment naive,not collected,not provided] Value found : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:11:42::906 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [SJCRH]: in column [collection_event] found 1 values Not of type: collection event [0-9] : [colelcton event 3]
13:11:42::906 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [SJCRH]: in column [tumour_type] found 8 values not in a required category. Required Categories: [primary,metastatic,recurrent,refactory,not collected,not provided] Value found : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:11:42::906 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [SJCRH]: in column [age_in_years_at_collection] found 34 values have characters not contains in US ASCII numbers and pP-., : [10 mo, 15 mo, 23 mo, 16 mo, 16 mo, 22 mo, 14 mo, 23 mo, 18 mo, 8 mo, 8 mo, 8 mo, 17 mo, 5 mo, 20 mo, 20 mo, 16 mo, 19 mo, 22 mo, 22 mo, 22 mo, 4 mo, 18 mo, 22 mo, 18 mo, 13 mo, 8 mo, 6 mo, 5 mo, 12 mo, 9 mo, 16 mo, 6 mo, 22 mo]
13:11:42::907 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [SJCRH]: in column [age_at_initial_diagnosis] found 34 values have characters not contains in US ASCII numbers and pP-., : [10 mo, 15 mo, 23 mo, 16 mo, 16 mo, 22 mo, 14 mo, 23 mo, 18 mo, 8 mo, 8 mo, 8 mo, 17 mo, 5 mo, 20 mo, 20 mo, 16 mo, 19 mo, 22 mo, 22 mo, 22 mo, 4 mo, 18 mo, 22 mo, 18 mo, 13 mo, 8 mo, 6 mo, 5 mo, 12 mo, 9 mo, 16 mo, 6 mo, 22 mo]
13:11:42::907 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [SJCRH]: in column [prior_treatment] found 1 values not in a required category. Required Categories: [yes,no,not provided,not collected] Value found : [not specified]
13:11:42::907 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model_validation.tsv] for provider [SJCRH]: in column [description] found 169 values have characters not contained in US ASCII Alphanumeric and ().',:;-/ : [h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor, h&e, high concordance between xenograft and patient tumor]
13:11:42::907 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [SJCRH]: in column [collection_date] found 77 values not of type: [MMM YYYY] three letter month and 4 digit year : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:11:42::907 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [SJCRH]: Duplicates found in column [patient_id]: [SJEWS063834, SJOS030645, SJNBL030721, SJRHB000026, SJOS046149, SJRB030240, SJRHB011, SJRHB012, SJOS013768, SJOS030605, SJRHB046156, SJRHB013759, SJRHB013758, SJRB012408, SJOS063833, SJEWS049193, SJOS001107]
13:11:42::907 INFO org.pdxfinder.dataloaders.updog.Updog : Using UPDOG to import UMCG PDX data from [/home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/UMCG]
Reading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/UMCG/UMCG_metadata-patient.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/UMCG/UMCG_metadata-sharing.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/UMCG/UMCG_metadata-model_validation.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/UMCG/UMCG_metadata-model.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/UMCG/UMCG_metadata-checklist.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/UMCG/UMCG_metadata-sample.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/UMCG/UMCG_metadata-loader.tsv13:11:48::806 INFO ders.updog.tablevalidation.ErrorReporter : Limiting output to the first 50 errors:
13:11:48::806 ERROR ders.updog.tablevalidation.ErrorReporter : 1 validation errors found:
13:11:48::806 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [UMCG]: in column [collection_date] found 5 values not of type: [MMM YYYY] three letter month and 4 digit year : [2012-02-01, 2012-04-01, 2012-07-01, 2012-07-01, 2012-07-01]
13:11:48::806 INFO org.pdxfinder.dataloaders.updog.Updog : Using UPDOG to import VHIO-PC PDX data from [/home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/VHIO-PC]
Reading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/VHIO-PC/VHIO-PC_metadata-patient.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/VHIO-PC/VHIO-PC_metadata-sample.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/VHIO-PC/VHIO-PC_metadata-model.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/VHIO-PC/VHIO-PC_metadata-loader.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/VHIO-PC/VHIO-PC_metadata-sharing.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/VHIO-PC/VHIO-PC_metadata-model_validation.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/VHIO-PC/VHIO-PC_metadata-checklist.tsv13:11:48::871 INFO ders.updog.tablevalidation.ErrorReporter : Limiting output to the first 50 errors:
13:11:48::871 ERROR ders.updog.tablevalidation.ErrorReporter : 10 validation errors found:
13:11:48::871 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [VHIO-PC]: in column [sex] found 1 values not in a required category. Required Categories: [male,female,other,not collected,not provided] Value found : [not specified]
13:11:48::871 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [VHIO-PC]: in column [ethnicity_assessment_method] found 43 values genetic : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:11:48::872 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [VHIO-PC]: in column [collection_event] found 43 values Not of type: collection event [0-9] : [collection1, collection1, collection1, collection1, collection1, collection1, collection1, collection1, collection1, collection1, collection1, collection1, collection1, collection1, collection1, collection1, collection1, collection1, collection1, collection1, collection1, collection1, collection2, collection1, collection1, collection1, collection1, collection1, collection1, collection1, collection2, collection1, collection2, collection1, collection1, collection1, collection1, collection1, collection1, collection1, collection1, collection1, collection1]
13:11:48::872 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [VHIO-PC]: in column [tumour_type] found 3 values not in a required category. Required Categories: [primary,metastatic,recurrent,refactory,not collected,not provided] Value found : [not specified, not specified, not specified]
13:11:48::872 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [VHIO-PC]: in column [provider_type] found 43 values not in a required category. Required Categories: [academia,industry,academia and industry,CRO,pharma] Value found : [academia , academia , academia , academia , academia , academia , academia , academia , academia , academia , academia , academia , academia , academia , academia , academia , academia , academia , academia , academia , academia , academia , academia , academia , academia , academia , academia , academia , academia , academia , academia , academia , academia , academia , academia , academia , academia , academia , academia , academia , academia , academia , academia ]
13:11:48::872 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model_validation.tsv] for provider [VHIO-PC]: in column [passages_tested] found 43 values have characters not contains in US ASCII numbers and pP-., : [not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided, not provided]
13:11:48::872 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [VHIO-PC]: in column [age_at_initial_diagnosis] found 43 values have characters not contains in US ASCII numbers and pP-., : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:11:48::872 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [VHIO-PC]: in column [initial_diagnosis] found 17 values have characters not contained in US ASCII Alphanumeric and ().',:;-/ : [pancreatic carcinoma - infiltrating ductal adenocarcinoma (idac) + intraductal papillary mucinous neoplasm (ipmn), pancreatic carcinoma - infiltrating ductal adenocarcinoma (idac) + intraductal papillary mucinous neoplasm (ipmn), pancreatic carcinoma , pancreatic carcinoma , pancreatic carcinoma , pancreatic carcinoma , pancreatic carcinoma , pancreatic carcinoma , pancreatic carcinoma , pancreatic carcinoma , pancreatic carcinoma , pancreatic carcinoma , pancreatic carcinoma , pancreatic carcinoma , pancreatic carcinoma , pancreatic carcinoma , pancreatic carcinoma ]
13:11:48::872 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [VHIO-PC]: in column [diagnosis] found 17 values have characters not contained in US ASCII Alphanumeric and ().',:;-/ : [pancreatic carcinoma - infiltrating ductal adenocarcinoma (idac) + intraductal papillary mucinous neoplasm (ipmn), pancreatic carcinoma - infiltrating ductal adenocarcinoma (idac) + intraductal papillary mucinous neoplasm (ipmn), pancreatic carcinoma , pancreatic carcinoma , pancreatic carcinoma , pancreatic carcinoma , pancreatic carcinoma , pancreatic carcinoma , pancreatic carcinoma , pancreatic carcinoma , pancreatic carcinoma , pancreatic carcinoma , pancreatic carcinoma , pancreatic carcinoma , pancreatic carcinoma , pancreatic carcinoma , pancreatic carcinoma ]
13:11:48::872 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [VHIO-PC]: in column [collection_date] found 43 values not of type: [MMM YYYY] three letter month and 4 digit year : [2011-09-07, 2011-09-21, 2011-11-30, 2011-12-16, 2012-01-18, 2012-02-10, 2012-03-28, 2012-06-01, 2012-11-28, 2017-05-16, 2017-07-05, 2017-07-28, 2017-11-27, 2018-06-29, 2018-09-17, 2018-10-17, 2019-01-30, 2019-03-08, 2019-03-11, 2019-03-19, 2019-04-01, 2019-05-28, 2019-09-23, 2019-05-28, 2016-02-18, 2016-10-10, 2017-05-23, 2017-10-26, 2018-02-01, 2018-08-06, 2019-02-25, 2018-09-18, 2018-10-09, 2018-11-27, 2018-11-28, 2018-12-10, 2019-01-22, 2019-03-12, 2019-03-29, 2019-04-11, 2019-05-15, 2019-11-27, 2019-12-23]
13:11:48::872 INFO org.pdxfinder.dataloaders.updog.Updog : Using UPDOG to import LIH PDX data from [/home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/LIH]
Reading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/LIH/LIH_metadata-sharing.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/LIH/LIH_metadata-model_validation.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/LIH/LIH_metadata-sample.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/LIH/LIH_metadata-loader.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/LIH/LIH_metadata-model.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/LIH/LIH_sampleplatform-data.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/LIH/LIH_metadata-patient.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/LIH/LIH_metadata-checklist.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/LIH/treatment/patienttreatment-Sheet1.tsv13:11:49::769 INFO ders.updog.tablevalidation.ErrorReporter : Limiting output to the first 50 errors:
13:11:49::770 ERROR ders.updog.tablevalidation.ErrorReporter : 7 validation errors found:
13:11:49::770 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [LIH]: in column [ethnicity_assessment_method] found 40 values genetic : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:11:49::770 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [LIH]: in column [treatment_naive_at_collection] found 4 values not in a required category. Required Categories: [treatment naive,not treatment naive,not collected,not provided] Value found : [not specified, not specified, not specified, not specified]
13:11:49::770 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [LIH]: in column [age_in_years_at_collection] found 1 values have characters not contains in US ASCII numbers and pP-., : [not specified]
13:11:49::770 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model_validation.tsv] for provider [LIH]: in column [passages_tested] found 11 values have characters not contains in US ASCII numbers and pP-., : [0, 2, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:11:49::770 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [LIH]: in column [age_at_initial_diagnosis] found 1 values have characters not contains in US ASCII numbers and pP-., : [not specified]
13:11:49::770 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [LIH]: in column [prior_treatment] found 4 values not in a required category. Required Categories: [yes,no,not provided,not collected] Value found : [not specified, not specified, not specified, not specified]
13:11:49::770 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [LIH]: Duplicates found in column [patient_id]: [LIH0394, LIH0384, LIH0188, LIH0347, LIH0831, LIH0304, LIH0192, LIH0281]
13:11:49::770 INFO org.pdxfinder.dataloaders.updog.Updog : Using UPDOG to import PPTC PDX data from [/home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/PPTC]
Reading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/PPTC/PPTC_metadata-patient.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/PPTC/PPTC_metadata-loader.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/PPTC/PPTC_metadata-sharing.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/PPTC/PPTC_metadata-model.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/PPTC/PPTC_metadata-model_validation.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/PPTC/PPTC_metadata-sample.tsvReading tsv file /home/afollette/Finder_Data_Repositories/pdxfinder-data/data/UPDOG/PPTC/PPTC_metadata-checklist.tsv13:11:49::834 INFO ders.updog.tablevalidation.ErrorReporter : Limiting output to the first 50 errors:
13:11:49::834 ERROR ders.updog.tablevalidation.ErrorReporter : 14 validation errors found:
13:11:49::834 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-loader.tsv] for provider [PPTC]: Missing value(s) in required column [internal_url]
13:11:49::834 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [PPTC]: Missing value(s) in required column [sample_id]
13:11:49::834 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [PPTC]: in column [sex] found 4 values not in a required category. Required Categories: [male,female,other,not collected,not provided] Value found : [unknown, unknown, unknown, unknown]
13:11:49::834 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [PPTC]: in column [ethnicity_assessment_method] found 261 values genetic : [derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data, derived from genetic data]
13:11:49::835 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [PPTC]: in column [treatment_naive_at_collection] found 109 values not in a required category. Required Categories: [treatment naive,not treatment naive,not collected,not provided] Value found : [unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown (24 days post dx), unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown]
13:11:49::835 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [PPTC]: in column [sharable] found 261 values not in a required category. Required Categories: [yes,no,not provided] Value found : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:11:49::835 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [PPTC]: in column [tumour_type] found 97 values not in a required category. Required Categories: [primary,metastatic,recurrent,refactory,not collected,not provided] Value found : [relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, not specified, not specified, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, not specified, relapse, relapse, not specified, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse, not specified, relapse, relapse, post-treatment, relapse, relapse, relapse, relapse, relapse, relapse, not specified, relapse, relapse, relapse, not specified, not specified, relapse, not specified, relapse, relapse, relapse, relapse, post-treatment, not specified, relapse, post-treatment, not specified, relapse, relapse, relapse, relapse, relapse, relapse, relapse, relapse]
13:11:49::835 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sharing.tsv] for provider [PPTC]: in column [provider_type] found 261 values not in a required category. Required Categories: [academia,industry,academia and industry,CRO,pharma] Value found : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:11:49::835 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-model_validation.tsv] for provider [PPTC]: in column [passages_tested] found 223 values have characters not contains in US ASCII numbers and pP-., : [not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, 8 or 21, 16 or 22, 2 or 3, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified, not specified]
13:11:49::835 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [PPTC]: in column [prior_treatment] found 261 values not in a required category. Required Categories: [yes,no,not provided,not collected] Value found : [prior chemotherapy, no prior tx, no prior tx, no prior tx, prior chemotherapy, no prior tx, no prior tx, prior chemotherapy, prior chemotherapy, no prior tx, no prior tx, no prior tx, no prior tx, unknown, unknown, unknown, prior chemotherapy, no prior tx, prior chemotherapy, prior chemotherapy, no prior tx, no prior tx, no prior tx, prior chemotherapy, no prior tx, prior chemotherapy, no prior tx, no prior tx, no prior tx, no prior tx, no prior tx, no prior tx, prior chemotherapy, prior chemotherapy, no prior tx, prior chemotherapy, no prior tx, no prior tx, no prior tx, no prior tx, no prior tx, no prior tx, no prior tx, no prior tx, no prior tx, no prior tx, no prior tx, no prior tx, no prior tx, no prior tx, prior chemotherapy, no prior tx, prior chemotherapy, no prior tx, prior chemotherapy, prior chemotherapy, prior chemotherapy, prior chemotherapy, prior chemotherapy, prior chemotherapy, prior chemotherapy, prior chemotherapy, prior chemotherapy, prior chemotherapy, no prior tx, unknown, no prior tx, vinc+dox+ cyclo, vp16+ifos; ifos+cbdca +etop, cisplatin, cyclophosphamide, doxorubicin, etoposide, melphalan, total body irradiation, prior chemotherapy, prior chemotherapy, no prior tx, multiple rounds of chemotherapy, radiation, mibg, immunotherapy; mln-8237, irinotecan, temozolomide, prior chemotherapy, prior chemotherapy, prior chemotherapy, prior chemotherapy, no prior tx, no prior tx, prior chemotherapy, prior chemotherapy, no prior tx, no prior tx, prior chemotherapy, prior chemotherapy, no prior tx, no prior tx, no prior tx, prior chemotherapy, prior chemotherapy, prior chemotherapy, prior chemotherapy, prior chemotherapy, prior chemotherapy, no prior tx, no prior tx, unknown, unknown, unknown (24 days post dx), no prior tx, no prior tx, no prior tx, no prior tx, no prior tx, no prior tx, prior chemotherapy, no prior tx, no prior tx, xrt, cytox,cddp,vcr,vp-16,carbo,tt, unknown, unknown, unknown, unknown, unknown, unknown, cytox,cddp,vcr,vp-16,carbo,tt, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, no prior tx, no prior tx, no prior tx, no prior tx, unknown, unknown, no prior tx, no prior tx, no prior tx, ifosfamide/carboplatin/etoposide, no prior tx, no prior tx, no prior tx, no prior tx, no prior tx, no prior tx, no prior tx, no prior tx, prior chemotherapy, vcr, vp-16, ctx, cddp, carbo, no prior tx, arac, dauno, 6-tg-vp-16, 5-azac, no prior tx, ctx, dox, cddp, vm-26, cisplatin, etoposide, vincristine, doxorubicin, crizotinib, mibg, topotecan, cyclophosphamide, ctx, dox, cddp, vm-26, unknown, no prior tx, unknown, no prior tx, unknown, unknown, unknown, no prior tx, no prior tx, no prior tx, no prior tx, no prior tx, unknown, unknown, no prior tx, no prior tx, no prior tx, no prior tx, no prior tx, unknown, no prior tx, unknown, no prior tx, no prior tx, no prior tx, unknown, no prior tx, unknown, unknown, unknown, unknown, unknown, unknown, no prior tx, unknown, unknown, unknown, unknown, unknown, unknown, unknown, unknown, no prior tx, unknown, no prior tx, unknown, no prior tx, unknown, no prior tx, unknown, no prior tx, unknown, unknown, unknown, unknown, unknown, no prior tx, no prior tx, no prior tx, no prior tx, no prior tx, no prior tx, no prior tx, no prior tx, no prior tx, no prior tx, no prior tx, no prior tx, chemotherapy with vincristine, cyclophosphamide, dactinomycin, and doxorubicin, no prior tx, no prior tx, unknown, dtic/dox, post chemotherapy, vac+, unknown, no prior tx, unknown, unknown]
13:11:49::835 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [PPTC]: in column [collection_date] found 26 values not of type: [MMM YYYY] three letter month and 4 digit year : [2010-04-23, 2011-10-21, 2011-06-24, 2011-08-23, 2011-12-14, 2012-03-13, 2012-03-13, 2012-08-09, 2013-04-24, 2013-11-16, 2014-01-10, 2014-12-05, 2015-01-07, 2014-10-31, 2015-02-10, 2015-06-22, 2014-11-12, 2015-10-14, 2015-12-22, 2016-03-26, 2016-02-26, 2016-02-26, 2015-08-19, 2016-01-29, 2015-04-13, 2016-05-11]
13:11:49::835 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-patient.tsv] for provider [PPTC]: Duplicates found in column [patient_id]: [P0015, P0007, P0238, P0017, P0028, P0105, P0067, P0199, P0047, P0201, P0046, P0079, P0173, P0021, P0080]
13:11:49::835 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [PPTC]: Broken one_to_one relation [(metadata-sample.tsv) sample_id -> model_id (metadata-sample.tsv)]: in [metadata-sample.tsv] one-to-one found 21 relationships with conflicts [(,ICb-1078MB), (,ICb-1140MB), (,ICb-1197MB), (,ICb-1487MB), (,OS-51-CHLX), (,ICb-1494MB), (,ICb-1572MB), (,ICb-1595MB), (,IBs-P1215DIPG), (,ICb-2164MB), (,IBs-W0128DIPG), (,IC-1128GBM), (,OS-9), (,IC-1425EPN), (,ICb-3400MB), (,IC-2305GBM), (,ICb-8008MB), (,ICb-984MB), (,ICb-J1017MB), (,IC-3752GBM), (,IC-9320GCT)]
13:11:49::835 ERROR ders.updog.tablevalidation.ErrorReporter : Error in [metadata-sample.tsv] for provider [PPTC]: Broken one_to_many relation [(metadata-sample.tsv) sample_id -> patient_id (metadata-sample.tsv)]: in [metadata-sample.tsv] one-to-many found 441 relationships with conflicts [(P0119,), (P0118,), (P0126,), (P0125,), (P0224,), (P0106,), (P0117,), (P0138,), (P0215,), (P0100,), (P0133,), (P0099,), (P0110,), (P0102,), (P0124,), (P0101,), (P0112,), (P0123,), (P0140,), (P0130,), (P0141,), (P0119,), (P0118,), (P0126,), (P0125,), (P0224,), (P0106,), (P0117,), (P0138,), (P0215,), (P0100,), (P0133,), (P0099,), (P0110,), (P0102,), (P0124,), (P0101,), (P0112,), (P0123,), (P0140,), (P0130,), (P0141,), (P0119,), (P0118,), (P0126,), (P0125,), (P0224,), (P0106,), (P0117,), (P0138,), (P0215,), (P0100,), (P0133,), (P0099,), (P0110,), (P0102,), (P0124,), (P0101,), (P0112,), (P0123,), (P0140,), (P0130,), (P0141,), (P0119,), (P0118,), (P0126,), (P0125,), (P0224,), (P0106,), (P0117,), (P0138,), (P0215,), (P0100,), (P0133,), (P0099,), (P0110,), (P0102,), (P0124,), (P0101,), (P0112,), (P0123,), (P0140,), (P0130,), (P0141,), (P0119,), (P0118,), (P0126,), (P0125,), (P0224,), (P0106,), (P0117,), (P0138,), (P0215,), (P0100,), (P0133,), (P0099,), (P0110,), (P0102,), (P0124,), (P0101,), (P0112,), (P0123,), (P0140,), (P0130,), (P0141,), (P0119,), (P0118,), (P0126,), (P0125,), (P0224,), (P0106,), (P0117,), (P0138,), (P0215,), (P0100,), (P0133,), (P0099,), (P0110,), (P0102,), (P0124,), (P0101,), (P0112,), (P0123,), (P0140,), (P0130,), (P0141,), (P0119,), (P0118,), (P0126,), (P0125,), (P0224,), (P0106,), (P0117,), (P0138,), (P0215,), (P0100,), (P0133,), (P0099,), (P0110,), (P0102,), (P0124,), (P0101,), (P0112,), (P0123,), (P0140,), (P0130,), (P0141,), (P0119,), (P0118,), (P0126,), (P0125,), (P0224,), (P0106,), (P0117,), (P0138,), (P0215,), (P0100,), (P0133,), (P0099,), (P0110,), (P0102,), (P0124,), (P0101,), (P0112,), (P0123,), (P0140,), (P0130,), (P0141,), (P0119,), (P0118,), (P0126,), (P0125,), (P0224,), (P0106,), (P0117,), (P0138,), (P0215,), (P0100,), (P0133,), (P0099,), (P0110,), (P0102,), (P0124,), (P0101,), (P0112,), (P0123,), (P0140,), (P0130,), (P0141,), (P0119,), (P0118,), (P0126,), (P0125,), (P0224,), (P0106,), (P0117,), (P0138,), (P0215,), (P0100,), (P0133,), (P0099,), (P0110,), (P0102,), (P0124,), (P0101,), (P0112,), (P0123,), (P0140,), (P0130,), (P0141,), (P0119,), (P0118,), (P0126,), (P0125,), (P0224,), (P0106,), (P0117,), (P0138,), (P0215,), (P0100,), (P0133,), (P0099,), (P0110,), (P0102,), (P0124,), (P0101,), (P0112,), (P0123,), (P0140,), (P0130,), (P0141,), (P0119,), (P0118,), (P0126,), (P0125,), (P0224,), (P0106,), (P0117,), (P0138,), (P0215,), (P0100,), (P0133,), (P0099,), (P0110,), (P0102,), (P0124,), (P0101,), (P0112,), (P0123,), (P0140,), (P0130,), (P0141,), (P0119,), (P0118,), (P0126,), (P0125,), (P0224,), (P0106,), (P0117,), (P0138,), (P0215,), (P0100,), (P0133,), (P0099,), (P0110,), (P0102,), (P0124,), (P0101,), (P0112,), (P0123,), (P0140,), (P0130,), (P0141,), (P0119,), (P0118,), (P0126,), (P0125,), (P0224,), (P0106,), (P0117,), (P0138,), (P0215,), (P0100,), (P0133,), (P0099,), (P0110,), (P0102,), (P0124,), (P0101,), (P0112,), (P0123,), (P0140,), (P0130,), (P0141,), (P0119,), (P0118,), (P0126,), (P0125,), (P0224,), (P0106,), (P0117,), (P0138,), (P0215,), (P0100,), (P0133,), (P0099,), (P0110,), (P0102,), (P0124,), (P0101,), (P0112,), (P0123,), (P0140,), (P0130,), (P0141,), (P0119,), (P0118,), (P0126,), (P0125,), (P0224,), (P0106,), (P0117,), (P0138,), (P0215,), (P0100,), (P0133,), (P0099,), (P0110,), (P0102,), (P0124,), (P0101,), (P0112,), (P0123,), (P0140,), (P0130,), (P0141,), (P0119,), (P0118,), (P0126,), (P0125,), (P0224,), (P0106,), (P0117,), (P0138,), (P0215,), (P0100,), (P0133,), (P0099,), (P0110,), (P0102,), (P0124,), (P0101,), (P0112,), (P0123,), (P0140,), (P0130,), (P0141,), (P0119,), (P0118,), (P0126,), (P0125,), (P0224,), (P0106,), (P0117,), (P0138,), (P0215,), (P0100,), (P0133,), (P0099,), (P0110,), (P0102,), (P0124,), (P0101,), (P0112,), (P0123,), (P0140,), (P0130,), (P0141,), (P0119,), (P0118,), (P0126,), (P0125,), (P0224,), (P0106,), (P0117,), (P0138,), (P0215,), (P0100,), (P0133,), (P0099,), (P0110,), (P0102,), (P0124,), (P0101,), (P0112,), (P0123,), (P0140,), (P0130,), (P0141,), (P0119,), (P0118,), (P0126,), (P0125,), (P0224,), (P0106,), (P0117,), (P0138,), (P0215,), (P0100,), (P0133,), (P0099,), (P0110,), (P0102,), (P0124,), (P0101,), (P0112,), (P0123,), (P0140,), (P0130,), (P0141,), (P0119,), (P0118,), (P0126,), (P0125,), (P0224,), (P0106,), (P0117,), (P0138,), (P0215,), (P0100,), (P0133,), (P0099,), (P0110,), (P0102,), (P0124,), (P0101,), (P0112,), (P0123,), (P0140,), (P0130,), (P0141,)]
13:11:49::836 INFO org.pdxfinder.utils.TransformPDMR : No data Loading or transformation at the moment, the tomcat server is running for browser based access, to Load data use program argument: -transformPDMR
13:11:49::963 INFO orm.jpa.AbstractEntityManagerFactoryBean : Closing JPA EntityManagerFactory for persistence unit 'default'
13:11:49::971 INFO com.zaxxer.hikari.HikariDataSource : HikariPool-1 - Shutdown initiated...
13:11:49::982 INFO com.zaxxer.hikari.HikariDataSource : HikariPool-1 - Shutdown completed.