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PDCMFinder / pdxfinder

PDX Finder performs integration, standardization, analysis and visualization of the complex and diverse data associated with PDX mouse models for the cancer community.
https://www.pdxfinder.org/
Apache License 2.0
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Run validator on existing datasets #497

Closed zperova closed 3 years ago

zperova commented 3 years ago

Description

As a developer, I want to have all the datasets according to the most recent template.

Acceptance criteria

Afollet commented 3 years ago

@zperova Here are the suspects. Error count/provider. The count is subject to change: 1 provider [UMCG] 2 provider [NKI] 3 provider [Curie-BC] 4 provider [Curie-LC] 5 provider [Curie-OC] 5 provider [IRCC-GC] 6 provider [IRCC-CRC] 6 provider [UOM-BC] 6 provider [VHIO-BC] 7 provider [LIH] 7 provider [PMLB] 7 provider [UOC-BC] 7 provider [VHIO-CRC] 9 provider [HCI-BCM] 10 provider [VHIO-PC] 12 provider [PDMR] 12 provider [SJCRH] 13 provider [CRL] 14 provider [PPTC] 14 provider [WUSTL] 17 provider [MDAnderson] 18 provider [DFCI-CPDM]

It seems TRACE and Wistar-MDAnderson-Penn are missing from this list which is suspicious. I would suspect they need to be examined as well.

I know/working with PDMR, PPTC, PMLB, and NKI and I would prefer to clean those in addition to whatever else I need to clean.

Afollet commented 3 years ago

I created a document on how to use the validator with postman and some other details: https://www.ebi.ac.uk/seqdb/confluence/display/MouseInformatics/Posting+to+Validator+Microservice I need to update the legal values for tumour_type, but the service is running. @CsabaHalmagyi @mauroz77

Afollet commented 3 years ago

@zperova done