Annotated projects not passing the validator

[wouter-l]

I'm trying to verify quite a few new SDRF tables with parse_sdrf validate-sdrf --sdrf_file $file. As a sanity check, I tried verifying the existing projects in the latest version on master. For multiple of them I get validation errors though (and for even more of them, quite a few warnings). One example is PXD000527.

[ypriverol]

Can you let me know which ones? did you pull the master from sdrf-pipelines master and build locally the version?

[wouter-l]

There was an issue with my setup indeed. I fixed that, and ran it again. There are still a couple with error messages though.

The issues:

• For PXD002222, PXD004705, PXD004939: ERROR: Value '50 mmu' does not match required pattern

• For PXD009623-dda, PXD009623-dia, PXD010698, PXD010705 and PXD010708 : ERROR: Value '20 mmu' does not match required pattern

• For PMID32668389 and PXD004612: issue with the column order ('assay name' should be moved more to the end). It also missing 'comment[technical replicate]' and 'comment[proteomics data acquisition method]'.

• For PXD008841: ERROR: Value 'not pooled' does not match required pattern

• For PXD019185_PXD018883: ERROR: Value 'pooled' does not match required pattern ERROR: Value 'not pooled' does not match required pattern