run 008 - compare invalid document

[amnonkhen]

Running instructions: see #25

Definition of done:

• [x] all output related to this task should be saved in the shared directory of this run (/nfs/production/tburdett/workstreams/fairification/checklists/data/run008)
• [x] generate the invalid documents, grouped in directory according to type, e.g. "missing mandatory", "bad pattern", etc.
• [x] the results of sending those documents for validation in biovalidator
• [x] The analysis of the results: did we get the expected errors from biovalidator
• [x] analyse the problems with invalid patterns being accepted by the json schema
  • see ticket #53

[snathanvj]

I have executed the script for mandatory and enum errors , details are in #38

[snathanvj]

erroneous files are in same directory with error_type in file name otherwise all done.

[snathanvj]

generated files are here

/nfs/production/tburdett/workstreams/fairification/checklists/data/run008/invalid

biovalidator outputs are here:

/nfs/production/tburdett/workstreams/fairification/checklists/data/run008/invalid/validation_result Comparison results are here:

/nfs/production/tburdett/workstreams/fairification/checklists/data/run008/enum_error_comparison.txt /nfs/production/tburdett/workstreams/fairification/checklists/data/run008/mandatory_error_comparison.txt Note: regexp pattern error and malformed json error not covered here

[ESapenaVentura]

• unmodified files: /nfs/production/tburdett/workstreams/fairification/checklists/data/run008/jsons/original/
• Errored pattern files: /nfs/production/tburdett/workstreams/fairification/checklists/data/run008/jsons/invalid_pattern
• Extra file that indicates what was changed: /nfs/production/tburdett/workstreams/fairification/checklists/data/run008/pattern_invalidation_error_report.csv

Will do the biovalidator output/comparison now

[ESapenaVentura]

Pattern validation

I have prepared a spreadsheet that contains some details about the validations that did not function correctly (aka, should have invalid value but it does not). I suspect this may be a problem of the regex and validation, rather than the schemas or the script not working correctly - Currently investigating

[ESapenaVentura]

There are 7 unique patterns:

• [+-]?[0-9]+.?[0-9]*
• (0|((0.)|([1-9][0-9].?))[0-9])([Ee][+-]?[0-9]+)?
• [+-]?(0|((0.)|([1-9][0-9].?))[0-9])([Ee][+-]?[0-9]+)?
• ([+-]?(0|((0.)|([1-9][0-9].?))[0-9])([Ee][+-]?[0-9]+)?)|((^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$))
• [+-]?[0-9]+
• ^150|1[0-4][0-9]|[1-9][0-9]|[0-9]|not provided$
• ((0|((0.)|([1-9][0-9].?))[0-9])([Ee][+-]?[0-9]+)?)|((^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$))

[ESapenaVentura]

All the patterns validate against the 123 part of the invalid value __XYZ_BANANA_123%$£. Possible options are:

• Accept that and try another invalid value
• Talk with ENA to understand if validation is supposed to be unanchored - if the regexp validation is expected or not