Incompatibilities with LinkML

jfy133 commented 1 day ago

Test cases

Linting

$ linkml lint ancient.yml 
/home/james/git/mixs-minas/extension-ancient/src/mixs/schema/ancient.yml
  warning  Enum 'DamageTreatmentEnum' does not have recommended slot 'description'  (recommended)
  warning  Enum 'LibTypeEnum' does not have recommended slot 'description'  (recommended)
  warning  Enum 'BioCulturalLabel' does not have recommended slot 'description'  (recommended)
  warning  Enum 'LibStrand' does not have recommended slot 'description'  (recommended)
  warning  Subset 'combination_classes' does not have recommended slot 'description'  (recommended)
  warning  Subset 'sequencing' does not have recommended slot 'description'  (recommended)
  warning  Subset 'environment' does not have recommended slot 'description'  (recommended)
  warning  Subset 'nucleic acid sequence source' does not have recommended slot 'description'  (recommended)
  warning  Subset 'investigation' does not have recommended slot 'description'  (recommended)
  warning  Subset 'ethics' does not have recommended slot 'description'  (recommended)
  warning  Permissible value of Enum 'DamageTreatmentEnum' has name 'partial-udg'  (standard_naming)
  warning  Permissible value of Enum 'DamageTreatmentEnum' has name 'full-udg'  (standard_naming)
  warning  Permissible value of Enum 'BioCulturalLabel' has name 'BC P'  (standard_naming)
  warning  Permissible value of Enum 'BioCulturalLabel' has name 'BC MC'  (standard_naming)
  warning  Permissible value of Enum 'BioCulturalLabel' has name 'BC CL'  (standard_naming)
  warning  Permissible value of Enum 'BioCulturalLabel' has name 'BC CV'  (standard_naming)
  warning  Permissible value of Enum 'BioCulturalLabel' has name 'BC CNV'  (standard_naming)
  warning  Permissible value of Enum 'BioCulturalLabel' has name 'BC R'  (standard_naming)
  warning  Permissible value of Enum 'BioCulturalLabel' has name 'BC CB'  (standard_naming)
  warning  Permissible value of Enum 'BioCulturalLabel' has name 'BC OC'  (standard_naming)
  warning  Permissible value of Enum 'BioCulturalLabel' has name 'BC O'  (standard_naming)
  warning  Permissible value of Enum 'BioCulturalLabel' has name 'BC NC'  (standard_naming)

✖ Found 22 problems in 1 schema

Validating against test data

$ linkml validate -s /home/james/git/mixs-minas/extension-ancient/src/mixs/schema/ancient.yml minas-ancient-test.csv  --target-class Ancient
[ERROR] [minas-ancient-test.csv/0] Additional properties are not allowed ('sample_id' was unexpected) in /
[ERROR] [minas-ancient-test.csv/0] 'Natural History Museum London 2' is not of type 'array', 'null' in /collection_context_name
[ERROR] [minas-ancient-test.csv/0] 'Non-udg' is not of type 'array' in /damage_treatment
[ERROR] [minas-ancient-test.csv/0] '2024-07-01' is not a 'date-time' in /dna_extraction_date
[ERROR] [minas-ancient-test.csv/0] 'Museum of Mongolia' is not of type 'array', 'null' in /ethical_authority
[ERROR] [minas-ancient-test.csv/0] '2024-01-01' is not a 'date-time' in /ethical_date
[ERROR] [minas-ancient-test.csv/0] 'GN12112322' is not of type 'array', 'null' in /ethical_id
[ERROR] [minas-ancient-test.csv/0] 'XYZ' is not of type 'array', 'null' in /experimental_procedures
[ERROR] [minas-ancient-test.csv/0] 12 is not of type 'array', 'null' in /lib_concentration
[ERROR] [minas-ancient-test.csv/0] '10.10023/1203981' is not of type 'array', 'null' in /lib_preparation_protocol
[ERROR] [minas-ancient-test.csv/0] 'FALSE' is not of type 'boolean', 'null' in /neg_cont_status
[ERROR] [minas-ancient-test.csv/0] 12 is not of type 'array', 'null' in /num_capture_amp_cycles
[ERROR] [minas-ancient-test.csv/0] 'formalin' is not of type 'array', 'null' in /preservational_treatment
[ERROR] [minas-ancient-test.csv/0] 1920 is not of type 'string', 'null' in /recovery_date
[ERROR] [minas-ancient-test.csv/0] 'acetone' is not of type 'array', 'null' in /samp_decontam_pretreat
[ERROR] [minas-ancient-test.csv/0] 10900 is not of type 'string' in /sample_age
[ERROR] [minas-ancient-test.csv/0] 'C14' is not of type 'array', 'null' in /sample_age_inference_methods
[ERROR] [minas-ancient-test.csv/0] 'BC MC' is not of type 'array', 'null' in /biocultural_label
[ERROR] [minas-ancient-test.csv/0] 'Microbes only' is not of type 'array', 'null' in /ethics_perm_scope
[ERROR] [minas-ancient-test.csv/0] 'single' is not of type 'array', 'null' in /lib_strandedness
[ERROR] [minas-ancient-test.csv/0] 'Y. pestis' is not of type 'array', 'null' in /probe_set
[ERROR] [minas-ancient-test.csv/0] 'UDI configurs' is not of type 'array', 'null' in /mid_config
[ERROR] [minas-ancient-test.csv/1] Additional properties are not allowed ('sample_id' was unexpected) in /
[ERROR] [minas-ancient-test.csv/1] 'cultural_era' is a required property in /
[ERROR] [minas-ancient-test.csv/1] 'damage_treatment' is a required property in /
[ERROR] [minas-ancient-test.csv/1] 'sample_age' is a required property in /
[ERROR] [minas-ancient-test.csv/2] Additional properties are not allowed ('sample_id' was unexpected) in /
[ERROR] [minas-ancient-test.csv/2] 'cultural_era' is a required property in /
[ERROR] [minas-ancient-test.csv/2] 'damage_treatment' is a required property in /
[ERROR] [minas-ancient-test.csv/2] 'sample_age' is a required property in /

minas-ancient-test.csv

jfy133 commented 1 day ago

For validation:

multivalued doesn't seem to mean what we think it does
optional columns don't seem to be supported (although that might be valid in this context, the sample_id column would come from the core mixs terms which I am avoiding at the moment)
Need to check if there is just a date object,not just date-time
LinkML seems to have a specific representation of boolean which does not include FALSE or false
string does not allow pure numbers (sample_age) -> formatting requirement? or switch to integer (with second column for unit)

jfy133 commented 1 day ago

Question to TWG: how closely to linkml do they plan to conform?

MIxS-MInAS / extension-ancient

Incompatibilities with LinkML #5

Test cases