Trouble getting Jinja "if" statements to work

[dirkdevriendt]

something like "valueUrl": "{{gender|lower}}" works
while "valueUrl": "pato:{% if gender == 'F' %}0000383{% else %}0000384{% endif %}" does not

Reference from the docs:
https://github.com/CLARIAH/COW/wiki/12.-example:-if-statement-converting-sex-variable-and-values-appropriately

When using the online cattle.datalegend.net tool, I get the expected result, but using the command line with the exact same json metadata files, the algorithm seems to skip the triples or includes incomplete URIs
I don't think there is a way to increase the logging level and get a better idea of where things go awry?

I can post a complete example if this is not an obvious error/misunderstanding on my end and a test case would help.

[rijpma]

Hi @dirkdevriendt , yes could you maybe post a few lines of the data and the relevant block of the metadata file?

[dirkdevriendt]

Thanks @rijpma !
Love what the tool does, BTW

A simple example would be the following csv:

id_subject,family_member,relation,gender
1,2,"F","M"
2,2,"P","M"

with the following metadata:

{
 "@context": [
  "https://raw.githubusercontent.com/CLARIAH/COW/master/csvw.json",
  {"@language": "en", "@base": "https://example.com/id/"},
  {
   ...
   "fhho": "http://www.owl-ontologies.com/Ontology1172270693.owl#",
   "pato": "http://purl.obolibrary.org/obo/pato#",
   "ro":   "http://purl.obolibrary.org/obo/ro#",
   "obi":  "http://purl.obolibrary.org/obo/obi#"
  }
],
 "tableSchema": {
  "aboutUrl": "ExampleData/subject_{id_subject}",
  "primaryKey": "id_subject",
  "columns": [
    {
        "name": "id_subject",
        "titles": [ "id_subject", "study subject ID" ],
        "datatype": "integer",
        "@id": "https://example.com/id/test.csv/column/id_subject",
        "propertyUrl": "rdf:type",
        "valueUrl": "fhho:Person"
   },
    {
        "name": "relation",
        "titles": [ "relation", "relation to the main study subject" ],
        "dc:description": "The family relation of the subject to the main study subject",
        "datatype": "string",
        "@id": "CheckSuccesfulDataset_SUBJECTUNIQUE.csv/column/relation",
        "aboutUrl": "ExampleData/subject_{family_member}",
        "propertyUrl": "{% if relation == 'M' %}fhho:has_natural_mother{% elif relation == 'F' %}fhho:has_natural_father{% else %}owl:sameAs{% endif %}",
        "valueUrl": "ExampleData/subject_{id_subject}"
    },
    {
        "name": "gender",
        "titles": [ "gender", "lowercase gender code of the study subject" ],
        "datatype": "string",
        "@id": "https://example.com/id/test.csv/column/gender",
        "propertyUrl": "gender",
        "valueUrl": "{{gender|lower}}"
   },
   {
        "name": "gender_PATO",
        "titles": [ "gender_PATO", "PATO gender of the study subject" ],
        "virtual": true,
        "datatype": "string",
        "@id": "https://example.com/id/test.csv/column/gender_PATO",
        "propertyUrl": "ro:0000086",
        "valueUrl": "pato:{% if gender == 'F' %}0000383{% else %}0000384{% endif %}"
    }
  ]
 },
...
 "@id": "https://example.com/id/test.csv"
}

Which in cattle.datalegend.net yields, as expected:
(let's ignore the unprompted iisg.amsterdam references and the subject_1 fhho:has_natural_father subject_1. I don't know if that is as designed)

...
<https://example.com/id/ExampleData/subject_1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.owl-ontologies.com/Ontology1172270693.owl#Person> <https://iisg.amsterdam/test/assertion/fa1ddd59/2022-11-21T13:24> .
<https://example.com/id/ExampleData/subject_1> <http://purl.obolibrary.org/obo/ro#0000086> <http://purl.obolibrary.org/obo/pato#0000384> <https://iisg.amsterdam/test/assertion/fa1ddd59/2022-11-21T13:24> .
<https://example.com/id/ExampleData/subject_2> <https://example.com/id/gender> <https://example.com/id/m> <https://iisg.amsterdam/test/assertion/fa1ddd59/2022-11-21T13:24> .
<https://example.com/id/ExampleData/subject_1> <https://example.com/id/fhho:has_natural_father> <https://example.com/id/ExampleData/subject_1> <https://iisg.amsterdam/test/assertion/fa1ddd59/2022-11-21T13:24> .
<https://example.com/id/ExampleData/subject_2> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.owl-ontologies.com/Ontology1172270693.owl#Person> <https://iisg.amsterdam/test/assertion/fa1ddd59/2022-11-21T13:24> .
<https://example.com/id/ExampleData/subject_2> <http://purl.obolibrary.org/obo/ro#0000086> <http://purl.obolibrary.org/obo/pato#0000384> <https://iisg.amsterdam/test/assertion/fa1ddd59/2022-11-21T13:24> .
<https://example.com/id/ExampleData/subject_2> <https://example.com/id/owl:sameAs> <https://example.com/id/ExampleData/subject_2> <https://iisg.amsterdam/test/assertion/fa1ddd59/2022-11-21T13:24> .
<https://example.com/id/ExampleData/subject_1> <https://example.com/id/gender> <https://example.com/id/m> <https://iisg.amsterdam/test/assertion/fa1ddd59/2022-11-21T13:24> .
...

While the cow_tool --processes 1 convert test.csv command yields:
(note: cow_tool --version returns 1.21)
cow_tool handles, AFAICT, the fhho:has_natural_father subject inversion correctly, but does not fill in the predicate and drops the gender_PATO rule entirely

<https://example.com/id/ExampleData/subject_1> <https://example.com/id/gender> <https://example.com/id/m> <https://example.com/id/test/assertion/aefe5ca2/2022-11-21T13:23> .
<https://example.com/id/ExampleData/subject_1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.owl-ontologies.com/Ontology1172270693.owl#Person> <https://example.com/id/test/assertion/aefe5ca2/2022-11-21T13:23> .
<https://example.com/id/ExampleData/subject_2> <https://example.com/id/> <https://example.com/id/ExampleData/subject_1> <https://example.com/id/test/assertion/aefe5ca2/2022-11-21T13:23> .
<https://example.com/id/ExampleData/subject_2> <https://example.com/id/gender> <https://example.com/id/m> <https://example.com/id/test/assertion/aefe5ca2/2022-11-21T13:23> .
<https://example.com/id/ExampleData/subject_2> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.owl-ontologies.com/Ontology1172270693.owl#Person> <https://example.com/id/test/assertion/aefe5ca2/2022-11-21T13:23> .
<https://example.com/id/ExampleData/subject_2> <https://example.com/id/> <https://example.com/id/ExampleData/subject_2> <https://example.com/id/test/assertion/aefe5ca2/2022-11-21T13:23> .
...