Query HDF metadata with SPARQL#

Metadata in form of JSON-LD can be queried using SPARQL:

import rdflib
from ontolutils import SSNO, PIVMETA

import h5rdmtoolbox as h5tbx
from h5rdmtoolbox import jsonld

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
Cell In[1], line 2
      1 import rdflib
----> 2 from ontolutils import SSNO, PIVMETA
      4 import h5rdmtoolbox as h5tbx
      5 from h5rdmtoolbox import jsonld

ImportError: cannot import name 'SSNO' from 'ontolutils' (/home/docs/checkouts/readthedocs.org/user_builds/h5rdmtoolbox/envs/v1.6.0/lib/python3.8/site-packages/ontolutils/__init__.py)

Example file:

with h5tbx.File() as h5:
    ds = h5.create_dataset('u', data=[1,2,3,4], attrs={'standard_name': 'coeff', 'units': 'm/s'})
    ds.rdf.predicate['standard_name'] = SSNO.hasStandardName
    ds.rdf.object['standard_name'] = PIVMETA.piv_correlation_coefficient
    h5.dump()

/(1)

Extract metadata:

json_str = jsonld.dumps(
        h5.hdf_filename,
        indent=2,
        context={'m4i': 'http://w3id.org/nfdi4ing/metadata4ing#',
                 'foaf': 'http://xmlns.com/foaf/0.1/'}
    )
print(json_str)

{
  "@context": {
    "foaf": "http://xmlns.com/foaf/0.1/",
    "hdf5": "http://purl.allotrope.org/ontologies/hdf5/1.8#",
    "m4i": "http://w3id.org/nfdi4ing/metadata4ing#",
    "standard_name": "https://matthiasprobst.github.io/ssno#hasStandardName"
  },
  "@graph": [
    {
      "@id": "_:N6",
      "@type": "hdf5:File",
      "hdf5:rootGroup": {
        "@id": "_:N5",
        "@type": "hdf5:Group",
        "hdf5:member": {
          "@id": "_:N7",
          "@type": "hdf5:Dataset",
          "hdf5:attribute": [
            {
              "@id": "_:N8",
              "@type": "hdf5:Attribute",
              "hdf5:name": "standard_name",
              "hdf5:value": "coeff"
            },
            {
              "@id": "_:N9",
              "@type": "hdf5:Attribute",
              "hdf5:name": "units",
              "hdf5:value": "m/s"
            }
          ],
          "hdf5:datatype": "H5T_INTEGER",
          "hdf5:dimension": 1,
          "hdf5:name": "/u",
          "hdf5:size": 4,
          "hdf5:value": {
            "@id": "https://matthiasprobst.github.io/pivmeta#piv_correlation_coefficient"
          },
          "standard_name": {
            "@id": "https://matthiasprobst.github.io/pivmeta#piv_correlation_coefficient"
          }
        },
        "hdf5:name": "/"
      }
    }
  ]
}

SPARQL query:

sparql_query_str = """
PREFIX hdf5: <http://purl.allotrope.org/ontologies/hdf5/1.8#>
PREFIX ssno: <https://matthiasprobst.github.io/ssno#>

SELECT  ?name ?sn
{
    ?obj a hdf5:Dataset .
    ?obj hdf5:name ?name .
    ?obj ssno:hasStandardName ?sn .
}
"""

g = rdflib.Graph().parse(data=json_str, format='json-ld')
qres = g.query(sparql_query_str)

for name, sn in qres:
    print(str(name), str(sn))

/u https://matthiasprobst.github.io/pivmeta#piv_correlation_coefficient

Find dataset with specific standard_name:

def find_dataset_from_standard_name(hdf_filename, sn, limit=1):
    sparql_query_str = """
    PREFIX hdf5: <http://purl.allotrope.org/ontologies/hdf5/1.8#>
    PREFIX ssno: <https://matthiasprobst.github.io/ssno#>
    
    SELECT ?name
    {
        ?obj a hdf5:Dataset .
        ?obj hdf5:name ?name .
    """
    sparql_query_str += f"?obj ssno:hasStandardName <{sn}> .\n}}"
    g = rdflib.Graph().parse(data=json_str, format='json-ld')
    qres = g.query(sparql_query_str)

    if limit == 1:
        for name in qres:
            return str(name[0])
    else:
        return [str(name[0]) for name in qres]

find_dataset_from_standard_name(
    h5.hdf_filename,
    'https://matthiasprobst.github.io/pivmeta#piv_correlation_coefficient',
    limit=1
)

'/u'

def find_attribute_from_name(hdf_filename, name, limit=1):
    sparql_query_str = f"""
    PREFIX hdf5: <http://purl.allotrope.org/ontologies/hdf5/1.8#>
    
    SELECT  ?name
    {{
        ?obj a ?type .
        ?obj hdf5:name ?name .
        ?obj hdf5:attribute ?attr .
        ?attr hdf5:name "{name}" .
        VALUES ?type {{  hdf5:Group hdf5:Dataset }}
    }}
    """
    g = rdflib.Graph().parse(data=json_str, format='json-ld')
    qres = g.query(sparql_query_str)

    if limit == 1:
        for name in qres:
            return str(name[0])
    else:
        return [str(name[0]) for name in qres]

find_attribute_from_name(h5.hdf_filename, 'codeRepository', 1)

Documentation

Query HDF metadata with SPARQL

Query HDF metadata with SPARQL#