Prefixes (Namespaces) for alphanumeric identifiers not passed to turtle serialisation

[cmaumet]

Hi @satra, @trungdong,

I am trying to use Namespace to specify prefixes for our alphanumeric identifiers and though this works fine with provn, it can't get it to work with the turtle serialisation. Any help would be greatly appreciated!

Here is a minimal example:

from prov.model import ProvDocument, Namespace, QualifiedName
import urllib.request
import csv

# Get a list of preferred prefixes form online csv file
csv_url = "https://raw.githubusercontent.com/incf-nidash/nidm/master/nidm/nidm-results/terms/prefixes.csv"
prefix_file = urllib.request.urlopen(
    csv_url).read().decode('utf-8').splitlines()
prefixes = dict()
reader = csv.reader(prefix_file)
for alphanum_id, prefix, uri in reader:
    prefixes[uri] = Namespace(prefix, uri)['']

## Example of prefixes dictionnary
# prefixes = dict(
#     [("http://purl.org/nidash/nidm#NIDM_0000170",
#       Namespace('nidm_groupName',
#                 'http://purl.org/nidash/nidm#NIDM_0000170')['']),
#      ("http://purl.org/nidash/nidm#NIDM_0000165",
#       Namespace('nidm_NIDMResultsExporter',
#                 'http://purl.org/nidash/nidm#NIDM_0000165')[''])],
#     )

g = ProvDocument()

group_name_uri = "http://purl.org/nidash/nidm#NIDM_0000170"
ex = Namespace('ex', 'http://example/')

g.entity(ex['group1'], {prefixes[group_name_uri]: "Group 1"})

print(g.serialize(format='provn'))
print("---")
print(g.serialize(format='rdf', rdf_format="turtle"))

and the output:

document
  prefix ex <http://example/>
  prefix nidm_groupName <http://purl.org/nidash/nidm#NIDM_0000170>

  entity(ex:group1, [nidm_groupName:="Group 1"])
endDocument

---
@prefix ex: <http://example/> .
@prefix nidm_groupName: <http://purl.org/nidash/nidm#NIDM_0000170> .
@prefix ns1: <http://purl.org/nidash/nidm#> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

ex:group1 a prov:Entity ;
    ns1:NIDM_0000170 "Group 1"^^xsd:string .

I would like ns1:NIDM_0000170 to be replaced by nidm_groupName: in the turtle document.

[satra]

PR submitted: RDFLib/rdflib#660

[satra]

@cmaumet - i tested with this.

from prov.model import ProvDocument, Namespace, QualifiedName
import pandas as pd

df = pd.read_csv('https://raw.githubusercontent.com/incf-nidash/nidm/master/nidm/nidm-results/terms/prefixes.csv')
df['Namespace'] = df[['Preferred prefix', 'URI']].apply(lambda x: Namespace(x['Preferred prefix'], x['URI']), axis=1)
prefixes = dict(df[['URI', 'Namespace']].values)
g = ProvDocument()

group_name_uri = "http://purl.org/nidash/nidm#NIDM_0000170"

for prefix in prefixes:
    if prefix == group_name_uri:
        g.add_namespace(prefixes[prefix])

group_name_uri = "http://purl.org/nidash/nidm#NIDM_0000170"
ex = Namespace('ex', 'http://example/')
g.entity(ex['group1'], {group_name_uri: "Group 1"})

print(g.serialize(format='provn'))
print("---")
print(g.serialize(format='rdf', rdf_format="turtle"))

[cmaumet]

Thank you @satra!

[satra]

this has been superceded by this PR, which takes performance into account: RDFLib/rdflib#649