Add serialisation using JSON-LD 1.1

nidmresults/exporter.py

@@ -8,7 +8,6 @@
 @copyright: University of Warwick 2013-2014
 """
 
-
 from prov.model import ProvBundle, ProvDocument
 import os
 import datetime
@@ -22,7 +21,10 @@
 import tempfile
 import zipfile
 from builtins import input
-
+# Needed for export using JSON-LD 1.1
+import pyld as ld
+import json
+import sys
 
 class NIDMExporter():
 
@@ -685,13 +687,27 @@ def save_prov_to_files(self, showattributes=False):
         with open(ttl_file, 'w') as ttl_fid:
             ttl_fid.write(ttl_txt)
 
-        # print(json_context)
-        jsonld_file = os.path.join(self.export_dir, 'nidm.json')
+        # JSON-LD (deprecated kept for background compatibility w/ viewers)
+        jsonld_file = os.path.join(self.export_dir, 'nidm_deprecated.json')
         jsonld_txt = self.doc.serialize(format='rdf', rdf_format='json-ld',
                                         context=json_context)
         with open(jsonld_file, 'w') as jsonld_fid:
             jsonld_fid.write(jsonld_txt)
 
+        # JSON-LD using specification 1.1 (a.k.a "nice" JSON-LD)
+        jsonld_11 = json.dumps(ld.jsonld.compact(
+            json.loads(jsonld_txt), "http://purl.org/nidash/context"))
+
+        # If python 2 convert string to unicode to avoid 
+        # 'must be unicode not str' error
+        if (sys.version_info < (3, 0)):
+            jsonld_11 = unicode(jsonld_11)
+
+        jsonld_11_file = os.path.join(self.export_dir, 'nidm.json')
+
+        with open(jsonld_11_file, "w") as fid:
+            fid.write(jsonld_11)
+
         # provjsonld_file = os.path.join(self.export_dir, 'nidm.provjsonld')
         # provjsonld_txt = self.doc.serialize(format='jsonld')
         # with open(provjsonld_file, 'w') as provjsonld_fid:

nidmresults/objects/generic.py

@@ -37,6 +37,25 @@ def __init__(self, oid=None):
                 oid = NIIRI.qname(Identifier(oid))
             self.id = oid
 
+    # the next three methods build a .file property
+    # with a dedicated function call on "set" that can
+    # be used to implement external ID mappings
+    # e.g. DataLad can replace '_map_fileid()' to provides
+    # its internal file IDs based on the filename associated
+    # with a NIDMFile object
+    @property
+    def file(self):
+        return getattr(self, '_file', None)
+
+    @file.setter
+    def file(self, fileobj):
+        if isinstance(fileobj, NIDMFile):
+            self._map_fileid(fileobj)
+        self._file = fileobj
+
+    def _map_fileid(self, fileobj):
+        pass
+
     def __str__(self):
         value = ""
         if hasattr(self, 'value'):

requirements.txt

@@ -3,4 +3,6 @@ rdflib-jsonld
 prov>=1.5.0
 nibabel
 numpy
-future
+future
+requests
+pyld