Issue 9 merge in context jsonld to registration schema

Pipfile

@@ -14,6 +14,7 @@ fastjsonschema = "*"
 jsonref = "*"
 pyyaml = "*"
 click = "*"
+pyld = "*"
 
 [requires]
 python_version = "3.8"

examples/examples.md

@@ -10,6 +10,7 @@ We provide the examples in YAML so that they're easier to read (and because JSON
 $ python convert.py minimal_registration.yaml
 {
     "@context": "https://raw.githubusercontent.com/IGSN/igsn-json/master/schema.igsn.org/json/registration/v0.1/context.jsonld",
+    "@id": "https://csiro.au/bogus_igsn/XXXCSIRO0001",
     "igsn": "XXXCSIRO0001",
     "registrant": {
         "name": "CSIRO",
@@ -55,10 +56,11 @@ Let's walk through the examples we've got...
 
 ## Minimal registration
 
-This is the minimal set of metadata required to define an IGSN - the `registrant` field pointing to the allocating agent, and the identifier itself. Not very useful but easy to do:
+This is the minimal set of metadata required to define an IGSN - the `registrant` field pointing to the allocating agent, an `@id` tag that identifies the JSON document, and the identifier itself. Not very useful but easy to do:
 
 ```yaml
 "@context": https://raw.githubusercontent.com/IGSN/igsn-json/master/schema.igsn.org/json/registration/v0.1/context.jsonld
+"@id": https://csiro.au/bogus_igsns/XXXCSIRO0001
 igsn: XXXCSIRO0001
 registrant:
   name: CSIRO
@@ -168,6 +170,7 @@ We'll say that an archeology team from ANU, in collaboration with the Museum of
 
 ```yaml
 "@context": https://raw.githubusercontent.com/IGSN/igsn-json/master/schema.igsn.org/json/registration/v0.1/context.jsonld
+@id: https://mfo.org/specimens/XXXMFO0001
 igsn: XXXMFO0001
 registrant:
   name: Museum of Fictional Objects
@@ -205,6 +208,7 @@ The team have also sampled the stratigraphic horizon that this tooth was found i
 
 ```yaml
 "@context": https://raw.githubusercontent.com/IGSN/igsn-json/master/schema.igsn.org/json/registration/v0.1/context.jsonld
+@id: https://mfo.org/specimens/XXXMFO0002
 igsn: XXXMFO0002
 registrant:
   $ref: http://igsn.org/XXXMFO001#registrant

examples/full_registration.yaml

@@ -10,6 +10,9 @@
 # IGSN data to be valid.
 "@context": https://raw.githubusercontent.com/IGSN/igsn-json/master/schema.igsn.org/json/registration/v0.1/context.jsonld
 
+# The ID tag identifies this document
+"@id": https://csiro.au/bogus/igsn/XXXCSIRO0001
+
 # This is the identifier that we are talking about. All identifier objects
 # have a 'kind' key indicating what sort of identifier they are, and an id
 # key pointing to a URI or resource definition

examples/lifecycle_1.yaml

@@ -6,6 +6,7 @@
 --- # tooth
 
 "@context": https://raw.githubusercontent.com/IGSN/igsn-json/master/schema.igsn.org/json/registration/v0.1/context.jsonld
+"@id": "https://mfo.org/specimens/XXXMFO0001"
 
 igsn: XXXMFO0001
 
@@ -51,6 +52,7 @@ log:
 
 # Registration of the sediment horizon
 "@context": https://raw.githubusercontent.com/IGSN/igsn-json/master/schema.igsn.org/json/registration/v0.1/context.jsonld
+"@id": "https://mfo.org/specimens/XXXMFO0002"
 
 igsn: XXXMFO0002
 

examples/lifecycle_2.yaml

@@ -7,6 +7,7 @@
 --- # tooth
 
 "@context": https://raw.githubusercontent.com/IGSN/igsn-json/master/schema.igsn.org/json/registration/v0.1/context.jsonld
+"@id": "https://mfo.org/specimens/XXXMFO0001"
 
 igsn: XXXMFO0001
 
@@ -61,6 +62,7 @@ log:
 
 # Registration of the sediment horizon
 "@context": https://raw.githubusercontent.com/IGSN/igsn-json/master/schema.igsn.org/json/registration/v0.1/context.jsonld
+"@id": "https://mfo.org/specimens/XXXMFO0002"
 
 igsn: XXXMFO0002
 

examples/lifecycle_3.yaml

@@ -7,6 +7,7 @@
 --- # tooth
 
 "@context": https://raw.githubusercontent.com/IGSN/igsn-json/master/schema.igsn.org/json/registration/v0.1/context.jsonld
+"@id": "https://mfo.org/specimens/XXXMFO0001"
 
 igsn: XXXMFO0001
 
@@ -82,6 +83,7 @@ log:
 
 # Registration of the sediment horizon
 "@context": https://raw.githubusercontent.com/IGSN/igsn-json/master/schema.igsn.org/json/registration/v0.1/context.jsonld
+"@id": "https://mfo.org/specimens/XXXMFO0002"
 
 igsn: XXXMFO0002
 
@@ -134,6 +136,7 @@ log:
 --- # tooth sample for CSIRO
 
 "@context": https://raw.githubusercontent.com/IGSN/igsn-json/master/schema.igsn.org/json/registration/v0.1/context.jsonld
+"@id": "https://csiro.au/lab-samples/XXXCSIRO001"
 
 igsn: XXXCSIRO001
 

examples/minimal_registration.yaml

@@ -10,6 +10,9 @@
 # IGSN data to be valid.
 "@context": https://raw.githubusercontent.com/IGSN/igsn-json/master/schema.igsn.org/json/registration/v0.1/context.jsonld
 
+# The ID tag identifies this document
+"@id": https://csiro.au/bogus/igsn/XXXCSIRO0001
+
 # This is the identifier that we are talking about. All identifier objects
 # have a 'kind' key indicating what sort of identifier they are, and an id
 # key pointing to a URI or resource definition

schema.igsn.org/json/registration/v0.1/main.schema.json

@@ -8,6 +8,10 @@
     "@context": {
       "const": "https://raw.githubusercontent.com/IGSN/igsn-json/master/schema.igsn.org/json/registration/v0.1/context.jsonld"
     },
+    "@id": {
+      "type": "string",
+      "description": "An identifier for this JSON document (e.g. 'http://example-agent.org/igsn/id/XXXAGENT00234')"
+    },
     "igsn": {
       "$ref": "identifiers.schema.json#/definitions/igsnPid"
     },
@@ -56,5 +60,5 @@
     },
     "log": { "$ref": "eventLog.schema.json" }
   },
-  "required": ["@context", "igsn", "registrant"]
+  "required": ["@context", "@id", "igsn", "registrant"]
 }

setup.cfg

@@ -10,6 +10,7 @@ extend-ignore =
 console_output_stype = progress
 log_level = INFO
 junit_family = legacy
+norecursedirs=tests/helpers
 addopts = 
     --junitxml='tests/reports/test-output.junit.xml' 
     # --cov=app --cov-report term --cov-report xml --cov-report html 

tests/conftest.py

@@ -1,12 +1,15 @@
 from pathlib import Path
+import sys
 
 import pytest
 import jsonref as json
 from fastjsonschema import compile as compile_schema
 
-
 # Get the root directory of the project
 ROOT = Path(__file__).parent.parent.absolute()
+TEST_DIR = ROOT / "tests"
+HELPERS = ROOT / "tests" / "helpers"
+sys.path.append(str(HELPERS))
 
 
 @pytest.fixture()
@@ -29,7 +32,7 @@ def schema_home():
         "host": "https://raw.githubusercontent.com",
         "org": "IGSN",
         "repo": "igsn-json",
-        "branch": "master",
+        "branch": "issue-9-Merge_in_context_jsonld_to_registration_schema",
     }
     return f"{github['host']}/{github['org']}/{github['repo']}/{github['branch']}"
 

tests/helpers/examples.py

@@ -0,0 +1,39 @@
+from pathlib import Path
+import json
+from collections import defaultdict
+
+# Example files from examples folder
+EXAMPLES = Path(__file__).parent.parent.parent / "examples"
+
+
+def filenames(extension=None):
+    """
+    Returns all the example files from the examples directory
+
+    Example files have both a JSON and YAML extension
+    """
+    files = defaultdict(list)
+    for fname in EXAMPLES.iterdir():
+        files[fname.stem].append(fname.suffix)
+    names = [name for name, ext in files.items() if set(ext) == {".yaml", ".json"}]
+
+    # Wrap in extension if required
+    if extension is not None:
+        return [EXAMPLES / f"{name}.{extension}" for name in names]
+    else:
+        return names
+
+
+def json_examples():
+    "Get all the JSON-formatted example data"
+    docs = {}
+    for name, jfile in zip(filenames(), filenames("json")):
+        with open(jfile, "rb") as source:
+            data = json.load(source)
+
+        if isinstance(data, list):
+            for idx, document in enumerate(data):
+                docs[f"{name}_doc_{id}"] = document
+        else:
+            docs[name] = data
+    return docs