Allow to add entries to context

tests/test_cli.py

@@ -661,3 +661,111 @@ def test_performance_add_multiple_accessed_with_paths(
         by_id = {r["trov:arrangement"]["@id"]: r for r in accessed}
         assert by_id["arrangement/0"]["trov:boundTo"] == "/mnt/a"
         assert "trov:boundTo" not in by_id["arrangement/1"]
+
+
+class TestExtraContextCLI:
+    """Tests for --extra-context CLI option."""
+
+    def test_extra_context_prefix_mapping(
+        self, runner, tmp_path, temp_workspace, trs_profile
+    ):
+        """--extra-context PREFIX=URI adds a prefix mapping dict to @context."""
+        tro_file = tmp_path / "tro.jsonld"
+        result = runner.invoke(
+            cli,
+            [
+                "--declaration",
+                str(tro_file),
+                "--profile",
+                trs_profile,
+                "--extra-context",
+                "ex=http://example.org/",
+                "arrangement",
+                "add",
+                "--comment",
+                "test",
+                str(temp_workspace),
+            ],
+        )
+        assert result.exit_code == 0, result.output
+        with open(tro_file) as f:
+            data = json.load(f)
+        assert {"ex": "http://example.org/"} in data["@context"]
+
+    def test_extra_context_multiple(
+        self, runner, tmp_path, temp_workspace, trs_profile
+    ):
+        """Multiple --extra-context PREFIX=URI flags all appear in @context."""
+        tro_file = tmp_path / "tro.jsonld"
+        result = runner.invoke(
+            cli,
+            [
+                "--declaration",
+                str(tro_file),
+                "--profile",
+                trs_profile,
+                "--extra-context",
+                "ex=http://example.org/",
+                "--extra-context",
+                "foaf=http://xmlns.com/foaf/0.1/",
+                "arrangement",
+                "add",
+                str(temp_workspace),
+            ],
+        )
+        assert result.exit_code == 0, result.output
+        with open(tro_file) as f:
+            data = json.load(f)
+        assert {"ex": "http://example.org/"} in data["@context"]
+        assert {"foaf": "http://xmlns.com/foaf/0.1/"} in data["@context"]
+
+    def test_extra_context_invalid_format(
+        self, runner, tmp_path, temp_workspace, trs_profile
+    ):
+        """--extra-context value that is not PREFIX=URI produces an error."""
+        tro_file = tmp_path / "tro.jsonld"
+        result = runner.invoke(
+            cli,
+            [
+                "--declaration",
+                str(tro_file),
+                "--profile",
+                trs_profile,
+                "--extra-context",
+                "https://example.org/vocab.jsonld",
+                "arrangement",
+                "add",
+                str(temp_workspace),
+            ],
+        )
+        assert result.exit_code != 0
+
+    def test_extra_context_base_context_preserved(
+        self, runner, tmp_path, temp_workspace, trs_profile
+    ):
+        """The standard base @context entry is always present even with extra context."""
+        tro_file = tmp_path / "tro.jsonld"
+        runner.invoke(
+            cli,
+            [
+                "--declaration",
+                str(tro_file),
+                "--profile",
+                trs_profile,
+                "--extra-context",
+                "ex=http://example.org/",
+                "arrangement",
+                "add",
+                str(temp_workspace),
+            ],
+        )
+        with open(tro_file) as f:
+            data = json.load(f)
+        base = data["@context"][0]
+        assert "trov" in base
+
+    def test_cli_help_shows_extra_context(self, runner):
+        """--extra-context option is visible in CLI help output."""
+        result = runner.invoke(cli, ["--help"])
+        assert result.exit_code == 0
+        assert "extra-context" in result.output

tests/test_tro_utils.py

@@ -2363,3 +2363,88 @@ def test_verification_result_is_valid_property(self):
 
         bad = VerificationResult(files_missing_in_arrangement=["x"])
         assert not bad.is_valid
+
+
+class TestExtraContext:
+    """Tests for extra vocabulary support in @context."""
+
+    def test_extra_context_default_empty(self):
+        """TransparentResearchObject.extra_context defaults to an empty list."""
+        tro = TransparentResearchObject()
+        assert tro.extra_context == []
+
+    def test_extra_context_dict_in_jsonld(self):
+        """A dict extra_context entry appears in the serialised @context."""
+        tro = TransparentResearchObject()
+        tro.extra_context = [{"ex": "http://example.org/"}]
+        data = tro.to_jsonld()
+        assert {"ex": "http://example.org/"} in data["@context"]
+
+    def test_extra_context_multiple_entries(self):
+        """Multiple extra_context dict entries all appear in @context."""
+        tro = TransparentResearchObject()
+        tro.extra_context = [
+            {"ex": "http://example.org/"},
+            {"foaf": "http://xmlns.com/foaf/0.1/"},
+        ]
+        data = tro.to_jsonld()
+        assert {"ex": "http://example.org/"} in data["@context"]
+        assert {"foaf": "http://xmlns.com/foaf/0.1/"} in data["@context"]
+
+    def test_extra_context_base_context_still_present(self):
+        """The standard base context is always the first entry in @context."""
+        tro = TransparentResearchObject()
+        tro.extra_context = [{"ex": "http://example.org/"}]
+        data = tro.to_jsonld()
+        base = data["@context"][0]
+        assert "trov" in base
+        assert "rdf" in base
+
+    def test_extra_context_roundtrip(self, tmp_path):
+        """Extra context dict entries survive a save/load roundtrip."""
+        tro = TransparentResearchObject()
+        tro.extra_context = [
+            {"ex": "http://example.org/"},
+            {"foaf": "http://xmlns.com/foaf/0.1/"},
+        ]
+        filepath = tmp_path / "tro_with_extra_ctx.jsonld"
+        tro.save(str(filepath))
+
+        loaded = TransparentResearchObject.load(str(filepath))
+        assert {"ex": "http://example.org/"} in loaded.extra_context
+        assert {"foaf": "http://xmlns.com/foaf/0.1/"} in loaded.extra_context
+
+    def test_extra_context_via_tro_facade(self, tmp_path):
+        """TRO facade propagates extra_context to the underlying model."""
+        tro_file = tmp_path / "tro.jsonld"
+        tro = TRO(
+            filepath=str(tro_file),
+            extra_context=[{"ex": "http://example.org/"}],
+        )
+        tro.save()
+
+        with open(tro_file) as f:
+            data = json.load(f)
+        assert {"ex": "http://example.org/"} in data["@context"]
+
+    def test_extra_context_via_tro_facade_extends_existing(self, tmp_path):
+        """TRO facade appends extra_context to any context already in the file."""
+        tro_file = tmp_path / "tro.jsonld"
+        # First save with one extra context entry
+        tro = TRO(
+            filepath=str(tro_file),
+            extra_context=[{"ex": "http://example.org/"}],
+        )
+        tro.save()
+
+        # Re-open and add a second entry
+        tro2 = TRO(
+            filepath=str(tro_file),
+            extra_context=[{"foaf": "http://xmlns.com/foaf/0.1/"}],
+        )
+        tro2.save()
+
+        with open(tro_file) as f:
+            data = json.load(f)
+        assert {"ex": "http://example.org/"} in data["@context"]
+        assert {"foaf": "http://xmlns.com/foaf/0.1/"} in data["@context"]

tro_utils/cli.py

@@ -21,6 +21,24 @@ def _parse_arrangement_ref(value: str) -> tuple[str, str | None]:
     return (arrangement_id, path or None)
 
 
+def _parse_extra_context_value(ctx, param, value):
+    """Parse ``--extra-context`` values into JSON-LD context dicts.
+
+    Each value must be in ``PREFIX=URI`` form (e.g. ``ex=http://example.org/``).
+    """
+    result = []
+    for v in value:
+        if "=" not in v:
+            raise click.BadParameter(
+                f"{v!r} is not a valid PREFIX=URI mapping.",
+                param=param,
+                ctx=ctx,
+            )
+        prefix, _, uri = v.partition("=")
+        result.append({prefix: uri})
+    return result
+
+
 _TEMPLATES = {
     "default": {
         "description": "Default pretty template by Craig Willis",
@@ -104,6 +122,20 @@ def convert(self, value, param, ctx):
     required=False,
     help="TRO description (only used when creating a new TRO)",
 )
+@click.option(
+    "--extra-context",
+    "-c",
+    envvar="TRO_EXTRA_CONTEXT",
+    type=click.STRING,
+    required=False,
+    multiple=True,
+    callback=_parse_extra_context_value,
+    is_eager=False,
+    help=(
+        "Extra PREFIX=URI vocabulary mapping to append to @context "
+        "(e.g. ex=http://example.org/).  May be repeated."
+    ),
+)
 def cli(
     declaration,
     profile,
@@ -112,6 +144,7 @@ def cli(
     tro_creator,
     tro_name,
     tro_description,
+    extra_context,
 ):
     pass
 
@@ -308,6 +341,7 @@ def add(ctx, directory, ignore_dir, comment, from_snapshot):
     tro_name = ctx.params.get("tro_name")
     tro_description = ctx.params.get("tro_description")
     tro_creator = ctx.params.get("tro_creator")
+    extra_context = ctx.params.get("extra_context") or []
     tro = TRO(
         filepath=declaration,
         gpg_fingerprint=gpg_fingerprint,
@@ -316,6 +350,7 @@ def add(ctx, directory, ignore_dir, comment, from_snapshot):
         tro_creator=tro_creator,
         tro_name=tro_name,
         tro_description=tro_description,
+        extra_context=extra_context or None,
     )
     if from_snapshot:
         tro.add_arrangement_from_snapshot(from_snapshot, comment=comment)
@@ -430,11 +465,13 @@ def performance_add(ctx, comment, start, end, attribute, accessed, modified):
     gpg_fingerprint = ctx.params.get("gpg_fingerprint")
     gpg_passphrase = ctx.params.get("gpg_passphrase")
     profile = ctx.params.get("profile")
+    extra_context = ctx.params.get("extra_context") or []
     tro = TRO(
         filepath=declaration,
         gpg_fingerprint=gpg_fingerprint,
         gpg_passphrase=gpg_passphrase,
         profile=profile,
+        extra_context=extra_context or None,
     )
     tro.add_performance(
         start,

tro_utils/models/tro.py

@@ -56,6 +56,7 @@ class TransparentResearchObject(TROVModel):
     arrangements: list[ArtifactArrangement] = field(default_factory=list)
     performances: list[TrustedResearchPerformance] = field(default_factory=list)
     attributes: list[TROAttribute] = field(default_factory=list)
+    extra_context: list[dict] = field(default_factory=list)
 
     # ------------------------------------------------------------------
     # File I/O
@@ -326,7 +327,7 @@ def to_jsonld(self) -> dict[str, Any]:
                 graph_node["trov:hasPerformance"][i].update(extra)
 
         return {
-            "@context": _JSONLD_CONTEXT,
+            "@context": _JSONLD_CONTEXT + self.extra_context,
             "@graph": [graph_node],
         }
 
@@ -345,6 +346,9 @@ def from_jsonld(cls, data: dict[str, Any]) -> "TransparentResearchObject":
         """
         graph = data["@graph"][0]
 
+        raw_context = data.get("@context", [])
+        extra_context = list(raw_context[1:]) if isinstance(raw_context, list) else []
+
         vocab_version = Version(graph.get("trov:vocabularyVersion", "0.0.1"))
         if vocab_version < TROV_VOCABULARY_VERSION:
             raise RuntimeError(
@@ -417,4 +421,5 @@ def from_jsonld(cls, data: dict[str, Any]) -> "TransparentResearchObject":
             arrangements=arrangements,
             performances=performances,
             attributes=attributes,
+            extra_context=extra_context,
         )

tro_utils/tro_utils.py

@@ -44,6 +44,7 @@ def __init__(
         tro_creator=None,
         tro_name=None,
         tro_description=None,
+        extra_context=None,
     ):
         if filepath is None:
             self.basename = "some_tro"
@@ -80,6 +81,9 @@ def __init__(
         else:
             self._model = TransparentResearchObject.load(self.tro_filename)
 
+        if extra_context:
+            self._model.extra_context.extend(extra_context)
+
         self.gpg = gnupg.GPG(gnupghome=GPG_HOME, verbose=False)
         if gpg_fingerprint:
             self.gpg_key_id = self.gpg.list_keys().key_map[gpg_fingerprint]["keyid"]