Merge branch 'main' into metadata-passthrough

README.md

@@ -147,6 +147,8 @@ semantica doctor
 # Config file           pass    ~/.semantica/config.yaml
 ```
 
+**Running in a script or CI?** Progress bars are written only when stdout is an interactive terminal (or a Jupyter notebook), so piping and redirecting stay clean by default. Override with `SEMANTICA_DISABLE_PROGRESS=1` to silence progress everywhere, or `SEMANTICA_FORCE_PROGRESS=1` to keep it when stdout is redirected. `SEMANTICA_DISABLE_PROGRESS` takes precedence.
+
 <div align="center">
 
 If Semantica solves a real problem for you, a star helps others find it.
@@ -1561,11 +1563,11 @@ On-premises deployment · Private cloud · Custom domain implementations · SLA-
 
 ## Star History
 
-<a href="https://www.star-history.com/?repos=semantica-agi%2Fsemantica&type=date&legend=top-left">
+<a href="https://star-history.dera.page/#semantica-agi/semantica&amp;type=date&amp;legend=top-left">
  <picture>
-   <source media="(prefers-color-scheme: dark)" srcset="https://api.star-history.com/chart?repos=semantica-agi/semantica&type=date&theme=dark&legend=top-left" />
+   <source media="(prefers-color-scheme: dark)" srcset="https://star-history.dera.page/svg?repos=semantica-agi/semantica&amp;type=date&amp;theme=dark&amp;legend=top-left" />
-   <source media="(prefers-color-scheme: light)" srcset="https://api.star-history.com/chart?repos=semantica-agi/semantica&type=date&legend=top-left" />
+   <source media="(prefers-color-scheme: light)" srcset="https://star-history.dera.page/svg?repos=semantica-agi/semantica&amp;type=date&amp;legend=top-left" />
-   <img alt="Star History Chart" src="https://api.star-history.com/chart?repos=semantica-agi/semantica&type=date&legend=top-left" />
+   <img alt="Star History Chart" src="https://star-history.dera.page/svg?repos=semantica-agi/semantica&amp;type=date&amp;legend=top-left" />
  </picture>
 </a>
 

docs/reference/triplet_store.md

@@ -182,7 +182,7 @@ for row in result.bindings:
     store = TripletStore(
         backend="rdf4j",
         endpoint="http://localhost:8080/rdf4j-server",
-        repository_id="semantica",   # passed through **config
+        repository_id="semantica",   # selects the remote repository
     )
     ```
 

docs/reference/utils.md

@@ -77,7 +77,17 @@ Most users won't call utils directly: it's the **shared foundation** for all mod
     export SEMANTICA_LOG_LEVEL=DEBUG
     export SEMANTICA_LOG_FORMAT=json     # "json" | "text"
     export SEMANTICA_DISABLE_PROGRESS=true
+    export SEMANTICA_FORCE_PROGRESS=true
     ```
+
+    <Tip>
+      **Progress bars follow your terminal.** Console progress is written only when
+      stdout is an interactive terminal (or a Jupyter notebook), so piping or
+      redirecting output no longer fills logs with progress bars and escape
+      sequences. Set `SEMANTICA_DISABLE_PROGRESS` to silence progress even in a
+      terminal, or `SEMANTICA_FORCE_PROGRESS` to keep it when stdout is redirected.
+      `SEMANTICA_DISABLE_PROGRESS` wins if both are set.
+    </Tip>
   </Step>
 </Steps>
 

docs/storage-backends.md

@@ -35,7 +35,7 @@ This page is intentionally conservative: it distinguishes between an adapter exi
 | FalkorDB | LPG | Yes | Yes | Partial | Partial | Redis-based; provenance depends on node/edge properties, and multi-graph isolation depends on the selected graph name. |
 | Amazon Neptune | LPG | Yes | Yes | Partial | Partial | Use the property-graph endpoint; AWS auth, VPC, and endpoint configuration can affect local tests. Provenance depends on node/edge properties. |
 | Apache AGE | LPG | Yes | Yes | Partial | Partial | Runs through PostgreSQL/AGE; Cypher compatibility and property handling can differ from standalone LPG engines. |
-| RDF4J | RDF | Yes | Partial | Partial | Partial | Context separation relies on named graphs; triple-level provenance may require reification or graph-level metadata. `RDF4JStore(repository_id=...)` currently has no effect — the constructor always connects to the `"default"` repository regardless of the value passed; track a fix separately. |
+| RDF4J | RDF | Yes | Partial | Partial | Partial | Context separation relies on named graphs; triple-level provenance may require reification or graph-level metadata. |
 | Apache Jena | RDF | Yes | Partial | Partial | Partial | Named graphs are needed for context separation; backend configuration and transaction behavior matter. |
 | Blazegraph | RDF | Yes | Partial | Partial | Partial | Use quads/named graphs for context; IRI stability and graph naming matter for provenance. |
 | Anzo | RDF | Yes | Partial | Partial | Partial | Anzo deployments are environment-specific; validate `dataset_uri`/graphmart naming, named-graph support, and provenance mapping. |
@@ -107,7 +107,7 @@ from semantica.triplet_store import RDF4JStore
 
 store = RDF4JStore(
     endpoint='http://localhost:8080/rdf4j-server',
-    repository_id='semantica'  # currently has no effect; connects to "default" (see Known limitations)
+    repository_id='semantica'
 )
 ```
 

semantica/triplet_store/rdf4j_store.py

@@ -28,7 +28,7 @@ License: MIT
 
 import re
 from typing import Any, Dict, List, Optional
-from urllib.parse import urlparse
+from urllib.parse import quote, urlparse
 
 import requests
 from rdflib import Graph, Literal
@@ -67,7 +67,8 @@ class RDF4JStore:
             self.progress_tracker.enabled = True
 
         self.endpoint = endpoint.rstrip("/")
-        self.repository_id = config.get("repository_id", "default")
+        self.repository_id = repository_id or config.get("repository_id", "default")
+        self._encoded_repository_id = quote(self.repository_id, safe="")
         self.username = config.get("username")
         self.password = config.get("password")
         self.timeout = config.get("timeout", 30)
@@ -79,7 +80,7 @@ class RDF4JStore:
         """Connect to RDF4J server."""
         try:
             # Test connection
-            test_url = f"{self.endpoint}/repositories/{self.repository_id}"
+            test_url = f"{self.endpoint}/repositories/{self._encoded_repository_id}"
             response = requests.get(
                 test_url,
                 timeout=self.timeout,
@@ -100,11 +101,11 @@ class RDF4JStore:
 
     def _get_sparql_endpoint(self) -> str:
         """Get SPARQL query endpoint."""
-        return f"{self.endpoint}/repositories/{self.repository_id}"
+        return f"{self.endpoint}/repositories/{self._encoded_repository_id}"
 
     def _get_update_endpoint(self) -> str:
         """Get SPARQL Update endpoint."""
-        return f"{self.endpoint}/repositories/{self.repository_id}/statements"
+        return f"{self.endpoint}/repositories/{self._encoded_repository_id}/statements"
 
     def _is_construct_query(self, query: str) -> bool:
         """
@@ -163,7 +164,7 @@ class RDF4JStore:
         """
         # RDF4J transaction support
         transaction_url = (
-            f"{self.endpoint}/repositories/{self.repository_id}/transactions"
+            f"{self.endpoint}/repositories/{self._encoded_repository_id}/transactions"
         )
 
         try:

semantica/utils/progress_tracker.py

@@ -64,6 +64,29 @@ def _progress_disabled_from_env() -> bool:
         "on",
     )
 
+
+def _progress_forced_from_env() -> bool:
+    """Return whether console progress is forced on despite a non-interactive stdout."""
+    return os.getenv("SEMANTICA_FORCE_PROGRESS", "").strip().lower() in (
+        "1",
+        "true",
+        "yes",
+        "on",
+    )
+
+
+def _stdout_is_tty() -> bool:
+    """Return whether stdout is an interactive terminal.
+
+    Replacement streams do not always implement ``isatty`` and closed streams can
+    raise, so both cases are treated as non-interactive.
+    """
+    try:
+        return bool(sys.stdout is not None and sys.stdout.isatty())
+    except (AttributeError, ValueError):
+        return False
+
+
 # Try to import IPython for Jupyter support
 try:
     from IPython import get_ipython
@@ -1040,18 +1063,24 @@ class ProgressTracker:
         # Create displays
         self.displays: List[ProgressDisplay] = []
 
+        # Console output only suits an interactive stdout. When output is piped or
+        # redirected (scripts, CI logs) the progress bars and their escape
+        # sequences would otherwise drown the program's own output.
+        console_ok = _stdout_is_tty() or self.is_jupyter or _progress_forced_from_env()
+
         # Always try Jupyter first if available, fallback to console
         if IPYTHON_AVAILABLE:
             # Try to detect Jupyter - if available, use it
             if self.is_jupyter and not self.disable_jupyter_progress:
                 self.displays.append(JupyterProgressDisplay(use_emoji=use_emoji))
             # Also add console as fallback for immediate feedback
+            if console_ok:
                 self.displays.append(
                     ConsoleProgressDisplay(
                         use_emoji=use_emoji, update_interval=update_interval
                     )
                 )
-        else:
+        elif console_ok:
             self.displays.append(
                 ConsoleProgressDisplay(
                     use_emoji=use_emoji, update_interval=update_interval

tests/test_progress_tracker_regressions.py

@@ -12,6 +12,7 @@ import semantica.utils.progress_tracker as progress_module
 @pytest.fixture(autouse=True)
 def reset_progress_singletons(monkeypatch):
     monkeypatch.delenv("SEMANTICA_DISABLE_PROGRESS", raising=False)
+    monkeypatch.delenv("SEMANTICA_FORCE_PROGRESS", raising=False)
     progress_module.ProgressTracker._instance = None
     progress_module._global_tracker = None
     yield
@@ -19,6 +20,40 @@ def reset_progress_singletons(monkeypatch):
     progress_module._global_tracker = None
 
 
+class _FakeStdout:
+    """Minimal stdout stand-in with controllable TTY reporting."""
+
+    encoding = "utf-8"
+
+    def __init__(self, tty):
+        self._tty = tty
+        self.written = []
+
+    def isatty(self):
+        return self._tty
+
+    def write(self, text):
+        self.written.append(text)
+        return len(text)
+
+    def flush(self):
+        pass
+
+
+def _use_stdout(monkeypatch, tty):
+    """Point sys.stdout at a fake with the given TTY behaviour, outside Jupyter."""
+    stream = _FakeStdout(tty=tty)
+    monkeypatch.setattr(sys, "stdout", stream)
+    monkeypatch.setattr(
+        progress_module.ProgressTracker, "_detect_jupyter", lambda *_: False
+    )
+    return stream
+
+
+def _displays_of(tracker, display_cls):
+    return [d for d in tracker.displays if isinstance(d, display_cls)]
+
+
 def _install_tracker_as_singleton(tracker: progress_module.ProgressTracker) -> None:
     progress_module.ProgressTracker._instance = tracker
     progress_module._global_tracker = tracker
@@ -100,6 +135,67 @@ def test_disable_progress_env_prevents_reenable(monkeypatch):
     assert tracker.start_tracking(module="core", submodule="test") == ""
 
 
+def test_console_display_omitted_when_stdout_is_not_a_tty(monkeypatch):
+    _use_stdout(monkeypatch, tty=False)
+
+    tracker = progress_module.ProgressTracker(use_emoji=False, update_interval=0)
+
+    assert _displays_of(tracker, progress_module.ConsoleProgressDisplay) == []
+
+
+def test_console_display_present_when_stdout_is_a_tty(monkeypatch):
+    _use_stdout(monkeypatch, tty=True)
+
+    tracker = progress_module.ProgressTracker(use_emoji=False, update_interval=0)
+
+    assert _displays_of(tracker, progress_module.ConsoleProgressDisplay)
+
+
+def test_file_display_survives_non_tty_stdout(monkeypatch):
+    _use_stdout(monkeypatch, tty=False)
+
+    tracker = progress_module.ProgressTracker(use_emoji=False, update_interval=0)
+
+    assert _displays_of(tracker, progress_module.FileProgressDisplay)
+
+
+def test_force_progress_env_restores_console_display_on_non_tty(monkeypatch):
+    monkeypatch.setenv("SEMANTICA_FORCE_PROGRESS", "1")
+    _use_stdout(monkeypatch, tty=False)
+
+    tracker = progress_module.ProgressTracker(use_emoji=False, update_interval=0)
+
+    assert _displays_of(tracker, progress_module.ConsoleProgressDisplay)
+
+
+def test_disable_progress_env_beats_force_progress_env(monkeypatch):
+    monkeypatch.setenv("SEMANTICA_DISABLE_PROGRESS", "1")
+    monkeypatch.setenv("SEMANTICA_FORCE_PROGRESS", "1")
+    stream = _use_stdout(monkeypatch, tty=False)
+
+    tracker = progress_module.ProgressTracker(use_emoji=False, update_interval=0)
+    _install_tracker_as_singleton(tracker)
+
+    assert tracker.enabled is False
+    assert tracker.start_tracking(module="core", submodule="test") == ""
+    assert stream.written == []
+
+
+def test_non_tty_stdout_stays_silent_after_module_reenables_tracker(monkeypatch):
+    stream = _use_stdout(monkeypatch, tty=False)
+    tracker = progress_module.ProgressTracker(use_emoji=False, update_interval=0)
+    _install_tracker_as_singleton(tracker)
+
+    # Mirrors the ~20 modules that do `self.progress_tracker.enabled = True`.
+    tracker.enabled = True
+    tracking_id = tracker.start_tracking(
+        module="core", submodule="Semantica", message="Building"
+    )
+    tracker.update_progress(tracking_id, processed=1, total=1, message="Processing")
+
+    assert stream.written == []
+
+
 def test_build_knowledge_base_subprocess_does_not_deadlock():
     root = Path(__file__).resolve().parents[1]
     runtime_dir = root / "test_data" / "runtime" / f"build-regression-{os.getpid()}"

tests/triplet_store/test_rdf4j_store.py

@@ -22,6 +22,71 @@ def _make_connected_store():
 CONSTRUCT_QUERY = "CONSTRUCT { ?s ?p ?o } WHERE { ?s ?p ?o }"
 
 
+class TestRDF4JStoreInitialization(unittest.TestCase):
+
+    def test_explicit_repository_id_selects_repository(self):
+        response = MagicMock(status_code=200)
+
+        with patch(
+            "semantica.triplet_store.rdf4j_store.requests.get",
+            return_value=response,
+        ) as mock_get:
+            store = RDF4JStore(
+                endpoint="http://localhost:8080/rdf4j-server/",
+                repository_id="semantica",
+            )
+
+        self.assertEqual(store.repository_id, "semantica")
+        mock_get.assert_called_once_with(
+            "http://localhost:8080/rdf4j-server/repositories/semantica",
+            timeout=30,
+            auth=None,
+        )
+
+    def test_repository_id_is_encoded_as_a_single_url_path_segment(self):
+        response = MagicMock(status_code=200)
+
+        with patch(
+            "semantica.triplet_store.rdf4j_store.requests.get",
+            return_value=response,
+        ) as mock_get:
+            store = RDF4JStore(
+                endpoint="http://localhost:8080/rdf4j-server",
+                repository_id="team/repo ?#",
+            )
+
+        self.assertEqual(store.repository_id, "team/repo ?#")
+        mock_get.assert_called_once_with(
+            "http://localhost:8080/rdf4j-server/repositories/team%2Frepo%20%3F%23",
+            timeout=30,
+            auth=None,
+        )
+        self.assertEqual(
+            store._get_sparql_endpoint(),
+            "http://localhost:8080/rdf4j-server/repositories/team%2Frepo%20%3F%23",
+        )
+        self.assertEqual(
+            store._get_update_endpoint(),
+            "http://localhost:8080/rdf4j-server/repositories/"
+            "team%2Frepo%20%3F%23/statements",
+        )
+
+        transaction_response = MagicMock()
+        transaction_response.headers = {"Location": "/transactions/tx-1"}
+        with patch(
+            "semantica.triplet_store.rdf4j_store.requests.post",
+            return_value=transaction_response,
+        ) as mock_post:
+            self.assertEqual(store.begin_transaction(), "tx-1")
+
+        mock_post.assert_called_once_with(
+            "http://localhost:8080/rdf4j-server/repositories/"
+            "team%2Frepo%20%3F%23/transactions",
+            timeout=30,
+            auth=None,
+        )
+
+
 class TestRDF4JStoreIsConstructQuery(unittest.TestCase):
     def test_detects_uppercase(self):
         self.assertTrue(_make_connected_store()._is_construct_query(