Skip tests on HTTP 403 from remote APIs

Add a `skip_on_forbidden` decorator to gracefully handle HTTP 403 Forbidden responses from remote APIs in CI environments where outbound requests may be blocked. This prevents environment-based failures from being reported as test failures.

The decorator walks the exception chain to detect 403 responses across different API wrapper types, emits a warning, and skips the test rather than failing it. Applied to all remote test methods in test_composer.py and test_fetcher.py.

Author: JR-1991

tests/integration/test_composer.py

@@ -1,9 +1,11 @@
 import pytest
 import pyenzyme as pe
 from pyenzyme.tools import to_dict_wo_json_ld
+from tests.utils import skip_on_forbidden
 
 
 class TestComposer:
+    @skip_on_forbidden
     def test_compose(self):
         # Act
         doc = pe.compose(
@@ -23,6 +25,7 @@ def test_compose(self):
         expected_doc = pe.read_enzymeml("tests/fixtures/compose/expected_compose.json")
         assert to_dict_wo_json_ld(doc) == to_dict_wo_json_ld(expected_doc)
 
+    @skip_on_forbidden
     def test_compose_with_prefix(self):
         # Act
         doc = pe.compose(
@@ -42,6 +45,7 @@ def test_compose_with_prefix(self):
         expected_doc = pe.read_enzymeml("tests/fixtures/compose/expected_compose.json")
         assert to_dict_wo_json_ld(doc) == to_dict_wo_json_ld(expected_doc)
 
+    @skip_on_forbidden
     def test_compose_no_vessel(self):
         # Act
         doc = pe.compose(

tests/integration/test_fetcher.py

@@ -6,10 +6,12 @@
 from pyenzyme.fetcher.pubchem import fetch_pubchem
 from pyenzyme.fetcher.rhea import fetch_rhea
 from pyenzyme.fetcher.uniprot import fetch_uniprot
+from tests.utils import skip_on_forbidden
 
 
 class TestFetcher:
     @pytest.mark.remote
+    @skip_on_forbidden
     def test_fetch_chebi_to_small_molecule(self):
         small_molecule = fetch_chebi("CHEBI:15377")
         assert small_molecule is not None
@@ -26,6 +28,7 @@ def test_fetch_chebi_to_small_molecule(self):
         )
 
     @pytest.mark.remote
+    @skip_on_forbidden
     def test_fetch_chebi_to_small_molecule_with_id(self):
         small_molecule = fetch_chebi("CHEBI:15377", smallmol_id="s1")
         assert small_molecule is not None
@@ -42,11 +45,13 @@ def test_fetch_chebi_to_small_molecule_with_id(self):
         )
 
     @pytest.mark.remote
+    @skip_on_forbidden
     def test_fetch_chebi_to_small_molecule_invalid_id(self):
         with pytest.raises(ValueError):
             fetch_chebi("INVALID_ID")
 
     @pytest.mark.remote
+    @skip_on_forbidden
     def test_fetch_uniprot_to_protein(self):
         protein = fetch_uniprot("P07327")
         assert protein is not None
@@ -64,6 +69,7 @@ def test_fetch_uniprot_to_protein(self):
         assert protein.references[0] == "https://www.uniprot.org/uniprotkb/P07327"
 
     @pytest.mark.remote
+    @skip_on_forbidden
     def test_fetch_uniprot_to_protein_with_prefix(self):
         protein = fetch_uniprot("uniprot:P07327")
         assert protein is not None
@@ -81,6 +87,7 @@ def test_fetch_uniprot_to_protein_with_prefix(self):
         assert protein.references[0] == "https://www.uniprot.org/uniprotkb/P07327"
 
     @pytest.mark.remote
+    @skip_on_forbidden
     def test_fetch_uniprot_to_protein_with_id(self):
         protein = fetch_uniprot("P07327", protein_id="p1")
         assert protein is not None
@@ -98,6 +105,7 @@ def test_fetch_uniprot_to_protein_with_id(self):
         assert protein.references[0] == "https://www.uniprot.org/uniprotkb/P07327"
 
     @pytest.mark.remote
+    @skip_on_forbidden
     def test_fetch_rhea_to_reaction(self):
         reaction, small_molecules = fetch_rhea("RHEA:22864")
 
@@ -124,11 +132,13 @@ def test_fetch_rhea_to_reaction(self):
         assert reaction.products[0].species_id == small_molecules[0].id
 
     @pytest.mark.remote
+    @skip_on_forbidden
     def test_fetch_rhea_to_reaction_invalid_id(self):
         with pytest.raises(ValueError):
             fetch_rhea("INVALID_ID")
 
     @pytest.mark.remote
+    @skip_on_forbidden
     def test_fetch_pubchem_to_small_molecule(self):
         small_molecule = fetch_pubchem(cid="2244")
         assert small_molecule is not None
@@ -142,6 +152,7 @@ def test_fetch_pubchem_to_small_molecule(self):
         )
 
     @pytest.mark.remote
+    @skip_on_forbidden
     def test_fetch_pubchem_to_small_molecule_with_prefix(self):
         small_molecule = fetch_pubchem(cid="pubchem:2244")
         assert small_molecule is not None
@@ -155,11 +166,13 @@ def test_fetch_pubchem_to_small_molecule_with_prefix(self):
         )
 
     @pytest.mark.remote
+    @skip_on_forbidden
     def test_fetch_pubchem_to_small_molecule_invalid_id(self):
         with pytest.raises(httpx.HTTPStatusError):
             fetch_pubchem(cid="162176127617627")
 
     @pytest.mark.remote
+    @skip_on_forbidden
     def test_fetch_pdb_to_protein(self):
         protein = fetch_pdb("1a23")
         assert protein is not None
@@ -174,6 +187,7 @@ def test_fetch_pdb_to_protein(self):
         )
 
     @pytest.mark.remote
+    @skip_on_forbidden
     def test_fetch_pdb_to_protein_with_prefix(self):
         protein = fetch_pdb("pdb:1a23")
         assert protein is not None
@@ -188,6 +202,7 @@ def test_fetch_pdb_to_protein_with_prefix(self):
         )
 
     @pytest.mark.remote
+    @skip_on_forbidden
     def test_fetch_pdb_to_protein_invalid_id(self):
         with pytest.raises(ValueError):
             fetch_pdb("INVALID_ID")

tests/utils.py

@@ -0,0 +1,57 @@
+"""Test helpers shared across the integration suite."""
+
+import functools
+import warnings
+
+import pytest
+
+
+def _is_forbidden(exc: BaseException) -> bool:
+    """Return True if ``exc`` (or anything in its cause/context chain) represents
+    an HTTP 403 Forbidden response.
+
+    The fetchers wrap remote errors in different ways (``httpx.HTTPStatusError``,
+    ``requests`` errors, ``ChEBIError``, ``ConnectionError``, ``ValueError`` …),
+    so we walk the whole exception chain and check both the response status code
+    and the string representation.
+    """
+    seen: set[int] = set()
+    while exc is not None and id(exc) not in seen:
+        seen.add(id(exc))
+
+        response = getattr(exc, "response", None)
+        if getattr(response, "status_code", None) == 403:
+            return True
+
+        message = str(exc)
+        if "403" in message or "Forbidden" in message:
+            return True
+
+        exc = exc.__cause__ or exc.__context__
+
+    return False
+
+
+def skip_on_forbidden(func):
+    """Skip a remote test (with a warning) when the remote API returns HTTP 403.
+
+    Some databases block outbound requests from CI, which surfaces as a 403
+    Forbidden. That is an environment restriction, not a genuine test failure,
+    so we emit a warning and skip the test rather than fail it.
+    """
+
+    @functools.wraps(func)
+    def wrapper(*args, **kwargs):
+        try:
+            return func(*args, **kwargs)
+        except Exception as exc:
+            if _is_forbidden(exc):
+                warnings.warn(
+                    f"'{func.__name__}' received HTTP 403 Forbidden from a remote "
+                    f"API (likely blocked in this environment); skipping.",
+                    stacklevel=2,
+                )
+                pytest.skip(f"Remote API returned 403 Forbidden for {func.__name__}")
+            raise
+
+    return wrapper