Fix: curl manifest futilely includes external LungMAP files (#8027)

src/azul/service/index_service.py

@@ -29,6 +29,10 @@
     CatalogName,
     config,
 )
+from azul.drs import (
+    CompactDRSURI,
+    DRSURI,
+)
 from azul.filters import (
     Filters,
 )
@@ -86,16 +90,30 @@ def prepare_request(self, request: Search) -> Search:
         return request
 
     def _file_url(self, *, uuid: str, version: str, drs_uri: str | None) -> str | None:
+        # FIXME: Redundant implementations of file URLs and mirror URIs
+        #        https://github.com/DataBiosphere/azul/issues/8042
         if drs_uri is None:
             # To download a file we need its DRS URI
             return None
+        elif (
+            config.catalogs[self.catalog].atlas == 'lungmap'
+            and isinstance(DRSURI.parse(drs_uri), CompactDRSURI)
+        ):
+            # LungMAP contains fles not hosted on TDR. Downloading these files
+            # requires authentication that can't be provided by Azul, rendering
+            # our file URLs non-functional. If a user tries to follow such a
+            # URL, the request fails with a 401 status, so we avoid exposing
+            # them wherever possible.
+            return None
         else:
             return str(self.file_url_func(catalog=self.catalog,
                                           fetch=False,
                                           file_uuid=uuid,
                                           version=version))
 
     def _file_mirror_uri(self, source: SourceRef, file: JSON) -> str | None:
+        # FIXME: Redundant implementations of file URLs and mirror URIs
+        #        https://github.com/DataBiosphere/azul/issues/8042
         file_cls = self.plugin.file_class
         mirror_service = self.service.mirror_service(self.catalog)
         return mirror_service.mirror_uri(source, file_cls, file)

src/azul/service/manifest_service.py

@@ -87,6 +87,10 @@
 from azul.deployment import (
     aws,
 )
+from azul.drs import (
+    CompactDRSURI,
+    DRSURI,
+)
 from azul.field_type import (
     FieldType,
     FieldTypes,
@@ -1139,9 +1143,21 @@ def _azul_file_url(self,
                        file: JSON,
                        args: Mapping = frozendict()
                        ) -> str | None:
+        # FIXME: Redundant implementations of file URLs and mirror URIs
+        #        https://github.com/DataBiosphere/azul/issues/8042
         if file['drs_uri'] is None:
             # To download a file we need its DRS URI
             return None
+        elif (
+            config.catalogs[self.catalog].atlas == 'lungmap'
+            and isinstance(DRSURI.parse(json_str(file['drs_uri'])), CompactDRSURI)
+        ):
+            # LungMAP contains files not hosted on TDR. Downloading these files
+            # requires authentication that can't be provided by Azul, rendering
+            # our file URLs non-functional. If a user tries to follow such a
+            # URL, the request fails with a 401 status, so we avoid exposing
+            # them wherever possible.
+            return None
         else:
             special_fields = self.metadata_plugin.special_fields
             return str(self.file_url_func(catalog=self.catalog,
@@ -1151,6 +1167,8 @@ def _azul_file_url(self,
                                           **args))
 
     def _azul_mirror_uri(self, source: SourceRef, file: JSON) -> str | None:
+        # FIXME: Redundant implementations of file URLs and mirror URIs
+        #        https://github.com/DataBiosphere/azul/issues/8042
         file_cls = self.metadata_plugin.file_class
         return self.mirror_service.mirror_uri(source, file_cls, file)
 

src/azul/service/query_service.py

@@ -20,7 +20,7 @@
     Self,
 )
 
-import attr
+import attrs
 from furl import (
     furl,
 )
@@ -119,7 +119,7 @@ def process_response(self, response: R1) -> R2:
         raise NotImplementedError
 
 
-@attr.s(frozen=True, auto_attribs=True, kw_only=True)
+@attrs.frozen(kw_only=True)
 class OpenSearchChain[R0, R1, R2](OpenSearchStage[R0, R2]):
     """
     The result of wrapping a stage or chain in another stage.
@@ -150,7 +150,7 @@ def stages(self) -> Iterable[OpenSearchStage]:
             yield self.inner
 
 
-@attr.s(frozen=True, auto_attribs=True, kw_only=True)
+@attrs.frozen(kw_only=True)
 class _OpenSearchStage[R1, R2](OpenSearchStage[R1, R2], metaclass=ABCMeta):
     """
     A base implementation of a stage.
@@ -170,7 +170,7 @@ def wrap[R0](self, other: OpenSearchStage[R0, R1]) -> OpenSearchChain[R0, R1, R2
 TranslatedFilters = Mapping[FieldPath, Mapping[str, Sequence[PrimitiveJSON]]]
 
 
-@attr.s(frozen=True, auto_attribs=True, kw_only=True)
+@attrs.frozen(kw_only=True)
 class FilterStage(_OpenSearchStage[Response, Response]):
     """
     Converts the given filters to an OpenSearch query and adds that query as
@@ -268,7 +268,7 @@ def prepare_query(self, skip_field_paths: tuple[FieldPath] = ()) -> Query:
         return Q('bool', must=query_list)
 
 
-@attr.s(frozen=True, auto_attribs=True, kw_only=True)
+@attrs.frozen(kw_only=True)
 class AggregationStage(_OpenSearchStage[MutableJSON, MutableJSON]):
     """
     Cooperate with the given filter stage to augment the request with an
@@ -421,7 +421,7 @@ def _populate_accessible(self, aggs: MutableJSON) -> None:
         aggs[special_fields.accessible.name] = agg
 
 
-@attr.s(frozen=True, auto_attribs=True, kw_only=True)
+@attrs.frozen(kw_only=True)
 class SlicingStage(_OpenSearchStage[Response, Response]):
     """
     Augments the request with a document slice (known as a *source filter* in
@@ -450,7 +450,7 @@ def _prepared_slice(self) -> DocumentSlice | None:
 # FIXME: Elminate Eliminate reliance on Elasticsearch DSL
 #        https://github.com/DataBiosphere/azul/issues/4111
 
-@attr.s(frozen=True, auto_attribs=True, kw_only=True)
+@attrs.frozen(kw_only=True)
 class ToDictStage(_OpenSearchStage[Response, MutableJSON]):
 
     def prepare_request(self, request: Search) -> Search:
@@ -477,7 +477,7 @@ def sort_key_to_json(s: SortKey) -> AnyJSON:
     return list(s)
 
 
-@attr.s(auto_attribs=True, kw_only=True, frozen=True)
+@attrs.frozen(kw_only=True)
 class Pagination:
     order: str
     size: int
@@ -490,9 +490,9 @@ def advance(self,
                 search_before: SortKey | None,
                 search_after: SortKey | None
                 ) -> Self:
-        return attr.evolve(self,
-                           search_before=search_before,
-                           search_after=search_after)
+        return attrs.evolve(self,
+                            search_before=search_before,
+                            search_after=search_after)
 
     def link(self, *, previous: bool, **params: str) -> furl | None:
         """
@@ -521,7 +521,7 @@ class ResponsePagination(JSONTypedDict):
 ResponseTriple = tuple[JSONs, ResponsePagination, JSON]
 
 
-@attr.s(frozen=True, auto_attribs=True, kw_only=True)
+@attrs.frozen(kw_only=True)
 class PaginationStage(_OpenSearchStage[JSON, ResponseTriple]):
     """
     Handles the pagination of search results

test/azul_test_case.py

@@ -19,6 +19,7 @@
 from typing import (
     Callable,
     Iterable,
+    Mapping,
     Optional,
 )
 from unittest import (
@@ -54,6 +55,9 @@
 from azul.deployment import (
     aws,
 )
+from azul.lib.types import (
+    JSON,
+)
 from azul.logging import (
     configure_test_logging,
     get_test_logger,
@@ -509,6 +513,13 @@ def _patch_source_cache(cls):
         )
         cls.addClassPatch(patch_source_cache(hit=[cls.source.ref.id]))
 
+    @classmethod
+    def _source_config(cls) -> Mapping[str, JSON]:
+        return {
+            str(source.ref.spec): source.config.to_json()
+            for source in cls._sources()
+        }
+
 
 class DCP2TestCase(TDRTestCase):
     source = Source(
@@ -522,18 +533,39 @@ class DCP2TestCase(TDRTestCase):
 
     @classmethod
     def catalog_config(cls) -> dict[CatalogName, Config.Catalog]:
-        sources = {
-            str(source.ref.spec): source.config.to_json()
-            for source in cls._sources()
-        }
         return {
             cls.catalog: config.Catalog(name=cls.catalog,
                                         atlas='hca',
                                         internal=False,
                                         mirror_limit=None,
                                         plugins=dict(metadata=config.Catalog.Plugin(name='hca'),
                                                      repository=config.Catalog.Plugin(name='tdr_hca')),
-                                        sources=sources)
+                                        sources=cls._source_config())
+        }
+
+
+class LungmapTestCase(TDRTestCase):
+    source_spec = ('tdr:bigquery:gcp:datarepo-dev-5d9526e0:'
+                   'lungmap_dev_1bdcecde16be420888f478cd2133d11d__20220401_20220404')
+    source = Source(
+        config=SourceConfig(mirror=False),
+        ref=TDRSourceRef(
+            id='96c6482b-7949-4d6e-894b-371149e85134',
+            spec=TDRSourceSpec.parse(source_spec),
+            prefix=Prefix.of_everything
+        )
+    )
+
+    @classmethod
+    def catalog_config(cls) -> dict[CatalogName, Config.Catalog]:
+        return {
+            cls.catalog: config.Catalog(name=cls.catalog,
+                                        atlas='lungmap',
+                                        internal=False,
+                                        mirror_limit=-1,
+                                        plugins=dict(metadata=config.Catalog.Plugin(name='hca'),
+                                                     repository=config.Catalog.Plugin(name='tdr_hca')),
+                                        sources=cls._source_config())
         }
 
 
@@ -549,15 +581,14 @@ class AnvilTestCase(TDRTestCase):
 
     @classmethod
     def catalog_config(cls) -> dict[CatalogName, Config.Catalog]:
-        sources = {str(cls.source.ref.spec): cls.source.config.to_json()}
         return {
             cls.catalog: config.Catalog(name=cls.catalog,
                                         atlas='anvil',
                                         internal=False,
                                         mirror_limit=None,
                                         plugins=dict(metadata=config.Catalog.Plugin(name='anvil'),
                                                      repository=config.Catalog.Plugin(name='tdr_anvil')),
-                                        sources=sources)
+                                        sources=cls._source_config())
         }