diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 030af37..f27d3a0 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -13,7 +13,7 @@ repos: - id: mypy exclude: tests|examples args: [--ignore-missing-imports] - additional_dependencies: [types-PyYAML>=6.0.12.20250915] + additional_dependencies: [types-PyYAML>=6.0.12.20250915, types-requests>=2.33.0.20260503] - repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks rev: v2.15.0 hooks: diff --git a/pyproject.toml b/pyproject.toml index 5f3fba1..d92121a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -22,7 +22,9 @@ dependencies = [ "numpy>=2.4.2", "pydantic>=2.12.3", "scipy>=1.17.0", - "styxpodman" + "styxpodman", + "requests>=2.33.1", + "platformdirs>=4.9.6" ] [dependency-groups] @@ -34,7 +36,8 @@ dev = [ "pytest>=9.0.3", "pytest-cov>=7.0.0", "ruff>=0.14.7", - "types-pyyaml>=6.0.12.20250915" + "types-pyyaml>=6.0.12.20250915", + "types-requests>=2.33.0.20260503" ] docs = ["pdoc>=15.0.4"] validate = ["check-jsonschema>=0.37.1"] diff --git a/src/neuromaps_prime/fetcher.py b/src/neuromaps_prime/fetcher.py new file mode 100644 index 0000000..b22cf5b --- /dev/null +++ b/src/neuromaps_prime/fetcher.py @@ -0,0 +1,46 @@ +"""Helpers for grabbing from remote repositories.""" + +from pathlib import Path +from typing import Literal +from urllib.parse import urlparse + +from neuromaps_prime.remote import OSFStorage + + +def id_storage(uri: str) -> Literal["osf"] | None: + """Identify the storage type. + + Args: + uri: Remote URI to fetch data from + + Returns: + String indicating type of storage (one of 'osf') + """ + + def _find_host(storage: str, host: str) -> bool: + return storage == host or host.endswith(storage) + + host = urlparse(uri).hostname + if host is not None: + host = host.lower() + if _find_host(storage="osf.io", host=host): + return "osf" + return None + + +def download_and_validate(uri: str, dest: str | Path) -> None: + """Download and validate the file. + + Args: + uri: Remote URI to fetch data from + dest: Output file path name + token: Optional token to use for remote storage + + Raises: + ValueError: if storage cannot be identified from provided URI + """ + match id_storage(uri): + case "osf": + OSFStorage().download(uri, Path(dest)) + case _: + raise ValueError(f"Could not identify storage from uri: {uri}") diff --git a/src/neuromaps_prime/graph/builder.py b/src/neuromaps_prime/graph/builder.py index b378884..824ceca 100644 --- a/src/neuromaps_prime/graph/builder.py +++ b/src/neuromaps_prime/graph/builder.py @@ -10,11 +10,11 @@ from __future__ import annotations -from pathlib import Path +from pathlib import Path # noqa: TC003 (pydantic req'd) from typing import TYPE_CHECKING, Any, cast import yaml -from pydantic import BaseModel, Field +from pydantic import BaseModel from neuromaps_prime.graph.cache import GraphCache # noqa: TC001 (pydantic req'd) from neuromaps_prime.graph.models import ( @@ -48,7 +48,7 @@ class GraphBuilder(BaseModel): model_config = {"arbitrary_types_allowed": True} cache: GraphCache - data_dir: Path | None = Field(default=None) + data_dir: Path # ------------------------------------------------------------------ # # Public entry points # @@ -201,12 +201,8 @@ def _build_volume_edge( # Generic resource parsers # # ------------------------------------------------------------------ # - def _resolve_path(self, path: str) -> Path: - """Prepend data_dir to path when set, otherwise return as-is.""" - return (self.data_dir / path) if self.data_dir else Path(path) - def _parse_surface_annotations( - self, prefix: str, space: str, density: str, hemispheres: dict[str, Any] + self, prefix: str, space: str, density: str, annots: dict[str, Any] ) -> list[SurfaceAnnotation]: """Parse annotation entries from a surface type block. @@ -214,28 +210,31 @@ def _parse_surface_annotations( prefix: Name prefix derived from space or source/target space pair. space: Space identifier applied to every annotation. density: Density key (e.g. ``"32k"``) shared by all entries in this block. - hemispheres: Dict keyed by label → {hemi: path, ...} with optional + annots: Dict keyed by label → {annot: left, ...} with optional ``"references"`` and ``"notes"`` keys. Returns: List of :class:`SurfaceAnnotation` instances parsed from the block. """ annotations = [] - for label, value in hemispheres.items(): + for annot, value in annots.items(): # Grab references and notes once references = value.get("references") notes = value.get("notes") for hemi, path in value.items(): if hemi in ("notes", "references"): continue + name = f"{prefix}_{density}_{hemi}_{annot}" + ext = "func.gii" if "PC" in annot else "label.gii" annotations.append( SurfaceAnnotation( - name=f"{prefix}_{density}_{hemi}_{label}", + name=name, space=space, - label=label, + label=annot, density=density, hemisphere=hemi, - file_path=self._resolve_path(path), + uri=path, + file_path=self.data_dir / f"{name}.{ext}", references=references, notes=notes, ) @@ -262,8 +261,8 @@ def _parse_surface_entries( density: Density key (e.g. ``"32k"``) shared by all entries in this block. surf_type: Resource type string (e.g. ``"midthickness"``). hemispheres: Dict mapping hemisphere key to file path. - fixed_fields: Fields forwarded verbatim to every instance (e.g. space, - description). + fixed_fields: Dict of fields forwarded verbatim to every instance (e.g. + space, description). provider: Provider string injected for :class:`SurfaceTransform` entries; empty string for atlases. transform_refs: References list attached to the enclosing transform block, @@ -275,8 +274,9 @@ def _parse_surface_entries( extra = {"provider": provider} if cls is SurfaceTransform else {} return [ cls( - name=f"{prefix}_{density}_{hemi}_{surf_type}", - file_path=self._resolve_path(path), + name=(name := f"{prefix}_{density}_{hemi}_{surf_type}"), + uri=path, + file_path=self.data_dir / f"{name}.surf.gii", density=density, hemisphere=hemi, # type: ignore[arg-type] resource_type=surf_type, @@ -398,13 +398,15 @@ def _parse_volume_resources( for vol_type, vol_value in types.items(): if vol_type == "annotation": for annot_key, annot_dict in vol_value.items(): + name = f"{prefix}_{res}_{annot_key}.nii.gz" annotations.append( VolumeAnnotation( - name=f"{prefix}_{res}_{annot_key}", + name=name, space=space, label=annot_key, resolution=res, - file_path=self._resolve_path(annot_dict.get("uri")), + uri=annot_dict.get("uri"), + file_path=self.data_dir / name, references=annot_dict.get("references"), notes=annot_dict.get("notes"), ) @@ -412,10 +414,12 @@ def _parse_volume_resources( continue extra = {"provider": provider} if is_transform else {} + name = f"{prefix}_{res}_{vol_type}" result.append( cls( - name=f"{prefix}_{res}_{vol_type}", - file_path=self._resolve_path(vol_value), + name=name, + uri=vol_value, + file_path=self.data_dir / name, resolution=res, resource_type=vol_type, references=transform_refs, diff --git a/src/neuromaps_prime/graph/core.py b/src/neuromaps_prime/graph/core.py index 53adb3a..c0a47ea 100644 --- a/src/neuromaps_prime/graph/core.py +++ b/src/neuromaps_prime/graph/core.py @@ -10,11 +10,11 @@ from __future__ import annotations -import os from pathlib import Path from typing import Any, Literal import networkx as nx +from platformdirs import user_cache_dir from neuromaps_prime.graph.builder import GraphBuilder from neuromaps_prime.graph.cache import GraphCache @@ -33,6 +33,8 @@ from neuromaps_prime.graph.utils import GraphUtils from neuromaps_prime.niwrap import setup_runner +NEUROMAPS_DATA_DIR = Path(user_cache_dir("neuromaps_prime")) + class NeuromapsGraph(nx.MultiDiGraph): """Multi-directed graph of brain template spaces and their transformations.""" @@ -47,7 +49,7 @@ def __init__( image_overrides: dict[str, str] | None = None, verbose: int = 0, yaml_file: Path | None = None, - data_dir: Path | None = None, + data_dir: Path = NEUROMAPS_DATA_DIR, *, _testing: bool = False, **kwargs, # noqa: ANN003 (ignore annotation for kwargs) @@ -61,8 +63,7 @@ def __init__( image_overrides: Dictionary containing overrides for container tags. yaml_file: Path to the graph definition YAML. Defaults to the bundled ``neuromaps_graph.yaml``. - data_dir: Optional root directory prepended to all relative file - paths in the YAML. + data_dir: Directory to save remote data. Defaults to system cache directory. verbose: Verbosity level (0=WARNING, 1=INFO, 2+=DEBUG) _testing: When ``True``, skip YAML loading (for unit tests). **kwargs: Additional keyword arguments passed for runner setup. @@ -77,11 +78,11 @@ def __init__( **kwargs, ) # Resource locations - self.data_dir = next( - (Path(d) for d in (data_dir, os.getenv("NEUROMAPS_DATA")) if d), None - ) - self.yaml_path = yaml_file + if not data_dir.exists(): + data_dir.mkdir(parents=True, exist_ok=True) # Graph initialization + self.data_dir = data_dir + self.yaml_path = yaml_file self._cache = GraphCache() self.utils = GraphUtils(graph=self, cache=self._cache) self.surface_ops = SurfaceTransformOps(cache=self._cache, utils=self.utils) diff --git a/src/neuromaps_prime/graph/models.py b/src/neuromaps_prime/graph/models.py index 14934f2..fd3e214 100644 --- a/src/neuromaps_prime/graph/models.py +++ b/src/neuromaps_prime/graph/models.py @@ -1,10 +1,15 @@ """Models for resources in the neuromaps_prime graph.""" +import logging from collections.abc import Sequence from pathlib import Path from typing import Literal -from pydantic import BaseModel, Field, field_validator +from pydantic import BaseModel, Field + +from neuromaps_prime.fetcher import download_and_validate + +_logger = logging.getLogger(__name__) class Resource(BaseModel): @@ -13,33 +18,30 @@ class Resource(BaseModel): name: str description: str | None file_path: Path + uri: str | None = None references: Sequence[str | dict[str, str]] | None = None notes: Sequence[str] | None = None - @field_validator("file_path") - @classmethod - def validate_file_path(cls, v: Path) -> Path: - """Validate that the file exists at the given path. - - Args: - v: The file path to validate. - - Returns: - The validated file path. - - Raises: - FileNotFoundError: If the file does not exist. - """ - if not v.exists(): - raise FileNotFoundError(f"File path does not exist: {v}") - return v - def fetch(self) -> Path: - """Return the path to this resource's file. + """Return the path to this resource's file, downloading if necessary. Returns: Path to the resource file. + + Raises: + FileNotFoundError: if file cannot be fetched """ + if self.file_path.exists(): + return self.file_path + if self.uri is None: + raise FileNotFoundError("File does not exist and cannot be fetched.") + if (local_file := Path(self.uri)).exists(): + self.file_path = local_file + else: + _logger.info(f"Fetching {self.file_path.name} from remote server.") + download_and_validate(uri=self.uri, dest=self.file_path) + if not self.file_path.exists(): + raise FileNotFoundError("File does not exist.") return self.file_path def __repr__(self) -> str: diff --git a/src/neuromaps_prime/niwrap.py b/src/neuromaps_prime/niwrap.py index c67829c..c125ef3 100644 --- a/src/neuromaps_prime/niwrap.py +++ b/src/neuromaps_prime/niwrap.py @@ -122,7 +122,7 @@ def setup_runner( logging.DEBUG if verbose >= len(_LOG_LEVELS) - 1 else logging.WARNING ) - neuromaps_prime_logger = logging.getLogger("neuromaps-PRIME") + neuromaps_prime_logger = logging.getLogger("neuromaps_prime") neuromaps_prime_logger.setLevel(_LOG_LEVELS[log_level]) if not neuromaps_prime_logger.handlers: handler = logging.StreamHandler() diff --git a/src/neuromaps_prime/remote/__init__.py b/src/neuromaps_prime/remote/__init__.py new file mode 100644 index 0000000..8c81996 --- /dev/null +++ b/src/neuromaps_prime/remote/__init__.py @@ -0,0 +1,5 @@ +"""Module associated with remote storages.""" + +from .osf import OSFStorage + +__all__ = ["OSFStorage"] diff --git a/src/neuromaps_prime/remote/osf.py b/src/neuromaps_prime/remote/osf.py new file mode 100644 index 0000000..90cbfb5 --- /dev/null +++ b/src/neuromaps_prime/remote/osf.py @@ -0,0 +1,59 @@ +"""Model associated with fetching from OSF storages.""" + +import hashlib +from abc import ABC +from pathlib import Path + +import requests +from pydantic import BaseModel + + +class OSFHashes(BaseModel): + """Model for OSF hashes.""" + + md5: str + sha256: str | None = None + + +class OSFFileExtra(BaseModel): + """Model for alternative storage of OSF hashes.""" + + hashes: OSFHashes + + +class OSFFileMeta(BaseModel): + """Model for file metadata.""" + + name: str + size: int + extra: OSFFileExtra + + +class OSFStorage(BaseModel, ABC): + """Model for OSF storage. + + Note: This currently only works for storages that are publicly accessible. + """ + + chunk_size: int = 8192 + + def get_meta(self, url: str) -> OSFFileMeta: + """Get metadata from remote OSF file.""" + r = requests.get(url, params={"meta": ""}, timeout=90) + r.raise_for_status() + return OSFFileMeta(**r.json()["data"]["attributes"]) + + def download(self, url: str, dest: Path) -> None: + """Download remote OSF file.""" + meta = self.get_meta(url) + r = requests.get(url, stream=True, timeout=90) + r.raise_for_status() + + h = hashlib.md5(usedforsecurity=False) + with dest.open("wb") as f: + for chunk in r.iter_content(self.chunk_size): + f.write(chunk) + h.update(chunk) + + if (actual := h.hexdigest()) != meta.extra.hashes.md5: + raise ValueError(f"Checksum mismatch: {actual} != {meta.extra.hashes.md5}") diff --git a/src/neuromaps_prime/resources/edges/surface/human_chimpanzee.yaml b/src/neuromaps_prime/resources/edges/surface/human_chimpanzee.yaml new file mode 100644 index 0000000..3272f32 --- /dev/null +++ b/src/neuromaps_prime/resources/edges/surface/human_chimpanzee.yaml @@ -0,0 +1,20 @@ +- from: NCBR + to: fsaverage + surfaces: + human_chimpanzee: + 164k: + sphere: + left: share/Outputs/NCBR-fsaverage/src-fsaverage_to-NCBR_den-164k_hemi-L_sphere.surf.gii + right: share/Outputs/NCBR-fsaverage/src-fsaverage_to-NCBR_den-164k_hemi-R_sphere.surf.gii + white: + left: share/Outputs/NCBR-fsaverage/src-fsaverage_to-NCBR_den-164k_hemi-L_white.surf.gii + right: share/Outputs/NCBR-fsaverage/src-fsaverage_to-NCBR_den-164k_hemi-R_white.surf.gii + +- from: fsaverage + to: NCBR + surfaces: + human_chimpanzee: + 164k: + sphere: + left: share/Outputs/fsaverage-NCBR/src-NCBR_to-fsaverage_den-164k_hemi-L_sphere.surf.gii + right: share/Outputs/fsaverage-NCBR/src-NCBR_to-fsaverage_den-164k_hemi-R_sphere.surf.gii diff --git a/src/neuromaps_prime/resources/edges/surface/human_human.yaml b/src/neuromaps_prime/resources/edges/surface/human_human.yaml new file mode 100644 index 0000000..4bacc27 --- /dev/null +++ b/src/neuromaps_prime/resources/edges/surface/human_human.yaml @@ -0,0 +1,34 @@ +- from: CIVET + to: fsLR + surfaces: + neuromaps: + 41k: + sphere: + left: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a1700c4e0d5737206829c59/?view_only=b214f40525fe44b5bea3103478d08d0d + right: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a1700c5d06c4774c98294e9/?view_only=b214f40525fe44b5bea3103478d08d0d + 164k: + sphere: + left: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a1700c56d01f8af2c829920/?view_only=b214f40525fe44b5bea3103478d08d0d + right: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a1700c6346bfaa8ef809d16/?view_only=b214f40525fe44b5bea3103478d08d0d + +- from: CIVET + to: fsaverage + surfaces: + neuromaps: + 41k: + sphere: + left: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a17033581dec3a3edfdfb6b/?view_only=b214f40525fe44b5bea3103478d08d0d + right: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a17033481dec3a3edfdfb69/?view_only=b214f40525fe44b5bea3103478d08d0d + 164k: + sphere: + left: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a17033788c420c552cc6f0e/?view_only=b214f40525fe44b5bea3103478d08d0d + right: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a170336a9eebf8f0f82902d/?view_only=b214f40525fe44b5bea3103478d08d0d + +- from: fsLR + to: fsaverage + surfaces: + neuromaps: + 32k: + sphere: + left: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a17044383ffd4e634cc6e33/?view_only=b214f40525fe44b5bea3103478d08d0d + right: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a1704435720fc8dbacc710f/?view_only=b214f40525fe44b5bea3103478d08d0d diff --git a/src/neuromaps_prime/resources/nodes/chimpanzee/NCBR.yaml b/src/neuromaps_prime/resources/nodes/chimpanzee/NCBR.yaml new file mode 100644 index 0000000..794c9b7 --- /dev/null +++ b/src/neuromaps_prime/resources/nodes/chimpanzee/NCBR.yaml @@ -0,0 +1,24 @@ +NCBR: + species: chimpanzee + description: NCBR Chimpanzee Atlas + surfaces: + 41k: + sphere: + left: share/Inputs/NCBR/src-NCBR_den-41k_hemi-L_sphere.surf.gii + right: share/Inputs/NCBR/src-NCBR_den-41k_hemi-R_sphere.surf.gii + white: + left: share/Inputs/NCBR/src-NCBR_den-41k_hemi-L_white.surf.gii + right: share/Inputs/NCBR/src-NCBR_den-41k_hemi-R_white.surf.gii + 164k: + sphere: + left: share/Inputs/NCBR/src-NCBR_den-164k_hemi-L_sphere.surf.gii + right: share/Inputs/NCBR/src-NCBR_den-164k_hemi-R_sphere.surf.gii + midthickness: + left: share/Inputs/NCBR/src-NCBR_den-164k_hemi-L_midthickness.surf.gii + right: share/Inputs/NCBR/src-NCBR_den-164k_hemi-R_midthickness.surf.gii + white: + left: share/Inputs/NCBR/src-NCBR_den-164k_hemi-L_white.surf.gii + right: share/Inputs/NCBR/src-NCBR_den-164k_hemi-R_white.surf.gii + volumes: + 400um: + T1w: share/Inputs/NCBR/src-NCBR_res-0p40mm_T1w.nii diff --git a/src/neuromaps_prime/resources/nodes/human/CIVET.yaml b/src/neuromaps_prime/resources/nodes/human/CIVET.yaml new file mode 100644 index 0000000..fdc51c4 --- /dev/null +++ b/src/neuromaps_prime/resources/nodes/human/CIVET.yaml @@ -0,0 +1,55 @@ +# Surfaces sourced from neuromaps OSF +# (https://osf.io/4mw3a) +# Annotations are direct URL +CIVET: + species: human + description: CIVET Human Template + surfaces: + 41k: + sphere: + left: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a15f366ae88a491b17ee7f2/?view_only=b214f40525fe44b5bea3103478d08d0d + right: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a15f36600e86708937eea00/?view_only=b214f40525fe44b5bea3103478d08d0d + midthickness: + left: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a15f367ae88a491b17ee7f4/?view_only=b214f40525fe44b5bea3103478d08d0d + right: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a15f3689b96bc757282a3e1/?view_only=b214f40525fe44b5bea3103478d08d0d + white: + left: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a15f3669b96bc757282a3dd/?view_only=b214f40525fe44b5bea3103478d08d0d + right: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a15f366bfa98ff448cc7572/?view_only=b214f40525fe44b5bea3103478d08d0d + inflated: + left: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a15f0c9ae88a491b17ee5b6/?view_only=b214f40525fe44b5bea3103478d08d0d + right: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a15f366bfa98ff448cc7574/?view_only=b214f40525fe44b5bea3103478d08d0d + annotation: + RM_scalinghcp: + left: https://files.osf.io/v1/resources/4mw3a/providers/osfstorage/613100104e5ee5021029a221 + right: https://files.osf.io/v1/resources/4mw3a/providers/osfstorage/613100044e5ee5021929210c + references: + - https://doi.org/10.1126/science.aar2578 + notes: + - Reardon 2018 scalinghcp + RM_scalingnih: + left: https://files.osf.io/v1/resources/4mw3a/providers/osfstorage/6130ffd5af610c0216dfe093 + right: https://files.osf.io/v1/resources/4mw3a/providers/osfstorage/6130ffe24e5ee5021829148a + references: + - https://doi.org/10.1126/science.aar2578 + notes: + - Reardon 2018 RM_scalingnih + RM_scalingpnc: + left: https://files.osf.io/v1/resources/4mw3a/providers/osfstorage/6130ffedab8bca0225edc80c + right: https://files.osf.io/v1/resources/4mw3a/providers/osfstorage/6130fff94e5ee502182914c1 + references: + - https://doi.org/10.1126/science.aar2578 + notes: + - Reardon 2018 RM_scalingpnc + 164k: + sphere: + left: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a15f348c2575abdbd829ac5/?view_only=b214f40525fe44b5bea3103478d08d0d + right: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a15f3487ef401e8b5cc74d1/?view_only=b214f40525fe44b5bea3103478d08d0d + midthickness: + left: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a15f348e9bdf105947ee536/?view_only=b214f40525fe44b5bea3103478d08d0d + right: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a15f3689b96bc757282a3e1/?view_only=b214f40525fe44b5bea3103478d08d0d + white: + left: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a15f3489b96bc757282a3b8/?view_only=b214f40525fe44b5bea3103478d08d0d + right: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a15f345bfa98ff448cc7564/?view_only=b214f40525fe44b5bea3103478d08d0d + inflated: + left: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a15f348ae88a491b17ee7d5/?view_only=b214f40525fe44b5bea3103478d08d0d + right: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a15f348bfa98ff448cc7569/?view_only=b214f40525fe44b5bea3103478d08d0d diff --git a/src/neuromaps_prime/resources/nodes/human/fsaverage.yaml b/src/neuromaps_prime/resources/nodes/human/fsaverage.yaml new file mode 100644 index 0000000..16a6c01 --- /dev/null +++ b/src/neuromaps_prime/resources/nodes/human/fsaverage.yaml @@ -0,0 +1,85 @@ +# Surfaces sourced from neuromaps OSF +# (https://osf.io/4mw3a) +# Annotations are direct URL +fsaverage: + species: human + description: fsaverage Human Template + surfaces: + 10k: + sphere: + left: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a15f3d101ad20570d7eeb1b/?view_only=b214f40525fe44b5bea3103478d08d0d + right: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a15f3d17ef401e8b5cc752d/?view_only=b214f40525fe44b5bea3103478d08d0d + white: + left: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a15f3d100e86708937eea7a/?view_only=b214f40525fe44b5bea3103478d08d0d + right: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a15f3d17ef401e8b5cc752e/?view_only=b214f40525fe44b5bea3103478d08d0d + pial: + left: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a15f3d1bfa98ff448cc75b5/?view_only=b214f40525fe44b5bea3103478d08d0d + right: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a15f3d1bfa98ff448cc75b6/?view_only=b214f40525fe44b5bea3103478d08d0d + inflated: + left: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a15f3d1ae88a491b17ee845/?view_only=b214f40525fe44b5bea3103478d08d0d + right: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a15f3d19b96bc757282a455/?view_only=b214f40525fe44b5bea3103478d08d0d + annotation: + RM_genepc1: + left: https://files.osf.io/v1/resources/4mw3a/providers/osfstorage/60c2290118f70b01fca797eb + right: https://files.osf.io/v1/resources/4mw3a/providers/osfstorage/60c228f5f3ce9401fa24e521 + references: + - https://doi.org/10.1038/nature11405 + - https://doi.org/10.7554/eLife.72129 + notes: + - Abagen Gene PC1 + 164k: + sphere: + left: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a15f3784a4fb9e964cc78b5/?view_only=b214f40525fe44b5bea3103478d08d0d + right: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a15f378ae88a491b17ee7fc/?view_only=b214f40525fe44b5bea3103478d08d0d + white: + left: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a15f3797ef401e8b5cc74ed/?view_only=b214f40525fe44b5bea3103478d08d0d + right: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a15f345bfa98ff448cc7564/?view_only=b214f40525fe44b5bea3103478d08d0d + pial: + left: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a15f37801ad20570d7eeacd/?view_only=b214f40525fe44b5bea3103478d08d0d + right: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a15f3797a6372a22ecc762c/?view_only=b214f40525fe44b5bea3103478d08d0d + inflated: + left: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a15f3799b96bc757282a3f5/?view_only=b214f40525fe44b5bea3103478d08d0d + right: https://files.osf.io/v1/resources/nmxfh/providers/osfstorage/6a15f37800e86708937eea31/?view_only=b214f40525fe44b5bea3103478d08d0d + annotation: + RM_az10419369: + left: https://files.osf.io/v1/resources/4mw3a/providers/osfstorage/638543b0723a11190518c8a6 + right: https://files.osf.io/v1/resources/4mw3a/providers/osfstorage/638543a2c86e2818da88f993 + references: + - https://doi.org/10.1523/JNEUROSCI.2830-16.2016 + notes: + - Beliveau 2017 AZ10419369 + RM_cimbi36: + left: https://files.osf.io/v1/resources/4mw3a/providers/osfstorage/638543bf228a5a18987bc2c1 + right: https://files.osf.io/v1/resources/4mw3a/providers/osfstorage/638543cdc86e2818da88f9e7 + references: + - https://doi.org/10.1523/JNEUROSCI.2830-16.2016 + notes: + - Beliveau 2017 cimbi36 + RM_cumi101: + left: https://files.osf.io/v1/resources/4mw3a/providers/osfstorage/638543ea1daa6b183975935a + right: https://files.osf.io/v1/resources/4mw3a/providers/osfstorage/638543dbc86e2818d988f7ea + references: + - https://doi.org/10.1523/JNEUROSCI.2830-16.2016 + notes: + - Beliveau 2017 cumi101 + RM_dasb: + left: https://files.osf.io/v1/resources/4mw3a/providers/osfstorage/63854394228a5a18987bc26e + right: https://files.osf.io/v1/resources/4mw3a/providers/osfstorage/63854385c86e2818da88f94b + references: + - https://doi.org/10.1523/JNEUROSCI.2830-16.2016 + notes: + - Beliveau 2017 dasb + RM_sb207145: + left: https://files.osf.io/v1/resources/4mw3a/providers/osfstorage/638542c2c86e2818d588f461 + right: https://files.osf.io/v1/resources/4mw3a/providers/osfstorage/638542b2a98e5f1ac2103866 + references: + - https://doi.org/10.1523/JNEUROSCI.2830-16.2016 + notes: + - Beliveau 2017 sb207145 + RM_norgaard_flumazenil: + left: https://files.osf.io/v1/resources/4mw3a/providers/osfstorage/638553fe228a5a18d67bcac8 + right: https://files.osf.io/v1/resources/4mw3a/providers/osfstorage/6385540d228a5a18d67bcadd + references: + - https://doi.org/10.1016/j.neuroimage.2021.117878 + notes: + - Norgaard 2021 flumazenil diff --git a/src/neuromaps_prime/resources/nodes/macaque/Yerkes19.yaml b/src/neuromaps_prime/resources/nodes/macaque/Yerkes19.yaml index c238b9e..b9346bd 100644 --- a/src/neuromaps_prime/resources/nodes/macaque/Yerkes19.yaml +++ b/src/neuromaps_prime/resources/nodes/macaque/Yerkes19.yaml @@ -23,14 +23,14 @@ Yerkes19: left: resources/Yerkes19/annotations/parcellations/src-Yerkes19_den-10k_hemi-L_atlas-Yeo7Networks_desc-PC_annot.label.gii right: resources/Yerkes19/annotations/parcellations/src-Yerkes19_den-10k_hemi-R_atlas-Yeo7Networks_desc-PC_annot.label.gii notes: - - Yeo2011 7 Network parcellation (N=1000). Human-to-monkey. 10k surface density. - - left lookup file -> resources/Yerkes19/annotations/parcellations/src-Yerkes19_den-10k_hemi-L_atlas-Yeo7Networks_desc-PC_annot.txt - - right lookup file -> resources/Yerkes19/annotations/parcellations/src-Yerkes19_den-10k_hemi-R_atlas-Yeo7Networks_desc-PC_annot.txt + - Yeo2011 7 Network parcellation (N=1000). Human-to-monkey. 10k surface density. + - left lookup file -> resources/Yerkes19/annotations/parcellations/src-Yerkes19_den-10k_hemi-L_atlas-Yeo7Networks_desc-PC_annot.txt + - right lookup file -> resources/Yerkes19/annotations/parcellations/src-Yerkes19_den-10k_hemi-R_atlas-Yeo7Networks_desc-PC_annot.txt PC_MarkovMonkey: - left: resources/Yerkes19/annotations/parcellations/src-Yerkes19_den-10k_hemi-L_atlas-MarkovMonkey_desc-PC_annot.label.gii - right: resources/Yerkes19/annotations/parcellations/src-Yerkes19_den-10k_hemi-R_atlas-MarkovMonkey_desc-PC_annot.label.gii - notes: - - Markov monkey cortical parcellation, 10k surface density. + left: resources/Yerkes19/annotations/parcellations/src-Yerkes19_den-10k_hemi-L_atlas-MarkovMonkey_desc-PC_annot.label.gii + right: resources/Yerkes19/annotations/parcellations/src-Yerkes19_den-10k_hemi-R_atlas-MarkovMonkey_desc-PC_annot.label.gii + notes: + - Markov monkey cortical parcellation, 10k surface density. 32k: sphere: left: share/Inputs/Yerkes19/src-Yerkes19_den-32k_hemi-L_sphere.surf.gii @@ -51,134 +51,134 @@ Yerkes19: RM_auto_ampa: left: resources/Yerkes19/annotations/receptor_maps/src-Yerkes19_den-32k_hemi-L_acq-auto_trc-ampa_desc-RM_annot.func.gii references: - - https://doi.org/10.1007/s00429-021-02437-y - - https://doi.org/10.1038/s41593-023-01351-2 - notes: - - AMPA receptor density, radioligand [³H]AMPA. Ionotropic glutamate receptor. + - https://doi.org/10.1007/s00429-021-02437-y + - https://doi.org/10.1038/s41593-023-01351-2 + notes: + - AMPA receptor density, radioligand [³H]AMPA. Ionotropic glutamate receptor. RM_auto_cgp5: left: resources/Yerkes19/annotations/receptor_maps/src-Yerkes19_den-32k_hemi-L_acq-auto_trc-cgp5_desc-RM_annot.func.gii references: - - https://doi.org/10.1007/s00429-021-02437-y - - https://doi.org/10.1038/s41593-023-01351-2 + - https://doi.org/10.1007/s00429-021-02437-y + - https://doi.org/10.1038/s41593-023-01351-2 notes: - - GABA_B receptor density, radioligand [³H]CGP54626. Metabotropic inhibitory GABA receptor. + - GABA_B receptor density, radioligand [³H]CGP54626. Metabotropic inhibitory GABA receptor. RM_auto_damp: left: resources/Yerkes19/annotations/receptor_maps/src-Yerkes19_den-32k_hemi-L_acq-auto_trc-damp_desc-RM_annot.func.gii references: - - https://doi.org/10.1007/s00429-021-02437-y - - https://doi.org/10.1038/s41593-023-01351-2 - notes: - - M3 muscarinic receptor density, radioligand [³H]4-DAMP. Cholinergic receptor. + - https://doi.org/10.1007/s00429-021-02437-y + - https://doi.org/10.1038/s41593-023-01351-2 + notes: + - M3 muscarinic receptor density, radioligand [³H]4-DAMP. Cholinergic receptor. RM_auto_dpat: left: resources/Yerkes19/annotations/receptor_maps/src-Yerkes19_den-32k_hemi-L_acq-auto_trc-dpat_desc-RM_annot.func.gii - references: - - https://doi.org/10.1007/s00429-021-02437-y - - https://doi.org/10.1038/s41593-023-01351-2 - notes: - - 5-HT1A receptor density, radioligand [³H]8-OH-DPAT (dpat). Serotonin receptor. + references: + - https://doi.org/10.1007/s00429-021-02437-y + - https://doi.org/10.1038/s41593-023-01351-2 + notes: + - 5-HT1A receptor density, radioligand [³H]8-OH-DPAT (dpat). Serotonin receptor. RM_auto_dpmg: left: resources/Yerkes19/annotations/receptor_maps/src-Yerkes19_den-32k_hemi-L_acq-auto_trc-dpmg_desc-RM_annot.func.gii references: - - https://doi.org/10.1007/s00429-021-02437-y - - https://doi.org/10.1038/s41593-023-01351-2 - notes: - - D1 dopamine receptor density, radioligand [³H]SCH23390. Dopamine receptor. + - https://doi.org/10.1007/s00429-021-02437-y + - https://doi.org/10.1038/s41593-023-01351-2 + notes: + - D1 dopamine receptor density, radioligand [³H]SCH23390. Dopamine receptor. RM_auto_flum: left: resources/Yerkes19/annotations/receptor_maps/src-Yerkes19_den-32k_hemi-L_acq-auto_trc-flum_desc-RM_annot.func.gii references: - - https://doi.org/10.1007/s00429-021-02437-y - - https://doi.org/10.1038/s41593-023-01351-2 - notes: - - GABA_A/BZ receptor density, radioligand [³H]flumazenil. Benzodiazepine site of GABA_A receptor. + - https://doi.org/10.1007/s00429-021-02437-y + - https://doi.org/10.1038/s41593-023-01351-2 + notes: + - GABA_A/BZ receptor density, radioligand [³H]flumazenil. Benzodiazepine site of GABA_A receptor. RM_auto_kain: left: resources/Yerkes19/annotations/receptor_maps/src-Yerkes19_den-32k_hemi-L_acq-auto_trc-kain_desc-RM_annot.func.gii references: - - https://doi.org/10.1007/s00429-021-02437-y - - https://doi.org/10.1038/s41593-023-01351-2 - notes: - - Kainate receptor density, radioligand [³H]kainate. Ionotropic glutamate receptor. + - https://doi.org/10.1007/s00429-021-02437-y + - https://doi.org/10.1038/s41593-023-01351-2 + notes: + - Kainate receptor density, radioligand [³H]kainate. Ionotropic glutamate receptor. RM_auto_keta: left: resources/Yerkes19/annotations/receptor_maps/src-Yerkes19_den-32k_hemi-L_acq-auto_trc-keta_desc-RM_annot.func.gii references: - - https://doi.org/10.1007/s00429-021-02437-y - - https://doi.org/10.1038/s41593-023-01351-2 - notes: - - 5-HT2A receptor density, radioligand [³H]ketanserin. Serotonin receptor. + - https://doi.org/10.1007/s00429-021-02437-y + - https://doi.org/10.1038/s41593-023-01351-2 + notes: + - 5-HT2A receptor density, radioligand [³H]ketanserin. Serotonin receptor. RM_auto_mk80: left: resources/Yerkes19/annotations/receptor_maps/src-Yerkes19_den-32k_hemi-L_acq-auto_trc-mk80_desc-RM_annot.func.gii references: - - https://doi.org/10.1007/s00429-021-02437-y - - https://doi.org/10.1038/s41593-023-01351-2 - notes: - - NMDA receptor density, radioligand [³H]MK-801. Ionotropic glutamate receptor. + - https://doi.org/10.1007/s00429-021-02437-y + - https://doi.org/10.1038/s41593-023-01351-2 + notes: + - NMDA receptor density, radioligand [³H]MK-801. Ionotropic glutamate receptor. RM_auto_musc: left: resources/Yerkes19/annotations/receptor_maps/src-Yerkes19_den-32k_hemi-L_acq-auto_trc-musc_desc-RM_annot.func.gii references: - - https://doi.org/10.1007/s00429-021-02437-y - - https://doi.org/10.1038/s41593-023-01351-2 - notes: - - GABA_A receptor density, radioligand [³H]muscimol. Ionotropic inhibitory GABA receptor. + - https://doi.org/10.1007/s00429-021-02437-y + - https://doi.org/10.1038/s41593-023-01351-2 + notes: + - GABA_A receptor density, radioligand [³H]muscimol. Ionotropic inhibitory GABA receptor. RM_auto_oxot: left: resources/Yerkes19/annotations/receptor_maps/src-Yerkes19_den-32k_hemi-L_acq-auto_trc-oxot_desc-RM_annot.func.gii references: - - https://doi.org/10.1007/s00429-021-02437-y - - https://doi.org/10.1038/s41593-023-01351-2 - notes: - - M2 muscarinic receptor density, radioligand [³H]oxotremorine-M. Cholinergic receptor. + - https://doi.org/10.1007/s00429-021-02437-y + - https://doi.org/10.1038/s41593-023-01351-2 + notes: + - M2 muscarinic receptor density, radioligand [³H]oxotremorine-M. Cholinergic receptor. RM_auto_pire: left: resources/Yerkes19/annotations/receptor_maps/src-Yerkes19_den-32k_hemi-L_acq-auto_trc-pire_desc-RM_annot.func.gii - references: - - https://doi.org/10.1007/s00429-021-02437-y - - https://doi.org/10.1038/s41593-023-01351-2 - notes: - - M1 muscarinic receptor density, radioligand [³H]pirenzepine. Cholinergic receptor. + references: + - https://doi.org/10.1007/s00429-021-02437-y + - https://doi.org/10.1038/s41593-023-01351-2 + notes: + - M1 muscarinic receptor density, radioligand [³H]pirenzepine. Cholinergic receptor. RM_auto_praz: left: resources/Yerkes19/annotations/receptor_maps/src-Yerkes19_den-32k_hemi-L_acq-auto_trc-praz_desc-RM_annot.func.gii references: - - https://doi.org/10.1007/s00429-021-02437-y - - https://doi.org/10.1038/s41593-023-01351-2 - notes: - - α1-adrenergic receptor density, radioligand [³H]prazosin. Noradrenergic receptor. + - https://doi.org/10.1007/s00429-021-02437-y + - https://doi.org/10.1038/s41593-023-01351-2 + notes: + - α1-adrenergic receptor density, radioligand [³H]prazosin. Noradrenergic receptor. RM_auto_uk14: left: resources/Yerkes19/annotations/receptor_maps/src-Yerkes19_den-32k_hemi-L_acq-auto_trc-uk14_desc-RM_annot.func.gii references: - - https://doi.org/10.1007/s00429-021-02437-y - - https://doi.org/10.1038/s41593-023-01351-2 - notes: - - α2-adrenergic receptor density, radioligand [³H]UK-14304. Noradrenergic receptor. + - https://doi.org/10.1007/s00429-021-02437-y + - https://doi.org/10.1038/s41593-023-01351-2 + notes: + - α2-adrenergic receptor density, radioligand [³H]UK-14304. Noradrenergic receptor. MM: left: resources/Yerkes19/annotations/myelin_maps/src-Yerkes19_den-32k_hemi-L_desc-MM_annot.func.gii right: resources/Yerkes19/annotations/myelin_maps/src-Yerkes19_den-32k_hemi-R_desc-MM_annot.func.gii references: - - https://doi.org/10.1073/pnas.1721653115 + - https://doi.org/10.1073/pnas.1721653115 notes: - - Myelin map (bias corrected). MacaqueYerkes19 v1.2. + - Myelin map (bias corrected). MacaqueYerkes19 v1.2. SMM: left: resources/Yerkes19/annotations/smoothed_myelin_maps/src-Yerkes19_den-32k_hemi-L_desc-SMM_annot.func.gii right: resources/Yerkes19/annotations/smoothed_myelin_maps/src-Yerkes19_den-32k_hemi-R_desc-SMM_annot.func.gii references: - - https://doi.org/10.1073/pnas.1721653115 + - https://doi.org/10.1073/pnas.1721653115 notes: - - Smoothed myelin map (bias corrected). MacaqueYerkes19 v1.2. + - Smoothed myelin map (bias corrected). MacaqueYerkes19 v1.2. CT: left: resources/Yerkes19/annotations/cortical_thickness/src-Yerkes19_den-32k_hemi-L_desc-CT_annot.func.gii right: resources/Yerkes19/annotations/cortical_thickness/src-Yerkes19_den-32k_hemi-R_desc-CT_annot.func.gii references: - - https://doi.org/10.1073/pnas.1721653115 + - https://doi.org/10.1073/pnas.1721653115 notes: - - Cortical thickness. MacaqueYerkes19 v1.2. + - Cortical thickness. MacaqueYerkes19 v1.2. CV: left: resources/Yerkes19/annotations/curvature/src-Yerkes19_den-32k_hemi-L_desc-CV_annot.func.gii right: resources/Yerkes19/annotations/curvature/src-Yerkes19_den-32k_hemi-R_desc-CV_annot.func.gii references: - - https://doi.org/10.1073/pnas.1721653115 + - https://doi.org/10.1073/pnas.1721653115 notes: - - Curvature. MacaqueYerkes19 v1.2. + - Curvature. MacaqueYerkes19 v1.2. PC_Yeo7Networks: left: resources/Yerkes19/annotations/parcellations/src-Yerkes19_den-32k_hemi-L_atlas-Yeo7Networks_desc-PC_annot.label.gii notes: - - Yeo2011 7 Network parcellation (N=1000). Human-to-monkey. 32k surface density. - - left lookup file -> resources/Yerkes19/annotations/parcellations/src-Yerkes19_den-32k_hemi-L_atlas-Yeo7Networks_desc-PC_annot.txt + - Yeo2011 7 Network parcellation (N=1000). Human-to-monkey. 32k surface density. + - left lookup file -> resources/Yerkes19/annotations/parcellations/src-Yerkes19_den-32k_hemi-L_atlas-Yeo7Networks_desc-PC_annot.txt volumes: 500um: T1w: share/Inputs/Yerkes19/src-Yerkes19_res-0p50mm_T1w.nii diff --git a/tests/conftest.py b/tests/conftest.py index ffe0e82..ac02a98 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -2,18 +2,13 @@ from __future__ import annotations -import logging -import os from pathlib import Path from typing import TYPE_CHECKING, Any -import niwrap import pytest import yaml -from styxpodman import PodmanRunner from neuromaps_prime.graph import NeuromapsGraph -from neuromaps_prime.niwrap import resolve_runner from neuromaps_prime.resources import NEUROMAPSPRIME_GRAPH if TYPE_CHECKING: @@ -30,51 +25,6 @@ def pytest_collection_modifyitems(items: Sequence[pytest.Item]) -> None: item.add_marker(getattr(pytest.mark, marker)) -def pytest_addoption(parser: pytest.Parser) -> None: - """Add option(s) to pytest parser.""" - parser.addoption( - "--runner", - action="store", - default="local", - help="Styx runner type to use: ['local', 'docker', 'singularity']", - ) - parser.addoption( - "--data-dir", - action="store", - default=None, - help="Directory where test data is located.", - ) - - -@pytest.fixture(scope="session", autouse=True) -def niwrap_runner( - request: pytest.FixtureRequest, tmp_path_factory: pytest.TempPathFactory -) -> niwrap.Runner: - """Globally set niwrap runner for the testing suite.""" - # Set up niwrap runner - runner_type, runner_exec = resolve_runner( - request.config.getoption("--runner").lower() - ) - match runner_type: - case "docker": - niwrap.use_docker(docker_executable=runner_exec) - case "podman": - niwrap.set_global_runner( - # UserID = 0 currently necessary for some containers used - runner=PodmanRunner(podman_executable=runner_exec, podman_user_id=0) - ) - case "singularity": - niwrap.use_singularity(singularity_executable=runner_exec) - case _: - niwrap.use_local() - runner = niwrap.get_global_runner() - runner.data_dir = tmp_path_factory.mktemp(f"{os.urandom(8).hex()}") - # Set up logging for debugging - logger = logging.getLogger(runner.logger_name) - logger.setLevel(logging.DEBUG) - return runner - - def _mk(tmp_path: Path, name: str) -> str: path = tmp_path / name path.touch() @@ -156,13 +106,9 @@ def _rewrite_edge_files(tmp_path: Path, edge: dict[str, Any]) -> None: @pytest.fixture -def graph(tmp_path: Path, request: pytest.FixtureRequest) -> NeuromapsGraph: +def graph(tmp_path: Path) -> NeuromapsGraph: """Create a graph fixture to use for tests.""" - data_dir = request.config.getoption("--data-dir") - if data_dir is not None: - return NeuromapsGraph(runner="auto", data_dir=Path(data_dir).resolve()) - - graph = NeuromapsGraph(_testing=True) + graph = NeuromapsGraph(runner="auto", data_dir=tmp_path / ".cache", _testing=True) def _load_dict(paths: tuple[Path, ...]) -> list[dict[str, Any]]: return [yaml.safe_load(path.read_bytes()) for path in paths] diff --git a/tests/unit/graph/test_graph.py b/tests/unit/graph/test_graph.py index 50c52d4..bc9d128 100644 --- a/tests/unit/graph/test_graph.py +++ b/tests/unit/graph/test_graph.py @@ -65,6 +65,7 @@ def test_graph_build_yaml(self, tmp_path: Path) -> None: def test_graph_build(self, graph: NeuromapsGraph) -> None: """Test graph initialization.""" info = graph.utils.get_graph_info() + assert graph.data_dir.exists() assert info["num_nodes"] > 0 assert info["num_edges"] >= 0 assert info["num_surfaces"] > 0 diff --git a/tests/unit/graph/test_model.py b/tests/unit/graph/test_model.py index 5edf528..e1ede9a 100644 --- a/tests/unit/graph/test_model.py +++ b/tests/unit/graph/test_model.py @@ -2,7 +2,9 @@ from __future__ import annotations +from pathlib import Path from typing import TYPE_CHECKING, Any, Protocol +from unittest.mock import MagicMock, patch import pytest @@ -10,7 +12,6 @@ if TYPE_CHECKING: from collections.abc import Callable - from pathlib import Path @pytest.fixture @@ -107,15 +108,31 @@ def test_validate_and_fetch( obj = model_cls( name="test", description="testing description", - file_path=tmp_file, + uri=str(tmp_file), + file_path=Path("abc"), **extra_kwargs, ) + assert obj.file_path.name == "abc" + assert obj.fetch() == tmp_file + assert obj.file_path == tmp_file + + def test_fetch_existing_file_path(self, tmp_file: Path) -> None: + """Test resource instantiation and fetching.""" + obj = models.SurfaceAtlas( + name="test", + description="testing description", + space="Yerkes19", + density="32k", + hemisphere="left", + resource_type="surf_atlas", + file_path=tmp_file, + ) assert obj.file_path == tmp_file assert obj.fetch() == tmp_file - def test_missing_file(self) -> None: + def test_missing_file_no_uri(self) -> None: """Test missing file raises error.""" - with pytest.raises(FileNotFoundError, match="File path does not exist"): + with pytest.raises(FileNotFoundError, match="cannot be fetched"): models.SurfaceAtlas( name="invalid", description="missing", @@ -124,7 +141,26 @@ def test_missing_file(self) -> None: density="32k", hemisphere="left", resource_type="SurfaceAtlas", - ) + ).fetch() + + @patch("neuromaps_prime.graph.models.download_and_validate") + def test_fetch_raises_if_download_fails( + self, mock_download: MagicMock, tmp_path: Path + ) -> None: + """Test fetch raises if download doesn't produce file.""" + dest = tmp_path / "file.txt" + obj = models.SurfaceAnnotation( + name="test", + file_path=dest, + uri="https://files.osf.io/v1/resources/abcde", + space="Yerkes19", + density="32k", + hemisphere="left", + label="myelin", + ) + mock_download.return_value = None + with pytest.raises(FileNotFoundError, match="does not exist"): + obj.fetch() def test_description_optional(self, tmp_file: Path) -> None: """Test that description defaults to None for annotation models.""" diff --git a/tests/unit/remote/test_osf.py b/tests/unit/remote/test_osf.py new file mode 100644 index 0000000..80f9532 --- /dev/null +++ b/tests/unit/remote/test_osf.py @@ -0,0 +1,118 @@ +"""Unit tests for OSF remote storage.""" + +from __future__ import annotations + +import hashlib +from typing import TYPE_CHECKING +from unittest.mock import MagicMock, patch + +import pytest + +from neuromaps_prime.remote.osf import OSFFileExtra, OSFFileMeta, OSFHashes, OSFStorage + +if TYPE_CHECKING: + from pathlib import Path + +MOCK_MD5 = hashlib.md5(b"test content", usedforsecurity=False).hexdigest() + +MOCK_META = { + "data": { + "attributes": { + "name": "test.txt", + "size": 12, + "extra": {"hashes": {"md5": MOCK_MD5}}, + } + } +} + + +@pytest.fixture +def mock_meta_response() -> MagicMock: + """Mock metadata response object.""" + return MagicMock(json=MagicMock(return_value=MOCK_META)) + + +class TestOSFHashes: + """Test suite for validating OSF hashes.""" + + def test_sha256_optional(self) -> None: + """Test sha256 defaults to None when not provided.""" + h = OSFHashes(md5=MOCK_MD5) + assert h.sha256 is None + + def test_both_fields(self) -> None: + """Test both md5 and sha256 are stored correctly when provided.""" + h = OSFHashes(md5=MOCK_MD5, sha256="abc123") + assert h.sha256 == "abc123" + + +class TestOSFFileMeta: + """Test suite for OSF file metadata.""" + + def test_valid(self) -> None: + """Test metadata fields are correctly assigned on instantiation.""" + meta = OSFFileMeta( + name="test.txt", + size=12, + extra=OSFFileExtra(hashes=OSFHashes(md5=MOCK_MD5)), + ) + assert meta.name == "test.txt" + assert meta.extra.hashes.md5 == MOCK_MD5 + + +class TestOSFStorage: + """Test suite for OSFStorage download and metadata retrieval.""" + + @patch("neuromaps_prime.remote.osf.requests.get") + def test_get_meta(self, mock_get: MagicMock, mock_meta_response: MagicMock) -> None: + """Test get_meta returns parsed OSFFileMeta and calls correct URL.""" + mock_get.return_value = mock_meta_response + meta = OSFStorage().get_meta("https://files.osf.io/v1/resources/abcde") + assert meta.name == "test.txt" + assert meta.extra.hashes.md5 == MOCK_MD5 + mock_get.assert_called_once_with( + "https://files.osf.io/v1/resources/abcde", + params={"meta": ""}, + timeout=90, + ) + + @patch("neuromaps_prime.remote.osf.requests.get") + def test_get_meta_raises_on_http_error(self, mock_get: MagicMock) -> None: + """Test get_meta propagates HTTP errors from the remote server.""" + mock_get.return_value.raise_for_status.side_effect = Exception("HTTP Error") + with pytest.raises(Exception, match="HTTP Error"): + OSFStorage().get_meta("https://files.osf.io/v1/resources/abcde") + + @patch("neuromaps_prime.remote.osf.requests.get") + def test_download_valid( + self, mock_get: MagicMock, mock_meta_response: MagicMock, tmp_path: Path + ) -> None: + """Test download writes correct bytes to dest when checksum matches.""" + content = b"test content" + mock_download = MagicMock(iter_content=MagicMock(return_value=[content])) + mock_get.side_effect = [mock_meta_response, mock_download] + dest = tmp_path / "test.txt" + OSFStorage().download("https://files.osf.io/v1/resources/abcde", dest) + assert dest.read_bytes() == content + + @patch("neuromaps_prime.remote.osf.requests.get") + def test_download_checksum_mismatch( + self, mock_get: MagicMock, mock_meta_response: MagicMock, tmp_path: Path + ) -> None: + """Test download raises ValueError when downloaded content fails checksum.""" + mock_download = MagicMock( + iter_content=MagicMock(return_value=[b"wrong content"]) + ) + mock_get.side_effect = [mock_meta_response, mock_download] + with pytest.raises(ValueError, match="Checksum mismatch"): + OSFStorage().download( + "https://files.osf.io/v1/resources/abcde", tmp_path / "test.txt" + ) + + def test_default_chunk_size(self) -> None: + """Test chunk_size defaults to 8192.""" + assert OSFStorage().chunk_size == 8192 + + def test_custom_chunk_size(self) -> None: + """Test chunk_size is correctly set when provided.""" + assert OSFStorage(chunk_size=4096).chunk_size == 4096 diff --git a/tests/unit/test_fetcher.py b/tests/unit/test_fetcher.py new file mode 100644 index 0000000..6ecd840 --- /dev/null +++ b/tests/unit/test_fetcher.py @@ -0,0 +1,47 @@ +"""Unit tests for remote fetcher.""" + +from __future__ import annotations + +from typing import TYPE_CHECKING +from unittest.mock import MagicMock, patch + +import pytest + +from neuromaps_prime.fetcher import download_and_validate, id_storage + +if TYPE_CHECKING: + from pathlib import Path + + +class TestIDStorage: + """Test suite for identifying storage location.""" + + def test_osf(self) -> None: + """Test downloading from osf storage.""" + assert id_storage("https://osf.io/project") == "osf" + + def test_unknown(self) -> None: + """Test None returned if unknown uri.""" + assert id_storage("https://google.com") is None + + def test_invalid(self) -> None: + """Test None returned if invalid.""" + assert id_storage("") is None + + +class TestDownloadAndValidate: + """Test suite for fetching and validating from remote uri.""" + + def test_unknown_uri_raises(self, tmp_path: Path) -> None: + """Test unidentifiable uri raises ValueError.""" + with pytest.raises(ValueError, match="Could not identify storage"): + download_and_validate("https://google.com", tmp_path / "invalid.txt") + + @patch("neuromaps_prime.fetcher.OSFStorage") + def test_osf_calls_download(self, mock_cls: MagicMock, tmp_path: Path) -> None: + """Test OSF download.""" + mock_osf = mock_cls.return_value + mock_uri = "https://files.osf.io/v1/resources/abcde" + dest = tmp_path / "out.surf.gii" + download_and_validate(mock_uri, dest) + mock_osf.download.assert_called_once_with(mock_uri, dest) diff --git a/uv.lock b/uv.lock index c40581e..d1cb3f3 100644 --- a/uv.lock +++ b/uv.lock @@ -2,9 +2,12 @@ version = 1 revision = 3 requires-python = ">=3.11" resolution-markers = [ - "python_full_version >= '3.14' and sys_platform == 'win32'", - "python_full_version >= '3.14' and sys_platform == 'emscripten'", - "python_full_version >= '3.14' 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