From 2e2e95a1298b28d6910a4a75194290afd87660d9 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Mon, 1 May 2023 19:39:21 -0400
Subject: [PATCH 1/3] ENH: Parallel specification of next API

---
 bids_ng/__init__.py       |   0
 bids_ng/types/__init__.py |  18 ++++++
 bids_ng/types/api1.py     | 113 ++++++++++++++++++++++++++++++++++++++
 bids_ng/types/enums.py    |  17 ++++++
 bids_ng/types/utils.py    |  76 +++++++++++++++++++++++++
 5 files changed, 224 insertions(+)
 create mode 100644 bids_ng/__init__.py
 create mode 100644 bids_ng/types/__init__.py
 create mode 100644 bids_ng/types/api1.py
 create mode 100644 bids_ng/types/enums.py
 create mode 100644 bids_ng/types/utils.py

diff --git a/bids_ng/__init__.py b/bids_ng/__init__.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/bids_ng/types/__init__.py b/bids_ng/types/__init__.py
new file mode 100644
index 000000000..09c59a321
--- /dev/null
+++ b/bids_ng/types/__init__.py
@@ -0,0 +1,18 @@
+from .api1 import BIDSDataset, BIDSFile, File, Index, Label
+from .enums import Query
+from .utils import PaddedInt
+
+NONE, REQUIRED, OPTIONAL = tuple(Query)
+
+__all__ = (
+    "BIDSDataset",
+    "BIDSFile",
+    "File",
+    "Index",
+    "Label",
+    "NONE",
+    "OPTIONAL",
+    "REQUIRED",
+    "Query",
+    "PaddedInt",
+)
diff --git a/bids_ng/types/api1.py b/bids_ng/types/api1.py
new file mode 100644
index 000000000..357c0e733
--- /dev/null
+++ b/bids_ng/types/api1.py
@@ -0,0 +1,113 @@
+"""PyBIDS 1.0 API specification"""
+
+from pathlib import Path
+from typing import Any, Dict, List, Optional, Protocol, TypeVar, Union
+
+from .utils import PaddedInt
+
+try:
+    from typing import TypeAlias
+except ImportError:
+    from typing_extensions import TypeAlias
+
+
+# Datasets should be parameterizable on some kind of schema object.
+# External API users should not depend on it, so this is bound to Any,
+# but once a Schema type is defined for an API implementation, type checkers
+# should be able to introspect it.
+SchemaT = TypeVar("SchemaT")
+
+
+Index: TypeAlias = PaddedInt
+Label: TypeAlias = str
+
+
+class File(Protocol[SchemaT]):
+    """Generic file holder
+
+    This serves as a base class for :class:`BIDSFile` and can represent
+    non-BIDS files.
+    """
+
+    path: Path
+    relative_path: Path
+    dataset: Optional["BIDSDataset[SchemaT]"]
+
+    def __fspath__(self) -> str:
+        ...
+
+
+class BIDSFile(File[SchemaT], Protocol):
+    """BIDS file
+
+    This provides access to BIDS concepts such as path components
+    and sidecar metadata.
+
+    BIDS paths take the form::
+
+        [sub-<label>/[ses-<label>/]<datatype>/]<entities>_<suffix><extension>
+    """
+
+    entities: Dict[str, Union[Label, Index]]
+    datatype: Optional[str]
+    suffix: Optional[str]
+    extension: Optional[str]
+
+    @property
+    def metadata(self) -> Dict[str, Any]:
+        """Sidecar metadata aggregated according to inheritance principle"""
+
+
+class BIDSDataset(Protocol[SchemaT]):
+    """Interface to a single BIDS dataset.
+
+    This structure does not consider the contents of sub-datasets
+    such as `sourcedata/` or `derivatives/`.
+    """
+
+    root: Path
+    schema: SchemaT
+
+    dataset_description: Dict[str, Any]
+    """Contents of dataset_description.json"""
+
+    ignored: List[File[SchemaT]]
+    """Invalid files found in dataset"""
+
+    files: List[BIDSFile[SchemaT]]
+    """Valid files found in dataset"""
+
+    datatypes: List[str]
+    """Datatype directories found in dataset"""
+
+    modalities: List[str]
+    """BIDS "modalities" found in dataset"""
+
+    subjects: List[str]
+    """Subject/participant identifiers found in the dataset"""
+
+    entities: List[str]
+    """Entities (long names) found in any filename in the dataset"""
+
+    def get(self, **filters) -> List[BIDSFile[SchemaT]]:
+        """Query dataset for files"""
+
+    def get_entities(self, entity: str, **filters) -> List[Label | Index]:
+        """Query dataset for entity values"""
+
+    def get_metadata(self, term: str, **filters) -> List[Any]:
+        """Query dataset for metadata values"""
+
+
+class DatasetCollection(BIDSDataset[SchemaT], Protocol):
+    """Interface to a collection of BIDS dataset.
+
+    This structure allows the user to construct a single view of
+    multiple datasets, such as including source or derivative datasets.
+    """
+
+    primary: BIDSDataset[SchemaT]
+    datasets: List[BIDSDataset[SchemaT]]
+
+    def add_dataset(self, dataset: BIDSDataset[SchemaT]) -> None:
+        ...
diff --git a/bids_ng/types/enums.py b/bids_ng/types/enums.py
new file mode 100644
index 000000000..d90e24995
--- /dev/null
+++ b/bids_ng/types/enums.py
@@ -0,0 +1,17 @@
+from enum import Enum
+
+
+class Query(Enum):
+    """Special arguments for dataset querying
+
+    * `Query.NONE` - The field MUST NOT be present
+    * `Query.REQUIRED` - The field MUST be present, but may take any value
+    * `Query.OPTIONAL` - The field MAY be present, and may take any value
+
+    `Query.ANY` is a synonym for `Query.REQUIRED`. Its use is discouraged
+    and may be removed in the future.
+    """
+
+    NONE = 1
+    REQUIRED = ANY = 2
+    OPTIONAL = 3
diff --git a/bids_ng/types/utils.py b/bids_ng/types/utils.py
new file mode 100644
index 000000000..2bab4cf94
--- /dev/null
+++ b/bids_ng/types/utils.py
@@ -0,0 +1,76 @@
+import typing as ty
+
+
+class PaddedInt(int):
+    """Integer type that preserves zero-padding
+
+    Acts like an int in almost all ways except that string formatting
+    will keep the original zero-padding. Numeric format specifiers will
+    work with the integer value.
+
+    >>> PaddedInt(1)
+    1
+    >>> p2 = PaddedInt("02")
+    >>> p2
+    02
+    >>> str(p2)
+    '02'
+    >>> p2 == 2
+    True
+    >>> p2 in range(3)
+    True
+    >>> f"{p2}"
+    '02'
+    >>> f"{p2:s}"
+    '02'
+    >>> f"{p2!s}"
+    '02'
+    >>> f"{p2!r}"
+    '02'
+    >>> f"{p2:d}"
+    '2'
+    >>> f"{p2:03d}"
+    '002'
+    >>> f"{p2:f}"
+    '2.000000'
+    >>> {2: "val"}.get(p2)
+    'val'
+    >>> {p2: "val"}.get(2)
+    'val'
+
+    Note that arithmetic will break the padding.
+
+    >>> str(p2 + 1)
+    '3'
+    """
+
+    def __init__(self, val: ty.Union[str, int]) -> None:
+        self.sval = str(val)
+        if not self.sval.isdigit():
+            raise TypeError(
+                f"{self.__class__.__name__}() argument must be a string of digits "
+                f"or int, not {val.__class__.__name__!r}"
+            )
+
+    def __eq__(self, val: object) -> bool:
+        return val == self.sval or super().__eq__(val)
+
+    def __str__(self) -> str:
+        return self.sval
+
+    def __repr__(self) -> str:
+        return self.sval
+
+    def __format__(self, format_spec: str) -> str:
+        """Format a padded integer
+
+        If a format spec can be used on a string, apply it to the zero-padded string.
+        Otherwise format as an integer.
+        """
+        try:
+            return format(self.sval, format_spec)
+        except ValueError:
+            return super().__format__(format_spec)
+
+    def __hash__(self) -> int:
+        return super().__hash__()

From 8ca4ee7cca11b6dc71edc5b4e20101d42331f09e Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Tue, 2 May 2023 08:38:53 -0400
Subject: [PATCH 2/3] ENH: Add default implementations of File

---
 bids_ng/types/api1.py | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/bids_ng/types/api1.py b/bids_ng/types/api1.py
index 357c0e733..49e29a354 100644
--- a/bids_ng/types/api1.py
+++ b/bids_ng/types/api1.py
@@ -30,11 +30,16 @@ class File(Protocol[SchemaT]):
     """
 
     path: Path
-    relative_path: Path
     dataset: Optional["BIDSDataset[SchemaT]"]
 
     def __fspath__(self) -> str:
-        ...
+        return str(self.path)
+
+    @property
+    def relative_path(self) -> Path:
+        if self.dataset is None:
+            raise ValueError("No dataset root to construct relative path from")
+        return self.path.relative_to(self.dataset.root)
 
 
 class BIDSFile(File[SchemaT], Protocol):

From bcddeb1d28584a3b174557f3da72d4bbb2ddeb2c Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Tue, 2 May 2023 08:40:19 -0400
Subject: [PATCH 3/3] ENH: Start concrete implementations

---
 bids_ng/dataset.py | 119 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 119 insertions(+)
 create mode 100644 bids_ng/dataset.py

diff --git a/bids_ng/dataset.py b/bids_ng/dataset.py
new file mode 100644
index 000000000..1188af0a7
--- /dev/null
+++ b/bids_ng/dataset.py
@@ -0,0 +1,119 @@
+import os
+import re
+import typing as ty
+from functools import cached_property
+from pathlib import Path
+
+import bidsschematools as bst  # type: ignore[import]
+import bidsschematools.schema  # type: ignore[import]
+import bidsschematools.types  # type: ignore[import]
+
+from . import types as bt
+
+
+class BIDSValidationError(ValueError):
+    """Error arising from invalid files or values in a BIDS dataset"""
+
+
+class Schema:
+    schema: bst.types.Namespace
+
+    def __init__(
+        self,
+        schema: ty.Union[bst.types.Namespace, None] = None,
+    ):
+        if schema is None:
+            # Bundled
+            schema = bst.schema.load_schema()
+        self.schema = schema
+
+    @classmethod
+    def from_spec(cls, schema_spec: str) -> "Schema":
+        return cls(bst.schema.load_schema(schema_spec))
+
+    # Conveniences to avoid `schema.schema` pattern
+    @property
+    def objects(self) -> bst.types.Namespace:
+        return self.schema.objects
+
+    @property
+    def rules(self) -> bst.types.Namespace:
+        return self.schema.rules
+
+    @property
+    def meta(self) -> bst.types.Namespace:
+        return self.schema.meta
+
+
+default_schema = Schema()
+
+
+class File(bt.File[Schema]):
+    """Generic file holder
+
+    This serves as a base class for :class:`BIDSFile` and can represent
+    non-BIDS files.
+    """
+
+    def __init__(
+        self,
+        path: ty.Union[os.PathLike, str],
+        dataset: ty.Optional["BIDSDataset"] = None,
+    ):
+        self.path = Path(path)
+        self.dataset = dataset
+
+
+class BIDSFile(File, bt.BIDSFile[Schema]):
+    """BIDS file"""
+
+    pattern = re.compile(
+        r"""
+        (?:(?P<entities>(?:[a-z]+-[a-zA-Z0-9]+(?:_[a-z]+-[a-zA-Z0-9]+)*))_)?
+        (?P<suffix>[a-zA-Z0-9]+)
+        (?P<extension>\.[^/\\]+)$
+        """,
+        re.VERBOSE,
+    )
+
+    def __init__(
+        self,
+        path: ty.Union[os.PathLike, str],
+        dataset: ty.Optional["BIDSDataset"] = None,
+    ):
+        super().__init__(path, dataset)
+        self.entities = {}
+        self.datatype = None
+        self.suffix = None
+        self.extension = None
+
+        schema = default_schema if dataset is None else dataset.schema
+
+        if self.path.parent.name in schema.objects.datatypes:
+            self.datatype = self.path.parent.name
+
+        matches = self.pattern.match(self.path.name)
+        if matches is None:
+            return
+
+        entities, self.suffix, self.extension = matches.groups()
+
+        if entities:
+            found_entities = dict(ent.split("-") for ent in entities.split("_"))
+            self.entities = {
+                key: bt.Index(value) if entity.format == "index" else value
+                for key, entity in schema.rules.entities.items()
+                if (value := found_entities.get(entity.name)) is not None
+            }
+
+    @cached_property
+    def metadata(self) -> dict[str, ty.Any]:
+        """Sidecar metadata aggregated according to inheritance principle"""
+        if not self.dataset:
+            raise ValueError
+        # TODO
+        return {}
+
+
+class BIDSDataset(bt.BIDSDataset[Schema]):
+    ...