when schema is loaded selectors then get loaded. Now need to implement the hooks and adding metadata etc..

Author: AugustijnVrolijk

bidsbuilder/bidsDataset.py

@@ -1,20 +1,20 @@
-import bidsschematools, bidsschematools.schema
-
 from pathlib import Path
 
 from bidsbuilder.modules import *
 from bidsbuilder.util.util import checkPath, isDir, clearSchema
 from bidsbuilder.util.datasetTree import FileTree
+from bidsbuilder.util.schema import no_cache_load_schema
 from bidsbuilder.modules.commonFiles import resolveCoreClassType
+from bidsbuilder.interpreter.selectors import selectorHook
 from typing import TYPE_CHECKING
 
 if TYPE_CHECKING:
     from collections.abc import MutableMapping 
 
 class BidsDataset():
     initialised = False
-    schema = bidsschematools.schema.load_schema()
-    schema.pop("meta")
+
+    schema = no_cache_load_schema()
 
     def __init__(self, root:str = Path.cwd()):
         self.root = root
@@ -48,13 +48,18 @@ def _pop_from_schema(schema:'MutableMapping'):
 
         _pop_from_schema(self.schema.rules.files.common.tables)
         clearSchema(self.schema.rules.files.common, "tables")
-
-        print(self._tree_reference.children)
-            
         return
 
     def _interpret_skeletonBIDS(self):
+        f1 = self.tree.fetch("README")
+        f2 = self.tree.fetch("dataset_description.json")
+        #recursive_interpret(1, self.schema.rules.files.common)
+        print(self.schema.rules.dataset_metadata.dataset_description.selectors.funcs[0])
+        
+        print(self.schema.rules.dataset_metadata.dataset_description.selectors(f1))
+        print(self.schema.rules.dataset_metadata.dataset_description.selectors(f2))
 
+        print("hello")
         return
 
     @property

bidsbuilder/interpreter/fields_funcs.py

@@ -1,11 +1,10 @@
 import re
 
 from typing import Any, Union, TYPE_CHECKING
-from functools import wraps
 from bidsbuilder.util.datasetTree import FileTree
+from bidsbuilder.modules.coreModule import DatasetCore
 
 if TYPE_CHECKING:
-    from bidsbuilder.modules.coreModule import DatasetCore
     from bidsbuilder.bidsDataset import BidsDataset
 
 def schema():
@@ -17,7 +16,8 @@ def dataset(core:'DatasetCore') -> 'BidsDataset':
 def subject():
     return notImplemented()
 
-def path(core:'DatasetCore') -> str:
+def path(core:DatasetCore) -> str:
+    assert isinstance(core, DatasetCore)
     return core._tree_reference.relative_path
 
 def entities():

bidsbuilder/interpreter/selectors.py

@@ -55,10 +55,9 @@ def from_raw(cls, r_selector:list[str]) -> 'selectorHook':
         funcs = []
         for selector in r_selector:
             parser = SelectorParser.from_raw(selector)
-            abstract_syntax_tree = parser.parse()
-            func = selectorFunc(abstract_syntax_tree)
-            func.evaluate_static_nodes()
-            funcs.append(func)
+            sel_function = parser.parse()
+            sel_function.evaluate_static_nodes()
+            funcs.append(sel_function)
 
         return cls(funcs)
 
@@ -67,7 +66,7 @@ def __init__(self, funcs):
         return
 
     def __call__(self, *args, **kwargs):
-            
+
         #all(func(*args, **kwargs) for func in self.funcs) can be slower
         for func in self.funcs:
             if not func(*args, **kwargs):
@@ -430,7 +429,8 @@ def primary(self):
 
         elif cur.kind == "STRING":
             val = self.match("STRING")
-            return val
+            #need to trim outer " " or ' '
+            return val[1:-1]
 
         elif cur.kind == "LPAREN":
             self.match("LPAREN")

bidsbuilder/util/datasetTree.py

@@ -198,7 +198,7 @@ def relative_path(self) -> str:
         Directories include trailing slashes for simpler matching.
         """
         if self.parent is None:
-            return ''
+            return '/'
 
         return posixpath.join(self.parent.relative_path,f'{self.name}/')
 

bidsbuilder/util/schema.py

@@ -0,0 +1,74 @@
+import bidsschematools
+
+from functools import lru_cache
+from bidsschematools.types import Namespace
+from bidsschematools.schema import dereference, flatten_enums, _get_bids_version, _get_schema_version
+from bidsschematools.utils import get_bundled_schema_path
+
+from bidsbuilder.interpreter.selectors import selectorHook
+
+def recursive_interpret(rec_n, schema):
+        #recurse into a file, i.e.
+        #rec_n = 0 means we have a file, so then loops for each selector block, and then chooses selectors
+        #rec_n = 1 means we have a folder of files,
+        #rec_n = 2 means we have a folder of folders that need to be iterated all
+    if rec_n >= 1:
+        for key in schema.keys():
+            schema[key] = recursive_interpret((rec_n-1), schema[key])
+
+    else:
+        for sel in schema.keys():
+            t_selector = selectorHook.from_raw(schema[sel].selectors)
+            #the raw schema is cached
+            schema[sel]["selectors"] = t_selector
+
+    return schema
+
+@lru_cache
+def parse_load_schema(schema_path=None):
+    """Load and Parse the schema into a dictionary.
+
+    This function allows the schema, like BIDS itself, to be specified in
+    a hierarchy of directories and files.
+    Filenames (minus extensions) and directory names become keys
+    in the associative array (dict) of entries composed from content
+    of files and entire directories.
+
+    Parameters
+    ----------
+    schema_path : str, optional
+        Directory containing yaml files or yaml file. If ``None``, use the
+        default schema packaged with ``bidsschematools``.
+
+    Returns
+    -------
+    dict
+        Schema in dictionary form.
+
+    Notes
+    -----
+        This function is cached, so it will only be called once per schema path.
+    """
+    if schema_path is None:
+        schema_path = get_bundled_schema_path()
+        #lgr.info("No schema path specified, defaulting to the bundled schema, `%s`.", schema_path)
+    schema = Namespace.from_directory(schema_path)
+    if not schema.objects:
+        raise ValueError(f"objects subdirectory path not found in {schema_path}")
+    if not schema.rules:
+        raise ValueError(f"rules subdirectory path not found in {schema_path}")
+
+    dereference(schema)
+    flatten_enums(schema)
+
+    schema["bids_version"] = _get_bids_version(schema_path)
+    schema["schema_version"] = _get_schema_version(schema_path)
+    schema.pop("meta")
+    schema.rules["dataset_metadata"] = recursive_interpret(0, schema.rules.dataset_metadata)
+    #IMPORTANT, CAN ONLY SET BY DOING schema["KEY"] = , setting by doing schema.key = DOES NOT WORK
+    #maybe look at making a wrapper class of namespace which fixes the __setitem__
+    #recursive_interpret(1, self.schema.rules.files.common)
+
+    #look at iterating over the whole schema and interpreting all "selectors" 
+
+    return schema