remove hdf5_linkml - it doesn't make sense to be separate since it requires all the rest of the main package

hdf5_linkml/README.md

@@ -1,3 +0,0 @@
-# hdf5_linkml
-
-HDF5 adapter to linkml models

hdf5_linkml/pyproject.toml

@@ -1,20 +0,0 @@
-[tool.poetry]
-name = "hdf5-linkml"
-version = "0.1.0"
-description = "Adapt and load hdf5 files to linkml-pydantic models"
-authors = ["sneakers-the-rat <JLSaunders987@gmail.com>"]
-license = "AGPL-3.0"
-readme = "README.md"
-packages = [{include = "hdf5_linkml", from="src"}]
-
-[tool.poetry.dependencies]
-python = "^3.11"
-h5py = "^3.9.0"
-nwb_linkml = { path = '..', develop = true, optional = true }
-linkml = "^1.5.7"
-
-
-
-[build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"

hdf5_linkml/src/hdf5_linkml/io.py

@@ -1,31 +0,0 @@
-"""
-Base I/O class for loading and saving hdf5 files
-"""
-from typing import List
-
-from linkml_runtime.linkml_model import SchemaDefinition
-
-class H5File:
-    pass
-
-    # --------------------------------------------------
-    # Hooks
-    # --------------------------------------------------
-    def load_embedded_schema(self, h5f) -> List[dict]:
-        """
-        Load schema that are embedded within the hdf5 file
-        Returns:
-
-        """
-        pass
-
-    def translate_schema(self, schema: List[dict]) -> List[SchemaDefinition]:
-        """
-        Optionally translate schema from source language into LinkML
-
-        Args:
-            dict:
-
-        Returns:
-
-        """

hdf5_linkml/src/hdf5_linkml/nwb.py

@@ -1,68 +0,0 @@
-import pdb
-from pathlib import Path
-import h5py
-import json
-from hdf5_linkml.io import H5File
-from nwb_linkml.adapters import NamespacesAdapter
-from nwb_linkml.io import load_schema_file
-from linkml_runtime.linkml_model import SchemaDefinition
-
-DATASET = '/Users/jonny/Dropbox/lab/p2p_ld/data/nwb/sub-738651046_ses-760693773.nwb'
-
-
-class NWBH5File(H5File):
-
-    def __init__(self, file: Path):
-        self.file = Path(file)
-
-    def read(self):
-        with h5py.File(self.file, 'r') as h5f:
-            embedded_schema = self.load_embedded_schema(h5f)
-            translated_schema = self.translate_schema(embedded_schema)
-            pdb.set_trace()
-
-    def load_embedded_schema(self, h5f:h5py.File) -> List[dict]:
-        """
-        Stored in ``/specfications/{namespace}/{version}/{schema_files}``
-
-        Args:
-            h5f:
-
-        Returns:
-            [
-                {
-                    'namespace': "DECODED_JSON_OBJECT",
-                    'nwb.base': "DECODED_JSON_OBJECT",
-                    ...
-                },
-                {
-                    'namespace': "DECODED_JSON_OBJECT",
-                }
-            ]
-
-        """
-
-        namespaces = []
-        for ns_name, ns in h5f['specifications'].items():
-            ns_schema = {}
-            for version in ns.values():
-                for schema_name, schema in version.items():
-                    # read the source json binary string
-                    sch_str = schema[()]
-                    sch_dict = json.loads(sch_str)
-                    ns_schema[schema_name] = sch_dict
-            namespaces.append(ns_schema)
-        return namespaces
-
-    def translate_schema(self, schema:List[dict]) -> List[SchemaDefinition]:
-        translated = []
-        for ns_schema in schema:
-            # find namespace
-            namespace = ns_schema['namespace']
-            ns_schema_adapters = [load_schema_file(sch_name, schema_dict) for sch_name, schema_dict in ns_schema.items() if sch_name != 'namespace']
-            adapter = NamespacesAdapter(
-                namespaces=namespace,
-                schemas=ns_schema_adapters
-            )
-            res = adapter.build()
-            translated.extend(res.schema)

hdf5_linkml/tests/test_scratch.py

@@ -1,2 +0,0 @@
-
-