some vague sketching on mapping namespaces

docs/notes/translation.md

@@ -0,0 +1,27 @@
+# translation
+
+what operations do we need when translating between schema languages?
+
+- Iteration - control over "for what" in the source or target domain.
+  eg. we need to map "all attributes and properties to slots" but then the
+  other direction of selection where we need to do one of everything per item
+  in the source domain as well
+- dependence - source and target domain have different notions of linking
+- level shifting - need to translate when something is a language-level
+  item to a schema-level item/object/class
+
+
+
+Steps:
+- each namespaces or schema object creates one linkml schema file
+- namespaces: one map, just imports all the other schema
+- schema: actually create the object in the schema.
+  - Classes:
+    - Groups
+    - Enums (see below)
+  - Slots
+    - Attributes
+- new files: files not in the source domain
+  - enum classes
+
+- Rename items

nwb_linkml/io.py

@@ -27,8 +27,6 @@ def load_yaml(path:Path) -> dict:
 
     # apply maps
     maps = [m for m in Map.instances if m.phase == PHASES.postload]
-    print('got maps')
-    print(maps)
     for amap in maps:
         ns_dict = amap.apply(ns_dict)
     return ns_dict

nwb_linkml/linkml.py

@@ -0,0 +1,3 @@
+from linkml.generators.linkmlgen import LinkmlGenerator
+from linkml_runtime.linkml_model import SchemaDefinition
+from linkml_runtime.dumpers import yaml_dumper

nwb_linkml/maps/namespace.py

@@ -0,0 +1,29 @@
+"""
+Practice translation of namespaces to linkml just as a warmup to
+see what kind of operations we'll need
+
+Notes:
+    - Handling "namespace" imports within namespaces separately as prefixes
+"""
+from typing import List
+from dataclasses import dataclass
+
+
+from nwb_schema_language import Namespace
+from linkml.utils.schema_builder import SchemaBuilder
+
+from linkml_runtime.linkml_model import SchemaDefinition
+
+
+
+# top-level attributes
+def build_schema(namespace: Namespace) -> SchemaDefinition:
+    return SchemaDefinition(
+        id=namespace.name,
+        name=namespace.name,
+        title=namespace.full_name,
+        version=namespace.version,
+        imports=[schema.source for schema in namespace.schema_ if schema.source is not None]
+    )
+
+

nwb_linkml/maps/source.py

@@ -0,0 +1,13 @@
+"""
+Draft of a source to target mapping in pseudo-markup
+"""
+
+namespace_map = {
+    "source": "Namespace",
+    "outputs": [
+        {}
+    ],
+    "maps": [
+
+    ]
+}

nwb_schema_language/src/nwb_schema_language/datamodel/nwb_schema_language.py

@@ -1,9 +1,9 @@
 # Auto generated from nwb_schema_language.yaml by pythongen.py version: 0.0.1
 # Generation date: 2023-08-18T00:36:55
-# Schema: nwb-schema-language
+# Schema: nwb_schema_language
 #
 # id: https://w3id.org/p2p_ld/nwb-schema-language
-# description: Translation of the nwb-schema-language to LinkML
+# description: Translation of the nwb_schema_language to LinkML
 # license: GNU GPL v3.0
 
 import dataclasses

nwb_schema_language/src/nwb_schema_language/datamodel/schemaview.py

@@ -0,0 +1,7 @@
+from pathlib import Path
+from linkml_runtime.utils.schemaview import SchemaView
+
+SCHEMA_FILE = Path(__file__).parent.parent.resolve() / 'schema' / 'nwb_schema_language.yaml'
+
+schema_view = SchemaView(SCHEMA_FILE)
+

poetry.lock

@@ -1,5 +1,29 @@
 # This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
 
+[[package]]
+name = "antlr4-python3-runtime"
+version = "4.9.3"
+description = "ANTLR 4.9.3 runtime for Python 3.7"
+optional = false
+python-versions = "*"
+files = [
+    {file = "antlr4-python3-runtime-4.9.3.tar.gz", hash = "sha256:f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b"},
+]
+
+[[package]]
+name = "arrow"
+version = "1.2.3"
+description = "Better dates & times for Python"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "arrow-1.2.3-py3-none-any.whl", hash = "sha256:5a49ab92e3b7b71d96cd6bfcc4df14efefc9dfa96ea19045815914a6ab6b1fe2"},
+    {file = "arrow-1.2.3.tar.gz", hash = "sha256:3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1"},
+]
+
+[package.dependencies]
+python-dateutil = ">=2.7.0"
+
 [[package]]
 name = "attrs"
 version = "23.1.0"
@@ -29,6 +53,30 @@ files = [
     {file = "certifi-2023.7.22.tar.gz", hash = "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082"},
 ]
 
+[[package]]
+name = "cfgraph"
+version = "0.2.1"
+description = "rdflib collections flattening graph"
+optional = false
+python-versions = "*"
+files = [
+    {file = "CFGraph-0.2.1.tar.gz", hash = "sha256:b57fe7044a10b8ff65aa3a8a8ddc7d4cd77bf511b42e57289cd52cbc29f8fe74"},
+]
+
+[package.dependencies]
+rdflib = ">=0.4.2"
+
+[[package]]
+name = "chardet"
+version = "5.2.0"
+description = "Universal encoding detector for Python 3"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "chardet-5.2.0-py3-none-any.whl", hash = "sha256:e1cf59446890a00105fe7b7912492ea04b6e6f06d4b742b2c788469e34c82970"},
+    {file = "chardet-5.2.0.tar.gz", hash = "sha256:1b3b6ff479a8c414bc3fa2c0852995695c4a026dcd6d0633b2dd092ca39c1cf7"},
+]
+
 [[package]]
 name = "charset-normalizer"
 version = "3.2.0"
@@ -162,6 +210,17 @@ pandas = ["pandas"]
 rdflib = ["rdflib"]
 tests = ["coverage", "pytest"]
 
+[[package]]
+name = "decorator"
+version = "5.1.1"
+description = "Decorators for Humans"
+optional = false
+python-versions = ">=3.5"
+files = [
+    {file = "decorator-5.1.1-py3-none-any.whl", hash = "sha256:b8c3f85900b9dc423225913c5aace94729fe1fa9763b38939a95226f02d37186"},
+    {file = "decorator-5.1.1.tar.gz", hash = "sha256:637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330"},
+]
+
 [[package]]
 name = "deprecated"
 version = "1.2.14"
@@ -179,6 +238,44 @@ wrapt = ">=1.10,<2"
 [package.extras]
 dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "sphinx (<2)", "tox"]
 
+[[package]]
+name = "et-xmlfile"
+version = "1.1.0"
+description = "An implementation of lxml.xmlfile for the standard library"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "et_xmlfile-1.1.0-py3-none-any.whl", hash = "sha256:a2ba85d1d6a74ef63837eed693bcb89c3f752169b0e3e7ae5b16ca5e1b3deada"},
+    {file = "et_xmlfile-1.1.0.tar.gz", hash = "sha256:8eb9e2bc2f8c97e37a2dc85a09ecdcdec9d8a396530a6d5a33b30b9a92da0c5c"},
+]
+
+[[package]]
+name = "fqdn"
+version = "1.5.1"
+description = "Validates fully-qualified domain names against RFC 1123, so that they are acceptable to modern bowsers"
+optional = false
+python-versions = ">=2.7, !=3.0, !=3.1, !=3.2, !=3.3, !=3.4, <4"
+files = [
+    {file = "fqdn-1.5.1-py3-none-any.whl", hash = "sha256:3a179af3761e4df6eb2e026ff9e1a3033d3587bf980a0b1b2e1e5d08d7358014"},
+    {file = "fqdn-1.5.1.tar.gz", hash = "sha256:105ed3677e767fb5ca086a0c1f4bb66ebc3c100be518f0e0d755d9eae164d89f"},
+]
+
+[[package]]
+name = "graphviz"
+version = "0.20.1"
+description = "Simple Python interface for Graphviz"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "graphviz-0.20.1-py3-none-any.whl", hash = "sha256:587c58a223b51611c0cf461132da386edd896a029524ca61a1462b880bf97977"},
+    {file = "graphviz-0.20.1.zip", hash = "sha256:8c58f14adaa3b947daf26c19bc1e98c4e0702cdc31cf99153e6f06904d492bf8"},
+]
+
+[package.extras]
+dev = ["flake8", "pep8-naming", "tox (>=3)", "twine", "wheel"]
+docs = ["sphinx (>=5)", "sphinx-autodoc-typehints", "sphinx-rtd-theme"]
+test = ["coverage", "mock (>=4)", "pytest (>=7)", "pytest-cov", "pytest-mock (>=3)"]
+
 [[package]]
 name = "greenlet"
 version = "2.0.1"
@@ -318,6 +415,37 @@ files = [
 [package.dependencies]
 six = "*"
 
+[[package]]
+name = "isoduration"
+version = "20.11.0"
+description = "Operations with ISO 8601 durations"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "isoduration-20.11.0-py3-none-any.whl", hash = "sha256:b2904c2a4228c3d44f409c8ae8e2370eb21a26f7ac2ec5446df141dde3452042"},
+    {file = "isoduration-20.11.0.tar.gz", hash = "sha256:ac2f9015137935279eac671f94f89eb00584f940f5dc49462a0c4ee692ba1bd9"},
+]
+
+[package.dependencies]
+arrow = ">=0.15.0"
+
+[[package]]
+name = "jinja2"
+version = "3.1.2"
+description = "A very fast and expressive template engine."
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "Jinja2-3.1.2-py3-none-any.whl", hash = "sha256:6088930bfe239f0e6710546ab9c19c9ef35e29792895fed6e6e31a023a182a61"},
+    {file = "Jinja2-3.1.2.tar.gz", hash = "sha256:31351a702a408a9e7595a8fc6150fc3f43bb6bf7e319770cbc0db9df9437e852"},
+]
+
+[package.dependencies]
+MarkupSafe = ">=2.0"
+
+[package.extras]
+i18n = ["Babel (>=2.7)"]
+
 [[package]]
 name = "json-flattener"
 version = "0.1.9"
@@ -333,6 +461,17 @@ files = [
 click = "*"
 pyyaml = "*"
 
+[[package]]
+name = "jsonasobj"
+version = "1.3.1"
+description = "JSON as python objects"
+optional = false
+python-versions = "*"
+files = [
+    {file = "jsonasobj-1.3.1-py3-none-any.whl", hash = "sha256:b9e329dc1ceaae7cf5d5b214684a0b100e0dad0be6d5bbabac281ec35ddeca65"},
+    {file = "jsonasobj-1.3.1.tar.gz", hash = "sha256:d52e0544a54a08f6ea3f77fa3387271e3648655e0eace2f21e825c26370e44a2"},
+]
+
 [[package]]
 name = "jsonasobj2"
 version = "1.0.4"
@@ -347,6 +486,48 @@ files = [
 [package.dependencies]
 hbreader = "*"
 
+[[package]]
+name = "jsonpatch"
+version = "1.33"
+description = "Apply JSON-Patches (RFC 6902)"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*"
+files = [
+    {file = "jsonpatch-1.33-py2.py3-none-any.whl", hash = "sha256:0ae28c0cd062bbd8b8ecc26d7d164fbbea9652a1a3693f3b956c1eae5145dade"},
+    {file = "jsonpatch-1.33.tar.gz", hash = "sha256:9fcd4009c41e6d12348b4a0ff2563ba56a2923a7dfee731d004e212e1ee5030c"},
+]
+
+[package.dependencies]
+jsonpointer = ">=1.9"
+
+[[package]]
+name = "jsonpath-ng"
+version = "1.5.3"
+description = "A final implementation of JSONPath for Python that aims to be standard compliant, including arithmetic and binary comparison operators and providing clear AST for metaprogramming."
+optional = false
+python-versions = "*"
+files = [
+    {file = "jsonpath-ng-1.5.3.tar.gz", hash = "sha256:a273b182a82c1256daab86a313b937059261b5c5f8c4fa3fc38b882b344dd567"},
+    {file = "jsonpath_ng-1.5.3-py2-none-any.whl", hash = "sha256:f75b95dbecb8a0f3b86fd2ead21c2b022c3f5770957492b9b6196ecccfeb10aa"},
+    {file = "jsonpath_ng-1.5.3-py3-none-any.whl", hash = "sha256:292a93569d74029ba75ac2dc3d3630fc0e17b2df26119a165fa1d498ca47bf65"},
+]
+
+[package.dependencies]
+decorator = "*"
+ply = "*"
+six = "*"
+
+[[package]]
+name = "jsonpointer"
+version = "2.4"
+description = "Identify specific nodes in a JSON document (RFC 6901)"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*"
+files = [
+    {file = "jsonpointer-2.4-py2.py3-none-any.whl", hash = "sha256:15d51bba20eea3165644553647711d150376234112651b4f1811022aecad7d7a"},
+    {file = "jsonpointer-2.4.tar.gz", hash = "sha256:585cee82b70211fa9e6043b7bb89db6e1aa49524340dde8ad6b63206ea689d88"},
+]
+
 [[package]]
 name = "jsonschema"
 version = "4.19.0"
@@ -360,9 +541,17 @@ files = [
 
 [package.dependencies]
 attrs = ">=22.2.0"
+fqdn = {version = "*", optional = true, markers = "extra == \"format\""}
+idna = {version = "*", optional = true, markers = "extra == \"format\""}
+isoduration = {version = "*", optional = true, markers = "extra == \"format\""}
+jsonpointer = {version = ">1.13", optional = true, markers = "extra == \"format\""}
 jsonschema-specifications = ">=2023.03.6"
 referencing = ">=0.28.4"
+rfc3339-validator = {version = "*", optional = true, markers = "extra == \"format\""}
+rfc3987 = {version = "*", optional = true, markers = "extra == \"format\""}
 rpds-py = ">=0.7.1"
+uri-template = {version = "*", optional = true, markers = "extra == \"format\""}
+webcolors = {version = ">=1.11", optional = true, markers = "extra == \"format\""}
 
 [package.extras]
 format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"]
@@ -382,6 +571,61 @@ files = [
 [package.dependencies]
 referencing = ">=0.28.0"
 
+[[package]]
+name = "linkml"
+version = "1.5.7"
+description = "Linked Open Data Modeling Language"
+optional = false
+python-versions = ">=3.7.6,<4.0.0"
+files = [
+    {file = "linkml-1.5.7-py3-none-any.whl", hash = "sha256:677f4c5809dc51b151b86accc69e77482ad86b9c1326a212cef9b4a2a9a96c10"},
+    {file = "linkml-1.5.7.tar.gz", hash = "sha256:bca3dd56837ced79749656843e1e20b8d1db1a89287e7b29d1ee145e4a75ad4d"},
+]
+
+[package.dependencies]
+antlr4-python3-runtime = ">=4.9.0,<4.10"
+click = ">=7.0"
+graphviz = ">=0.10.1"
+hbreader = "*"
+isodate = ">=0.6.0"
+jinja2 = ">=3.1.0"
+jsonasobj2 = ">=1.0.3,<2.0.0"
+jsonschema = {version = ">=4.0.0", extras = ["format"]}
+linkml-dataops = "*"
+linkml-runtime = ">=1.5.4"
+openpyxl = "*"
+parse = "*"
+prefixcommons = ">=0.1.7"
+prefixmaps = ">=0.1.3"
+pydantic = "*"
+pyjsg = ">=0.11.6"
+pyshex = ">=0.7.20"
+pyshexc = ">=0.8.3"
+python-dateutil = "*"
+pyyaml = "*"
+rdflib = ">=6.0.0"
+requests = ">=2.22"
+sqlalchemy = ">=1.4.31"
+watchdog = ">=0.9.0"
+
+[[package]]
+name = "linkml-dataops"
+version = "0.1.0"
+description = "LinkML Data Operations API"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "linkml_dataops-0.1.0-py3-none-any.whl", hash = "sha256:193cf7f659e5f07946d2c2761896910d5f7151d91282543b1363801f68307f4c"},
+    {file = "linkml_dataops-0.1.0.tar.gz", hash = "sha256:4550eab65e78b70dc3b9c651724a94ac2b1d1edb2fbe576465f1d6951a54ed04"},
+]
+
+[package.dependencies]
+jinja2 = "*"
+jsonpatch = "*"
+jsonpath-ng = "*"
+linkml-runtime = ">=1.1.6"
+"ruamel.yaml" = "*"
+
 [[package]]
 name = "linkml-runtime"
 version = "1.5.6"
@@ -432,6 +676,65 @@ profiling = ["gprof2dot"]
 rtd = ["jupyter_sphinx", "mdit-py-plugins", "myst-parser", "pyyaml", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx_book_theme"]
 testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 
+[[package]]
+name = "markupsafe"
+version = "2.1.3"
+description = "Safely add untrusted strings to HTML/XML markup."
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "MarkupSafe-2.1.3-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:cd0f502fe016460680cd20aaa5a76d241d6f35a1c3350c474bac1273803893fa"},
+    {file = "MarkupSafe-2.1.3-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:e09031c87a1e51556fdcb46e5bd4f59dfb743061cf93c4d6831bf894f125eb57"},
+    {file = "MarkupSafe-2.1.3-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:68e78619a61ecf91e76aa3e6e8e33fc4894a2bebe93410754bd28fce0a8a4f9f"},
+    {file = "MarkupSafe-2.1.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:65c1a9bcdadc6c28eecee2c119465aebff8f7a584dd719facdd9e825ec61ab52"},
+    {file = "MarkupSafe-2.1.3-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:525808b8019e36eb524b8c68acdd63a37e75714eac50e988180b169d64480a00"},
+    {file = "MarkupSafe-2.1.3-cp310-cp310-musllinux_1_1_aarch64.whl", hash = "sha256:962f82a3086483f5e5f64dbad880d31038b698494799b097bc59c2edf392fce6"},
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+    {file = "MarkupSafe-2.1.3-cp310-cp310-win32.whl", hash = "sha256:10bbfe99883db80bdbaff2dcf681dfc6533a614f700da1287707e8a5d78a8431"},
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+    {file = "MarkupSafe-2.1.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:bfce63a9e7834b12b87c64d6b155fdd9b3b96191b6bd334bf37db7ff1fe457f2"},
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+    {file = "MarkupSafe-2.1.3.tar.gz", hash = "sha256:af598ed32d6ae86f1b747b82783958b1a4ab8f617b06fe68795c7f026abbdcad"},
+]
+
 [[package]]
 name = "mdurl"
 version = "0.1.2"
@@ -454,13 +757,28 @@ develop = true
 
 [package.dependencies]
 linkml-runtime = "^1.1.24"
+pydantic = "<2"
 
 [package.extras]
 docs = []
 
 [package.source]
 type = "directory"
-url = "nwb-schema-language"
+url = "nwb_schema_language"
+
+[[package]]
+name = "openpyxl"
+version = "3.1.2"
+description = "A Python library to read/write Excel 2010 xlsx/xlsm files"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "openpyxl-3.1.2-py2.py3-none-any.whl", hash = "sha256:f91456ead12ab3c6c2e9491cf33ba6d08357d802192379bb482f1033ade496f5"},
+    {file = "openpyxl-3.1.2.tar.gz", hash = "sha256:a6f5977418eff3b2d5500d54d9db50c8277a368436f4e4f8ddb1be3422870184"},
+]
+
+[package.dependencies]
+et-xmlfile = "*"
 
 [[package]]
 name = "packaging"
@@ -473,6 +791,17 @@ files = [
     {file = "packaging-23.1.tar.gz", hash = "sha256:a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f"},
 ]
 
+[[package]]
+name = "parse"
+version = "1.19.1"
+description = "parse() is the opposite of format()"
+optional = false
+python-versions = "*"
+files = [
+    {file = "parse-1.19.1-py2.py3-none-any.whl", hash = "sha256:371ed3800dc63983832159cc9373156613947707bc448b5215473a219dbd4362"},
+    {file = "parse-1.19.1.tar.gz", hash = "sha256:cc3a47236ff05da377617ddefa867b7ba983819c664e1afe46249e5b469be464"},
+]
+
 [[package]]
 name = "pluggy"
 version = "1.2.0"
@@ -488,6 +817,17 @@ files = [
 dev = ["pre-commit", "tox"]
 testing = ["pytest", "pytest-benchmark"]
 
+[[package]]
+name = "ply"
+version = "3.11"
+description = "Python Lex & Yacc"
+optional = false
+python-versions = "*"
+files = [
+    {file = "ply-3.11-py2.py3-none-any.whl", hash = "sha256:096f9b8350b65ebd2fd1346b12452efe5b9607f7482813ffca50c22722a807ce"},
+    {file = "ply-3.11.tar.gz", hash = "sha256:00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3"},
+]
+
 [[package]]
 name = "prefixcommons"
 version = "0.1.12"
@@ -593,6 +933,21 @@ files = [
 [package.extras]
 plugins = ["importlib-metadata"]
 
+[[package]]
+name = "pyjsg"
+version = "0.11.10"
+description = "Python JSON Schema Grammar interpreter"
+optional = false
+python-versions = "*"
+files = [
+    {file = "PyJSG-0.11.10-py3-none-any.whl", hash = "sha256:10af60ff42219be7e85bf7f11c19b648715b0b29eb2ddbd269e87069a7c3f26d"},
+    {file = "PyJSG-0.11.10.tar.gz", hash = "sha256:4bd6e3ff2833fa2b395bbe803a2d72a5f0bab5b7285bccd0da1a1bc0aee88bfa"},
+]
+
+[package.dependencies]
+antlr4-python3-runtime = ">=4.9.3,<4.10.0"
+jsonasobj = ">=1.2.1"
+
 [[package]]
 name = "pyparsing"
 version = "3.1.1"
@@ -607,6 +962,47 @@ files = [
 [package.extras]
 diagrams = ["jinja2", "railroad-diagrams"]
 
+[[package]]
+name = "pyshex"
+version = "0.8.1"
+description = "Python ShEx Implementation"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "PyShEx-0.8.1-py3-none-any.whl", hash = "sha256:6da1b10123e191abf8dcb6bf3e54aa3e1fcf771df5d1a0ed453217c8900c8e6a"},
+    {file = "PyShEx-0.8.1.tar.gz", hash = "sha256:3c5c4d45fe27faaadae803cb008c41acf8ee784da7868b04fd84967e75be70d0"},
+]
+
+[package.dependencies]
+cfgraph = ">=0.2.1"
+chardet = "*"
+pyshexc = "0.9.1"
+rdflib-shim = "*"
+requests = ">=2.22.0"
+shexjsg = ">=0.8.2"
+sparqlslurper = ">=0.5.1"
+sparqlwrapper = ">=1.8.5"
+urllib3 = "*"
+
+[[package]]
+name = "pyshexc"
+version = "0.9.1"
+description = "PyShExC - Python ShEx compiler"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "PyShExC-0.9.1-py2.py3-none-any.whl", hash = "sha256:efc55ed5cb2453e9df569b03e282505e96bb06597934288f3b23dd980ef10028"},
+    {file = "PyShExC-0.9.1.tar.gz", hash = "sha256:35a9975d4b9afeb20ef710fb6680871756381d0c39fbb5470b3b506581a304d3"},
+]
+
+[package.dependencies]
+antlr4-python3-runtime = ">=4.9.3,<4.10.0"
+chardet = "*"
+jsonasobj = ">=1.2.1"
+pyjsg = ">=0.11.10"
+rdflib-shim = "*"
+shexjsg = ">=0.8.1"
+
 [[package]]
 name = "pytest"
 version = "7.4.0"
@@ -640,6 +1036,20 @@ files = [
 [package.dependencies]
 pytest = ">=2.8.1"
 
+[[package]]
+name = "python-dateutil"
+version = "2.8.2"
+description = "Extensions to the standard Python datetime module"
+optional = false
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
+files = [
+    {file = "python-dateutil-2.8.2.tar.gz", hash = "sha256:0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86"},
+    {file = "python_dateutil-2.8.2-py2.py3-none-any.whl", hash = "sha256:961d03dc3453ebbc59dbdea9e4e11c5651520a876d0f4db161e8674aae935da9"},
+]
+
+[package.dependencies]
+six = ">=1.5"
+
 [[package]]
 name = "pytrie"
 version = "0.4.0"
@@ -723,6 +1133,35 @@ html = ["html5lib (>=1.0,<2.0)"]
 lxml = ["lxml (>=4.3.0,<5.0.0)"]
 networkx = ["networkx (>=2.0.0,<3.0.0)"]
 
+[[package]]
+name = "rdflib-jsonld"
+version = "0.6.1"
+description = "rdflib extension adding JSON-LD parser and serializer"
+optional = false
+python-versions = "*"
+files = [
+    {file = "rdflib-jsonld-0.6.1.tar.gz", hash = "sha256:eda5a42a2e09f80d4da78e32b5c684bccdf275368f1541e6b7bcddfb1382a0e0"},
+    {file = "rdflib_jsonld-0.6.1-py2.py3-none-any.whl", hash = "sha256:bcf84317e947a661bae0a3f2aee1eced697075fc4ac4db6065a3340ea0f10fc2"},
+]
+
+[package.dependencies]
+rdflib = ">=5.0.0"
+
+[[package]]
+name = "rdflib-shim"
+version = "1.0.3"
+description = "Shim for rdflib 5 and 6 incompatibilities"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "rdflib_shim-1.0.3-py3-none-any.whl", hash = "sha256:7a853e7750ef1e9bf4e35dea27d54e02d4ed087de5a9e0c329c4a6d82d647081"},
+    {file = "rdflib_shim-1.0.3.tar.gz", hash = "sha256:d955d11e2986aab42b6830ca56ac6bc9c893abd1d049a161c6de2f1b99d4fc0d"},
+]
+
+[package.dependencies]
+rdflib = ">=5.0.0"
+rdflib-jsonld = "0.6.1"
+
 [[package]]
 name = "referencing"
 version = "0.30.2"
@@ -759,6 +1198,31 @@ urllib3 = ">=1.21.1,<3"
 socks = ["PySocks (>=1.5.6,!=1.5.7)"]
 use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
+[[package]]
+name = "rfc3339-validator"
+version = "0.1.4"
+description = "A pure python RFC3339 validator"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+files = [
+    {file = "rfc3339_validator-0.1.4-py2.py3-none-any.whl", hash = "sha256:24f6ec1eda14ef823da9e36ec7113124b39c04d50a4d3d3a3c2859577e7791fa"},
+    {file = "rfc3339_validator-0.1.4.tar.gz", hash = "sha256:138a2abdf93304ad60530167e51d2dfb9549521a836871b88d7f4695d0022f6b"},
+]
+
+[package.dependencies]
+six = "*"
+
+[[package]]
+name = "rfc3987"
+version = "1.3.8"
+description = "Parsing and validation of URIs (RFC 3986) and IRIs (RFC 3987)"
+optional = false
+python-versions = "*"
+files = [
+    {file = "rfc3987-1.3.8-py2.py3-none-any.whl", hash = "sha256:10702b1e51e5658843460b189b185c0366d2cf4cff716f13111b0ea9fd2dce53"},
+    {file = "rfc3987-1.3.8.tar.gz", hash = "sha256:d3c4d257a560d544e9826b38bc81db676890c79ab9d7ac92b39c7a253d5ca733"},
+]
+
 [[package]]
 name = "rich"
 version = "13.5.2"
@@ -883,6 +1347,84 @@ files = [
     {file = "rpds_py-0.9.2.tar.gz", hash = "sha256:8d70e8f14900f2657c249ea4def963bed86a29b81f81f5b76b5a9215680de945"},
 ]
 
+[[package]]
+name = "ruamel-yaml"
+version = "0.17.32"
+description = "ruamel.yaml is a YAML parser/emitter that supports roundtrip preservation of comments, seq/map flow style, and map key order"
+optional = false
+python-versions = ">=3"
+files = [
+    {file = "ruamel.yaml-0.17.32-py3-none-any.whl", hash = "sha256:23cd2ed620231677564646b0c6a89d138b6822a0d78656df7abda5879ec4f447"},
+    {file = "ruamel.yaml-0.17.32.tar.gz", hash = "sha256:ec939063761914e14542972a5cba6d33c23b0859ab6342f61cf070cfc600efc2"},
+]
+
+[package.dependencies]
+"ruamel.yaml.clib" = {version = ">=0.2.7", markers = "platform_python_implementation == \"CPython\" and python_version < \"3.12\""}
+
+[package.extras]
+docs = ["ryd"]
+jinja2 = ["ruamel.yaml.jinja2 (>=0.2)"]
+
+[[package]]
+name = "ruamel-yaml-clib"
+version = "0.2.7"
+description = "C version of reader, parser and emitter for ruamel.yaml derived from libyaml"
+optional = false
+python-versions = ">=3.5"
+files = [
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+python-versions = "*"
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+pandas = ["pandas (>=1.3.5)"]
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+
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+aiosqlite = ["aiosqlite", "greenlet (!=0.4.17)", "typing-extensions (!=3.10.0.1)"]
+asyncio = ["greenlet (!=0.4.17)"]
+asyncmy = ["asyncmy (>=0.2.3,!=0.2.4,!=0.2.6)", "greenlet (!=0.4.17)"]
+mariadb-connector = ["mariadb (>=1.0.1,!=1.1.2,!=1.1.5)"]
+mssql = ["pyodbc"]
+mssql-pymssql = ["pymssql"]
+mssql-pyodbc = ["pyodbc"]
+mypy = ["mypy (>=0.910)"]
+mysql = ["mysqlclient (>=1.4.0)"]
+mysql-connector = ["mysql-connector-python"]
+oracle = ["cx-oracle (>=7)"]
+oracle-oracledb = ["oracledb (>=1.0.1)"]
+postgresql = ["psycopg2 (>=2.7)"]
+postgresql-asyncpg = ["asyncpg", "greenlet (!=0.4.17)"]
+postgresql-pg8000 = ["pg8000 (>=1.29.1)"]
+postgresql-psycopg = ["psycopg (>=3.0.7)"]
+postgresql-psycopg2binary = ["psycopg2-binary"]
+postgresql-psycopg2cffi = ["psycopg2cffi"]
+postgresql-psycopgbinary = ["psycopg[binary] (>=3.0.7)"]
+pymysql = ["pymysql"]
+sqlcipher = ["sqlcipher3-binary"]
+
 [[package]]
 name = "typing-extensions"
 version = "4.7.1"
@@ -916,6 +1572,20 @@ files = [
     {file = "typing_extensions-4.7.1.tar.gz", hash = "sha256:b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2"},
 ]
 
+[[package]]
+name = "uri-template"
+version = "1.3.0"
+description = "RFC 6570 URI Template Processor"
+optional = false
+python-versions = ">=3.7"
+files = [
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+
+[package.extras]
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+
 [[package]]
 name = "urllib3"
 version = "2.0.4"
@@ -933,6 +1603,60 @@ secure = ["certifi", "cryptography (>=1.9)", "idna (>=2.0.0)", "pyopenssl (>=17.
 socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
 zstd = ["zstandard (>=0.18.0)"]
 
+[[package]]
+name = "watchdog"
+version = "3.0.0"
+description = "Filesystem events monitoring"
+optional = false
+python-versions = ">=3.7"
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+    {file = "watchdog-3.0.0.tar.gz", hash = "sha256:4d98a320595da7a7c5a18fc48cb633c2e73cda78f93cac2ef42d42bf609a33f9"},
+]
+
+[package.extras]
+watchmedo = ["PyYAML (>=3.10)"]
+
+[[package]]
+name = "webcolors"
+version = "1.13"
+description = "A library for working with the color formats defined by HTML and CSS."
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "webcolors-1.13-py3-none-any.whl", hash = "sha256:29bc7e8752c0a1bd4a1f03c14d6e6a72e93d82193738fa860cbff59d0fcc11bf"},
+    {file = "webcolors-1.13.tar.gz", hash = "sha256:c225b674c83fa923be93d235330ce0300373d02885cef23238813b0d5668304a"},
+]
+
+[package.extras]
+docs = ["furo", "sphinx", "sphinx-copybutton", "sphinx-inline-tabs", "sphinx-notfound-page", "sphinxext-opengraph"]
+tests = ["pytest", "pytest-cov"]
+
 [[package]]
 name = "wrapt"
 version = "1.15.0"
@@ -1035,4 +1759,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.11"
-content-hash = "32b9026599bc647c7c91a582f2629cd4bf23ca6bbedecd62ac455cfde4c8ed5c"
+content-hash = "90f5eaedd0572c26dfac8a9f2fed0c8ec50f70a54b7bff03a43816f96cb60bb1"

pyproject.toml

@@ -7,18 +7,25 @@ license = "GPL-3.0"
 readme = "README.md"
 packages = [
     {include = "nwb_linkml"},
-#    {include = "nwb_schema_language", from="nwb-schema-language/src"}
+    {include = "nwb_schema_language", from="nwb_schema_language/src"}
 ]
 
 [tool.poetry.dependencies]
 python = "^3.11"
 pyyaml = "^6.0"
 linkml-runtime = "^1.5.6"
-nwb_schema_language = { path = './nwb-schema-language', develop = true }
+nwb_schema_language = { path = './nwb_schema_language', develop = true }
 pydantic = "<2"
 rich = "^13.5.2"
+linkml = "^1.5.7"
 
 
+[tool.poetry.group.dev.dependencies]
+pytest = "^7.4.0"
+
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"
+
+
+[tool.pytest.ini_options]

tests/fixtures.py

@@ -0,0 +1,22 @@
+import pytest
+from typing import Dict
+
+
+from nwb_linkml import io
+import shutil
+from pathlib import Path
+
+@pytest.fixture(scope="session")
+def tmp_output_dir() -> Path:
+    path = Path(__file__).parent.resolve() / '__tmp__'
+    if path.exists():
+        shutil.rmtree(str(path))
+    path.mkdir()
+
+    return path
+
+
+@pytest.fixture(scope="session")
+def nwb_core_fixture() -> Dict[str, io.NamespaceBundle]:
+    nwb_core = io.load_nwb_core()
+    return nwb_core

tests/test_namespace.py

@@ -0,0 +1,13 @@
+import pytest
+
+from .fixtures import nwb_core_fixture, tmp_output_dir
+
+from nwb_linkml.maps.namespace import build_schema
+from linkml_runtime.dumpers import yaml_dumper
+
+def test_namespace_to_linkml(nwb_core_fixture, tmp_output_dir):
+    output_file = tmp_output_dir / 'nwb.namespace.yml'
+    schema = build_schema(nwb_core_fixture['nwb-core']['namespace'].namespaces[0])
+
+    yaml_dumper.dump(schema, output_file)
+