Convert LinkML to ttl during poetry install and poetry run pytest

build.py

@@ -0,0 +1,44 @@
+#!/usr/bin/env python3
+
+import os
+import subprocess
+import sys
+from linkml.generators.shaclgen import ShaclGenerator
+import linkml._version as linkml_version
+
+
+def convert_to_shacl(input_file: str, output_file: str):
+    # Generate shacl
+    shacl_shapes = ShaclGenerator(input_file).serialize()
+
+    comment = (
+        f"# This SHACL file was auto-generated with LinkML {linkml_version.__version__}.\n"
+        f"#Changes will be overwritten on install.\n"
+        f"# Source file: {input_file}\n"
+        "\n"
+    )
+
+    # Run the command and redirect output to the output file
+    with open(output_file, "w") as outfile:
+        outfile.write(comment)
+        outfile.write(shacl_shapes)
+
+
+def convert_folder_recursively(path: str, force: bool = False):
+    # recursively iterate through subfolders searching for yaml files
+    for root, _, files, in os.walk(path):
+        for file in files:
+
+            # skip non-yaml files
+            if not file.endswith(".yaml"):
+                continue
+
+            input_file = os.path.join(root, file)
+            output_file = input_file.replace(".yaml", ".ttl")
+            if force or not os.path.exists(output_file) or os.path.getmtime(input_file) > os.path.getmtime(output_file):
+                print("Converting", input_file)
+                convert_to_shacl(input_file, output_file)
+
+
+if __name__ == "__main__":
+    convert_folder_recursively("rocrate_validator/profiles", force="--force" in sys.argv)

pyproject.toml

@@ -51,9 +51,13 @@ pytest-xdist = "^3.6.1"
 max-line-length = 120
 
 [build-system]
-requires = ["poetry-core"]
+requires = ["poetry-core", "linkml"]
 build-backend = "poetry.core.masonry.api"
 
+[tool.poetry.build]
+generate-setup-file = false
+script = "build.py"
+
 [tool.poetry.scripts]
 rocrate-validator = "rocrate_validator.cli:cli"
 

tests/conftest.py

@@ -15,8 +15,9 @@
 # calculate the absolute path of the rocrate-validator package
 # and add it to the system path
 import os
+import subprocess
 
-from pytest import fixture
+from pytest import fixture, hookimpl
 
 import rocrate_validator.log as logging
 
@@ -37,6 +38,12 @@
 PROFILES_PATH = os.path.abspath(f"{CURRENT_PATH}/../rocrate_validator/profiles")
 
 
+@hookimpl(tryfirst=True)
+def pytest_configure():
+    # make sure all linkml files are converted to shacl
+    subprocess.run(["python", "build.py"], check=True)
+
+
 @fixture
 def random_path():
     return "/tmp/random_path"