using ontology_helper to check against POSIXPath before download (#…

…197)

* using ontology_helper and check against FilreReference

* no more TODO

* checking ontology availability before posixPath check

* test with no ontology

* adapted test

* adapted test

* test with extra annotations

* proper fixture

* is_ontology_available property and TODO

* adapted test

* resetting ontology availability

* test with simple regex

nb2workflow/nbadapter.py

@@ -65,6 +65,7 @@ class ModOntology(Ontology):
     def __init__(self, ontology_path):
         super().__init__(ontology_path)
         self.lock = Lock()
+        self._is_ontology_available = True
 
     def get_datatype_restriction(self, param_uri):
         self.lock.acquire()
@@ -74,6 +75,11 @@ def get_datatype_restriction(self, param_uri):
             logger.warning(f'Unknown datatype for owl_uri {param_uri}')
         return dt
 
+    @property
+    def is_ontology_available(self):
+        # TODO will be developed properly in the ontology_helper
+        return self._is_ontology_available
+
 ontology = ModOntology(oda_ontology_path)
 oda_prefix = str([x[1] for x in ontology.g.namespaces() if x[0] == 'oda'][0])
 
@@ -813,9 +819,15 @@ def download_file(self, file_url, tmpdir):
     def handle_url_params(self, parameters, tmpdir, context={}):
         adapted_parameters = copy.deepcopy(parameters)
         exceptions = []
+        posix_path_with_annotations_pattern = re.compile(rf"^{re.escape(oda_prefix)}.*_POSIXPath_")
         for input_par_name, input_par_obj in self.input_parameters.items():
-            # TODO use oda_api.ontology_helper
-            if input_par_obj['owl_type'] == f"{oda_prefix}POSIXPath":
+            if ontology.is_ontology_available:
+                parameter_hierarchy = ontology.get_parameter_hierarchy(input_par_obj['owl_type'])
+                is_posix_path = f"{oda_prefix}POSIXPath" in parameter_hierarchy
+            else:
+                is_posix_path = f"{oda_prefix}POSIXPath" == input_par_obj['owl_type'] or \
+                                posix_path_with_annotations_pattern.match(input_par_obj['owl_type']) is not None
+            if is_posix_path:
                 arg_par_value = parameters.get(input_par_name, None)
                 if arg_par_value is None:
                     arg_par_value = input_par_obj['default_value']

tests/conftest.py

@@ -10,6 +10,9 @@
 
 import nb2workflow.service
 from importlib import reload
+import rdflib as rdf
+
+from oda_api.ontology_helper import ODA, ODAS
 
 @pytest.fixture
 def test_notebook():
@@ -51,6 +54,7 @@ def app(test_notebook):
     app = nb2workflow.service.app
     app.notebook_adapters = nb2workflow.nbadapter.find_notebooks(test_notebook)
     nb2workflow.service.setup_routes(app)
+    nb2workflow.nbadapter.ontology._is_ontology_available = True
     print("creating app")
     return app
 
@@ -63,10 +67,19 @@ def app_low_download_limit():
     for nb, nba_obj in app_low_download_limit.notebook_adapters.items():
         nba_obj.max_download_size = 1
     nb2workflow.service.setup_routes(app_low_download_limit)
+    nb2workflow.nbadapter.ontology._is_ontology_available = True
     print("creating app with low limit on the download of files")
     return app_low_download_limit
 
 
+# TODO improve this, as it requires changes also in the oda_api
+@pytest.fixture
+def app_not_available_ontology():
+    nb2workflow.nbadapter.ontology._is_ontology_available = False
+    yield
+
+
+
 def kill_child_processes(parent_pid, sig=signal.SIGTERM):
     try:
         parent = psutil.Process(parent_pid)

tests/test_input_types.py

@@ -15,18 +15,30 @@ def app():
     app = nb2workflow.service.app
     app.notebook_adapters = nb2workflow.nbadapter.find_notebooks(testfiles_path)
     nb2workflow.service.setup_routes(app)
+    nb2workflow.nbadapter.ontology._is_ontology_available = True
     print("creating app")
     return app
 
-
 def test_posix_download_file(client):
     r = client.get('/api/v1.0/get/testposixpath')
     assert r.json['output']['output_file_download'] == 'file not downloaded'
 
+def test_posix_download_file_no_ontology(client, app_not_available_ontology):
+    r = client.get('/api/v1.0/get/testposixpath', query_string={'fits_file_path': 'https://fits.gsfc.nasa.gov/samples/testkeys.fits'})
+    assert r.json['output']['output_file_download'] == 'file downloaded successfully'
+
+def test_posix_download_file_no_ontology_extra_annotations(client, app_not_available_ontology):
+    r = client.get('/api/v1.0/get/testposixpath_extra_annotated', query_string={'fits_file_path': 'https://fits.gsfc.nasa.gov/samples/testkeys.fits'})
+    assert r.json['output']['output_file_download'] == 'file downloaded successfully'
+
 def test_posix_download_file_with_arg(client):
     r = client.get('/api/v1.0/get/testposixpath', query_string={'fits_file_path': 'https://fits.gsfc.nasa.gov/samples/testkeys.fits'})
     assert r.json['output']['output_file_download'] == 'file downloaded successfully'
 
+def test_posix_download_file_extra_annotations(client):
+    r = client.get('/api/v1.0/get/testposixpath_extra_annotated', query_string={'fits_file_path': 'https://fits.gsfc.nasa.gov/samples/testkeys.fits'})
+    assert r.json['output']['output_file_download'] == 'file downloaded successfully'
+
 def test_posix_download_file_with_arg_low_download_limit(client, app_low_download_limit):
     r = client.get('/api/v1.0/get/testposixpath', query_string={'fits_file_path': 'https://fits.gsfc.nasa.gov/samples/testkeys.fits'})
     assert r.json['output'] == {}

tests/test_nbadapter.py

@@ -84,7 +84,7 @@ def test_find_notebooks(caplog):
     assert 'Ignoring pattern.' in caplog.text
 
     nbas = find_notebooks(nb_dir)
-    assert len(nbas) == 8
+    assert len(nbas) == 9
 
     nbas = find_notebooks(nb_dir, pattern=r'.*bool')
     assert len(nbas) == 1

tests/testfiles/testposixpath_extra_annotated.ipynb

@@ -0,0 +1,74 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "parameters"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "fits_file_path = \"test.fits\" # oda:POSIXPath ; oda:label \"Test file path\" ; oda:description \"Description test file path\" ."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "output_file_download = 'file not downloaded'\n",
+    "if os.path.exists(fits_file_path) is True:\n",
+    "    output_file_download = 'file downloaded successfully'"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "outputs"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "output_file_download"
+   ]
+  }
+ ],
+ "metadata": {
+  "interpreter": {
+   "hash": "767d51c1340bd893661ea55ea3124f6de3c7a262a8b4abca0554b478b1e2ff90"
+  },
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}