forked from enviPath/enviPy
Tobias O
d06bd0d4fd
This is an initial implementation that creates a working minimal .i6z document. It passes schema validation and can be imported into IUCLID. Caveat: IUCLID files target individual compounds. Pathway is not actually covered by the format. It can be added in either soil or water and soil OECD endpoints. **I currently only implemented the soil endpoint for all data.** This sort of works, and I can report all degradation products in a pathway (not a nice view, but we can report many transformation products and add a diagram attachment in the future). Adding additional information is an absolute pain, as we need to explicitly map each type of information to the relevant OECD field. I use the XSD scheme for validation, but unfortunately the IUCLID parser is not fully compliant and requires a specific order, etc. The workflow is: finding the AI structure from the XSD scheme -> make the scheme validation pass -> upload to IUCLID to get obscure error messages -> guess what could be wrong -> repeat 💣 New specifications get released once per year, so we will have to update accordingly. I believe that this should be a more expensive feature, as it requires significant effort to uphold. Currently implemented for root compound only in SOIL: - Soil Texture 2 - Soil Texture 1 - pH value - Half-life per soil sample / scenario (mapped to disappearance; not sure about that). - CEC - Organic Matter (only Carbon) - Moisture content - Humidity <img width="2123" alt="image.png" src="attachments/d29830e1-65ef-4136-8939-1825e0959c62"> <img width="2124" alt="image.png" src="attachments/ac9de2ac-bf68-4ba4-b40b-82f810a9de93"> <img width="2139" alt="image.png" src="attachments/5674c7e6-865e-420e-974a-6b825b331e6c"> Reviewed-on: enviPath/enviPy#338 Co-authored-by: Tobias O <tobias.olenyi@envipath.com> Co-committed-by: Tobias O <tobias.olenyi@envipath.com>
203 lines
6.7 KiB
Python
203 lines
6.7 KiB
Python
from django.test import TestCase, override_settings
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from django.urls import reverse
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from django.conf import settings as s
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from epdb.logic import UserManager, PackageManager
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from epdb.models import Pathway, Edge
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@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
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class PathwayViewTest(TestCase):
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fixtures = ["test_fixtures_incl_model.jsonl.gz"]
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@classmethod
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def setUpClass(cls):
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super(PathwayViewTest, cls).setUpClass()
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cls.user1 = UserManager.create_user(
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"user1",
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"user1@envipath.com",
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"SuperSafe",
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set_setting=True,
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add_to_group=True,
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is_active=True,
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)
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cls.user1_default_package = cls.user1.default_package
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cls.package = PackageManager.create_package(cls.user1, "Test", "Test Pack")
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def setUp(self):
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self.client.force_login(self.user1)
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def test_predict_pathway(self):
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response = self.client.post(
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reverse("pathways"),
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{
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"name": "Test Pathway",
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"description": "Just a Description",
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"predict": "predict",
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"smiles": "CCN(CC)C(=O)C1=CC(=CC=C1)CO",
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},
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)
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self.assertEqual(response.status_code, 302)
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pathway_url = response["Location"]
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pw = Pathway.objects.get(url=pathway_url)
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self.assertEqual(self.user1_default_package, pw.package)
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self.assertEqual(pw.name, "Test Pathway")
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self.assertEqual(pw.description, "Just a Description")
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self.assertEqual(len(pw.root_nodes), 1)
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self.assertEqual(
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pw.root_nodes.first().default_node_label.smiles, "CCN(CC)C(=O)C1=CC(CO)=CC=C1"
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)
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first_level_nodes = {
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# Edge 1
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"CCN(CC)C(=O)C1=CC(C=O)=CC=C1",
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# Edge 2
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"CCNC(=O)C1=CC(CO)=CC=C1",
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"CC=O",
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# Edge 3
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"CCNCC",
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"O=C(O)C1=CC(CO)=CC=C1",
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}
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predicted_nodes = set()
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edges = Edge.objects.filter(start_nodes__in=[pw.root_nodes.first()])
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for edge in edges:
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for n in edge.end_nodes.all():
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predicted_nodes.add(n.default_node_label.smiles)
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self.assertEqual(first_level_nodes, predicted_nodes)
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def test_predict_package_pathway(self):
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response = self.client.post(
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reverse("package pathway list", kwargs={"package_uuid": str(self.package.uuid)}),
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{
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"name": "Test Pathway",
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"description": "Just a Description",
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"predict": "predict",
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"smiles": "CCN(CC)C(=O)C1=CC(=CC=C1)CO",
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},
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)
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self.assertEqual(response.status_code, 302)
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pathway_url = response["Location"]
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pw = Pathway.objects.get(url=pathway_url)
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self.assertEqual(self.package, pw.package)
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self.assertEqual(pw.name, "Test Pathway")
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self.assertEqual(pw.description, "Just a Description")
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self.assertEqual(len(pw.root_nodes), 1)
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self.assertEqual(
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pw.root_nodes.first().default_node_label.smiles, "CCN(CC)C(=O)C1=CC(CO)=CC=C1"
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)
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first_level_nodes = {
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# Edge 1
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"CCN(CC)C(=O)C1=CC(C=O)=CC=C1",
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# Edge 2
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"CCNC(=O)C1=CC(CO)=CC=C1",
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"CC=O",
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# Edge 3
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"CCNCC",
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"O=C(O)C1=CC(CO)=CC=C1",
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}
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predicted_nodes = set()
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edges = Edge.objects.filter(start_nodes__in=[pw.root_nodes.first()])
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for edge in edges:
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for n in edge.end_nodes.all():
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predicted_nodes.add(n.default_node_label.smiles)
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self.assertEqual(first_level_nodes, predicted_nodes)
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def test_set_aliases(self):
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alias_1 = "Alias 1"
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alias_2 = "Alias 2"
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response = self.client.post(
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reverse("package pathway list", kwargs={"package_uuid": str(self.package.uuid)}),
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{
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"name": "Test Pathway",
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"description": "Just a Description",
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"predict": "predict",
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"smiles": "CCN(CC)C(=O)C1=CC(=CC=C1)CO",
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},
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)
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self.assertEqual(response.status_code, 302)
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pathway_url = response["Location"]
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pw = Pathway.objects.get(url=pathway_url)
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response = self.client.post(
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reverse(
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"package pathway detail",
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kwargs={"package_uuid": str(pw.package.uuid), "pathway_uuid": str(pw.uuid)},
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),
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{"aliases": [alias_1, alias_2]},
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)
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pw = Pathway.objects.get(url=pathway_url)
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self.assertEqual(len(pw.aliases), 2)
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response = self.client.post(
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reverse(
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"package pathway detail",
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kwargs={"package_uuid": str(pw.package.uuid), "pathway_uuid": str(pw.uuid)},
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),
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{"aliases": [alias_1]},
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)
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pw = Pathway.objects.get(url=pathway_url)
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self.assertEqual(len(pw.aliases), 1)
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response = self.client.post(
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reverse(
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"package pathway detail",
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kwargs={"package_uuid": str(pw.package.uuid), "pathway_uuid": str(pw.uuid)},
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),
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{
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# We have to set an empty string to avoid that the parameter is removed
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"aliases": ""
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},
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)
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pw = Pathway.objects.get(url=pathway_url)
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self.assertEqual(len(pw.aliases), 0)
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@override_settings(FLAGS={**s.FLAGS, "IUCLID_EXPORT": True})
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def test_pathway_detail_shows_iuclid_export_action_when_enabled(self):
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pathway = Pathway.create(self.package, "CCO", name="IUCLID Export Pathway")
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response = self.client.get(
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reverse(
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"package pathway detail",
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kwargs={
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"package_uuid": str(pathway.package.uuid),
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"pathway_uuid": str(pathway.uuid),
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},
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)
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)
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self.assertEqual(response.status_code, 200)
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self.assertContains(response, f"/api/v1/pathway/{pathway.uuid}/export/iuclid")
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@override_settings(FLAGS={**s.FLAGS, "IUCLID_EXPORT": False})
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def test_pathway_detail_hides_iuclid_export_action_when_disabled(self):
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pathway = Pathway.create(self.package, "CCO", name="IUCLID Export Pathway")
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response = self.client.get(
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reverse(
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"package pathway detail",
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kwargs={
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"package_uuid": str(pathway.package.uuid),
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"pathway_uuid": str(pathway.uuid),
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},
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)
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)
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self.assertEqual(response.status_code, 200)
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self.assertNotContains(response, f"/api/v1/pathway/{pathway.uuid}/export/iuclid")
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