Merge pull request #529 from Steinbeck-Lab/development

Development

.github/workflows/test.yml

@@ -1,4 +1,4 @@
-name: API workflow
+name: test
 
 on:
   push:
@@ -31,10 +31,6 @@ jobs:
         python -m pip install --upgrade pip
         pip3 install --upgrade setuptools pip
         pip3 install --no-cache-dir -r requirements.txt
-        pip3 install rdkit
-        python3 -m pip uninstall -y imantics
-        pip3 install imantics==0.1.12
-        pip3 install openbabel-wheel
         pip3 install --no-deps decimer-segmentation==1.1.3
         pip3 install --no-deps decimer==2.3.0
         pip3 install --no-deps STOUT-pypi==2.0.5

app/modules/toolkits/cdk_wrapper.py

@@ -28,7 +28,7 @@ def setup_jvm():
 
     if not isJVMStarted():
         paths = {
-            "cdk-2.9": "https://github.com/cdk/cdk/releases/download/cdk-2.9/cdk-2.9.jar",
+            "cdk-2.10": "https://github.com/cdk/cdk/releases/download/cdk-2.10/cdk-2.10.jar",
             "SugarRemovalUtility-jar-with-dependencies": "https://github.com/JonasSchaub/SugarRemoval/releases/download/v1.3.2/SugarRemovalUtility-jar-with-dependencies.jar",
             "centres": "https://github.com/SiMolecule/centres/releases/download/1.0/centres.jar",
             "opsin-cli-2.8.0-jar-with-dependencies": "https://github.com/dan2097/opsin/releases/download/2.8.0/opsin-cli-2.8.0-jar-with-dependencies.jar",

tests/test_classyfire.py

@@ -1,4 +1,3 @@
-"""
 import pytest
 from app.modules.classyfire import classify, result
 import asyncio
@@ -19,7 +18,11 @@ def test_valid_classyfire(valid_smiles):
     result_ = loop.run_until_complete(classify(valid_smiles))
     assert result_["query_type"] == "STRUCTURE"
     id_ = result_["id"]
-    classified = loop.run_until_complete(result(id_))
+    while True:
+        classified = loop.run_until_complete(result(id_))
+        if classified["classification_status"] == "Done":
+            break
+        asyncio.run(asyncio.sleep(2))
     assert classified["classification_status"] == "Done"
     assert classified["entities"][0]["class"]["name"] == "Imidazopyrimidines"
 
@@ -29,10 +32,13 @@ def test_invalid_classyfire(invalid_smiles):
     result_ = loop.run_until_complete(classify(invalid_smiles))
     assert result_["query_input"] == "invalid_smiles"
     id_ = result_["id"]
-    classified = loop.run_until_complete(result(id_))
+    while True:
+        classified = loop.run_until_complete(result(id_))
+        if classified["classification_status"] == "Done":
+            break
+        asyncio.run(asyncio.sleep(2))
     assert classified["classification_status"] == "Done"
     assert (
         classified["invalid_entities"][0]["report"][0]
         == "Cannot process the input SMILES string, please check again"
     )
-"""

tests/test_functions.py

@@ -158,7 +158,7 @@ def test_all_rdkit_descriptors(test_smiles_descriptors):
         0,
         1.0,
         0,
-        62.12,
+        61.98,
     )
     assert expected_result == descriptors