From 071f20b4f369331ee4ccafec138897ac62bc90e8 Mon Sep 17 00:00:00 2001
From: Kohulan <kohulan.rajan@uni-jena.de>
Date: Mon, 13 Jan 2025 14:33:22 +0100
Subject: [PATCH 1/3] feat: upgrade to CDK 2.10

---
 .github/workflows/test.yml          | 4 ----
 app/modules/toolkits/cdk_wrapper.py | 2 +-
 tests/test_classyfire.py            | 8 +++++---
 3 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index a4f6b55..4d5b15e 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -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
diff --git a/app/modules/toolkits/cdk_wrapper.py b/app/modules/toolkits/cdk_wrapper.py
index 6f2e9ba..c33704f 100644
--- a/app/modules/toolkits/cdk_wrapper.py
+++ b/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",
diff --git a/tests/test_classyfire.py b/tests/test_classyfire.py
index 263d3c1..1ae6663 100644
--- a/tests/test_classyfire.py
+++ b/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"
 
@@ -35,4 +38,3 @@ def test_invalid_classyfire(invalid_smiles):
         classified["invalid_entities"][0]["report"][0]
         == "Cannot process the input SMILES string, please check again"
     )
-"""

From c9c488310d1128b05be2fccce4df85859d07433a Mon Sep 17 00:00:00 2001
From: Kohulan <kohulan.rajan@uni-jena.de>
Date: Mon, 13 Jan 2025 14:47:44 +0100
Subject: [PATCH 2/3] fix: classyfire test

---
 tests/test_classyfire.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/tests/test_classyfire.py b/tests/test_classyfire.py
index 1ae6663..185c638 100644
--- a/tests/test_classyfire.py
+++ b/tests/test_classyfire.py
@@ -32,7 +32,11 @@ 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]

From f2074011fc7c3a4c6f1986abaebafb4ca37da134 Mon Sep 17 00:00:00 2001
From: Kohulan <kohulan.rajan@uni-jena.de>
Date: Mon, 13 Jan 2025 14:58:49 +0100
Subject: [PATCH 3/3] fix: functions test

---
 .github/workflows/test.yml | 2 +-
 tests/test_functions.py    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 4d5b15e..344ce26 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -1,4 +1,4 @@
-name: API workflow
+name: test
 
 on:
   push:
diff --git a/tests/test_functions.py b/tests/test_functions.py
index 1bee37f..e7db5e2 100644
--- a/tests/test_functions.py
+++ b/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