ncats · KeithKelleher · Mar 28, 2023
diff --git a/Dockerfile b/Dockerfile
@@ -0,0 +1,12 @@
+FROM openjdk:8-jdk as buildContainer
+
+RUN apt-get update
+RUN apt-get install -y maven
+
+WORKDIR /opt/app
+COPY . /opt/app
+
+RUN chmod +x ./make.sh
+RUN bash ./make.sh
+
+CMD bash
diff --git a/README.md b/README.md
@@ -22,7 +22,7 @@ target/lychi-0.5.1-jar-with-dependencies.jar
 The self-contained jar file can be invoked directly. For example:
 
 ```
-java -jar target/lychi-0.5.1-jar-with-dependencies.jar tests/standardizer_case1.smi
+java -jar target/lychi-0.7.1-jar-with-dependencies.jar tests/standardizer_case1.smi
 ```
 
 
diff --git a/api/api.py b/api/api.py
@@ -0,0 +1,55 @@
+from flask import Flask, request, jsonify, render_template
+import subprocess
+import tempfile
+import os
+
+lychify = Flask("lychify")
+
+@lychify.route('/')
+def index():
+    return render_template('index.html')
+
+@lychify.route('/standardize', methods=['POST'])
+def standardize():
+    # Get the list of SMILES objects from the request
+    smiles_list = request.json['smiles_list']
+    counter = 0
+    if len(smiles_list) == 0:
+        return jsonify({'result': []})
+    # Write the SMILES objects to a temporary file
+    with tempfile.NamedTemporaryFile(delete=False, mode='w') as f:
+        for obj in smiles_list:
+            if ("id" in obj):
+                f.write(obj['smiles'] + '\t' + str(obj['id']) + '\n')
+            else:
+                counter += 1
+                f.write(obj["smiles"] + '\t' + "no_id:" + str(counter) + '\n')
+        filepath = f.name
+
+    # Create the command to call the Java application with the input file
+    command = ['java', '-jar', 'lychi-0.7.1-jar-with-dependencies.jar', filepath]
+
+    # Call the Java application using subprocess
+    process = subprocess.run(command, capture_output=True, text=True)
+
+    # Remove the temporary file
+    os.remove(filepath)
+
+    # Check if the command completed successfully
+    if process.returncode != 0:
+        return jsonify({'error': 'Failed to run Java application',
+                        'output': process.stdout.strip().split('\n')})
+
+    # Parse the output from the Java application and format the response
+    output = process.stdout.strip().split('\n')
+    formatted_output = []
+    for i, line in enumerate(output):
+        smiles, id, lychi = line.split('\t')
+        formatted_output.append({'smiles': smiles, 'id': id, 'lychi': lychi})
+
+    # Return the formatted output as a JSON response
+    return jsonify({'result': formatted_output})
+
+
+if __name__ == '__main__':
+    lychify.run(debug=True)
diff --git a/api/lychi-0.7.1-jar-with-dependencies.jar b/api/lychi-0.7.1-jar-with-dependencies.jar
diff --git a/api/templates/index.html b/api/templates/index.html
@@ -0,0 +1,18 @@
+<!doctype html>
+<html>
+<head>
+    <title>lychify</title>
+</head>
+<body>
+<h1>Welcome to lychify!</h1>
+<p>This is a web service to calculate lychi keys for any given chemical structure. See the repo here: <a href="https://github.com/ncats/lychi">https://github.com/ncats/lychi</a>.</p>
+<p>To use this application, send a POST request to /standardize with a JSON payload containing a list of SMILES strings. The response will contain a JSON payload with the standardized SMILES strings.</p>
+<p>Here's an example payload:</p>
+<pre>{
+  "smiles_list": [
+    {"smiles": "CCO", "id": "1"},
+    {"smiles": "COC", "id": "2"}
+  ]
+}</pre>
+</body>
+</html>
diff --git a/api/testapi.py b/api/testapi.py
@@ -0,0 +1,31 @@
+import requests
+
+url = 'http://localhost:5000/standardize'
+
+response = requests.post(url, json={'smiles_list': []})
+print (response.json())
+
+long_smiles = "".join(['C' for i in range(10)])
+response = requests.post(url, json={'smiles_list': [{"smiles": long_smiles}]})
+print(response.json())
+
+invalid_list = [
+    {'smiles':'invalid','id':'1'},
+    {'smiles':'SMILES','id':'2'},
+    {'smiles':'strings','id':'3'}
+]
+response = requests.post(url, json={'smiles_list': invalid_list})
+print(response.json())  # Should return an error message or an empty result
+
+duplicate_list = [
+    {"smiles": "C", "id": "1"},
+    {"smiles": "CC", "id": "2"},
+    {"smiles": "C", "id": "3"},
+    {"smiles": "CCC", "id": "4"}
+]
+response = requests.post(url, json={'smiles_list': duplicate_list})
+print(response.json())
+
+aminophylline = [{"smiles":"Cn1c2nc[nH]c2c(=O)n(C)c1=O", "id": "aminophylline"}]
+response = requests.post(url, json={'smiles_list': aminophylline})
+print(response.json())
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -0,0 +1,7 @@
+version: '3'
+services:
+  dev:
+    build:
+      context: .
+      dockerfile: Dockerfile
+    tty: true