Fix load of models that depend on non thread-safe dependencies

A problem was detected when loading TensorFlow models in different threads inside the same JVM. That happened after load a TensorFlow model and then try to import a new TensorFlow model. This was caused by a dependency of TensorFlow (protobuf) that was being reloaded but it already existed in the JVM (through the 1st thread).

The workaround was to share the problematic module (Tensorflow) across the sub-interpreters of Python. This is a workaround for the issues with CPython extensions.

Author: Paulo Pereira

openml-python-common/README.md

@@ -40,3 +40,15 @@ export PATH=$ANACONDA_PATH/envs/myenv/bin:$PATH
 export LD_LIBRARY_PATH=$ANACONDA_PATH/envs/myenv/lib/python3.6/site-packages/jep:$LD_LIBRARY_PATH
 export LD_PRELOAD=$ANACONDA_PATH/envs/myenv/lib/libpython3.6m.so
 ```
+
+7. If you need to share Python modules across sub-interpreters, you will need to create a "python-packages.xml" file where you define the modules to be shared. By default the provider is already sharing the "numpy" and "tensorflow" modules. This is a workaround for the issues with CPython extensions.
+    - Remember that this file should be added to the classpath of your program.
+
+```
+<?xml version="1.0"?>
+<python>
+   <package>my_package_1</package>
+   <package>my_package_2</package>
+</python>
+
+``` 

openml-python-common/pom.xml

@@ -42,16 +42,16 @@
             <groupId>com.feedzai</groupId>
             <artifactId>openml-utils</artifactId>
         </dependency>
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-databind</artifactId>
+            <scope>provided</scope>
+        </dependency>
         <dependency>
             <groupId>com.feedzai</groupId>
             <artifactId>openml-utils</artifactId>
             <scope>test</scope>
             <type>test-jar</type>
         </dependency>
-        <dependency>
-            <groupId>com.fasterxml.jackson.core</groupId>
-            <artifactId>jackson-databind</artifactId>
-            <scope>provided</scope>
-        </dependency>
     </dependencies>
 </project>

openml-python-common/src/main/java/com/feedzai/openml/python/jep/instance/JepInstance.java

@@ -15,12 +15,16 @@
  */
 package com.feedzai.openml.python.jep.instance;
 
+import com.feedzai.openml.python.modules.SharedModulesParser;
+import com.google.common.collect.ImmutableSet;
 import com.google.common.util.concurrent.Uninterruptibles;
 import jep.Jep;
+import jep.JepConfig;
 import jep.JepException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.util.Set;
 import java.util.concurrent.BlockingQueue;
 import java.util.concurrent.LinkedBlockingQueue;
 import java.util.concurrent.TimeUnit;
@@ -97,8 +101,18 @@ public void stop() {
      */
     @Override
     public void run() {
-
-        try (final Jep jep = new Jep(false)) {
+        final Set<String> sharedModules = ImmutableSet.<String>builder()
+                .add("tensorflow")
+                .add("numpy")
+                .addAll(new SharedModulesParser().getSharedModules())
+                .build();
+        logger.debug("Python modules to be shared: {}", String.join(",", sharedModules.toString()));
+
+        final JepConfig jepConfig = new JepConfig()
+                .addSharedModules(sharedModules.toArray(new String[0]))
+                .setInteractive(false);
+
+        try (final Jep jep = new Jep(jepConfig)) {
             while (this.running) {
                 this.evaluationQueue.take().evaluate(jep);
             }

openml-python-common/src/main/java/com/feedzai/openml/python/modules/SharedModulesParser.java

@@ -0,0 +1,117 @@
+/*
+ * Copyright (c) 2018 Feedzai
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ *  Unless required by applicable law or agreed to in writing, software
+ *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  See the License for the specific language governing permissions and
+ *  limitations under the License.
+ */
+
+package com.feedzai.openml.python.modules;
+
+import com.google.common.collect.ImmutableSet;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.w3c.dom.Document;
+import org.w3c.dom.NodeList;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import java.io.InputStream;
+import java.util.Set;
+
+/**
+ * Class responsible for parsing a XML file in order to retrieve the name of the Python modules to be shared across
+ * sub-interpreters.
+ *
+ * @author Paulo Pereira (paulo.pereira@feedzai.com)
+ * @since 0.1.5
+ */
+public class SharedModulesParser {
+
+    /**
+     * Logger.
+     */
+    private static final Logger logger = LoggerFactory.getLogger(SharedModulesParser.class);
+
+    /**
+     * Default value for {@link #xmlFile}.
+     */
+    private static final String DEFAULT_XML_FILE = "python-packages.xml";
+
+    /**
+     * The filename of a XML file with the name of the Python modules to be shared across sub-interpreters.
+     */
+    private final String xmlFile;
+
+    /**
+     * Constructor.
+     *
+     * @param xmlFileName The name of a XML file.
+     */
+    public SharedModulesParser(final String xmlFileName) {
+        this.xmlFile = xmlFileName;
+    }
+
+    /**
+     * Constructor.
+     */
+    public SharedModulesParser() {
+        this(DEFAULT_XML_FILE);
+    }
+
+    /**
+     * Gets the {@link InputStream} of {@link #xmlFile} that exists in the current classpath.
+     *
+     * @return The {@link InputStream} of {@link #xmlFile}.
+     */
+    private InputStream getXMLInputStream() {
+        final ClassLoader classLoader = getClass().getClassLoader();
+        return classLoader.getResourceAsStream(this.xmlFile);
+    }
+
+    /**
+     * Parses the {@link #xmlFile} to retrieve the name of the Python modules to be shared across sub-interpreters.
+     *
+     * @return A {@link Set} with the name of the Python modules to be shared across sub-interpreters.
+     * @throws Exception If there is an error while parsing {@link #xmlFile}.
+     */
+    private Set<String> parseXMLFile() throws Exception {
+        final ImmutableSet.Builder<String> sharedModulesBuilder = ImmutableSet.builder();
+        final DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
+        final DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
+
+        try (final InputStream xmlFile = getXMLInputStream()) {
+            final Document doc = dBuilder.parse(xmlFile);
+            doc.getDocumentElement().normalize();
+
+            final NodeList nList = doc.getElementsByTagName("package");
+            for (int i = 0; i < nList.getLength(); i++) {
+                sharedModulesBuilder.add(nList.item(i).getFirstChild().getNodeValue());
+            }
+        }
+        return sharedModulesBuilder.build();
+    }
+
+    /**
+     * Retrieves a {@link Set} with the name of the Python modules to be shared across sub-interpreters.
+     *
+     * @return The name of the Python modules to be shared across sub-interpreters.
+     */
+    public Set<String> getSharedModules() {
+        Set<String> sharedModules = ImmutableSet.of();
+        try {
+            sharedModules = parseXMLFile();
+        } catch (final Exception e) {
+            logger.warn("Problem while getting the XML file with the Python modules to be shared.", e);
+        }
+        return sharedModules;
+    }
+}

openml-python-common/src/main/java/com/feedzai/openml/python/modules/package-info.java

@@ -0,0 +1,23 @@
+/*
+ * Copyright (c) 2018 Feedzai
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ *  Unless required by applicable law or agreed to in writing, software
+ *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  See the License for the specific language governing permissions and
+ *  limitations under the License.
+ */
+
+/**
+ * This package contains logic for parsing XML files to retrieve the name of the Python modules to be shared across
+ * sub-interpreters.
+ *
+ * @since 0.1.5
+ */
+package com.feedzai.openml.python.modules;

openml-python-common/src/test/java/com/feedzai/openml/python/jep/instance/JepInstanceTest.java

@@ -0,0 +1,67 @@
+/*
+ * Copyright (c) 2018 Feedzai
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ *  Unless required by applicable law or agreed to in writing, software
+ *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  See the License for the specific language governing permissions and
+ *  limitations under the License.
+ */
+
+package com.feedzai.openml.python.jep.instance;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+/**
+ * Contains the tests for the wrapper for the Jep object.
+ *
+ * @author Paulo Pereira (paulo.pereira@feedzai.com)
+ * @since 0.1.5
+ */
+public class JepInstanceTest {
+
+    /**
+     * The wrapper for the Jep object used in the tests.
+     */
+    private JepInstance jepInstance;
+
+    /**
+     * Initializes an instance of {@link JepInstance}.
+     */
+    @Before
+    public void setUp() {
+        this.jepInstance = new JepInstance();
+        this.jepInstance.start();
+    }
+
+    /**
+     * Tears downs the instance of {@link JepInstance}.
+     */
+    @After
+    public void tearDown() {
+        this.jepInstance.stop();
+    }
+
+    /**
+     * Tests the submission of evaluations on a {@link JepInstance}.
+     *
+     * @throws Exception If there is a problem while getting the result.
+     */
+    @Test
+    public void submitEvaluationTest() throws Exception {
+        final String result = this.jepInstance.submitEvaluation((jep) -> jep.getValue("1 + 2")).get().toString();
+        assertThat(result)
+            .as("The result of the evaluation")
+            .isEqualTo("3");
+    }
+}

openml-python-common/src/test/java/com/feedzai/openml/python/jep/instance/package-info.java

@@ -0,0 +1,22 @@
+/*
+ * Copyright (c) 2018 Feedzai
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ *  Unless required by applicable law or agreed to in writing, software
+ *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  See the License for the specific language governing permissions and
+ *  limitations under the License.
+ */
+
+/**
+ * This package contains the unit-tests for {@link com.feedzai.openml.python.jep.instance}.
+ *
+ * @since 0.1.5
+ */
+package com.feedzai.openml.python.jep.instance;

openml-python-common/src/test/java/com/feedzai/openml/python/modules/SharedModulesParserTest.java

@@ -0,0 +1,71 @@
+/*
+ * Copyright (c) 2018 Feedzai
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ *  Unless required by applicable law or agreed to in writing, software
+ *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  See the License for the specific language governing permissions and
+ *  limitations under the License.
+ */
+
+package com.feedzai.openml.python.modules;
+
+import org.assertj.core.util.Files;
+import org.junit.Test;
+
+import java.io.File;
+import java.util.Set;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+/**
+ * Tests the retrieving of the modules to be shared across sub-interpreters from a XML file.
+ *
+ * @author Paulo Pereira (paulo.pereira@feedzai.com)
+ * @since 0.1.5
+ */
+public class SharedModulesParserTest {
+
+    /**
+     * Tests the retrieving of the shared modules from a valid XML file with name of two modules to be shared.
+     */
+    @Test
+    public void validXMLFileTest() {
+        final Set<String> sharedPythonPackages = new SharedModulesParser().getSharedModules();
+        assertThat(sharedPythonPackages)
+                .as("Set of shared modules.")
+                .hasSize(2)
+                .contains("my_package_1", "my_package_2");
+    }
+
+    /**
+     * Tests the retrieving of the shared modules from an empty file.
+     */
+    @Test
+    public void emptyFileTest() {
+        final File file = Files.newTemporaryFile();
+        file.deleteOnExit();
+
+        final SharedModulesParser sharedModulesParser = new SharedModulesParser(file.getAbsolutePath());
+        assertThat(sharedModulesParser.getSharedModules())
+                .as("Set of shared modules.")
+                .hasSize(0);
+    }
+
+    /**
+     * Tests the retrieving of the shared modules from a non existing file.
+     */
+    @Test
+    public void nonExistingFileTest() {
+        final SharedModulesParser sharedModulesParser = new SharedModulesParser("non_existing_file");
+        assertThat(sharedModulesParser.getSharedModules())
+                .as("Set of shared modules.")
+                .hasSize(0);
+    }
+}