Merge pull request #1 from twosigma/jarek/base_individual_component

jarek/base: create beakerx kernel base as individual component

.gitignore

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+# IntelliJ
+.idea/
+.iml
+
+# Gradle
+.gradle/
+/build/
+*/build/

README.md

@@ -1 +1,7 @@
-# an empty repository
+# BeakerX: Beaker kernel base  
+
+### Build and Install (linux and mac)
+
+```
+./gradlew clean install
+```

base-api/build.gradle

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+version 'unspecified'
+
+repositories {
+    mavenCentral()
+}
+
+dependencies {
+    compile group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: '2.6.5'
+    compile group: 'org.apache.commons', name: 'commons-lang3', version: '3.6'
+    compile group: 'org.apache.commons', name: 'commons-text', version: '1.1'
+    compile group: 'commons-io', name: 'commons-io', version: '2.5'
+    compile group: 'org.slf4j', name: 'slf4j-log4j12', version: '1.7.25'
+    compile group: 'net.sf.py4j', name: 'py4j', version: '0.10.7'
+    compile group: "commons-codec", name: "commons-codec", version: "1.9"
+    compile group: 'com.google.code.gson', name: 'gson', version: '2.3.1'
+    testCompile group: 'junit', name: 'junit', version: '4.12'
+}
+
+publishing {
+    publications {
+        maven(MavenPublication) {
+            groupId 'com.twosigma'
+            artifactId 'beakerx-kernel-base-api'
+            version "$beakerxVersion"
+            from components.java
+        }
+    }
+}

base-api/src/main/java/com/twosigma/beakerx/AutotranslationService.java

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+/*
+ *  Copyright 2018 TWO SIGMA OPEN SOURCE, LLC
+ *
+ *  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.twosigma.beakerx;
+
+public interface AutotranslationService {
+
+  String BEAKERX = "beakerx";
+
+  String update(String name, String json);
+
+  String get(String name);
+
+  String close();
+
+  String getContextAsString();
+}

base-api/src/main/java/com/twosigma/beakerx/BeakerXClient.java

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+/*
+ *  Copyright 2018 TWO SIGMA OPEN SOURCE, LLC
+ *
+ *  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.twosigma.beakerx;
+
+import java.util.List;
+import java.util.concurrent.SynchronousQueue;
+
+public interface BeakerXClient {
+
+  String CODE_CELL_PATH = "codecell";
+
+  String URL_ARG = "urlarg";
+
+  void showProgressUpdate(String message, int progress);
+
+  void delBeaker();
+
+  String update(String name, Object value);
+
+  Object set(String name, Object value);
+
+  Object get(final String name);
+
+  SynchronousQueue<Object> getMessageQueue(String channel);
+
+  List<CodeCell> getCodeCells(String tagFilter);
+
+  void runByTag(String tag);
+
+  String getContext();
+
+  String urlArg(String argName);
+}

base-api/src/main/java/com/twosigma/beakerx/BeakerXClientManager.java

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+/*
+ *  Copyright 2018 TWO SIGMA OPEN SOURCE, LLC
+ *
+ *  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.twosigma.beakerx;
+
+
+public class BeakerXClientManager {
+
+  public static String BEAKER_X_CLIENT_MANAGER_PATH = BeakerXClientManager.class.getName();
+  public static String BEAKER_X_CLIENT_MANAGER_GET = BeakerXClientManager.class.getSimpleName() + ".get()";
+  public static String BEAKER_X_CLIENT_MANAGER = BeakerXClientManager.class.getName() + ".get()";
+
+  private static BeakerXClient beakerXClientInst;
+
+  public static BeakerXClient register(BeakerXClient beakerXClient) {
+    beakerXClientInst = beakerXClient;
+    return beakerXClientInst = beakerXClient;
+  }
+
+  public static BeakerXClient get() {
+    return beakerXClientInst;
+  }
+
+}

base-api/src/main/java/com/twosigma/beakerx/ClassLoaderSwitcher.java

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+/*
+ *  Copyright 2018 TWO SIGMA OPEN SOURCE, LLC
+ *
+ *  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.twosigma.beakerx;
+
+import com.twosigma.beakerx.evaluator.BaseEvaluator;
+
+public class ClassLoaderSwitcher {
+
+  private ClassLoader oldld;
+  private BaseEvaluator baseEvaluator;
+
+  public ClassLoaderSwitcher(BaseEvaluator baseEvaluator) {
+    this.baseEvaluator = baseEvaluator;
+  }
+
+  public void start() {
+    this.oldld = Thread.currentThread().getContextClassLoader();
+    Thread.currentThread().setContextClassLoader(baseEvaluator.getClassLoader());
+  }
+
+  public void end() {
+    Thread.currentThread().setContextClassLoader(oldld);
+  }
+}

base-api/src/main/java/com/twosigma/beakerx/ClasspathManager.java

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+/*
+ *  Copyright 2018 TWO SIGMA OPEN SOURCE, LLC
+ *
+ *  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.twosigma.beakerx;
+
+import com.twosigma.beakerx.kernel.KernelManager;
+
+import java.util.List;
+import java.util.stream.Collectors;
+
+public class ClasspathManager {
+
+  public static List<String> getJars() {
+    List<String> pathsAsStrings = KernelManager.get().getClasspath().getPathsAsStrings();
+    return pathsAsStrings.stream()
+            .filter(x -> x.endsWith(".jar")).collect(Collectors.toList());
+  }
+}

base-api/src/main/java/com/twosigma/beakerx/CodeCell.java

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+/*
+ *  Copyright 2014 TWO SIGMA OPEN SOURCE, LLC
+ *
+ *  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.twosigma.beakerx;
+
+import java.io.IOException;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.core.JsonGenerator;
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.JsonSerializer;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.SerializerProvider;
+
+import com.twosigma.beakerx.jvm.serialization.BeakerObjectConverter;
+import com.twosigma.beakerx.jvm.serialization.ObjectDeserializer;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class CodeCell {
+  private final static Logger logger = LoggerFactory.getLogger(CodeCell.class.getName());
+  @JsonProperty("execution_count")
+  private String executionCount;
+  @JsonProperty("cell_type")
+  private String cellType;
+  private Object outputs;
+  private Object metadata;
+  private String source;
+
+  public CodeCell() { }
+
+  public String getExecutionCount() {
+    return executionCount;
+  }
+
+  public void setExecutionCount(String executionCount) {
+    this.executionCount = executionCount;
+  }
+
+  public String getCellType() {
+    return cellType;
+  }
+
+  public void setCellType(String cellType) {
+    this.cellType = cellType;
+  }
+
+  public Object getOutputs() {
+    return outputs;
+  }
+
+  public void setOutputs(Object outputs) {
+    this.outputs = outputs;
+  }
+
+  public Object getMetadata() {
+    return metadata;
+  }
+
+  public void setMetadata(Object metadata) {
+    this.metadata = metadata;
+  }
+
+  public String getSource() {
+    return source;
+  }
+
+  public void setSource(String source) {
+    this.source = source;
+  }
+
+  public static class Serializer extends JsonSerializer<CodeCell> {
+
+    private final BeakerObjectConverter objectSerializerProvider;
+
+    public Serializer(BeakerObjectConverter osp) {
+      objectSerializerProvider = osp;
+    }
+
+    private BeakerObjectConverter getObjectSerializer() {
+      return objectSerializerProvider;
+    }
+
+    @Override
+    public void serialize(CodeCell value,
+        JsonGenerator jgen,
+        SerializerProvider provider)
+        throws IOException, JsonProcessingException {
+
+      synchronized (value) {
+        jgen.writeStartObject();
+        jgen.writeStringField("type", "CodeCell");
+        jgen.writeStringField("execution_count", value.executionCount);
+        jgen.writeStringField("cell_type", value.cellType);
+        jgen.writeFieldName("outputs");
+        if (!getObjectSerializer().writeObject(value.outputs, jgen, true))
+          jgen.writeString(value.outputs.toString());
+        jgen.writeFieldName("metadata");
+        if (!getObjectSerializer().writeObject(value.metadata, jgen, true))
+          jgen.writeString(value.metadata.toString());
+        jgen.writeStringField("source", value.source);
+        jgen.writeEndObject();
+      }
+    }
+  }
+
+  public static class DeSerializer implements ObjectDeserializer {
+
+    private final BeakerObjectConverter parent;
+
+    public DeSerializer(BeakerObjectConverter p) {
+      parent = p;
+      parent.addKnownBeakerType("CodeCell");
+    }
+
+    @Override
+    public Object deserialize(JsonNode n, ObjectMapper mapper) {
+      CodeCell o = null;
+      try {
+        String executionCount=null, cellType=null, source=null;
+        Object outputs=null;
+        Object metadata=null;
+        if (n.has("execution_count"))
+          executionCount = n.get("execution_count").asText();
+        if (n.has("cell_type"))
+          cellType = n.get("cell_type").asText();
+        if (n.has("source"))
+          source = n.get("source").asText();
+        if (n.has("outputs"))
+          outputs = parent.deserialize(n.get("outputs"), mapper);
+        if (n.has("metadata"))
+          metadata = parent.deserialize(n.get("metadata"), mapper);
+
+        o = new CodeCell();
+        o.setExecutionCount(executionCount);
+        o.setCellType(cellType);
+        o.setSource(source);
+        o.setOutputs(outputs);
+        o.setMetadata(metadata);
+      } catch (Exception e) {
+        logger.error("exception deserializing CodeCell ", e);
+        e.printStackTrace();
+      }
+      return o;
+    }
+
+    @Override
+    public boolean canBeUsed(JsonNode n) {
+      return n.has("type") && n.get("type").asText().equals("CodeCell");
+    }
+  }
+
+}