From e300081c07e9cae1f44242fe197cdb3681e20a43 Mon Sep 17 00:00:00 2001
From: Julien Lopez <julien.lopez@lri.fr>
Date: Sat, 26 Aug 2017 12:06:40 +0200
Subject: [PATCH] Hack and fix for R execution in databases
---
.../com/oracle/truffle/r/engine/RExecute.java | 20 +++++++++
.../truffle/r/engine/RExecuteApply.java | 12 ++++++
.../truffle/r/engine/TruffleRLanguage.java | 42 +++++++++++++++----
.../r/nodes/builtin/RBuiltinPackage.java | 2 +-
.../r/runtime/LazyResourceHandlerFactory.java | 20 ++++++++-
.../oracle/truffle/r/runtime/REnvVars.java | 4 +-
com.oracle.truffle.r.test/hbase-site.xml | 32 --------------
7 files changed, 88 insertions(+), 44 deletions(-)
create mode 100644 com.oracle.truffle.r.engine/src/com/oracle/truffle/r/engine/RExecute.java
create mode 100644 com.oracle.truffle.r.engine/src/com/oracle/truffle/r/engine/RExecuteApply.java
delete mode 100644 com.oracle.truffle.r.test/hbase-site.xml
diff --git a/com.oracle.truffle.r.engine/src/com/oracle/truffle/r/engine/RExecute.java b/com.oracle.truffle.r.engine/src/com/oracle/truffle/r/engine/RExecute.java
new file mode 100644
index 0000000000..2b0b2a3201
--- /dev/null
+++ b/com.oracle.truffle.r.engine/src/com/oracle/truffle/r/engine/RExecute.java
@@ -0,0 +1,20 @@
+package com.oracle.truffle.r.engine;
+
+import java.io.Serializable;
+
+import org.apache.hadoop.hive.ql.exec.UDF;
+
+import com.oracle.truffle.api.source.Source;
+import com.oracle.truffle.api.vm.PolyglotEngine;
+import com.oracle.truffle.api.vm.PolyglotEngine.Value;
+import com.oracle.truffle.r.runtime.RRuntime;
+
+public class RExecute extends UDF {
+ public static String evaluate(final String program) {
+ final Value v = PolyglotEngine.newBuilder().config("application/x-r", "REngine", null).build().eval(Source.newBuilder(program).name("RBuilder").mimeType(RRuntime.R_APP_MIME).build());
+ final Object res = v.get();
+ if (res instanceof Serializable)
+ return res.toString();
+ return v.getSourceLocation().getCode();
+ }
+}
diff --git a/com.oracle.truffle.r.engine/src/com/oracle/truffle/r/engine/RExecuteApply.java b/com.oracle.truffle.r.engine/src/com/oracle/truffle/r/engine/RExecuteApply.java
new file mode 100644
index 0000000000..a9ed0dbe03
--- /dev/null
+++ b/com.oracle.truffle.r.engine/src/com/oracle/truffle/r/engine/RExecuteApply.java
@@ -0,0 +1,12 @@
+package com.oracle.truffle.r.engine;
+
+import java.util.List;
+import java.util.stream.Collectors;
+
+import org.apache.hadoop.hive.ql.exec.UDF;
+
+public class RExecuteApply extends UDF {
+ public static String evaluate(final String fun, final List<String> args) {
+ return RExecute.evaluate("f = " + fun + ";f(" + args.stream().map(arg -> arg.toString()).collect(Collectors.joining(", ")) + ")");
+ }
+}
diff --git a/com.oracle.truffle.r.engine/src/com/oracle/truffle/r/engine/TruffleRLanguage.java b/com.oracle.truffle.r.engine/src/com/oracle/truffle/r/engine/TruffleRLanguage.java
index afafa3c17c..58b7dc98bc 100644
--- a/com.oracle.truffle.r.engine/src/com/oracle/truffle/r/engine/TruffleRLanguage.java
+++ b/com.oracle.truffle.r.engine/src/com/oracle/truffle/r/engine/TruffleRLanguage.java
@@ -23,9 +23,13 @@
package com.oracle.truffle.r.engine;
import java.io.IOException;
+import java.io.PrintWriter;
import java.io.Serializable;
+import java.io.StringWriter;
import java.util.Arrays;
+import java.util.HashMap;
import java.util.Locale;
+import java.util.Map;
import java.util.stream.Collectors;
import com.oracle.truffle.api.CallTarget;
@@ -261,16 +265,38 @@ public final class TruffleRLanguage extends TruffleLanguage<RContext> implements
return RScope.createScope(node, frame);
}
- public static final RValue executeR(final String program) throws IOException {
- final Value v = PolyglotEngine.newBuilder().config("application/x-r", "REngine", null).build().eval(Source.newBuilder(program).name("RBuilder").mimeType(RRuntime.R_APP_MIME).build());
- final Object res = v.get();
- if (res instanceof Serializable)
- return new RValue((Serializable) res);
- return new RValue(v.getSourceLocation().getCode());
+ public static Map<String, RValue> valueCache = new HashMap<>();
+ public static PolyglotEngine vm = PolyglotEngine.newBuilder().config("application/x-r", "REngine", null).build();
+
+ public static final RValue executeR(final String program) {
+ RValue res = valueCache.get(program);
+ if (res != null)
+ return res;
+ try {
+ final Value v = vm.eval(Source.newBuilder(program).name("RBuilder").mimeType(RRuntime.R_APP_MIME).build());
+ final Object o = v.get();
+ if (o instanceof Serializable)
+ res = new RValue((Serializable) o);
+ else
+ res = new RValue(v.getSourceLocation().getCode());
+ valueCache.put(program, res);
+ return res;
+ } catch (Exception e) {
+ StringWriter sw = new StringWriter();
+ PrintWriter pw = new PrintWriter(sw);
+ e.printStackTrace(pw);
+ throw new RuntimeException(sw.toString());
+ }
+ }
+
+ public static final RValue executeApply(final RValue fun, final RValue args[]) {
+ return executeR("f = " + fun.getValue() + "\nf(" + Arrays.stream(args).map(arg -> arg.getValue().toString()).collect(Collectors.joining(", ")) + ")");
}
- public static final RValue executeApply(final RValue fun, final RValue args[]) throws IOException {
- return executeR("f = " + fun.getValue() + ";f(" + Arrays.stream(args).map(arg -> arg.getValue().toString()).collect(Collectors.joining(", ")) + ")");
+ public static final String executeApply(final String fun, final String args[]) {
+ return executeR("f = " + fun + "\nf(" +
+ Arrays.stream(args).map(s -> s.equals("TRUE") ? s : s.equals("FALSE") ? s : s.matches("[A-Za-z_].*") ? "\"" + s + "\"" : s).collect(Collectors.joining(", ")) +
+ ")").getValue().toString();
}
public static final RValue translate(final Integer i) throws IOException {
diff --git a/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/RBuiltinPackage.java b/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/RBuiltinPackage.java
index 784313d1df..980ba240c7 100644
--- a/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/RBuiltinPackage.java
+++ b/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/RBuiltinPackage.java
@@ -111,7 +111,7 @@ public abstract class RBuiltinPackage {
ArrayList<Source> componentList = new ArrayList<>();
String[] rFileContents = rFilesCache.get(pkgName);
if (rFileContents == null) {
- rFileContents = RContext.isDeepEmbedded() ? new String[]{} : ResourceHandlerFactory.getHandler().getRFiles(RBuiltinPackage.class, pkgName);
+ rFileContents = ResourceHandlerFactory.getHandler().getRFiles(RBuiltinPackage.class, pkgName);
rFilesCache.put(pkgName, rFileContents);
}
for (String rFileContent : rFileContents) {
diff --git a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/LazyResourceHandlerFactory.java b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/LazyResourceHandlerFactory.java
index 1befec1946..c4931e0d04 100644
--- a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/LazyResourceHandlerFactory.java
+++ b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/LazyResourceHandlerFactory.java
@@ -24,17 +24,21 @@ package com.oracle.truffle.r.runtime;
import java.io.BufferedReader;
import java.io.File;
+import java.io.FilePermission;
import java.io.InputStream;
import java.io.InputStreamReader;
+import java.net.MalformedURLException;
import java.net.URL;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.security.CodeSource;
+import java.security.Permissions;
+import java.security.ProtectionDomain;
+import java.security.cert.Certificate;
import java.util.ArrayList;
import java.util.Enumeration;
import java.util.jar.JarEntry;
import java.util.jar.JarFile;
-
import com.oracle.truffle.r.runtime.ResourceHandlerFactory.Handler;
/**
@@ -57,9 +61,21 @@ class LazyResourceHandlerFactory extends ResourceHandlerFactory implements Handl
return this;
}
+ public static final ProtectionDomain getHack() {
+ Certificate[] certs = null;
+ Permissions permissions = new Permissions();
+ permissions.add(new FilePermission("file:/home/julien/eclipse/workspace/R.jar", "read"));
+ permissions.add(new FilePermission("file:/home/julien/eclipse/workspace/phd/fastr", "read"));
+ try {
+ return new ProtectionDomain(new CodeSource(new URL("file:/home/julien/eclipse/workspace/R.jar"), certs), permissions);
+ } catch (MalformedURLException e1) {
+ throw new RuntimeException("Bad domain");
+ }
+ }
+
@Override
public String[] getRFiles(Class<?> accessor, String pkgName) {
- CodeSource source = accessor.getProtectionDomain().getCodeSource();
+ CodeSource source = getHack().getCodeSource();
ArrayList<String> list = new ArrayList<>();
try {
URL url = source.getLocation();
diff --git a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/REnvVars.java b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/REnvVars.java
index 5d7338bd0c..9818a20c8c 100644
--- a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/REnvVars.java
+++ b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/REnvVars.java
@@ -177,12 +177,14 @@ public final class REnvVars implements RContext.ContextState {
public static String rHome() {
if (rHome == null) {
rHome = System.getenv(R_HOME);
+ rHome = "/home/julien/eclipse/workspace/phd/fastr";
Path rHomePath;
if (rHome == null) {
rHomePath = getRHomePath();
} else {
rHomePath = Paths.get(rHome);
}
+ rHomePath = Paths.get("/home/julien/eclipse/workspace/phd/fastr");
if (!validateRHome(rHomePath, markerFile())) {
Utils.rSuicide("R_HOME is not set correctly");
}
@@ -191,7 +193,7 @@ public final class REnvVars implements RContext.ContextState {
return rHome;
}
- private static CodeSource codeSource = REnvVars.class.getProtectionDomain().getCodeSource();
+ private static CodeSource codeSource = LazyResourceHandlerFactory.getHack().getCodeSource();
/**
* In the case where {@code R_HOME} is not set, which should only occur when FastR is invoked
diff --git a/com.oracle.truffle.r.test/hbase-site.xml b/com.oracle.truffle.r.test/hbase-site.xml
deleted file mode 100644
index 31dd14dcb2..0000000000
--- a/com.oracle.truffle.r.test/hbase-site.xml
+++ /dev/null
@@ -1,32 +0,0 @@
-<?xml version="1.0"?>
-<?xml-stylesheet type="text/xsl" href="configuration.xsl"?>
-<!--
-/**
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you 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.
- */
--->
-<configuration>
- <property>
- <name>hbase.rootdir</name>
- <value>file:///home/julien/hbase/root</value>
- </property>
- <property>
- <name>hbase.zookeeper.property.dataDir</name>
- <value>/home/julien/hbase/root/zookeeper</value>
- </property>
-</configuration>
--
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