From 4ed1ade4c858238f18f101d5663905d53ada0f6d Mon Sep 17 00:00:00 2001
From: Lukas Stadler <lukas.stadler@oracle.com>
Date: Wed, 19 Jul 2017 15:17:48 +0200
Subject: [PATCH] implement unzip builtin
---
.../oracle/truffle/r/library/utils/Unzip.java | 165 ++++++++++++++++++
.../r/nodes/builtin/base/IsTypeFunctions.java | 2 +-
.../foreign/CallAndExternalFunctions.java | 2 +
.../com/oracle/truffle/r/runtime/RError.java | 3 +-
.../com/oracle/truffle/r/runtime/ffi/DLL.java | 2 +-
.../truffle/r/test/ExpectedTestOutput.test | 15 ++
.../r/test/builtins/TestBuiltin_unzip.java | 53 ++++++
7 files changed, 239 insertions(+), 3 deletions(-)
create mode 100644 com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/utils/Unzip.java
create mode 100644 com.oracle.truffle.r.test/src/com/oracle/truffle/r/test/builtins/TestBuiltin_unzip.java
diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/utils/Unzip.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/utils/Unzip.java
new file mode 100644
index 0000000000..334edb9283
--- /dev/null
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/utils/Unzip.java
@@ -0,0 +1,165 @@
+/*
+ * Copyright (c) 2017, 2017, Oracle and/or its affiliates. All rights reserved.
+ * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
+ *
+ * This code is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU General Public License version 2 only, as
+ * published by the Free Software Foundation.
+ *
+ * This code is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
+ * version 2 for more details (a copy is included in the LICENSE file that
+ * accompanied this code).
+ *
+ * You should have received a copy of the GNU General Public License version
+ * 2 along with this work; if not, write to the Free Software Foundation,
+ * Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * Please contact Oracle, 500 Oracle Parkway, Redwood Shores, CA 94065 USA
+ * or visit www.oracle.com if you need additional information or have any
+ * questions.
+ */
+package com.oracle.truffle.r.library.utils;
+
+import static com.oracle.truffle.r.nodes.builtin.CastBuilder.Predef.logicalValue;
+import static com.oracle.truffle.r.nodes.builtin.CastBuilder.Predef.singleElement;
+import static com.oracle.truffle.r.nodes.builtin.CastBuilder.Predef.stringValue;
+import static com.oracle.truffle.r.nodes.builtin.CastBuilder.Predef.toBoolean;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.function.Predicate;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipInputStream;
+
+import com.oracle.truffle.api.CompilerDirectives.TruffleBoundary;
+import com.oracle.truffle.api.dsl.Specialization;
+import com.oracle.truffle.r.nodes.builtin.RExternalBuiltinNode;
+import com.oracle.truffle.r.runtime.RError;
+import com.oracle.truffle.r.runtime.RError.Message;
+import com.oracle.truffle.r.runtime.Utils;
+import com.oracle.truffle.r.runtime.data.RDataFactory;
+import com.oracle.truffle.r.runtime.data.RIntVector;
+import com.oracle.truffle.r.runtime.data.RNull;
+import com.oracle.truffle.r.runtime.data.model.RAbstractStringVector;
+import com.oracle.truffle.r.runtime.nodes.RBaseNode;
+
+public abstract class Unzip extends RExternalBuiltinNode.Arg7 {
+
+ static {
+ Casts casts = new Casts(Unzip.class);
+ casts.arg(0, "zipfile").mustBe(stringValue()).asStringVector().mustBe(singleElement()).findFirst();
+ casts.arg(1, "files").allowNull().mustBe(stringValue()).asStringVector();
+ casts.arg(2, "exdir").mustBe(stringValue()).asStringVector().mustBe(singleElement()).findFirst();
+ casts.arg(3, "list").mustBe(logicalValue()).asLogicalVector().mustBe(singleElement()).findFirst().map(toBoolean());
+ casts.arg(4, "overwrite").mustBe(logicalValue()).asLogicalVector().mustBe(singleElement()).findFirst().map(toBoolean());
+ casts.arg(5, "junkpaths").mustBe(logicalValue()).asLogicalVector().mustBe(singleElement()).findFirst().map(toBoolean());
+ casts.arg(6, "setTimes").mustBe(logicalValue()).asLogicalVector().mustBe(singleElement()).findFirst().map(toBoolean());
+ }
+
+ @Specialization
+ @TruffleBoundary
+ protected Object unzip(String zipfile, @SuppressWarnings("unused") RNull files, String exdir, boolean list, boolean overwrite, boolean junkpaths, boolean setTimes) {
+ return unzip(zipfile, (RAbstractStringVector) null, exdir, list, overwrite, junkpaths, setTimes);
+ }
+
+ @Override
+ protected RBaseNode getErrorContext() {
+ return RError.SHOW_CALLER;
+ }
+
+ @Specialization
+ @TruffleBoundary
+ protected Object unzip(String zipfile, RAbstractStringVector files, String exdir, boolean list, boolean overwrite, boolean junkpaths, boolean setTimes) {
+ if (list) {
+ return list(zipfile);
+ }
+ Predicate<String> filter;
+ boolean[] found;
+ if (files == null) {
+ found = null;
+ filter = x -> true;
+ } else {
+ found = new boolean[files.getLength()];
+ filter = x -> {
+ for (int i = 0; i < files.getLength(); i++) {
+ if (x.equals(files.getDataAt(i))) {
+ found[i] = true;
+ return true;
+ }
+ }
+ return false;
+ };
+ }
+
+ File targetDir = new File(exdir);
+ if (!targetDir.exists() || !targetDir.isDirectory()) {
+ throw error(Message.GENERIC, "invalid target directory");
+ }
+ try (ZipInputStream stream = new ZipInputStream(new FileInputStream(Utils.tildeExpand(zipfile)))) {
+ ZipEntry entry;
+ ArrayList<String> extracted = new ArrayList<>();
+ byte[] buffer = new byte[2048];
+ while ((entry = stream.getNextEntry()) != null) {
+ if (filter.test(entry.getName())) {
+ File target = new File(targetDir, junkpaths ? new File(entry.getName()).getName() : entry.getName());
+ if (!target.exists() || overwrite) {
+ try (FileOutputStream output = new FileOutputStream(target)) {
+ extracted.add(target.getPath());
+ int length;
+ while ((length = stream.read(buffer)) > 0) {
+ output.write(buffer, 0, length);
+ }
+ }
+ if (setTimes) {
+ target.setLastModified(entry.getTime());
+ }
+ }
+ }
+ }
+ if (files != null) {
+ for (int i = 0; i < found.length; i++) {
+ if (!found[i]) {
+ warning(Message.FILE_NOT_FOUND_IN_ZIP);
+ break;
+ }
+ }
+ }
+ RIntVector result = RDataFactory.createIntVector(new int[]{0}, true);
+ result.setAttr("extracted", RDataFactory.createStringVector(extracted.toArray(new String[0]), true));
+ return result;
+ } catch (IOException e) {
+ throw error(Message.GENERIC, "error while extracting zip: " + e.getMessage());
+ }
+ }
+
+ @SuppressWarnings("deprecation")
+ private Object list(String zipfile) {
+ try (ZipInputStream stream = new ZipInputStream(new FileInputStream(Utils.tildeExpand(zipfile)))) {
+ ArrayList<ZipEntry> entryList = new ArrayList<>();
+ ZipEntry entry;
+ while ((entry = stream.getNextEntry()) != null) {
+ entryList.add(entry);
+ }
+ String[] names = new String[entryList.size()];
+ double[] sizes = new double[entryList.size()];
+ String[] dates = new String[entryList.size()];
+ for (int i = 0; i < entryList.size(); i++) {
+ entry = entryList.get(i);
+ names[i] = entry.getName();
+ sizes[i] = entry.getSize();
+ // rounding up to minutes
+ Date date = new Date(entry.getTime() + (30 * 1000));
+ dates[i] = String.format("%04d-%02d-%02d %02d:%02d", date.getYear() + 1900, date.getMonth() + 1, date.getDate(), date.getHours(), date.getMinutes());
+ }
+ return RDataFactory.createList(new Object[]{RDataFactory.createStringVector(names, true), RDataFactory.createDoubleVector(sizes, true), RDataFactory.createStringVector(dates, true)});
+ } catch (IOException e) {
+ throw error(Message.GENERIC, "error while extracting zip: " + e.getMessage());
+ }
+ }
+}
diff --git a/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/IsTypeFunctions.java b/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/IsTypeFunctions.java
index 124bb99da5..58c61e58ea 100644
--- a/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/IsTypeFunctions.java
+++ b/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/IsTypeFunctions.java
@@ -600,7 +600,7 @@ public class IsTypeFunctions {
return RRuntime.LOGICAL_FALSE;
}
- private boolean typesMatch(RType expected, RType actual) {
+ private static boolean typesMatch(RType expected, RType actual) {
return expected == RType.Numeric ? actual == RType.Integer || actual == RType.Double : actual == expected;
}
diff --git a/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/foreign/CallAndExternalFunctions.java b/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/foreign/CallAndExternalFunctions.java
index 7f0f565864..ad7d504a4e 100644
--- a/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/foreign/CallAndExternalFunctions.java
+++ b/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/foreign/CallAndExternalFunctions.java
@@ -62,6 +62,7 @@ import com.oracle.truffle.r.library.tools.ToolsTextFactory.DoTabExpandNodeGen;
import com.oracle.truffle.r.library.utils.CountFieldsNodeGen;
import com.oracle.truffle.r.library.utils.Crc64NodeGen;
import com.oracle.truffle.r.library.utils.DownloadNodeGen;
+import com.oracle.truffle.r.library.utils.UnzipNodeGen;
import com.oracle.truffle.r.library.utils.MenuNodeGen;
import com.oracle.truffle.r.library.utils.ObjectSizeNodeGen;
import com.oracle.truffle.r.library.utils.RprofNodeGen;
@@ -760,6 +761,7 @@ public class CallAndExternalFunctions {
case "signrank_free":
return new SignrankFreeNode();
case "unzip":
+ return UnzipNodeGen.create();
case "addhistory":
case "loadhistory":
case "savehistory":
diff --git a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RError.java b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RError.java
index 983421fd3a..c9cefc000a 100644
--- a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RError.java
+++ b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RError.java
@@ -892,7 +892,8 @@ public final class RError extends RuntimeException implements TruffleException {
NO_BINDING_FOR("no binding for \"%s\""),
INVALID_SUBSTRING_ARGS("invalid substring arguments"),
OBJECT_SIZE_ESTIMATE("The object size is only estimated."),
- REPLACING_IN_NON_CHAR_OBJ("replacing substrings in a non-character object");
+ REPLACING_IN_NON_CHAR_OBJ("replacing substrings in a non-character object"),
+ FILE_NOT_FOUND_IN_ZIP("requested file not found in the zip file");
public final String message;
final boolean hasArgs;
diff --git a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/ffi/DLL.java b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/ffi/DLL.java
index 37031964a3..0573b87c6a 100644
--- a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/ffi/DLL.java
+++ b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/ffi/DLL.java
@@ -459,7 +459,7 @@ public class DLL {
invokeVoidCallNode.execute(new NativeCallInfo(pkgInit, initFunc, dllInfo), new Object[]{dllInfo});
} catch (ReturnException ex) {
// An error call can, due to condition handling, throw this which we must
- // propogate
+ // propagate
throw ex;
} catch (Throwable ex) {
if (RContext.isInitialContextInitialized()) {
diff --git a/com.oracle.truffle.r.test/src/com/oracle/truffle/r/test/ExpectedTestOutput.test b/com.oracle.truffle.r.test/src/com/oracle/truffle/r/test/ExpectedTestOutput.test
index 995ee48459..8bd3b2c347 100644
--- a/com.oracle.truffle.r.test/src/com/oracle/truffle/r/test/ExpectedTestOutput.test
+++ b/com.oracle.truffle.r.test/src/com/oracle/truffle/r/test/ExpectedTestOutput.test
@@ -72953,6 +72953,21 @@ Slot "y":
[1] 77 88
+##com.oracle.truffle.r.test.builtins.TestBuiltin_unzip.testunzip#
+#n <- tempfile(); writeBin(con=n,c(67324752L, 10L, 1851785216L, -273200397L, 99292L, 65536L, 262144L, <<<NEWLINE>>>1868955676L, 1414869359L, -1560084471L, -1386647737L, 1968795463L, <<<NEWLINE>>>16780152L, 128260L, 1311744L, 1345388544L, 503447883L, 2563L, <<<NEWLINE>>>1610612736L, -1219824786L, 25418991L, 16777216L, 67108864L, 6144L, <<<NEWLINE>>>16777216L, -1543503872L, 129L, 1869571584L, 89412913L, 1201865472L, <<<NEWLINE>>>2020956527L, 67174411L, 501L, 5124L, 88821760L, 6L, 16777472L, <<<NEWLINE>>>18944L, 16128L))<<<NEWLINE>>>length(unzip(n,list=T))<<<NEWLINE>>>names(unzip(n,list=T))<<<NEWLINE>>>unzip(n,list=T)[1:2]<<<NEWLINE>>>target <- tempdir()<<<NEWLINE>>>v <- unzip(n,exdir=target, files=c('bar','baz'))<<<NEWLINE>>>v<<<NEWLINE>>>file.exists(paste0(target, '/foo1'))<<<NEWLINE>>>v <- unzip(n,exdir=target)<<<NEWLINE>>>length(v)<<<NEWLINE>>>file.exists(v)<<<NEWLINE>>>readBin(paste0(target, '/foo1'), what='raw', n=1000)
+[1] 3
+[1] "Name" "Length" "Date"
+ Name Length
+1 foo1 1
+Warning message:
+In unzip(n, exdir = target, files = c("bar", "baz")) :
+ requested file not found in the zip file
+character(0)
+[1] FALSE
+[1] 1
+[1] TRUE
+[1] 31
+
##com.oracle.truffle.r.test.builtins.TestBuiltin_utf8ToInt.testUtf8ToInt#
#utf8ToInt('')
integer(0)
diff --git a/com.oracle.truffle.r.test/src/com/oracle/truffle/r/test/builtins/TestBuiltin_unzip.java b/com.oracle.truffle.r.test/src/com/oracle/truffle/r/test/builtins/TestBuiltin_unzip.java
new file mode 100644
index 0000000000..4f755e7ab1
--- /dev/null
+++ b/com.oracle.truffle.r.test/src/com/oracle/truffle/r/test/builtins/TestBuiltin_unzip.java
@@ -0,0 +1,53 @@
+/*
+ * Copyright (c) 2017, 2017, Oracle and/or its affiliates. All rights reserved.
+ * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
+ *
+ * This code is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU General Public License version 2 only, as
+ * published by the Free Software Foundation.
+ *
+ * This code is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
+ * version 2 for more details (a copy is included in the LICENSE file that
+ * accompanied this code).
+ *
+ * You should have received a copy of the GNU General Public License version
+ * 2 along with this work; if not, write to the Free Software Foundation,
+ * Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * Please contact Oracle, 500 Oracle Parkway, Redwood Shores, CA 94065 USA
+ * or visit www.oracle.com if you need additional information or have any
+ * questions.
+ */
+package com.oracle.truffle.r.test.builtins;
+
+import org.junit.Test;
+
+import com.oracle.truffle.r.test.TestBase;
+
+public class TestBuiltin_unzip extends TestBase {
+
+ @Test
+ public void testunzip() {
+ // writes out a small dummy zip file
+ assertEval("n <- tempfile(); writeBin(con=n,c(67324752L, 10L, 1851785216L, -273200397L, 99292L, 65536L, 262144L, \n" +
+ "1868955676L, 1414869359L, -1560084471L, -1386647737L, 1968795463L, \n" +
+ "16780152L, 128260L, 1311744L, 1345388544L, 503447883L, 2563L, \n" +
+ "1610612736L, -1219824786L, 25418991L, 16777216L, 67108864L, 6144L, \n" +
+ "16777216L, -1543503872L, 129L, 1869571584L, 89412913L, 1201865472L, \n" +
+ "2020956527L, 67174411L, 501L, 5124L, 88821760L, 6L, 16777472L, \n" +
+ "18944L, 16128L))\n" +
+ "length(unzip(n,list=T))\n" +
+ "names(unzip(n,list=T))\n" +
+ "unzip(n,list=T)[1:2]\n" + // leave out date (depends on time zone)
+ "target <- tempdir()\n" +
+ "v <- unzip(n,exdir=target, files=c('bar','baz'))\n" +
+ "v\n" +
+ "file.exists(paste0(target, '/foo1'))\n" +
+ "v <- unzip(n,exdir=target)\n" +
+ "length(v)\n" +
+ "file.exists(v)\n" +
+ "readBin(paste0(target, '/foo1'), what='raw', n=1000)");
+ }
+}
--
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