Grammar Remake

versions/development/parsers/README.md

@@ -1,8 +1,10 @@
-# Parsers for WDL
+# Grammars and Parsers
 
-This directory contains pregenerated parsers for WDL in a variety of languages. Except for the Java parser, all of these are provided *as-is*. We believe that they work but do not have the resources to validate that claim. However if you're willing to help us fix any issues you come across we'll work with you to do so."
+At the moment, WDL is transitioning away from `Hermes` as its primary grammar definition and parser generation tool and moving
+towards [Antlr4](https://www.antlr.org/). The motivation for this transition was to provide a grammar language which would 
+be more familiar to more people as well as employing a well supported and actively developed tool for generating the parsers.
+Antlr4 grammars are written as an EBNF and the tool itself supports 9 different target languages currently. 
 
-# How to rebuild
-
-Typing `make` in this directory will trigger builds for all of the languages and produce the appropriate files. This requires you to have [Hermes](https://github.com/scottfrazer/hermes) installed on your system. To do this you might need to use a virtualenv, e.g. ``mkvirtualenv py3 -p `which python3` ``
+Please note that hermes grammars will be removed from the specification at some point in the future, and this feature should
+be considered deprecated.
 

versions/development/parsers/antlr4/.gitignore

@@ -0,0 +1,16 @@
+*.interp
+*.tokens
+WdlLexer.py
+WdlParser.py
+WdlParserListener.py
+WdlParserVisitor.py
+WdlLexer.js
+WdlParser.js
+WdlParserListener.js
+WdlParserVisitor.js
+WdlLexerPython.py
+target/
+.idea/
+*.jar
+node_modules/
+build/

versions/development/parsers/antlr4/Java/.mvn/wrapper/MavenWrapperDownloader.java

@@ -0,0 +1,117 @@
+/*
+ * Copyright 2007-present the original author or authors.
+ *
+ * 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.
+ */
+import java.net.*;
+import java.io.*;
+import java.nio.channels.*;
+import java.util.Properties;
+
+public class MavenWrapperDownloader {
+
+    private static final String WRAPPER_VERSION = "0.5.5";
+    /**
+     * Default URL to download the maven-wrapper.jar from, if no 'downloadUrl' is provided.
+     */
+    private static final String DEFAULT_DOWNLOAD_URL = "https://repo.maven.apache.org/maven2/io/takari/maven-wrapper/"
+        + WRAPPER_VERSION + "/maven-wrapper-" + WRAPPER_VERSION + ".jar";
+
+    /**
+     * Path to the maven-wrapper.properties file, which might contain a downloadUrl property to
+     * use instead of the default one.
+     */
+    private static final String MAVEN_WRAPPER_PROPERTIES_PATH =
+            ".mvn/wrapper/maven-wrapper.properties";
+
+    /**
+     * Path where the maven-wrapper.jar will be saved to.
+     */
+    private static final String MAVEN_WRAPPER_JAR_PATH =
+            ".mvn/wrapper/maven-wrapper.jar";
+
+    /**
+     * Name of the property which should be used to override the default download url for the wrapper.
+     */
+    private static final String PROPERTY_NAME_WRAPPER_URL = "wrapperUrl";
+
+    public static void main(String args[]) {
+        System.out.println("- Downloader started");
+        File baseDirectory = new File(args[0]);
+        System.out.println("- Using base directory: " + baseDirectory.getAbsolutePath());
+
+        // If the maven-wrapper.properties exists, read it and check if it contains a custom
+        // wrapperUrl parameter.
+        File mavenWrapperPropertyFile = new File(baseDirectory, MAVEN_WRAPPER_PROPERTIES_PATH);
+        String url = DEFAULT_DOWNLOAD_URL;
+        if(mavenWrapperPropertyFile.exists()) {
+            FileInputStream mavenWrapperPropertyFileInputStream = null;
+            try {
+                mavenWrapperPropertyFileInputStream = new FileInputStream(mavenWrapperPropertyFile);
+                Properties mavenWrapperProperties = new Properties();
+                mavenWrapperProperties.load(mavenWrapperPropertyFileInputStream);
+                url = mavenWrapperProperties.getProperty(PROPERTY_NAME_WRAPPER_URL, url);
+            } catch (IOException e) {
+                System.out.println("- ERROR loading '" + MAVEN_WRAPPER_PROPERTIES_PATH + "'");
+            } finally {
+                try {
+                    if(mavenWrapperPropertyFileInputStream != null) {
+                        mavenWrapperPropertyFileInputStream.close();
+                    }
+                } catch (IOException e) {
+                    // Ignore ...
+                }
+            }
+        }
+        System.out.println("- Downloading from: " + url);
+
+        File outputFile = new File(baseDirectory.getAbsolutePath(), MAVEN_WRAPPER_JAR_PATH);
+        if(!outputFile.getParentFile().exists()) {
+            if(!outputFile.getParentFile().mkdirs()) {
+                System.out.println(
+                        "- ERROR creating output directory '" + outputFile.getParentFile().getAbsolutePath() + "'");
+            }
+        }
+        System.out.println("- Downloading to: " + outputFile.getAbsolutePath());
+        try {
+            downloadFileFromURL(url, outputFile);
+            System.out.println("Done");
+            System.exit(0);
+        } catch (Throwable e) {
+            System.out.println("- Error downloading");
+            e.printStackTrace();
+            System.exit(1);
+        }
+    }
+
+    private static void downloadFileFromURL(String urlString, File destination) throws Exception {
+        if (System.getenv("MVNW_USERNAME") != null && System.getenv("MVNW_PASSWORD") != null) {
+            String username = System.getenv("MVNW_USERNAME");
+            char[] password = System.getenv("MVNW_PASSWORD").toCharArray();
+            Authenticator.setDefault(new Authenticator() {
+                @Override
+                protected PasswordAuthentication getPasswordAuthentication() {
+                    return new PasswordAuthentication(username, password);
+                }
+            });
+        }
+        URL website = new URL(urlString);
+        ReadableByteChannel rbc;
+        rbc = Channels.newChannel(website.openStream());
+        FileOutputStream fos = new FileOutputStream(destination);
+        fos.getChannel().transferFrom(rbc, 0, Long.MAX_VALUE);
+        fos.close();
+        rbc.close();
+    }
+
+}

versions/development/parsers/antlr4/Java/.mvn/wrapper/maven-wrapper.properties

@@ -0,0 +1,2 @@
+distributionUrl=https://repo.maven.apache.org/maven2/org/apache/maven/apache-maven/3.6.1/apache-maven-3.6.1-bin.zip
+wrapperUrl=https://repo.maven.apache.org/maven2/io/takari/maven-wrapper/0.5.5/maven-wrapper-0.5.5.jar

versions/development/parsers/antlr4/Java/README.md

@@ -0,0 +1,22 @@
+# WDL Java Parser
+
+This directory provides a parser implemented in java. The parser is built on top of the Base [WDLBaseLexer.java](src/main/java/org/openwdl/wdl/parser/WDLBaseLexer.java)
+
+# Requirements
+- Java 7+
+
+# Building
+
+Building the project can be accomplished using the packaged maven wrapper.
+
+```bash
+./mvnw -DskipTests clean package
+```
+
+# Running tests
+
+There are a number of tests which can be run using surefire.
+
+```bash
+./mvnw test
+```