merging fixes from 2.x branch

Author: paxtonhare

.gitignore

@@ -9,6 +9,7 @@ marklogic-data-hub/bin/
 marklogic-data-hub/src/main/resources/ml-modules/root/trace-ui
 quick-start/bin/
 build/
+out/
 releases/
 .classpath
 .project

.travis/Dockerfile-java

@@ -1,18 +1,27 @@
 FROM centos:centos7
 
 ENV LANG C.UTF-8
-ENV JAVA_VERSION 8u131
-ENV BUILD_VERSION b11
-ENV SUM d54c1d3a095b4ff2b6607d096fa80163
+ENV JAVA_VERSION 8u141
+ENV BUILD_VERSION b15
+ENV SUM 336fa29ff2bb4ef291e347e091f7f4a7
+
+# Get any CentOS updates then clear the Docker cache
+RUN yum makecache fast && \
+    yum -y update && yum clean all
+
+# Install MarkLogic dependencies
 RUN yum -y install glibc.i686 \
     gdb.x86_64 redhat-lsb.x86_64 vim \
     bzip2 \
     unzip \
-    wget \
-    xz-utils 2>&1 > /dev/null
+    xz-utils 2>&1 > /dev/null \
+    && yum clean all
+
+# Install the initscripts package so MarkLogic starts ok
+RUN yum -y install initscripts && yum clean all
 
 # Downloading Java
-RUN wget --no-cookies --no-check-certificate --header "Cookie: oraclelicense=accept-securebackup-cookie" "http://download.oracle.com/otn-pub/java/jdk/$JAVA_VERSION-$BUILD_VERSION/$SUM/jdk-$JAVA_VERSION-linux-x64.rpm" -O /tmp/jdk-8-linux-x64.rpm
+RUN curl -s -L -C - -b "oraclelicense=accept-securebackup-cookie" -o /tmp/jdk-8-linux-x64.rpm http://download.oracle.com/otn-pub/java/jdk/$JAVA_VERSION-$BUILD_VERSION/$SUM/jdk-$JAVA_VERSION-linux-x64.rpm
 RUN yum -y install /tmp/jdk-8-linux-x64.rpm
 
 RUN alternatives --install /usr/bin/java jar /usr/java/latest/bin/java 200000
@@ -21,6 +30,9 @@ RUN alternatives --install /usr/bin/javac javac /usr/java/latest/bin/javac 20000
 
 ENV JAVA_HOME /usr/java/latest
 
+# Set the Path
+ENV PATH /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/MarkLogic/mlcmd/bin
+
 # Install MarkLogic
 COPY ./MarkLogic.rpm /tmp/MarkLogic.rpm
 
@@ -29,6 +41,7 @@ RUN yum -y install /tmp/MarkLogic.rpm 2>&1 > /dev/null
 # Expose MarkLogic Server ports - add additional ones for your REST, etc
 # endpoints
 EXPOSE 7997-8020
+EXPOSE 5005
 
 # init
 COPY .travis/startml.sh /tmp/startml.sh
@@ -41,7 +54,7 @@ VOLUME /marklogic-data-hub
 ADD ./ /marklogic-data-hub
 WORKDIR /marklogic-data-hub
 
-RUN ./gradlew build -x test 2>&1 > /dev/null
+RUN ./gradlew resolveAllDependencies
 
 # Define default command (which avoids immediate shutdown)
-CMD /tmp/startml.sh && ./gradlew test
+CMD /tmp/startml.sh && ./gradlew clean && ./gradlew test

.travis/Dockerfile-ml

@@ -1,3 +1,11 @@
+allprojects {
+    task resolveAllDependencies {
+        doLast {
+            configurations.all { it.resolve() }
+        }
+    }
+}
+
 subprojects {
     apply plugin: 'java'
 

build.gradle

@@ -2,7 +2,11 @@ version: '2'
 services:
   marklogic:
     image: marklogiccommunity/marklogic-datahub-1x
+    build:
+      context: .
+      dockerfile: ./.travis/Dockerfile-ml
     ports:
-      - "8000-8020"
+      - "5005:5005"
+      - "8000-8020:8000-8020"
     volumes:
       - .:/marklogic-data-hub

docker-compose.yml

@@ -3,7 +3,7 @@ plugins {
     id 'java'
     id 'maven-publish'
     id 'com.jfrog.bintray' version '1.7.2'
-    id 'com.marklogic.ml-gradle' version '2.6.0'
+    id 'com.marklogic.ml-gradle' version '2.8.0'
     id 'com.moowork.node' version '1.1.1'
 }
 
@@ -20,8 +20,10 @@ targetCompatibility = 1.8
 
 dependencies {
     compile 'com.marklogic:marklogic-client-api:4.0.1'
-    compile 'com.marklogic:ml-javaclient-util:4.0.alpha4'
-    compile 'com.marklogic:ml-app-deployer:2.6.0'
+    compile('com.marklogic:ml-javaclient-util:4.0.alpha4') {
+      exclude group: 'com.marklogic', module: 'marklogic-xcc'
+    }
+    compile 'com.marklogic:ml-app-deployer:2.8.0'
     compile 'commons-io:commons-io:2.4'
     testCompile 'junit:junit:4.12'
     testCompile 'xmlunit:xmlunit:1.3'

marklogic-data-hub/build.gradle

@@ -55,6 +55,7 @@
 import org.springframework.web.client.ResourceAccessException;
 
 import java.io.File;
+import java.io.FileOutputStream;
 import java.io.IOException;
 import java.nio.file.*;
 import java.nio.file.attribute.BasicFileAttributes;
@@ -448,7 +449,10 @@ public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IO
                                 JsonNode xored = JsonXor.xor(hubFile, file.toFile());
                                 if (xored.size() > 0) {
                                     ObjectMapper objectMapper = new ObjectMapper();
-                                    objectMapper.writerWithDefaultPrettyPrinter().writeValue(file.toFile(), xored);
+                                    FileOutputStream fileOutputStream = new FileOutputStream(file.toFile());
+                                    objectMapper.writerWithDefaultPrettyPrinter().writeValue(fileOutputStream, xored);
+                                    fileOutputStream.flush();
+                                    fileOutputStream.close();
                                 }
                                 else {
                                     FileUtils.forceDelete(file.toFile());

marklogic-data-hub/src/main/java/com/marklogic/hub/DataHub.java

@@ -94,7 +94,7 @@ private void initializeActiveSession(CommandContext context) {
 
         this.modulesLoader = new DefaultModulesLoader(xccAssetLoader);
         this.threadPoolTaskExecutor = new ThreadPoolTaskExecutor();
-        this.threadPoolTaskExecutor.setCorePoolSize(16);
+        this.threadPoolTaskExecutor.setCorePoolSize(2);
 
         // 10 minutes should be plenty of time to wait for REST API modules to be loaded
         this.threadPoolTaskExecutor.setAwaitTerminationSeconds(60 * 10);

marklogic-data-hub/src/main/java/com/marklogic/hub/deploy/commands/LoadHubModulesCommand.java

@@ -90,14 +90,13 @@ public AbstractFlow(String entityName, String flowName, FlowType type,
 
     public static AbstractFlow loadFromFile(File file) {
         AbstractFlow entity = null;
+        FileInputStream is = null;
         try {
-            FileInputStream is = new FileInputStream(file);
+            is = new FileInputStream(file);
             DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
             factory.setNamespaceAware(true);
-            DocumentBuilder builder = null;
-            builder = factory.newDocumentBuilder();
+            DocumentBuilder builder = factory.newDocumentBuilder();
             Document doc = builder.parse(is);
-            is.close();
             entity = new SimpleFlow(doc.getDocumentElement());
         } catch (FileNotFoundException e) {
             e.printStackTrace();
@@ -108,6 +107,15 @@ public static AbstractFlow loadFromFile(File file) {
         } catch (IOException e) {
             e.printStackTrace();
         }
+        finally {
+            if (is != null) {
+                try {
+                    is.close();
+                }
+                catch(IOException e) {}
+            }
+
+        }
         return entity;
     }
 

marklogic-data-hub/src/main/java/com/marklogic/hub/flow/AbstractFlow.java

@@ -30,7 +30,9 @@ declare function debug:enable($enabled as xs:boolean)
 
     xdmp:document-insert(
       "/com.marklogic.hub/settings/__debug_enabled__.xml",
-      element debug:is-debugging-enabled { if ($enabled) then 1 else 0 })
+      element debug:is-debugging-enabled { if ($enabled) then 1 else 0 },
+      xdmp:default-permissions(),
+      "hub-core-module")
     ',
     map:new((map:entry("enabled", $enabled))),
     map:new(map:entry("database", xdmp:modules-database()))