Merge pull request #580 from kbase/develop

Release 0.13.0

.classpath

@@ -1,9 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry excluding=".gitignore" kind="src" path="test"/>
-	<classpathentry kind="src" path="performance"/>
 	<classpathentry kind="src" path="server_scripts"/>
 	<classpathentry excluding=".gitignore" kind="src" path="src"/>
+	<classpathentry kind="src" path="performanceanddevelopment"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER">
 		<attributes>
 			<attribute name="module" value="true"/>
@@ -56,7 +55,6 @@
 	<classpathentry kind="lib" path="/jars/lib/jars/hamcrest/hamcrest-core-1.3.jar"/>
 	<classpathentry kind="lib" path="/jars/lib/jars/kbase/auth2/kbase-auth2test-0.2.4.jar"/>
 	<classpathentry kind="lib" path="/jars/lib/jars/kafka/kafka-clients-2.1.0.jar"/>
-	<classpathentry kind="lib" path="/jars/lib/jars/mongo/mongo-java-driver-3.8.2.jar"/>
 	<classpathentry kind="lib" path="/jars/lib/jars/kbase/shock/shock-client-0.1.0.jar"/>
 	<classpathentry kind="lib" path="/jars/lib/jars/amazon/V2/eventstream-1.0.1.jar"/>
 	<classpathentry kind="lib" path="/jars/lib/jars/annotation/javax.annotation-api-1.3.2.jar"/>
@@ -77,7 +75,6 @@
 		</attributes>
 	</classpathentry>
 	<classpathentry kind="lib" path="/jars/lib/jars/kbase/common/kbase-common-0.1.0.jar" sourcepath="/jars/lib/jars/kbase/common/kbase-common-0.1.0-sources.jar"/>
-	<classpathentry kind="lib" path="/jars/lib/jars/kbase/sample/SampleServiceClient-0.1.0-alpha22.jar"/>
 	<classpathentry kind="lib" path="/jars/lib/jars/arangodb/arangodb-java-driver-6.7.2.jar">
 		<attributes>
 			<attribute name="javadoc_location" value="jar:platform:/resource/jars/lib/jars/arangodb/arangodb-java-driver-6.7.2-javadoc.jar!/"/>
@@ -104,5 +101,7 @@
 	<classpathentry kind="lib" path="/jars/lib/jars/apache_commons/http/httpcore-4.4.5.jar"/>
 	<classpathentry kind="lib" path="/jars/lib/jars/apache_commons/http/httpmime-4.5.8.jar"/>
 	<classpathentry kind="lib" path="/jars/lib/jars/picocli/picocli-4.6.1.jar"/>
+	<classpathentry kind="lib" path="/jars/lib/jars/kbase/sample/SampleServiceClient-0.1.1.jar"/>
+	<classpathentry kind="lib" path="/jars/lib/jars/mongo/mongo-java-driver-3.12.10.jar"/>
 	<classpathentry kind="output" path="bin"/>
 </classpath>

.travis.yml

@@ -41,7 +41,7 @@ install:
   - export ARANGO_JS=$(pwd)/arangodb3-$ARANGODB_VER/usr/share/arangodb3/js/
 
   # set up handle service
-  - export HS_COMMIT=aae2f70120e75d2ccccab1b1c01dbb9e8327eee8
+  - export HS_COMMIT=08e18379817e16db920501b66ba62b66598f506c
   - export LOG_COMMIT=b549c557e3c519e0a55eadf7863a93db25cd6806
   - git clone https://github.com/kbase/handle_service2.git
   - cd handle_service2/
@@ -56,7 +56,7 @@ install:
   - cd ../..
 
   # set up sample service
-  - export SAMPLE_COMMIT=695bb800cb3babe2084e93c260affcd10018d3e7
+  - export SAMPLE_COMMIT=6813fb148e95db2b11db6eea04f4d1d45cbb7119
   - git clone https://github.com/kbase/sample_service.git
   - cd sample_service
   - git checkout $SAMPLE_COMMIT
@@ -66,6 +66,11 @@ install:
 
   - cd $HOMEDIR
 
+  # set up blobstore
+  - wget -O blobstore https://github.com/kbase/blobstore/releases/download/v0.1.2/blobstore_linux_amd64
+  - chmod a+x blobstore
+  - export BLOBEXE=$(pwd)/blobstore
+
   # install python dependencies
   - cd python_dependencies
   - pipenv install --dev
@@ -94,8 +99,7 @@ script:
   - sed -i "s#^test.minio.exe.*#test.minio.exe=$MINIOD#" test.cfg
   - sed -i "s#^test.mongo.wired_tiger.*#test.mongo.wired_tiger=$WIRED_TIGER#" test.cfg
   - sed -i "s#^test.jars.dir.*#test.jars.dir=$JARSDIR#" test.cfg
-  - sed -i "s#^test.shock.version.*#test.shock.version=0.9.6#" test.cfg
-  - sed -i "s#^test.shock.exe.*#test.shock.exe=$SHOCKEXE#" test.cfg
+  - sed -i "s#^test.blobstore.exe.*#test.blobstore.exe=$BLOBEXE#" test.cfg
   - sed -i "s#^test.handleservice.dir.*#test.handleservice.dir=$HSDIR#" test.cfg
   - sed -i "s#^test.sampleservice.dir.*#test.sampleservice.dir=$SAMPLE_DIR#" test.cfg
   - sed -i "s#^test.arango.exe.*#test.arango.exe=$ARANGO_EXE#" test.cfg

Makefile

@@ -69,10 +69,7 @@ compile-typespec:
 		$(SERVICE).spec
 	rm lib/biokbase/workspace/authclient.py
 
-test: test-client test-service
-
-test-client: test-service
-	$(ANT) test_client_import
+test: test-service
 
 test-service:
 	$(ANT) test

build.xml

@@ -33,19 +33,19 @@
     <include name="jna/jna-3.4.0.jar"/>
     <include name="servlet/servlet-api-2.5.jar"/>
     <include name="syslog4j/syslog4j-0.9.46.jar"/>
-    <include name="joda/joda-time-2.2.jar"/>
     <include name="annotation/javax.annotation-api-1.3.2.jar"/>
   </fileset>
 
   <fileset dir="${jardir}" id="clientserverlib">
     <include name="junit/junit-4.12.jar"/>
     <include name="hamcrest/hamcrest-core-1.3.jar"/>
     <include name="kbase/common/kbase-common-0.1.0.jar"/>
+    <!-- joda is required for kbase-common -->
+    <include name="joda/joda-time-2.2.jar"/>
     <include name="kbase/auth/kbase-auth-0.4.4.jar"/>
     <include name="jackson/jackson-annotations-2.9.9.jar"/>
     <include name="jackson/jackson-core-2.9.9.jar"/>
     <include name="jackson/jackson-databind-2.9.9.jar"/>
-    <include name="${commonjar}"/>
   </fileset>
 
   <fileset dir="${jardir}" id="shocklib">
@@ -62,14 +62,14 @@
     <include name="apache_commons/commons-io-2.4.jar"/>
     <include name="apache_commons/commons-lang3-3.1.jar"/>
     <include name="picocli/picocli-4.6.1.jar"/>
-    <include name="mongo/mongo-java-driver-3.8.2.jar"/>
+    <include name="mongo/mongo-java-driver-3.12.10.jar"/>
     <include name="slf4j/slf4j-api-1.7.7.jar"/>
     <include name="logback/logback-core-1.1.2.jar"/>
     <include name="logback/logback-classic-1.1.2.jar"/>
     <include name="google/guava-14.0.1.jar"/>
     <include name="kafka/kafka-clients-2.1.0.jar"/>
     <include name="kbase/handle/AbstractHandleClient-1.0.0.jar"/>
-    <include name="kbase/sample/SampleServiceClient-0.1.0-alpha22.jar"/>
+    <include name="kbase/sample/SampleServiceClient-0.1.1.jar"/>
   </fileset>
 
   <fileset dir="${jardir}" id="s3lib">
@@ -351,75 +351,6 @@
     <fail message="Test failure detected, check test results." if="test.failed" />
   </target>
 
-  <target name="test_quick_no_handle_coverage"
-          depends="test_quick_no_handle"
-          description="run most tests and generate test report">
-    <delete file="${test.reports.dir}/merged_jacoco.exec"/>
-    <jacoco:merge destfile="${test.reports.dir}/merged_jacoco.exec">
-      <fileset dir="${test.reports.dir}" includes="*.exec"/>
-    </jacoco:merge>
-    <jacoco:report>
-      <executiondata>
-        <file file="${test.reports.dir}/merged_jacoco.exec"/>
-      </executiondata>
-      <structure name="${package} Unit Tests">
-        <classfiles>
-          <fileset dir="${classes}">
-            <exclude name="**/test/**"/>
-          </fileset>
-        </classfiles>
-        <sourcefiles encoding="UTF-8">
-          <fileset dir="${src}">
-            <exclude name="**/test/**"/>
-          </fileset>
-        </sourcefiles>
-      </structure>
-      <html destdir="${test.reports.dir}/html"/>
-      <csv destfile="${test.reports.dir}/coverage-report.csv"/>
-      <xml destfile="${test.reports.dir}/coverage-report.xml"/>
-    </jacoco:report>
-  </target>
-
-  <target name="test_quick_no_handle"
-      depends="compile"
-      description="run tests other than the *LongTest.java and HandleAndShockTest tests">
-    <echo message="starting ${package} tests"/>
-    <delete file="${test.reports.dir}/ws.exec"/>
-    <jacoco:coverage destfile="${test.reports.dir}/ws.exec"
-         excludes="org/*:junit/*">
-      <junit fork="yes" maxmemory="3G" failureproperty="test.failed">
-        <classpath refid="test.classpath"/>
-        <formatter type="plain" usefile="false" />
-        <sysproperty key="test.cfg" value="./test.cfg"/>
-        <batchtest>
-          <fileset dir="${src}">
-            <include name="**/test/**/**Test.java"/>
-            <exclude name="**/test/**/**LongTest.java"/>
-            <exclude name="**/test/**/HandleAndShockTest.java"/>
-          </fileset>
-        </batchtest>
-      </junit>
-    </jacoco:coverage>
-    <fail message="Test failure detected, check test results." if="test.failed" />
-  </target>
-
-  <target name="test_client_import" depends="compile" description="make sure the client jar contains all files">
-    <javac destdir="${test}" srcdir="${test}" includeantruntime="false" target="1.6" source="1.6"
-          debug="true" classpathref="test.client.import.classpath">
-      <src path="${test}"/>
-      <exclude name="performance/**"/>
-      <exclude name="debugging/**"/>
-      <exclude name="sorting/**"/>
-      <exclude name="s3presignedurl/**"/>
-    </javac>
-    <junit fork="yes" failureproperty="test.failed">
-      <classpath refid="test.client.import.classpath"/>
-      <formatter type="plain" usefile="false" />
-      <test name="TestClientImport"/>
-    </junit>
-    <fail message="Test failure detected, check test results." if="test.failed" />
-  </target>
-
   <target name="script" depends="compile" description="create cli script">
     <pathconvert targetos="unix" property="lib.classpath" refid="applicationjars"/>
     <echo file="./update_workspace_database_schema">#!/bin/sh

deploy.cfg.example

@@ -10,6 +10,11 @@ mongodb-host = localhost
 # Name of the workspace mongo database
 mongodb-database = workspace
 
+# Setting for the MongoDB retryWrites connection parameter.
+# See https://www.mongodb.com/docs/manual/core/retryable-writes/
+# 'true' is true, anything else is false.
+#mongodb-retrywrites = false
+
 # The user name for an account with readWrite access to the database
 #mongodb-user = add username here
 

deployment/conf/.templates/deployment.cfg.templ

@@ -1,6 +1,7 @@
 [Workspace]
 mongodb-database={{ default .Env.mongodb_database "workspace" }}
 mongodb-type-database={{ default .Env.mongodb_type_database "workspace_type_db" }}
+mongodb-retrywrites={{ default .Env.mongodb_retrywrites "false" }}
 mongodb-pwd={{ default .Env.mongodb_pwd "" }}
 ws-admin={{ default .Env.ws_admin "scanonadmin" }}
 # backend user is wstest globus user in ci