From 7854fb6edd7be905bf93d92fbfeefc5775863d12 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 10 Sep 2015 21:14:09 +0200
Subject: [PATCH] Move utils tests to utils
---
public/biopet-utils/pom.xml | 18 +++++++++++++
.../src/test/resources/log4j.properties | 25 +++++++++++++++++++
.../sasc/biopet/utils/ConfigUtilsTest.scala | 0
.../lumc/sasc/biopet/utils/PackageTest.scala | 0
.../sasc/biopet/utils/config/ConfigTest.scala | 0
.../biopet/utils/config/ConfigValueTest.scala | 0
.../utils/config/ConfigurableTest.scala | 0
.../utils/intervals/BedRecordListTest.scala | 0
.../utils/intervals/BedRecordTest.scala | 0
9 files changed, 43 insertions(+)
create mode 100644 public/biopet-utils/src/test/resources/log4j.properties
rename public/{biopet-framework => biopet-utils}/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala (100%)
rename public/{biopet-framework => biopet-utils}/src/test/scala/nl/lumc/sasc/biopet/utils/PackageTest.scala (100%)
rename public/{biopet-framework => biopet-utils}/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigTest.scala (100%)
rename public/{biopet-framework => biopet-utils}/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigValueTest.scala (100%)
rename public/{biopet-framework => biopet-utils}/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigurableTest.scala (100%)
rename public/{biopet-framework => biopet-utils}/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordListTest.scala (100%)
rename public/{biopet-framework => biopet-utils}/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordTest.scala (100%)
diff --git a/public/biopet-utils/pom.xml b/public/biopet-utils/pom.xml
index d0f8a7c75..30bae7c8d 100644
--- a/public/biopet-utils/pom.xml
+++ b/public/biopet-utils/pom.xml
@@ -13,6 +13,24 @@
<dependencies>
+ <dependency>
+ <groupId>org.testng</groupId>
+ <artifactId>testng</artifactId>
+ <version>6.8</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.mockito</groupId>
+ <artifactId>mockito-all</artifactId>
+ <version>1.9.5</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.scalatest</groupId>
+ <artifactId>scalatest_2.10</artifactId>
+ <version>2.2.1</version>
+ <scope>test</scope>
+ </dependency>
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
diff --git a/public/biopet-utils/src/test/resources/log4j.properties b/public/biopet-utils/src/test/resources/log4j.properties
new file mode 100644
index 000000000..501af6758
--- /dev/null
+++ b/public/biopet-utils/src/test/resources/log4j.properties
@@ -0,0 +1,25 @@
+#
+# Biopet is built on top of GATK Queue for building bioinformatic
+# pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+# SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+# should also be able to execute Biopet tools and pipelines.
+#
+# Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+#
+# Contact us at: sasc@lumc.nl
+#
+# A dual licensing mode is applied. The source code within this project that are
+# not part of GATK Queue is freely available for non-commercial use under an AGPL
+# license; For commercial users or users who do not want to follow the AGPL
+# license, please contact us to obtain a separate license.
+#
+
+# Set root logger level to DEBUG and its only appender to A1.
+log4j.rootLogger=ERROR, A1
+
+# A1 is set to be a ConsoleAppender.
+log4j.appender.A1=org.apache.log4j.ConsoleAppender
+
+# A1 uses PatternLayout.
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala b/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
similarity index 100%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
rename to public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/PackageTest.scala b/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/PackageTest.scala
similarity index 100%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/PackageTest.scala
rename to public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/PackageTest.scala
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigTest.scala b/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigTest.scala
similarity index 100%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigTest.scala
rename to public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigTest.scala
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigValueTest.scala b/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigValueTest.scala
similarity index 100%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigValueTest.scala
rename to public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigValueTest.scala
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigurableTest.scala b/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigurableTest.scala
similarity index 100%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigurableTest.scala
rename to public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigurableTest.scala
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordListTest.scala b/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordListTest.scala
similarity index 100%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordListTest.scala
rename to public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordListTest.scala
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordTest.scala b/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordTest.scala
similarity index 100%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordTest.scala
rename to public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordTest.scala
--
GitLab