<commit_before><?xml version="1.0" encoding="UTF-8"?>
<!--
  ~    Copyright 2016 OICR
  ~
  ~    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.
  -->

<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
    <modelVersion>4.0.0</modelVersion>
    <parent>
        <groupId>io.dockstore</groupId>
        <artifactId>dockstore</artifactId>
        <version>1.2.0-alpha.7-SNAPSHOT</version>
        <relativePath>../pom.xml</relativePath>
    </parent>
    <artifactId>dockstore-integration-testing</artifactId>
    <packaging>jar</packaging>

    <properties>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
    </properties>

    <dependencies>
        <dependency>
            <groupId>io.dockstore</groupId>
            <artifactId>dockstore-webservice</artifactId>
            <version>1.2.0-alpha.7-SNAPSHOT</version>
        </dependency>

        <!-- testing -->
        <dependency>
            <groupId>io.dockstore</groupId>
            <artifactId>dockstore-common</artifactId>
            <version>1.2.0-alpha.7-SNAPSHOT</version>
            <scope>test</scope>
            <type>test-jar</type>
        </dependency>

        <dependency>
            <groupId>io.dropwizard</groupId>
            <artifactId>dropwizard-testing</artifactId>
            <version>${dropwizard.version}</version>
            <scope>test</scope>
            <exclusions>
                <exclusion>
                    <groupId>org.mockito</groupId>
                    <artifactId>mockito-core</artifactId>
                </exclusion>
            </exclusions>
        </dependency>

        <dependency>
            <groupId>commons-io</groupId>
            <artifactId>commons-io</artifactId>
        </dependency>
        <dependency>
            <groupId>org.apache.commons</groupId>
            <artifactId>commons-configuration2</artifactId>
        </dependency>

        <dependency>
            <groupId>org.assertj</groupId>
            <artifactId>assertj-core</artifactId>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>junit</groupId>
            <artifactId>junit</artifactId>
            <version>4.12</version>
            <scope>test</scope>
        </dependency>

        <dependency>
            <groupId>ch.qos.logback</groupId>
            <artifactId>logback-classic</artifactId>
            <scope>runtime</scope>
            <optional>true</optional>
        </dependency>
        <dependency>
            <groupId>ch.qos.logback</groupId>
            <artifactId>logback-core</artifactId>
            <scope>runtime</scope>
            <optional>true</optional>
        </dependency>
        <dependency>
            <groupId>com.github.stefanbirkner</groupId>
            <artifactId>system-rules</artifactId>
            <scope>test</scope>
        </dependency>

        <!-- mocking -->
        <dependency>
            <groupId>org.powermock</groupId>
            <artifactId>powermock-core</artifactId>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>org.powermock</groupId>
            <artifactId>powermock-module-junit4</artifactId>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>org.powermock</groupId>
            <artifactId>powermock-api-mockito</artifactId>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>org.powermock</groupId>
            <artifactId>powermock-api-easymock</artifactId>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>org.easymock</groupId>
            <artifactId>easymock</artifactId>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>org.mockito</groupId>
            <artifactId>mockito-core</artifactId>
            <scope>test</scope>
        </dependency>
    </dependencies>


    <build>
        <plugins>
            <plugin>
                <groupId>org.codehaus.mojo</groupId>
                <artifactId>cobertura-maven-plugin</artifactId>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
            </plugin>
            <plugin>
                <artifactId>maven-dependency-plugin</artifactId>
                <executions>
                    <execution>
                        <id>analyze</id>
                        <goals>
                            <goal>analyze-only</goal>
                        </goals>
                        <configuration>
                            <failOnWarning>true</failOnWarning>
                            <outputXML>true</outputXML>
                            <ignoreNonCompile>true</ignoreNonCompile>
                            <usedDependencies>
                                <!--                                <usedDependency>joda-time:joda-time</usedDependency>-->
                                <usedDependency>commons-io:commons-io</usedDependency>
                                <usedDependency>org.apache.commons:commons-configuration2</usedDependency>
                            </usedDependencies>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <groupId>net.alchim31.maven</groupId>
                <artifactId>scala-maven-plugin</artifactId>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-clean-plugin</artifactId>
                <executions>
                    <execution>
                        <id>clean-test-download</id>
                        <phase>install</phase>
                        <goals>
                            <goal>clean</goal>
                        </goals>
                        <configuration>
                            <excludeDefaultDirectories>true</excludeDefaultDirectories>
                            <filesets>
                                <fileset>
                                    <directory>cromwell-workflow-logs</directory>
                                </fileset>
                                <fileset>
                                    <includes>
                                        <include>Cromwell.stderr.txt</include>
                                        <include>Cromwell.stdout.txt</include>
                                    </includes>
                                </fileset>
                            </filesets>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
        </plugins>
    </build>

    <profiles>
        <profile>
            <id>confidential-tests</id>
            <build>
                <plugins>
                    <plugin>
                        <groupId>org.apache.maven.plugins</groupId>
                        <artifactId>maven-failsafe-plugin</artifactId>
                        <version>${maven-fire.version}</version>
                        <configuration>
                            <includes>
                                <!-- standard inclusions -->
                                <include>**/IT*.java</include><commit_msg>Cleaning up downloaded plugins (#647)<commit_after><?xml version="1.0" encoding="UTF-8"?>
<!--
  ~    Copyright 2016 OICR
  ~
  ~    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.
  -->

<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
    <modelVersion>4.0.0</modelVersion>
    <parent>
        <groupId>io.dockstore</groupId>
        <artifactId>dockstore</artifactId>
        <version>1.2.0-alpha.7-SNAPSHOT</version>
        <relativePath>../pom.xml</relativePath>
    </parent>
    <artifactId>dockstore-integration-testing</artifactId>
    <packaging>jar</packaging>

    <properties>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
    </properties>

    <dependencies>
        <dependency>
            <groupId>io.dockstore</groupId>
            <artifactId>dockstore-webservice</artifactId>
            <version>1.2.0-alpha.7-SNAPSHOT</version>
        </dependency>

        <!-- testing -->
        <dependency>
            <groupId>io.dockstore</groupId>
            <artifactId>dockstore-common</artifactId>
            <version>1.2.0-alpha.7-SNAPSHOT</version>
            <scope>test</scope>
            <type>test-jar</type>
        </dependency>

        <dependency>
            <groupId>io.dropwizard</groupId>
            <artifactId>dropwizard-testing</artifactId>
            <version>${dropwizard.version}</version>
            <scope>test</scope>
            <exclusions>
                <exclusion>
                    <groupId>org.mockito</groupId>
                    <artifactId>mockito-core</artifactId>
                </exclusion>
            </exclusions>
        </dependency>

        <dependency>
            <groupId>commons-io</groupId>
            <artifactId>commons-io</artifactId>
        </dependency>
        <dependency>
            <groupId>org.apache.commons</groupId>
            <artifactId>commons-configuration2</artifactId>
        </dependency>

        <dependency>
            <groupId>org.assertj</groupId>
            <artifactId>assertj-core</artifactId>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>junit</groupId>
            <artifactId>junit</artifactId>
            <version>4.12</version>
            <scope>test</scope>
        </dependency>

        <dependency>
            <groupId>ch.qos.logback</groupId>
            <artifactId>logback-classic</artifactId>
            <scope>runtime</scope>
            <optional>true</optional>
        </dependency>
        <dependency>
            <groupId>ch.qos.logback</groupId>
            <artifactId>logback-core</artifactId>
            <scope>runtime</scope>
            <optional>true</optional>
        </dependency>
        <dependency>
            <groupId>com.github.stefanbirkner</groupId>
            <artifactId>system-rules</artifactId>
            <scope>test</scope>
        </dependency>

        <!-- mocking -->
        <dependency>
            <groupId>org.powermock</groupId>
            <artifactId>powermock-core</artifactId>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>org.powermock</groupId>
            <artifactId>powermock-module-junit4</artifactId>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>org.powermock</groupId>
            <artifactId>powermock-api-mockito</artifactId>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>org.powermock</groupId>
            <artifactId>powermock-api-easymock</artifactId>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>org.easymock</groupId>
            <artifactId>easymock</artifactId>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>org.mockito</groupId>
            <artifactId>mockito-core</artifactId>
            <scope>test</scope>
        </dependency>
    </dependencies>


    <build>
        <plugins>
            <plugin>
                <groupId>org.codehaus.mojo</groupId>
                <artifactId>cobertura-maven-plugin</artifactId>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
            </plugin>
            <plugin>
                <artifactId>maven-dependency-plugin</artifactId>
                <executions>
                    <execution>
                        <id>analyze</id>
                        <goals>
                            <goal>analyze-only</goal>
                        </goals>
                        <configuration>
                            <failOnWarning>true</failOnWarning>
                            <outputXML>true</outputXML>
                            <ignoreNonCompile>true</ignoreNonCompile>
                            <usedDependencies>
                                <!--                                <usedDependency>joda-time:joda-time</usedDependency>-->
                                <usedDependency>commons-io:commons-io</usedDependency>
                                <usedDependency>org.apache.commons:commons-configuration2</usedDependency>
                            </usedDependencies>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <groupId>net.alchim31.maven</groupId>
                <artifactId>scala-maven-plugin</artifactId>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-clean-plugin</artifactId>
                <executions>
                    <execution>
                        <id>clean-test-download</id>
                        <phase>install</phase>
                        <goals>
                            <goal>clean</goal>
                        </goals>
                        <configuration>
                            <excludeDefaultDirectories>true</excludeDefaultDirectories>
                            <filesets>
                                <fileset>
                                    <directory>cromwell-workflow-logs</directory>
                                </fileset>
                                <fileset>
                                    <includes>
                                        <include>Cromwell.stderr.txt</include>
                                        <include>Cromwell.stdout.txt</include>
                                    </includes>
                                </fileset>
                                <fileset>
                                    <directory>src/test/resources/pluginsTest1/plugins</directory>
                                    <excludes>
                                        <exclude>*abled.txt</exclude>
                                    </excludes>
                                </fileset>
                                <fileset>
                                    <directory>src/test/resources/pluginsTest2/plugins</directory>
                                    <excludes>
                                        <exclude>*abled.txt</exclude>
                                    </excludes>
                                </fileset>
                            </filesets>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
        </plugins>
    </build>

    <profiles>
        <profile>
            <id>confidential-tests</id>
            <build>
                <plugins>
                    <plugin>
                        <groupId>org.apache.maven.plugins</groupId>
                        <artifactId>maven-failsafe-plugin</artifactId>
                        <version>${maven-fire.version}</version>
                        <configuration>
                            <includes>
                                <!-- standard inclusions -->
                                <include>**/IT*.java</include>
{'fraction_non_alphanumeric': 0.11443286762964718, 'fraction_numerical': 0.006097560975609756, 'mean_word_length': 1.3081021997540647, 'pattern_counts': {'":': 0, '<': 575, '<?xml version=': 2, '>': 575, 'https://': 0, 'lorem ipsum': 0, 'www.': 4, 'xml': 8}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 23, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4642933', 'n_tokens_mistral': 4657, 'n_tokens_neox': 4041, 'n_words': 561}