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Feature/update more dependencies (#342)
* Restlet 2.3.7, AWS, jersey Jackson update * org.codehaus.jackson still used by some dependencies instead of com.fasterxml.jackson * Make zip64 library more standard by using commons-compress instead of odd rare library * can now use standard Linux tools like unzip to view bundles * New tools are still compatible with old bundles
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‎README.md

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@@ -94,8 +94,8 @@ When this is complete:
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(This runs all unit tests and integration tests that only require postgres as a prerequisite)
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mvn clean install -DskipITs=false -P extITs,embeddedTomcat
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(runs all unit tests and all integration tests including those that require Oozie)
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mvn clean install -DskipITs=false -P allITs,embeddedTomcat
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(runs all unit tests and all integration tests including those that require Oozie or take longer than can fix on Travis-CI)
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mvn clean install -DskipITs=false -P longITs,embeddedTomcat
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(runs all unit tests and just the long integration tests that take longer than can run on Travis-CI)
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In the last case, the extended integration tests profile is used to trigger integration tests that run our command line utilities.
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In order to point your command-line tools at the web service brought up by the integration tests, you will need to comment out your crontab and modify your SeqWare ~/.seqware/settings to include:

‎pom.xml

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@@ -21,8 +21,8 @@
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<seqware_meta_db_host>localhost</seqware_meta_db_host>
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<!-- while merging com.amazonaws.services.s3.transfer.MultipleFileUpload , I couldn't compile without setting a version here -->
24-
<aws-java-sdk.version>1.10.77</aws-java-sdk.version>
25-
<jackson.version>1.9.13</jackson.version>
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<aws-java-sdk.version>1.11.15</aws-java-sdk.version>
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<jackson.version>2.4.4</jackson.version>
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<spring.version>4.2.6.RELEASE</spring.version>
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<hibernate.version>5.1.0.Final</hibernate.version>
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<hibernate.jpa.version>1.0.0.Final</hibernate.jpa.version>
@@ -35,7 +35,7 @@
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<commons-exec.version>1.3</commons-exec.version>
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<postgresql.version>9.4-1201-jdbc41</postgresql.version>
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<guava.version>19.0</guava.version>
38-
<restlet.version>2.2.2</restlet.version>
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<restlet.version>2.3.7</restlet.version>
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<opencsv.version>2.3</opencsv.version>
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<maven-assembly-plugin.version>2.6</maven-assembly-plugin.version>
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<jetty-maven-plugin.version>6.1.26</jetty-maven-plugin.version>
@@ -59,6 +59,8 @@
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<powermock.version>1.6.5</powermock.version>
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<findbugs.version>3.0.3</findbugs.version>
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<maven-pmd-plugin.version>3.6</maven-pmd-plugin.version>
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<slf4j.version>1.7.21</slf4j.version>
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<old-jersey.version>1.19.1</old-jersey.version>
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<skipITs>true</skipITs>
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<!-- Needs to be set for memory issues, but must be overrideable from the command line for Bionimbus for unknown reasons -->
@@ -196,22 +198,22 @@
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<dependency>
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<groupId>org.slf4j</groupId>
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<artifactId>slf4j-api</artifactId>
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<version>1.7.6</version>
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<version>${slf4j.version}</version>
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</dependency>
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<dependency>
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<groupId>org.slf4j</groupId>
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<artifactId>slf4j-log4j12</artifactId>
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<version>1.7.6</version>
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<version>${slf4j.version}</version>
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</dependency>
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<dependency>
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<groupId>org.slf4j</groupId>
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<artifactId>jul-to-slf4j</artifactId>
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<version>1.7.6</version>
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<version>${slf4j.version}</version>
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</dependency>
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<dependency>
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<groupId>org.slf4j</groupId>
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<artifactId>jcl-over-slf4j</artifactId>
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<version>1.7.6</version>
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<version>${slf4j.version}</version>
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</dependency>
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<dependency>
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<groupId>log4j</groupId>
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<version>4.1</version>
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</dependency>
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<dependency>
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<groupId>ch.enterag</groupId>
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<artifactId>zip64</artifactId>
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<version>1.03</version>
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<groupId>commons-collections</groupId>
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<artifactId>commons-collections</artifactId>
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<version>3.2.1</version>
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</dependency>
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<dependency>
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<groupId>commons-digester</groupId>
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<artifactId>commons-digester</artifactId>
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<version>1.8</version>
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</dependency>
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<!-- https://mvnrepository.com/artifact/org.apache.commons/commons-compress -->
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<dependency>
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<groupId>org.apache.commons</groupId>
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<artifactId>commons-compress</artifactId>
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<version>1.12</version>
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</dependency>
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<dependency>
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<groupId>commons-dbutils</groupId>
@@ -377,26 +390,44 @@
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</exclusions>
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</dependency>
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393+
<!-- enforce for dependencies but replaced by com.fasterxml.jackson in our code -->
394+
<dependency>
395+
<groupId>org.codehaus.jackson</groupId>
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<artifactId>jackson-mapper-asl</artifactId>
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<version>1.9.13</version>
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</dependency>
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<dependency>
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<groupId>org.codehaus.jackson</groupId>
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<artifactId>jackson-core-asl</artifactId>
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<version>1.9.13</version>
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</dependency>
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<dependency>
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<groupId>com.fasterxml.jackson.core</groupId>
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<artifactId>jackson-annotations</artifactId>
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<version>${jackson.version}</version>
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</dependency>
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<!-- https://mvnrepository.com/artifact/com.fasterxml.jackson.core/jackson-databind -->
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<dependency>
386-
<groupId>org.codehaus.jackson</groupId>
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<artifactId>jackson-mapper-asl</artifactId>
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<groupId>com.fasterxml.jackson.core</groupId>
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<artifactId>jackson-databind</artifactId>
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<version>${jackson.version}</version>
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</dependency>
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<dependency>
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<groupId>org.codehaus.jackson</groupId>
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<artifactId>jackson-jaxrs</artifactId>
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<groupId>com.fasterxml.jackson.core</groupId>
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<artifactId>jackson-core</artifactId>
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<version>${jackson.version}</version>
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</dependency>
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<dependency>
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<groupId>org.codehaus.jackson</groupId>
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<artifactId>jackson-xc</artifactId>
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<groupId>com.fasterxml.jackson.dataformat</groupId>
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<artifactId>jackson-dataformat-yaml</artifactId>
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<version>${jackson.version}</version>
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</dependency>
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<dependency>
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<groupId>org.yaml</groupId>
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<artifactId>snakeyaml</artifactId>
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<version>1.17</version>
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</dependency>
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<dependency>
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<groupId>org.springframework</groupId>
@@ -576,7 +607,7 @@
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<dependency>
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<groupId>org.codehaus.woodstox</groupId>
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<artifactId>stax2-api</artifactId>
579-
<version>3.1.3</version>
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<version>3.1.4</version>
580611
</dependency>
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<dependency>
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<groupId>xml-apis</groupId>
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<dependency>
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<groupId>com.sun.jersey</groupId>
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<artifactId>jersey-json</artifactId>
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<version>1.11.1</version>
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<version>${old-jersey.version}</version>
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</dependency>
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<dependency>
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<groupId>com.sun.jersey.contribs</groupId>
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<artifactId>jersey-moxy</artifactId>
706-
<version>1.11.1</version>
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<version>${old-jersey.version}</version>
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</dependency>
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<dependency>
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<groupId>com.sun.jersey.glassfish.v3.osgi</groupId>
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<artifactId>jersey-gf-server</artifactId>
711-
<version>1.11.1</version>
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<version>${old-jersey.version}</version>
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</dependency>
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<dependency>
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<groupId>com.sun.jersey</groupId>
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<artifactId>jersey-client</artifactId>
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<version>1.11.1</version>
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<version>${old-jersey.version}</version>
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</dependency>
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<dependency>
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<groupId>com.sun.jersey</groupId>
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<artifactId>jersey-grizzly</artifactId>
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<version>1.11.1</version>
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<version>${old-jersey.version}</version>
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</dependency>
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<dependency>
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<groupId>com.sun.jersey.glassfish.v3.osgi</groupId>
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<artifactId>jersey-gf-statsproviders</artifactId>
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<version>1.11.1</version>
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<version>${old-jersey.version}</version>
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</dependency>
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<dependency>
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<groupId>org.glassfish.hk2.external</groupId>
@@ -733,7 +764,7 @@
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<dependency>
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<groupId>com.sun.jersey.glassfish.v3.osgi</groupId>
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<artifactId>jersey-gf-servlet</artifactId>
736-
<version>1.11.1</version>
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<version>${old-jersey.version}</version>
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</dependency>
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<dependency>
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<groupId>org.codehaus.jettison</groupId>
@@ -743,17 +774,17 @@
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<dependency>
744775
<groupId>org.jvnet.mimepull</groupId>
745776
<artifactId>mimepull</artifactId>
746-
<version>1.8</version>
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<version>1.9.3</version>
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</dependency>
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<dependency>
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<groupId>com.sun.jersey.contribs</groupId>
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<artifactId>jersey-multipart</artifactId>
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<version>1.11.1</version>
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<version>${old-jersey.version}</version>
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</dependency>
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<dependency>
754785
<groupId>com.sun.jersey</groupId>
755786
<artifactId>jersey-core</artifactId>
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<version>1.11.1</version>
787+
<version>${old-jersey.version}</version>
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</dependency>
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<dependency>
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<groupId>junit</groupId>
@@ -831,7 +862,7 @@
831862
<dependency>
832863
<groupId>com.google.code.gson</groupId>
833864
<artifactId>gson</artifactId>
834-
<version>2.6.2</version>
865+
<version>2.7</version>
835866
</dependency>
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<dependency>
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<groupId>joda-time</groupId>
@@ -856,6 +887,27 @@
856887
<artifactId>commons-beanutils</artifactId>
857888
<version>1.9.2</version>
858889
</dependency>
890+
891+
<dependency>
892+
<groupId>asm</groupId>
893+
<artifactId>asm</artifactId>
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<version>3.3.1</version>
895+
</dependency>
896+
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<!-- explicitly define dependency to version 0.8.11 -->
898+
<dependency>
899+
<groupId>org.raml</groupId>
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<artifactId>raml-parser</artifactId>
901+
<version>0.8.14</version>
902+
</dependency>
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<!-- https://mvnrepository.com/artifact/com.google.code.findbugs/jsr305 -->
905+
<dependency>
906+
<groupId>com.google.code.findbugs</groupId>
907+
<artifactId>jsr305</artifactId>
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<version>3.0.0</version>
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</dependency>
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</dependencies>
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</dependencyManagement>
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‎seqware-admin-webservice/pom.xml

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<artifactId>jersey-client</artifactId>
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<type>jar</type>
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</dependency>
68+
<dependency>
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<groupId>javax.ws.rs</groupId>
70+
<artifactId>jsr311-api</artifactId>
71+
<version>1.1.1</version>
72+
</dependency>
73+
<!--
6874
<dependency>
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<groupId>com.sun.jersey</groupId>
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<artifactId>jersey-core</artifactId>
7177
</dependency>
78+
-->
7279
<dependency>
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<groupId>${project.groupId}</groupId>
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<artifactId>seqware-meta-db</artifactId>
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<version>${project.version}</version>
7683
</dependency>
77-
<dependency>
78-
<artifactId>jackson-core-asl</artifactId>
79-
<groupId>org.codehaus.jackson</groupId>
80-
<type>jar</type>
81-
</dependency>
8284
<dependency>
8385
<artifactId>jaxb-api</artifactId>
8486
<groupId>javax.xml.bind</groupId>
@@ -124,6 +126,14 @@
124126
<type>jar</type>
125127
<scope>runtime</scope>
126128
</dependency>
129+
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<!-- https://mvnrepository.com/artifact/com.fasterxml.jackson.core/jackson-annotations -->
131+
<dependency>
132+
<groupId>com.fasterxml.jackson.core</groupId>
133+
<artifactId>jackson-annotations</artifactId>
134+
<version>${jackson.version}</version>
135+
</dependency>
136+
127137
</dependencies>
128138

129139
<build>

‎seqware-admin-webservice/src/main/java/io/seqware/webservice/generated/model/File.java

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44
*/
55
package io.seqware.webservice.generated.model;
66

7-
import java.io.Serializable;
8-
import java.math.BigInteger;
9-
import java.util.Collection;
7+
import com.fasterxml.jackson.annotation.JsonIgnore;
8+
109
import javax.persistence.Basic;
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import javax.persistence.CascadeType;
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import javax.persistence.Column;
@@ -26,7 +25,9 @@
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import javax.validation.constraints.Size;
2726
import javax.xml.bind.annotation.XmlRootElement;
2827
import javax.xml.bind.annotation.XmlTransient;
29-
import org.codehaus.jackson.annotate.JsonIgnore;
28+
import java.io.Serializable;
29+
import java.math.BigInteger;
30+
import java.util.Collection;
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/**
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*

‎seqware-admin-webservice/src/main/java/io/seqware/webservice/generated/model/WorkflowRun.java

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44
*/
55
package io.seqware.webservice.generated.model;
66

7-
import java.io.Serializable;
8-
import java.sql.Timestamp;
9-
import java.util.Collection;
10-
import java.util.Date;
7+
import com.fasterxml.jackson.annotation.JsonIgnore;
8+
119
import javax.persistence.Basic;
1210
import javax.persistence.CascadeType;
1311
import javax.persistence.Column;
@@ -30,7 +28,10 @@
3028
import javax.validation.constraints.Size;
3129
import javax.xml.bind.annotation.XmlRootElement;
3230
import javax.xml.bind.annotation.XmlTransient;
33-
import org.codehaus.jackson.annotate.JsonIgnore;
31+
import java.io.Serializable;
32+
import java.sql.Timestamp;
33+
import java.util.Collection;
34+
import java.util.Date;
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3536
/**
3637
*

‎seqware-common/pom.xml

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@@ -180,9 +180,10 @@
180180
<artifactId>org.restlet.ext.jsslutils</artifactId>
181181
<scope>runtime</scope>
182182
</dependency>
183+
<!-- https://mvnrepository.com/artifact/org.apache.commons/commons-compress -->
183184
<dependency>
184-
<groupId>ch.enterag</groupId>
185-
<artifactId>zip64</artifactId>
185+
<groupId>org.apache.commons</groupId>
186+
<artifactId>commons-compress</artifactId>
186187
</dependency>
187188
<dependency>
188189
<groupId>net.sf.jopt-simple</groupId>
@@ -243,11 +244,6 @@
243244
<groupId>com.amazonaws</groupId>
244245
<artifactId>aws-java-sdk-core</artifactId>
245246
</dependency>
246-
<dependency>
247-
<groupId>org.codehaus.jackson</groupId>
248-
<artifactId>jackson-core-asl</artifactId>
249-
<scope>runtime</scope>
250-
</dependency>
251247
<dependency>
252248
<groupId>commons-codec</groupId>
253249
<artifactId>commons-codec</artifactId>

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