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#1 image for drs
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@michael-conway
michael-conway committed Feb 7, 2020
1 parent a31a5d9 commit f6cfa66
Showing 12 changed files with 470 additions and 227 deletions.
6 changes: 3 additions & 3 deletions Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
FROM tomcat:jre8-alpine
FROM adoptopenjdk/openjdk11
LABEL organization="NIEHS"
LABEL maintainer="mike.conway@nih.gov"
LABEL description="iRODS REST V2"
@@ -10,6 +10,6 @@ ENTRYPOINT ["/runit.sh"]



# build: docker build -t diceunc/ga4gh-dos:0.0.1 .
# build: docker build -t michael-conway/irods-rest2:1.0.0 .

# run: docker run -d --rm -p 8080:8080 -v /etc/irods-ext:/etc/irods-ext --add-host irods420.irodslocal:172.16.250.101 diceunc/ga4gh-dos:0.0.1
# run: docker run -d --rm -p 8080:8080 -v /etc/irods-ext:/etc/irods-ext michael-conway/irods-rest2:1.0.0
299 changes: 156 additions & 143 deletions pom.xml
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Original file line number Diff line number Diff line change
@@ -1,146 +1,153 @@
<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/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>org.irods</groupId>
<artifactId>irods-rest2</artifactId>
<packaging>jar</packaging>
<name>irods-rest2</name>
<version>1.0.0</version>
<properties>
<java.version>1.8</java.version>
<maven.compiler.source>${java.version}</maven.compiler.source>
<maven.compiler.target>${java.version}</maven.compiler.target>
<springfox-version>2.7.0</springfox-version>
<jargon.version>4.3.1.0-SNAPSHOT</jargon.version>
<spring.security.version>4.2.4.RELEASE</spring.security.version>
<spring.boot.starter.version>1.5.9.RELEASE</spring.boot.starter.version>
</properties>
<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
<version>1.5.9.RELEASE</version>
</parent>
<dependencies>
<dependency>
<groupId>org.irods.jargon</groupId>
<artifactId>jargon-core</artifactId>
<version>${jargon.version}</version>
</dependency>
<dependency>
<groupId>org.irods.jargon</groupId>
<artifactId>jargon-mdquery</artifactId>
<version>${jargon.version}</version>
</dependency>
<dependency>
<groupId>org.irods.jargon</groupId>
<artifactId>jargon-ticket</artifactId>
<version>${jargon.version}</version>
</dependency>
<dependency>
<groupId>org.irods.jargon</groupId>
<artifactId>jargon-extensions-if</artifactId>
<version>${jargon.version}</version>
</dependency>
<dependency>
<groupId>org.irods.jargon</groupId>
<artifactId>irodsext-data-typer</artifactId>
<version>${jargon.version}</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.mockito/mockito-all -->
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-all</artifactId>
<version>1.10.19</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-web</artifactId>
<exclusions>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>log4j-over-slf4j</artifactId>
</exclusion>
<exclusion>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-tomcat</artifactId>
<exclusions>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>log4j-over-slf4j</artifactId>
</exclusion>
</exclusions>
</dependency>
<!--SpringFox dependencies -->
<dependency>
<groupId>io.springfox</groupId>
<artifactId>springfox-swagger2</artifactId>
<version>${springfox-version}</version>
<exclusions>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>log4j-over-slf4j</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>io.springfox</groupId>
<artifactId>springfox-swagger-ui</artifactId>
<version>${springfox-version}</version>
<exclusions>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>log4j-over-slf4j</artifactId>
</exclusion>
</exclusions>
</dependency>

<dependency>
<groupId>com.fasterxml.jackson.datatype</groupId>
<artifactId>jackson-datatype-jsr310</artifactId>
</dependency>
<!-- Bean Validation API support -->
<dependency>
<groupId>javax.validation</groupId>
<artifactId>validation-api</artifactId>
</dependency>
<?xml version="1.0" encoding="UTF-8"?>
<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/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>org.irods</groupId>
<artifactId>irods-rest2</artifactId>
<packaging>jar</packaging>
<name>irods-rest2</name>
<version>1.0.0</version>
<properties>
<java.version>1.8</java.version>
<maven.compiler.source>${java.version}</maven.compiler.source>
<maven.compiler.target>${java.version}</maven.compiler.target>
<springfox-version>2.7.0</springfox-version>
<jargon.version>4.3.2.0-SNAPSHOT</jargon.version>
<spring.security.version>4.2.4.RELEASE</spring.security.version>
<spring.boot.starter.version>1.5.9.RELEASE</spring.boot.starter.version>
</properties>
<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
<version>1.5.9.RELEASE</version>
</parent>
<dependencies>

<dependency>
<groupId>org.irods.jargon</groupId>
<artifactId>jargon-core</artifactId>
<version>${jargon.version}</version>
</dependency>
<dependency>
<groupId>org.irods.jargon</groupId>
<artifactId>jargon-mdquery</artifactId>
<version>${jargon.version}</version>
</dependency>
<dependency>
<groupId>org.irods.jargon</groupId>
<artifactId>jargon-ticket</artifactId>
<version>${jargon.version}</version>
</dependency>
<dependency>
<groupId>org.irods.jargon</groupId>
<artifactId>jargon-extensions-if</artifactId>
<version>${jargon.version}</version>
</dependency>
<dependency>
<groupId>org.irods</groupId>
<artifactId>irodsext-jwt-service</artifactId>
<version>${jargon.version}</version>
</dependency>
<dependency>
<groupId>org.irods.jargon</groupId>
<artifactId>irodsext-data-typer</artifactId>
<version>${jargon.version}</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.mockito/mockito-all -->
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-all</artifactId>
<version>1.10.19</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-web</artifactId>
<exclusions>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>log4j-over-slf4j</artifactId>
</exclusion>
<exclusion>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-tomcat</artifactId>
<exclusions>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>log4j-over-slf4j</artifactId>
</exclusion>
</exclusions>
</dependency>
<!--SpringFox dependencies -->
<dependency>
<groupId>io.springfox</groupId>
<artifactId>springfox-swagger2</artifactId>
<version>${springfox-version}</version>
<exclusions>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>log4j-over-slf4j</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>io.springfox</groupId>
<artifactId>springfox-swagger-ui</artifactId>
<version>${springfox-version}</version>
<exclusions>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>log4j-over-slf4j</artifactId>
</exclusion>
</exclusions>
</dependency>

<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-test</artifactId>
<scope>test</scope>
<exclusions>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>log4j-over-slf4j</artifactId>
</exclusion>
</exclusions>
</dependency>

<dependency>
<dependency>
<groupId>com.fasterxml.jackson.datatype</groupId>
<artifactId>jackson-datatype-jsr310</artifactId>
</dependency>
<!-- Bean Validation API support -->
<dependency>
<groupId>javax.validation</groupId>
<artifactId>validation-api</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-test</artifactId>
<scope>test</scope>
<exclusions>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>log4j-over-slf4j</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.springframework.security</groupId>
<artifactId>spring-security-web</artifactId>
<exclusions>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>log4j-over-slf4j</artifactId>
</exclusion>
</exclusions>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>log4j-over-slf4j</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.springframework.security</groupId>
<artifactId>spring-security-config</artifactId>
<exclusions>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>log4j-over-slf4j</artifactId>
</exclusion>
</exclusions>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>log4j-over-slf4j</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.datatype</groupId>
@@ -165,8 +172,8 @@
<groupId>joda-time</groupId>
<artifactId>joda-time</artifactId>
</dependency>
</dependencies>
<build>
</dependencies>
<build>
<sourceDirectory>src/main/java</sourceDirectory>
<plugins>
<plugin>
@@ -188,10 +195,13 @@
<phase>validate</phase>
<configuration>
<tasks>
<delete file="${basedir}/src/test/resources/testing.properties" />
<touch file="${basedir}/src/test/resources/testing.properties"
<delete
file="${basedir}/src/test/resources/testing.properties" />
<touch
file="${basedir}/src/test/resources/testing.properties"
mkdirs="true" />
<echo file="${basedir}/src/test/resources/testing.properties"
<echo
file="${basedir}/src/test/resources/testing.properties"
append="true">
test.data.directory=${jargon.test.data.directory}
test.irods.admin=${jargon.test.irods.admin}
@@ -247,7 +257,7 @@
test.option.mount.basedir=${test.option.mount.basedir}
test.option.python=${test.option.python}
ga4gh.access.url=http://foo.com/ga4gh/drs/v1/objects

</echo>
</tasks>
</configuration>
@@ -261,10 +271,13 @@
<phase>validate</phase>
<configuration>
<tasks>
<delete file="${basedir}/src/test/resources/test.rest.properties" />
<touch file="${basedir}/src/test/resources/test.rest.properties"
<delete
file="${basedir}/src/test/resources/test.rest.properties" />
<touch
file="${basedir}/src/test/resources/test.rest.properties"
mkdirs="true" />
<echo file="${basedir}/src/test/resources/test.rest.properties"
<echo
file="${basedir}/src/test/resources/test.rest.properties"
append="true">
irods.host=${jargon.test.irods.host}
irods.port=${jargon.test.irods.port}
2 changes: 1 addition & 1 deletion src/main/java/org/irods/rest/api/FileBytesApiController.java
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Original file line number Diff line number Diff line change
@@ -45,6 +45,7 @@ public void fileBytes(String path, Integer offset, Integer limit, HttpServletRes
try {
IRODSAccount irodsAccount = contextAccountHelper
.irodsAccountFromAuthentication(irodsAuthentication.getName());
log.info("irodsAccount:{}", irodsAccount);

if (!irodsAuthentication.getTicket().isEmpty()) {
// use TicketClientSupport
@@ -59,7 +60,6 @@ public void fileBytes(String path, Integer offset, Integer limit, HttpServletRes
if (!irodsFile.exists()) {
log.info("file does not exist");
throw new IrodsRestRuntimeException("file not found");

}

InputStream input = new org.irods.jargon.core.pub.io.PackingIrodsInputStream(
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