Web, REST and SFTP server for the data submission sub-system.
The submission server is comprised of the following frameworks:
The SFTP interface is implemented using Apache MINA SSHD using a custom HDFS based virtual file system.
The metadata persistence layer is implemented using:
To compile, test and package the module, execute the following from the root of the repository:
mvn -am -pl dcc-submission/dcc-submission-serverBefore starting development it is necessary to download and extract a reference genome FASTA file and index:
wget https://artifacts.oicr.on.ca/artifactory/simple/dcc-dependencies/org/icgc/dcc/dcc-reference-genome/GRCh37/dcc-reference-genome-GRCh37.tar.gz
tar zxf dcc-reference-genome-GRCh37.tar.gz -C /tmpEnsure the FASTA file is correctly referenced from application.conf's reference.fasta configuration element.
To start the server in an IDE:
java -Dlogback.configurationFile=src/main/conf/logback.xml -Dlog.dir=target/logs org.icgc.dcc.submission.server.Main external src/test/conf/application.confTo start the server from the command line:
cd dcc
mvn -am -pl dcc-submission/dcc-submission-server -DskipTests=true
cd dcc-submission/dcc-submission-server
mvn exec:javaStart the server using an IDE by running:
org.icgc.dcc.submission.SubmissionMain external src/test/conf/application.confTo see the client interface, point your browser to http://localhost:5380/
To login to SFTP type:
sftp -P 5322 -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null admin@localhostUse the username admin and password adminspasswd to login to both HTTP and SFTP interfaces.
Sometimes it is needed to debug a running instance that has been packaged into a jar to investigate packaging issues. You can attach a debugger in your IDE by running the jared application with:
java -Dlogback.configurationFile=../conf/logback.xml -Dlog.dir=../logs -Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=1044 -Xmx4092m -jar ../lib/dcc-submission-server.jar external ../conf/application.conf