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RDSDS( Reference Data Set Distribution Service)

RDSDS is Client/Server Mode, this introduction will show how to deploy RDSDS with Binary Code.

DSDS-Client-Binary

RDSDS Client use ELIXIR AAI for authentication, make sure the client environment installed browser service. At the moment, RDSDS is running on ELIXIR Test environment, please be confirmed if you belong to ELIXIR Test VO (Virtual Organisation), if you can more details via https://perun.elixir-czech.cz/fed/registrar//registrar/?vo=elixir_test

Support: Windows 10 Pro, Centos 7, Fedora 28, Ubuntu and MacOS

If you can't run this file. Please check the file format, if it is plain text file, please execute this command : chomd +x

DSDS WorkFlow

image

Login with ELIXIR AAI or Google Account

image image

Commandlines

JSON template

{
"SourceSiteName": "EMBL-EBI",
"TransferSource": "gsiftp://dsds-gridftp1.ebi.ac.uk:2811/gridftp/100files",
"Protocol": "gridftp",
"Hostname": "dsds-gridftp1.ebi.ac.uk",
"Port": "2811",
"FilePath": "/gridftp/100files",
"CreatorName": "Jinny Chien",
"CreatorEmail": "[email protected]",
"DatasetName": "marinemetagenomics"
}

Login to a client shell:

./dsds-client-cmd
(dsds>)_

Register single dataset

(dsds>)reg <filename.json

Register multiple datasets

(dsds>)reg <filename.json

Unregister a Data Set

If the data set status is not released, Data Provider can unregister it

Unregister dataset

(dsds>)unreg -d datasetPID

Declare a file to the Data Set

After Data Provider registered and got dataset PID. Then they can add file definition does not verify existence. This action does not check remote file’s existence.

JSON template

{
“FileName”: “/ERR268/ERR268106/ERR268106.fastq.gz”,
“DatasetPID”: “embl-ebi-20161117-23456”
}

declare to add a single file/multiple files to the dataset

(dsds>)declare <filename.json

declare to add multiple dataset

 (dsds>)declare <filename.json

Index a file/folder to the Data Set

After Data Provider registered and got dataset PID. Then they can add a file or folder (recursive) and verify files existence (remote sites).

Index to add a file/folder to the dataset

(dsds>)index -d datasetPID

Index a nominated folder to the dataset

(dsds>)index -d datasetPID -folder foldername

List details of the Data Set or Subscriber

This command will perform the file list of the specific dataset PID or list the subscribered dataset PID or the details of the specific dataset PID

List files of the dataset

(dsds>)list -d datasetPID

List different version files of the dataset

(dsds>)list -d datasetPID -v releaseversion

List active subscribed datasetPID

(dsds>)list -u username

Show detail of subscribed datasetPID

(dsds>)list -u username -d datasetPID

Verify the Data Set

Data Provider can verify that the defined dataset is available to be released and check the integrity

Verify file existence before dataset releases

(dsds>)verify -d datasetPID

Verify integrity checking after releasing

(dsds>)verify -d datasetPID -v release_version

Compare the difference

Data consumer search different version files of dataset to get the transfer list and perform the data transfer

Find difference between release versions

(dsds>)diff -d datasetPID -f release_version -t release_version

Release the Data Set

When data set is released, data transfer will be performed in backgrpund

Release the dataset and subscribers will get the notification when the registered dataset updates

(dsds>)release -d datasetPID -v release_version

Delete the file

Data Provider can delete one file from a dataset that they have not released yet. If the dataset is released, there will be a warning reminder

Delete a single file of the dataset

(dsds>)delete -d datasetPID -f filename

Subscription

Data consumer subscribes which data set he/she wants, then they will get the Emial notification on every release and data transfer will be run in background.

Add subscriber JSON template

{
"FullName": "Kevin EBI",
"Username": "Kevin",
"Email": "[email protected]",
"Organisation": "EMBL-EBI",
"Hostname": "hx-gridftp-test.ebi.ac.uk",
"Port": "2811",
"FilePath": "/data01/test/test_folder/"
}

Add subscriber

(dsds>)adduser <filename.json

Update subscriber

(dsds>)updateuser <filename.json

Delete subscriber

(dsds>)deluser -u username

Activate subscriber

(dsds>)activate -u username

Subscribe users and datasetPID

(dsds>)sub -u username -d datasetPID

Unsubscribe users and datasetPID

(dsds>)unsub -u username -d datasetPID

Show all command lines information

Display all available command list and its description to help Data Provider to choose.

Show all useful comment line information

(dsds>)help

Show help for specific command

(dsds>)help <command>