NGPIris 4.3.0

"Iris is a light-weight tool for interacting with a Boto3 backed Hitachi Content Platform"

NGP Iris 👁

NGP Iris is a light-weight tool for interacting with a Boto3 backed Hitachi Content Platform. NGP Iris is designed with two use cases in mind:

• A simple, clear, real-time interaction with NGPr file management
• Improving process flow for performing off-site data analysis by using automated transfer scripts

Getting started

Easy installation

pip install NGPIris

Requirements

• Anaconda or Miniconda for conda environment
• pip installed
• NGPr credentials

NGPr Credentials

• Receive your NGPr credentials from your local NGP admin
• Edit NGPIris/credentials.json

{
"endpoint" : "https://ACCESSNODESERVERNAME:PORT",
"aws_access_key_id" : "ALONGSTRINGOFCHARSTHATSYMBOLIZEYOURID",
"aws_secret_access_key" : "ANEVENLONGERSTRINGOFCHARSTHATSYMBOLIZEYOURPASSWORD",
"ngpi_password": "p@ssw0rd"
}

Introduction

NGP Iris provides two parts. A command line interface for intuitive manipulation of single files. And a python package to import easy to use file manipulation functions

Both of these modes of interaction pipe processes to the HCPManager class. This class is responsible for connecting to the specified endpoints with the provided access keys and manages the upload, download, and querying against the contents of the available buckets.

The connection is made on a higher resource level rather than client level. This will come to change in the future as more advanced features are introduced.

Usage

Command Line Interface

Successful installation means the command iris --help is active. Iris is constructed to have additional help for each subcommand. So, e.g., run iris -c CREDENTIALS -b BUCKET download --help to recieve all the download information.

Usage: iris [OPTIONS] COMMAND [ARGS]...

  NGP intelligence and repository interface software

Options:
  -c, --credentials PATH     File containing ep, id & key  [required]
  -b, --bucket TEXT          Bucket name  [required]
  -ep, --endpoint TEXT       Endpoint URL override
  -id, --access_key_id TEXT  Amazon key identifier override
  -key, --access_key TEXT    Amazon secret access key override
  -p, --password TEXT        NGPintelligence password
  -l, --logfile PATH         Logs activity to provided file
  --version                  Show the version and exit.
  --help                     Show this message and exit.

Commands:
  delete    Delete a file on the HCP
  download  Download files using a given query
  search    List all file hits for a given query by directly calling HCP
  upload    Upload fastq files / fastq folder structure
  utils     Advanced commands for specific purposes

Search for a file

iris -b BUCKETNAME -c CREDENTIALS_FILE search "MYDU*TESTFILE" --mode ngpr

This command will search the bucket BUCKETNAME for the object MYDU*TESTFILE.
The search command supports both asterix (*) completion and most regex.

--mode ngpr uses the NGPr search mode to find this file. This is the slowest mode, but also the one that has existed the longest.

To list the contents the entire bucket, use the command iris -b BUCKETNAME -c CREDENTIALS_FILE search "*" --mode ngpr The ngpr mode will take long while to complete this process, which is why other modes are in development.

Download a file

iris -b BUCKETNAME -c CREDENTIALS_FILE download /tmp/MYDUMBTESTFILE -o ./MYLOCALTESTFILE --silent --mode ngpr -f

This command will download your previously uploaded testfile, and put it in your current directory.
--mode ngpr uses the NGPr search mode to find this file. This is the slowest mode, but also the one that has existed the longest. Alternatively use --mode None to skip searching for the file altogether. This is lightening fast. But requires the file name to be exactly correct.
-f will overwrite any locally stored file with the same name
--silent will remove the download progress bar. Which is sometimes useful when scripting

Upload a file

iris -b BUCKETNAME -c CREDENTIALS_FILE upload FILE2UPLOAD -o /tmp/MYDUMBTESTFILE -s

This command will upload your test file as MYDUMBTESTFILE on the bucket BUCKETNAME.
-q verifies that only fastq files are uploaded -s removes the transfer speed info. Which can get very spammy in scripts.

iris -b BUCKETNAME -c CREDENTIALS_FILE upload FOLDER2UPLOAD/

This command will upload your entire folder, its contents and the substructure.

Delete a file

iris -b BUCKETNAME -c CREDENTIALS_FILE delete MYDUMBTESTFILE

This command will delete the file MYDUMBTESTFILE.
By default you will be prompted that you are certain that you wish to remove your file.

Additional commands

iris -c CREDENTIALS_FILE -b BUCKETNAME utils test-connection

This command tests if you can successfully connect to NGPRepository.

If it doesn't crash, it means you have correct credentials and an uninterrupted path to NGPRepository.

iris -c CREDENTIALS_FILE -b anything utils list-buckets

This command lists all the buckets of a tenent, that you at some point had admin access to. Note that you do not need to provide a valid bucketname for this command to successfully execute.

iris contains more commands and flags for additional operations. The help menu packaged with the program is always kept up to date, so refer to that to easily discover more.

For more use cases, check out the CLI file

As a package

For usage of Iris as a package see the package documentation

For an index of all HCPManager functionality, check out the source file

Development installation

git clone [e-mail]:genomic-medicine-sweden/NGPIris.git
cd NGPIris
bash setup.sh ENVNAME
source activate ENVNAME
Edit credentials.json
pytest tests/