"Iris is a light-weight tool for interacting with a Boto3 backed Hitachi Content Platform"
Project description
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
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.
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 -a -s
This command will upload your test file as MYDUMBTESTFILE
on the bucket BUCKETNAME.
-a
allows non-fastq file formats.
-s
removes the transfer speed info. Which can get very spammy in scripts.
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
contains more commands and flags for additional operations. Such as search, deleting, or doing things in a more nuanced way. 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 build
git clone git@github.com:genomic-medicine-sweden/NGPIris.git
cd NGPIris
bash setup.sh iris
source activate iris
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