irods_fcs's Introduction

irods-fcs

Summary

As of version 0.0.1, this Python3 module contains the basic functionality to

pull keyword/value parameter pairs from the headers of FCS files
if the file is registered in iRODS, filter the parameter pairs optionally via a list of desired keywords and translate the selected parameters into metadata tags that will annotate the corresponding iRODS data object.

These capabilities can be extended to become interoperable with

client side ingest: https://github.com/irods/irods_capability_automated_ingest
data policy via rules implemented in Python: https://github.com/irods/irods_rule_engine_plugin_python

We rely on the PyPI 'FlowCal' module at present

Setup

On Centos 7 with an iRODS 4.2.11 server installed, we can set up in this way:

(as root)  
# sudo apt install python3-tkinter python3-pip python36-virtualenv git
(as irods) 
$ virtualenv-3 ~/py3
$ . ~/py3/bin/activate
(py3) $ git clone http://github.com/d-w-moore/irods_fcs
(py3) $ pip install ./irods_fcs

Demonstration

Using a sample .FCS file:

# -- choose a subset of the available keywords in the file header (no filtering if keywords are not entered)

(py3) $ irods_fcs/src/demo.sh /tmp/01-ALL_651149252706-A8.fcs 
enter keywords > SMID TBID

# -- list the registered data object's metadata tags that were attached 

(py3) $ imeta ls -d  `ipwd`//01-ALL_651149252706-A8.fcs
AVUs defined for dataObj /tempZone/home/rods/01-ALL_651149252706-A8.fcs:
attribute: SMID
value: CA012-004_20OCT20_0024 00212_C1D15
units: 
----
attribute: TBID
value: 2e48cac4-566e-4d07-bf90-44fc3e568e12
units:

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