Feature #8404: allow environment variable replacement of path in leginon.cfg parsing - Leginon - Electron Microscopy Group

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Feature #8404

closed

allow environment variable replacement of path in leginon.cfg parsing

Added by Anchi Cheng over 4 years ago. Updated over 3 years ago.

Status:

Closed

Priority:

Urgent

Assignee:

Anchi Cheng

Category:

Target version:

Appion/Leginon 3.5

Start date:

12/20/2019

Due date:

% Done:

Estimated time:

Deliverable:

Description

SEMC starts to have more than one data storage system as we expand. We want to allow local staff with the same LDAP to collect to the different system depending on the leginon linux computer they log into.

Related issues 1 (0 open — 1 closed)

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Updated by Anchi Cheng over 4 years ago

Usage:

Use ${} to enclose the case sensitive variable name in leginon.cfg. For example

If you login as my_name and have an environment variable setup as

CRYOEM_BIG_STORAGE=data01

Then

[Images]
path: /${CRYOEM_BIG_STORAGE}/${USER}/leginon

is parsed as

[Images]
path: /data01/my_name/leginon

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Updated by Anchi Cheng over 4 years ago

Status changed from Assigned to Closed

works

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Updated by Shaker Krit almost 4 years ago

Status changed from Closed to In Test

The environment variable "CRYOEM_BIG_STORAGE" needs to be set withing "betaleginon" or "nccatleginon".

What changes have to be made for the transfer monitor script?

Anchi's suggestion is to have two different monitoring scripts each monitoring a different directory path (e.g. one for /ingest1data/beegfs another for /ingest1data/gpfs)

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