metagrate

Metadata Migrate

Usage at DLS

For use at DLS metagrate has been set up at /dls/science/groups/i04-1/software/max/metagrate

To use it:

1. Load the python environment

source /dls/science/groups/i04-1/software/max/load_py310.sh

2. See the (barebones) help screen:

$METAGRATE migrate --help

3. Migrate a metadata.csv file

$METAGRATE migrate SOURCE TEMPLATE --output OUTPUT

• SOURCE is the metadata.csv containing the tags you want to migrate, i.e. this file should be from a Fragalysis download of a target where you have renamed the CanonicalSites and added your own tags, etc.
• TEMPLATE is a metadata.csv downloaded from the working Fragalysis target you wish to move the tags to, i.e. if you have just done a fresh LHS upload and want to migrate tags from an old version of the target.
• OUTPUT is the optional name of the output CSV file.

N.B. because Fragalysis names all the metadata files metadata.csv it is recommended you rename all your input and output files so you don't forget where they came from

Some example files are provided in examples/

Debugging common errors

AssertionError: SOURCE Long code does not match TEMPLATE

If you see the following error, the CanonicalSites or observation longcodes between the two files are incompatible. Try running with the --no-rename-sites option to skip renaming the XCA sites and just migrate the "curator" tags.

AssertionError: SOURCE Long code does not match TEMPLATE: ('3vws_A_1004_1_3vws+A+1003+1', '3vws_A_1004_v1'). Try running 
with --no-rename-sites

Installation (not at DLS)

Install the following dependencies and clone this repository:

pip install pandas mpytools
git clone [email protected]:xchem/metagrate