Better terminology for "metadata" instances in the code, and in command line clients

[meren]

We have been calling a lot of things "metadata" throughout the development of anvi'o, when we should not have.

I already was upset about this situation (although failed, I attempted to fix it before too, i.e., #65). Finally when Susan Holmes (@spholmes) said "there is no such thing as metadata" during her last talk at the MBL, I decided to do something more concrete about this. Yes, everything is data, after all, and there should be better descriptions of what kind of data they are in the code than just calling things 'metadata' whenever it becomes challenging to find appropriate names.

I am going to start changing variable names and parameters that are called "metadata" into things such as "view data", "layer data", "additional view data", and such. This will stir things up in the codebase, previously-used parameters will be missing from command line clients, tests will fail, and our currently-quite-tiny user base will be upset because their batch scripts will not work. I will try to keep the damage to a minimum, and document everything. I am sorry for any inconvenience in advance, and I apologize for not doing a better job earlier.

[spholmes]

Of course I agree and the tack we took with phyloseq is to organize things as sample_data (any data, times samples were taken, clinical covariates etc.....that qualify samples) tax_table has all the data about the taxa and we are extending phyloseq to include many other `kinds of data'.

Thanks for listening...

Susan Holmes Professor, Statistics and BioX John Henry Fellow in Undergraduate Education Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/

[amaralzettler]

Hellos,

I suggest contextual data ­ this is what we started calling it in the GSC (Genomics Standards Consortium).

Linda

[meren]

This is done!

$ grep metadata * -nr | grep -v lib | grep -v svg
sandbox/anvi-script-upgrade-profile-db-v5-to-v6:37:        profile_db._exec('ALTER TABLE metadata_contigs RENAME TO atomic_data_contigs;')
sandbox/anvi-script-upgrade-profile-db-v5-to-v6:38:        profile_db._exec('ALTER TABLE metadata_splits RENAME TO atomic_data_splits;')

There is no instance of the word "metadata" in our codebase anymore.