Command line interface

# at place A, create some json
zoo init file.json  # validation checks on records at this stage
# more modifications
zoo commit -m 'new RNA virus assemblies from study'
dat share . # generates link asdew3es...

# in some faraway place B
dat clone asdew3es...
zoo add --db zika --cell new_study 
# rename
zoo drop --db zika --cell new_study --force
zoo add --db zika --cell renamed_study
# now we can do analyses, e.g. MSA against some flaviviruses
zoo commit -m 'new RNA viruses related to flavivirus'

# at some place C, somebody already cloned zoo B
zoo pull # new sequences now present
zoo status --db zika

# This is lucky because B got frustrated and deleted evrything.
zoo destroy --db zika

Example:

zoo init --db zika --cell a zoo/data/cell_a.json
# Initializing data cell.
# Inserted 3 entries into cell "a".

zoo add --db zika --cell a --primkey genbank.a zoo/data/cell_b.json
# Loading data cell.
# Index created on field "genbank.a".
# 1 documents inserted in cell "a".
# 3 duplicates skipped.

zoo add --db zika --cell a cell_c.json
# Loading data cell.
# 2 documents inserted in cell "a".

zoo init --db zika --cell c zoo/data/cell_c_change.json
zoo commit --db zika --cell c --ksize 3,4,5 --n 5 cell_c_change_commit

# now pull these changes to cell "a"


zoo drop --db zika --cell a --force
# Dropped cell "a" from database "zika".