Scripts to manage CSTB database.
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Need pyCouch module
Use replicate_database.py script :
usage: replicate_database.py [-h] [--db <str>] [--all] --url <str>
optional arguments:
-h, --help show this help message and exit
--db <str> Replicate database(s) corresponding to this regular expression
--all Replicate all databases in couchDB
--url <str> couchDB endpoint
For each database, this will create a backup database with bak and a timestamp in name.
For couchDB localized in http://localhost:5984
- Replicate all couchDB database
python replicate_database.py --url http://localhost:5984 --all
- Replicate taxon_tree database
python replicate_database.py --url http://localhost:5984 --db taxon_tree
- Replicate all crispr_rc01 databases
python replicate_database.py --url http://localhost:5984 --db crispr_rc01_v[0-9]+
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You can create view document from your own mapper with your regular expression or you can give depth parameters and regular expression will be created automatically.
Example of mapper file (it's the regular expression that will be created with depth 2):
{
'^[ACGT]{3}AA[ACGT]{18}$': 'organisms1',
'^[ACGT]{3}AC[ACGT]{18}$': 'organisms2',
'^[ACGT]{3}AG[ACGT]{18}$': 'organisms3',
'^[ACGT]{3}AT[ACGT]{18}$': 'organisms4',
'^[ACGT]{3}CA[ACGT]{18}$': 'organisms5',
'^[ACGT]{3}CC[ACGT]{18}$': 'organisms6',
'^[ACGT]{3}CG[ACGT]{18}$': 'organisms7',
'^[ACGT]{3}CT[ACGT]{18}$': 'organisms8',
'^[ACGT]{3}GA[ACGT]{18}$': 'organisms9',
'^[ACGT]{3}GC[ACGT]{18}$': 'organisms10',
'^[ACGT]{3}GG[ACGT]{18}$': 'organisms11',
'^[ACGT]{3}GT[ACGT]{18}$': 'organisms12',
'^[ACGT]{3}TA[ACGT]{18}$': 'organisms13',
'^[ACGT]{3}TC[ACGT]{18}$': 'organisms14',
'^[ACGT]{3}TG[ACGT]{18}$': 'organisms15',
'^[ACGT]{3}TT[ACGT]{18}$': 'organisms16'}
}
With depth 1 it will be :
{
"^[ACGT]{3}A[ACGT]{19}$": "organisms1",
"^[ACGT]{3}C[ACGT]{19}$": "organisms2",
"^[ACGT]{3}G[ACGT]{19}$": "organisms3",
"^[ACGT]{3}T[ACGT]{19}$": "organisms4"
}
python bin/create_view.py -d 2 -o data/view16.json
curl -X PUT http://couch_agent:couch@localhost:5984/my_db/_design/my_design -d @data/view16.json