Database options¶

BioPlate use sqlalchemy in order to manipulate sqlite3 database. Each database file are stock in the script under BioPlate/database/DBfiles.

Common database method¶

Plate database and plate historic database bot inherit of database parent class. Each function in commun should be call on an instance and by adding one of this suffix :

PlateDB : `_plate`

PlateHist : `_hplate`

Eg: For get method you will call it like that :

For PlateDB :

>>> from BioPlate.database.plate_db import PlateDB
>>> pdb = PlateDB()
>>> pdb.get_plate(96)

For PlateHist:

>>> from BioPlate.database.plate_historic_db import PlateHist
>>> ph = PlateHist()
>>> plate = ph.get_one_hplate("my Experiment 1", key="plate_name").plate_array

An exemple¶

>>> from BioPlate.database.plate_db import PlateDB
>>> pdb= PlateDB()
>>> pdb.add_plate( numWell =96,
       numColumns = 12,
       numRows = 8,
       surfWell = 0.29,
       maxVolWell = 200,
       workVolWell = 200,
       refURL = 'useful.url.reference.com')
>>> plate_96 = pdb.get_one_plate(96)
>>> plate_96
<plate N°1 : 96-12-8>
>>> plate_96.name
 None
>>> plate_96.surfWell
0.29
>>> update = {"name" : "plate_for_MTT_test", "surfWell" : 0.3}
>>> pdb.update_plate(update, 96)
>>> plate_96_update = pdb.get_one_plate(96)
>>> plate_96_update.name
plate_for_MTT_test
>>> plate_96_update.surfWell
0.3

Use case of PlateDB and PlateHist¶

Both of this database can be used to save informations, on general plate informations (PlateDB) or on a users defined plate (PlateHist).

PlateDB¶

This database will be used when always working with same plate format. This database are attended to be used to keep following informations :

Note

numWell :: number of well in plate created
numColumns :: number of column in plate created
numRows :: number of row in plate created
surfWell :: surface of one well (eg : in \(cm^2\))
maxVolWell :: maximum volume avaliable (eg : in \(\mu{L}\))
workVolWell :: volume use in each well (eg: in \(\mu{L}\))
refURL :: An url reference

PlateHist¶

This database will be used to save plate filed with value. This database is attended to be used to keep following informations :

Note

Plate_id :: id of plate in PlateDB
numWell :: number of well in plate
date :: date when plate is added to the database
plate_name :: name of the given plate (eg : “my expwriment 1”)
plate_array :: plate object

Get one plate object¶

>>> from BioPlate.database.plate_db import PlateDB
>>> pdb = PlateDB()
>>> pdb.get_one_plate(args, key="numWell")

Get plate object matching given elements¶

>>> from BioPlate.database.plate_db import PlateDB
>>> pdb = PlateDB()
>>> pdb.get_plate(self, **kwargs)

where **kwargs are pair of key, value you are looking for :

eg : ” numWell” = 96, “surfWell” = 0.29 .

This function return a list of object containing all element matching the query.

>>> pdb.get_plate(96)
>>> [<plate N°1 : 96-12-8>, <plate N°26 : cool name,  96-12-8>]

If no result, get retun an empty list.

Get all elements in given database¶

>>> from BioPlate.database.plate_db import PlateDB
>>> pdb = PlateDB()
>>> pdb.get_all_plate()

This function return all elements stock in the database object.

>>> pdb.get_all_plate()
>>> [<plate N°1 : 96-12-8>,  <plate N°2 : cool 24 plate, 24-6-4>, < ... >, <plate N°26 : cool name,  96-12-8>]

If database is empty, get_all return an empty list.

Update plate object in database¶

>>> from BioPlate.database.plate_db import PlateDB
>>> pdb = PlateDB()
>>> pdb.update_plate(self, dict_update, args, key="numWell")

where dict_update is a dictionary of key and value to update :

eg : {“name” : “plate_for_MTT_test”, “surfWell” : 0.3}

where args is value you are looking for :

eg : 96 for number of well

Where key is column name of data you looking for , by default key is numWell in both database.

Warning

Be carefull `args` and `key` should be enought specific to return a unique match, is recomended to use `id` as `key`.

This function return f”plate with {args} {key} updated” OR return “Use a more specific key to update the object”

Delete plate object in database¶

>>> from BioPlate.database.plate_db import PlateDB
>>> pdb = PlateDB()
>>> pdb.delete_plate(args, key="numWell")`

where args is value you are looking for :

eg : 96, key=”numWell”

Where key is column name of data you looking for , by default key is numWell in both database.

Warning

Be carefull `args` and `key` should be enought specific to return a unique match, is recomended to use `id` as `key`.

This function return f”plate with {args} {key} deleted” OR return “Use a more specific key to delete the object”