Databases usage

In this section, you will learn how to manipulate the databases files. Four types of operations on the files are provided by the msdb package and are described in the following paragraphs:

Read info : retrieve or get the content stored inside the databases files
Add info : add new content inside the databases files
Update info : modify existing content stored inside the databases files
Delete info : delete the content stored inside the databases files

These operations can be accessed through python functions that can only be used on an instance of a DB class. In other words, you will need to create an instance of the DB class (see create instance class).

import msdb

# Create an instance of the DB class
# I previously created a database called "test" with corresponding databases
# files on which the operations mentioned above can be performed

db = msdb.DB(db_name='test')
db

DB class - name  = test - folder = /home/johhn/Documents/databases

1. Get / read info¶

To retrieve the content stored inside the databases files, use the functions that start with the word 'get'. They are 12 get functions for which a short description is provided in Table 1.

Table 1. Description of the get functions.

Function names	Description
get_creators	Get the name and surname of persons that created the objects analyzed
get_devices	Get information about the analytical devices used to analyze objects
get_institutions	Get information about the institution performing analyses
get_lamps	Get information about the lamps used to perform analyses
get_materials	Get a list of materials found in objects
get_methods	Get information about the analytical methods used to investigate objects
get_objects	Get the information about the objects analyzed
get_projects	Get information about the projects within which objects are analyzed
get_techniques	Get a list of techniques used to create objects
get_types	Get a list of general object types
get_users	Get the name, surname, and initials of persons performing the analyses
get_white_standards	Get information about the white standards used for the analyses

For the time being, only two functions (get_objects and get_projects) allow for arguments to be passed in to perform queries on the returned dataframe (see figure below for an example).

Alt text — get_projects() function without and with arguments.

2. Add / create info¶

To add new content inside the databases files, use the functions that start with the word 'add'. They are 12 add functions for which a short description is provided in Table 2.

Table 2. Description of the add functions.

Function names	Description
add_creators	Add a new person that created the objects analyzed
add_devices	Add a new analytical device used to analyze objects
add_institutions	Add a new institution performing analyses
add_lamps	Add a new lamp used to perform analyses
add_materials	Add a new material found in objects
add_methods	Add a new analytical method to investigate objects
add_objects	Add a new objects to be analyzed
add_projects	Add a new project within which objects are analyzed
add_techniques	Add a new technique used to create objects
add_types	Add a new type of objects
add_users	Add a new person performing the analyses
add_white_standards	Add a new white standard used for the analyses

All the add functions return ipywidgets inside which you can enter the requested info before saving them by clicking on the 'record' button (see figure below for an example).

3. Update info¶

For the time being, one can only update the content of the two csv files (objects_info.csv and projects_info.csv), using the functions update_objects() and update_projects() respectively. These two functions works similarly and the way to use them is described below. There are two ways you can use these functions : with or with ipywidgets. Simply, set the parameters "widgets" fo each function to True or False to use one or the other way.

Method with ipywidgets

Method without ipywidgets

# For two projects ('2023-011' and '2023-555'), I assigned
# the value 'JD' (initials for John Doe) for the 'project_leader' column.

db.update_projects(
    column='project_leader',
    new_value='JD', 
    project_id=['2023-011', '2025-555']
)

4. Delete info¶

To delete content from the databases files, use the functions that start with the word 'delete'. They are 12 delete functions for which a short description is provided in Table 4.

Table 4. Description of the delete functions.

Function names	Description
delete_creators	Delete a person that created the objects analyzed
delete_devices	Delete an analytical device used to analyze objects
delete_institutions	Delete an institution performing analyses
delete_lamps	Delete a lamp used to perform analyses
delete_materials	Delete a material found in objects
delete_methods	Delete am analytical method to investigate objects
delete_objects	Delete an object to be analyzed
delete_projects	Delete a project within which objects are analyzed
delete_techniques	Delete a technique used to create objects
delete_types	Delete a type of objects
delete_users	Delete a person performing the analyses
delete_white_standards	Delete a white standard used for the analyses

You can always run the delete function directly without passing arguments. It will always display ipywidgets allowing you to select the item(s) to be deleted and then to click on the 'delete' button to effectively remove the item(s) from the databases files (see figure below for an example).