Manager Documentation¶

The classes and functions in this module have been designed to help manage existing and new projects using the Cookies module as well as the different utilities found in the Tools module.

Why a manager?¶

This module is intended to mesh with a Flask user interface. While the Flask server/client interface is not currently set up, we are developing the package so that it will be easier to implement.

Whenever a new website is made the RepoManagement and WebManagement classes are used.
- Whenever a new user is created in the Flask webpage, the UserManagement class is used.
- Whenever an existing user creates a new project, the ProjectManagement class is used.

This module does not have to be used to create a Flask webpage. The full repository can be used for higher level organization, or standalone projects can be made using the ProjectManagements _basic_project_ flag.

Example¶

Using DatabaseDispatcher to set up the proper databases using a YAML config file. This example is based on db_mana_test.py:

from OrthoEvol.Manager.management import ProjectManagement
from OrthoEvol.Manager.database_dispatcher import DatabaseDispatcher
from OrthoEvol.Manager.config import yml
from pkg_resources import resource_filename
from pathlib import Path
import yaml
import getpass
from datetime import datetime as d
import os

# Define job name
job_name = "jobname"

# Function to load configuration from YAML file
def load_config(file_name):
    file_path = resource_filename(yml.__name__, file_name)
    with open(file_path, 'r') as file:
        return yaml.load(file, Loader=yaml.FullLoader)

# Load project management configuration
pm_config = load_config("initialize_new.yml")
project_manager = ProjectManagement(**pm_config["Management_config"])

# Load and update database management configuration
db_config = load_config("databases.yml")
db_config.update(pm_config)

# Configure NCBI RefSeq release settings
ncbi_config = db_config['Database_config']['Full']['NCBI']['NCBI_refseq_release']
ncbi_config['upload_number'] = 12
ncbi_config['pbs_dict'] = {
    'author': getpass.getuser(),
    'description': 'This is a default pbs job.',
    'date': d.now().strftime('%a %b %d %I:%M:%S %p %Y'),
    'proj_name': 'OrthoEvol',
    'select': '1',
    'memgb': '6gb',
    'cput': '72:00:00',
    'wt': '2000:00:00',
    'job_name': job_name,
    'outfile': job_name + '.o',
    'errfile': job_name + '.e',
    'script': job_name,
    'log_name': job_name,
    'pbsworkdir': os.getcwd(),
    'cmd': f'python3.6 {os.path.join(os.getcwd(), job_name + ".py")}',
    'email': 'n/a'
}

# Save the updated configuration to a YAML file
config_file_path = project_manager.user_log / Path("upload_config.yml")
with open(str(config_file_path), 'w') as config_file:
    yaml.dump(db_config, config_file, default_flow_style=False)

# Initialize database dispatcher and execute dispatch functions
db_dispatcher = DatabaseDispatcher(config_file_path, project_manager)
db_dispatcher.dispatch(db_dispatcher.strategies, db_dispatcher.dispatcher, db_dispatcher.configuration)

Notes¶

Please view our BioSQL documentation and view some of the static/config related files.

Fork me on GitHub