class WebsiteManagement(RepoManagement):
"""Website Management for OrthoEvol."""
def __init__(self,
repo,
website,
host='0.0.0.0',
port='5252',
home=os.getcwd(),
new_website=False,
create_admin=False,
**kwargs):
"""Install a template for Flask using cookiecutter.
The official cookiecutter-flask template
(https://github.com/sloria/cookiecutter-flask) has been edited for our
own purposes. This app class uses cookiecutter hooks to deploy the
flask server.
:param repo (string): The name of the repository.
:param website (string): The name of the website. Not a url, so
it doesn't containt http://www.*.com.
(e.g. for www.vallenger-genetics.ml this parameter would be 'vallender-genetics')
:param host (string): The address to launch the flask app. Defaults to 0.0.0.0
:param port (string): The port to launch the flask app. Defaults to 5252
:param home (string or pathlike): The home path of the repository.
:param new_website (bool): Flag for creating a new website
:param create_admin: Flag for creating a new admin for the website via FLASK USER.
(Note: This parameter is not used currently in development.)
"""
if repo and website:
super().__init__(repo=repo, home=home, **kwargs)
# Website Deployment Information:
self.website = website
self.web_host = host
self.web_port = port
# Path to Flask's Web-Server Files
self.website_path = self.flask / Path(self.website)
self.Kitchen = Oven(repo=self.repo,
user=self.user,
website=self.website,
output_dir=self.flask)
logmsg = 'The Website Management class variables have been set.'
self.managementlog.info(logmsg)
if new_website is True:
logmsg = 'The website cookie is being prepared for the Oven.'
self.managementlog.info(logmsg)
self.Kitchen.bake_the_website(host=self.web_host,
port=self.web_port,
website_path=self.website_path)
def stop_server(self):
"""Stop the server running the website."""
class RepoManagement(Management):
"""Repository Management for OrthoEvol."""
def __init__(self,
repo,
user=None,
home=os.getcwd(),
new_user=False,
new_repo=False,
**kwargs):
"""Manage repositories.
This class has to be paired with a repository name. It gives the
option of creating a filesystem for a new user and a new repository
using cookiecutter.
This class maps the named repository, which includes top level access
to front facing web servers, important documents, and the top level
users directory.
:param repo (string): The name of the repository.
:param user (string): The name of the current user if any.
:param home (string or pathlike): The home path of the repository.
:param new_user (bool): Flag for creating a new user.
:param new_repo (bool): Flag for creating a new repository.
"""
# TODO-ROB change the home parameter to the output directory parameter
super().__init__(repo=repo, home=home, new_repo=new_repo, **kwargs)
self.repo = repo
# Users and Important Documentation:
self.docs = self.repo_path / Path('docs')
self.users = self.repo_path / Path('users')
# Web Servers:
self.repo_web = self.repo_path / Path('web')
self.repo_shiny = self.repo_web / Path('shiny')
self.ftp = self.repo_web / Path('ftp')
self.wasabi = self.repo_web / Path('wasabi')
self.flask = self.repo_web / Path('flask')
if user:
self.user = user # FROM Flask
self.user_path = self.users / Path(self.user)
self.Kitchen = Oven(repo=self.repo,
user=self.user,
output_dir=self.users)
self.managementlog.info(
'The Repository Management class variables have been set.')
if new_user is True:
self.managementlog.info(
'The user cookie is being prepared for the Oven.')
self.Kitchen.bake_the_user()
class Management(object):
def __init__(self, repo=None, home=os.getcwd(), new_repo=False, **kwargs):
"""Base class for directory management.
It maps the directories of the OrthoEvol-Script package using the
pathlib module, and turns the names of each important directory into
a pathlike object. The base class gives the option of creating a new
repository with cookiecutter.
:param repo (string): The name of the new repository to be created.
:param home (path or path-like): The home of the file calling this name.
When creating a new repository it is
best to explicitly name the home path.
:param new_repo (bool): Creates a new repository."""
self.repo = repo
self.file_home = Path(home) # Home of the file calling this class
self.managementlog = LogIt().default(logname="Management",
logfile=None)
# Below are path-like attributes that map various modules and directories.
# Cookies Module:
self.Kitchen = Oven(repo=self.repo, output_dir=self.file_home)
self.Pantry = self.Kitchen.Recipes
# Manager Module:
self.Manager = Path(
pkg_resources.resource_filename(Manager.__name__, ''))
self.BioSQL = self.Manager / Path('BioSQL')
self.SQLite3 = self.BioSQL / Path('sqlite')
self.MySQL = self.BioSQL / Path('mysql')
self.config = self.Manager / Path('config')
# Orthologs Module:
self.Orthologs = Path(
pkg_resources.resource_filename(Orthologs.__name__, ''))
self.Align = self.Orthologs / Path('Align')
self.Blast = self.Orthologs / Path('Blast')
self.GenBank = self.Orthologs / Path('GenBank')
self.Phylogenetics = self.Orthologs / Path('Phylogenetics')
# Tools Module:
self.Tools = Path(pkg_resources.resource_filename(Tools.__name__, ''))
self.ftp = self.Tools / Path('ftp')
self.logit = self.Tools / Path('logit')
self.mpi = self.Tools / Path('mpi')
self.mygene = self.Tools / Path('mygene')
self.pandoc = self.Tools / Path('pandoc')
self.parallel = self.Tools / Path('parallel')
self.pybasher = self.Tools / Path('pybasher')
self.send2server = self.Tools / Path('send2server')
self.sge = self.Tools / Path('sge')
self.slackify = self.Tools / Path('slackify')
self.otherutils = self.Tools / Path('otherutils')
if self.repo:
self.repo_path = self.file_home / Path(self.repo)
self.managementlog.info(
'The BaseManagement class variables have been set.')
# Make a new repository.
if new_repo is True:
self.managementlog.info(
'The repository cookie is being prepared for the Oven.')
self.Kitchen.bake_the_repo()
def __init__(self,
repo,
user,
project,
research=None,
research_type=None,
app=None,
home=os.getcwd(),
new_project=False,
new_research=False,
new_app=False,
**kwargs):
"""Manage the directories of the current project.
Each project requires a repository, user, and project name. It gives
the option of starting a new type of research within an existing
project. An application directory for the specific research/dataset
can also be generated
It gives access to the project directories including index
files, the raw data, the processed data, the project db_config_file,
and the web files for serving data.
:param repo (string): The name of the repository.
:param user (string): The name of the current user if any.
:param project(string): The name of the current project if any.
:param research (string): The name of the current type of research if any
:param research_type (string): The type of research (public or private)
:param app (string): The name of the application that the research.
:param home (string or pathlike): The home path of the repository.
:param new_project (bool): Flag for creating a new project.
:param new_research (bool): Flag for creating new research under a project.
:param new_app (bool): Flag for creating a new web app under a research target.
"""
# Standalone for child/self or full class hierarchy use
if project or (repo and user and project):
super().__init__(repo=repo,
user=user,
project=project,
home=home,
new_project=new_project,
**kwargs)
self.project = project
self.research = research
self.research_type = research_type
# Project Directories:
self.research_path = self.project_path / Path(
research_type) / Path(research)
self.project_archive = self.project_path / Path('archive')
self.project_database = self.user_db / Path(project)
# Dataset Directories:
self.project_index = self.research_path / Path('index')
self.data = self.research_path / Path('data')
self.raw_data = self.research_path / Path('raw_data')
self.project_web = self.research_path / Path('web')
if app:
self.app = app
self.app_path = self.project_web / Path(app)
logmsg = 'The User Management class variables have been set.'
self.managementlog.info(logmsg)
if new_research is True:
logmsg = 'The research cookie is being prepared for the Oven.'
self.managementlog.info(logmsg)
self.research_type = research_type
self.Kitchen = Oven(repo=self.repo,
user=self.user,
project=self.project,
output_dir=self.project_path)
self.Kitchen.bake_the_research(research_type=self.research_type,
research=self.research)
if new_app is True:
logmsg = 'The app cookie is being prepared for the Oven.'
self.managementlog.info(logmsg)
self.app = app
self.app_path = self.project_path / Path(research_type) / Path(
research) / Path('web')
self.Kitchen.bake_the_app(app=self.app)
def __init__(self,
repo,
user,
project=None,
db_config_file=None,
home=os.getcwd(),
new_user=False,
new_project=False,
new_db=False,
archive=False,
**kwargs):
"""Manages the current user's directories.
This class has to be paired with a repository and a user. It gives
access to user paths, and provides functionality for creating new
projects and new project db_config_file for the current user. It also
gives the option of creating a new user.
This class maps a users directory, which gives access to directories
for db_config_file (NCBI and proprietary), index files for quickly
retrieving project data, project log files, user affiliated journal
articles, and projects.
:param repo (string): The name of the repository.
:param user (string): The name of the current user if any.
:param project(string): The name of the current project if any.
:param home (string or pathlike): The home path of the repository.
:param new_user (bool): Flag for creating a new user.
:param new_project (bool): Flag for creating a new project.
"""
if user or (user and repo):
super().__init__(repo=repo,
user=user,
home=home,
new_user=new_user,
**kwargs)
self.user = user
# NCBI and Proprietary Database Repositories:
self.user_db = self.user_path / Path('databases')
self.user_archive = self.user_path / Path('archive')
self.ncbi_db_repo = self.user_db / Path('NCBI')
self.ncbi_taxonomy = self.ncbi_db_repo / Path('pub') / Path(
'taxonomy')
self.ncbi_refseq_release = self.ncbi_db_repo / Path(
'refseq') / Path('release')
self.blast_db = self.ncbi_db_repo / Path('blast') / Path('db')
self.windowmaker_files = self.ncbi_db_repo / Path('blast') / Path(
'windowmaker_files')
self.itis_db_repo = self.user_db / Path('ITIS')
# Index Files:
self.user_index = self.user_path / Path('index')
# User Log Files:
self.user_log = self.user_path / Path('log')
# Relevant Journal Articles:
self.manuscripts = self.user_path / Path('manuscripts')
self.other = self.user_path / Path('other')
# Projects
self.projects = self.user_path / Path('projects')
if project:
self.project = project
self.project_path = self.projects / Path(project)
else:
self.projects = home
self.Cookies = Path(Cookies.__path__[0])
self.project_cookie = self.Cookies / Path('new_project')
if project:
self.project = project
self.project_path = home / Path(project)
self.Kitchen = Oven(repo=self.repo,
user=self.user,
project=self.project,
output_dir=self.projects)
self.managementlog.info(
'The User Management class variables have been set.')
if new_project is True:
self.managementlog.info(
'The project cookie is being prepared for the Oven.')
self.Kitchen.bake_the_project()
if new_db is True:
self.managementlog.info(
'The database cookie is being prepared for the Oven.')
self.Kitchen.bake_the_db_repo(user_db=self.user_db,
db_path_dict=self.db_path_dict,
ncbi_db_repo=self.ncbi_db_repo)
class UserManagement(RepoManagement):
"""User Management for OrthoEvol."""
# TODO-ROB CREATE THESE IN A VIRTUAL ENVIRONMENT FOR EACH USER
# TODO-ROB The virtual environment can be the name of the user
# TODO-ROB When the user logs in, they will activate the virtual environment
# TODO-ROB USE SQL here to see if the user db contains the username
def __init__(self,
repo,
user,
project=None,
db_config_file=None,
home=os.getcwd(),
new_user=False,
new_project=False,
new_db=False,
archive=False,
**kwargs):
"""Manages the current user's directories.
This class has to be paired with a repository and a user. It gives
access to user paths, and provides functionality for creating new
projects and new project db_config_file for the current user. It also
gives the option of creating a new user.
This class maps a users directory, which gives access to directories
for db_config_file (NCBI and proprietary), index files for quickly
retrieving project data, project log files, user affiliated journal
articles, and projects.
:param repo (string): The name of the repository.
:param user (string): The name of the current user if any.
:param project(string): The name of the current project if any.
:param home (string or pathlike): The home path of the repository.
:param new_user (bool): Flag for creating a new user.
:param new_project (bool): Flag for creating a new project.
"""
if user or (user and repo):
super().__init__(repo=repo,
user=user,
home=home,
new_user=new_user,
**kwargs)
self.user = user
# NCBI and Proprietary Database Repositories:
self.user_db = self.user_path / Path('databases')
self.user_archive = self.user_path / Path('archive')
self.ncbi_db_repo = self.user_db / Path('NCBI')
self.ncbi_taxonomy = self.ncbi_db_repo / Path('pub') / Path(
'taxonomy')
self.ncbi_refseq_release = self.ncbi_db_repo / Path(
'refseq') / Path('release')
self.blast_db = self.ncbi_db_repo / Path('blast') / Path('db')
self.windowmaker_files = self.ncbi_db_repo / Path('blast') / Path(
'windowmaker_files')
self.itis_db_repo = self.user_db / Path('ITIS')
# Index Files:
self.user_index = self.user_path / Path('index')
# User Log Files:
self.user_log = self.user_path / Path('log')
# Relevant Journal Articles:
self.manuscripts = self.user_path / Path('manuscripts')
self.other = self.user_path / Path('other')
# Projects
self.projects = self.user_path / Path('projects')
if project:
self.project = project
self.project_path = self.projects / Path(project)
else:
self.projects = home
self.Cookies = Path(Cookies.__path__[0])
self.project_cookie = self.Cookies / Path('new_project')
if project:
self.project = project
self.project_path = home / Path(project)
self.Kitchen = Oven(repo=self.repo,
user=self.user,
project=self.project,
output_dir=self.projects)
self.managementlog.info(
'The User Management class variables have been set.')
if new_project is True:
self.managementlog.info(
'The project cookie is being prepared for the Oven.')
self.Kitchen.bake_the_project()
if new_db is True:
self.managementlog.info(
'The database cookie is being prepared for the Oven.')
self.Kitchen.bake_the_db_repo(user_db=self.user_db,
db_path_dict=self.db_path_dict,
ncbi_db_repo=self.ncbi_db_repo)
# TODO-ROB: Determine what type of database as well.
def zip_mail(self, comp_filename, zip_path, destination=''):
"""Zip and mail a file or folder.
:param comp_filename:
:param zip_path:
:param destination: (Default value = '')
"""
pass