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database_settings.py

DatabaseSettings

Source code in src/spyglass/utils/database_settings.py 
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class DatabaseSettings:
    def __init__(
        self,
        user_name=None,
        host_name=None,
        debug=False,
        target_database=None,
        exec_user=None,
        exec_pass=None,
        test_mode=False,
    ):
        """Class to manage common database settings

        Roles:
        - dj_guest:  select for all prefix
        - dj_collab: select for all prefix, all for user prefix
        - dj_user:   select for all prefix, all for user prefix, all for shared
        - dj_admin:     all for all prefix

        Note: To add dj_user role to all those with common access, run:
            query = "SELECT user, host FROM mysql.db WHERE Db LIKE 'common%';"
            users = dj.conn().query(query).fetchall()
            for user in users:
                dj.conn().query(f"GRANT dj_user TO '{user[0][0]}'@'%';")

        Parameters
        ----------
        user_name : str, optional
            The name of the user to add to the database. Default from dj.config
        host_name : str, optional
            The name of the host to add to the database. Default from dj.config
        debug : bool, optional
            Default False. If True, pprint sql instead of running
        target_database : str, optional
            Default is mysql. Can also be docker container id
        exec_user : str, optional
            User for executing commands. If None, use dj.config
        exec_pass : str, optional
            Password for executing commands. If None, use dj.config
        test_mode : bool, optional
            Default False. If True, prepend sudo to commands for use in CI/CD
            Only true in github actions, not true in local testing.
        """
        self.shared_modules = [f"{m}{ESC}" for m in SHARED_MODULES]
        self.user = user_name or dj.config["database.user"]
        self.host = (
            host_name or dj.config["database.host"] or "lmf-db.cin.ucsf.edu"
        )
        self.debug = debug
        self.target_database = target_database or "mysql"
        self.exec_user = exec_user or dj.config["database.user"]
        self.exec_pass = exec_pass or dj.config["database.password"]
        self.test_mode = test_mode

    @property
    def _create_roles_dict(self):
        return dict(
            guest=[
                f"{CREATE_ROLE}`dj_guest`;\n",
                f"{GRANT_SEL}`%`.* TO `dj_guest`;\n",
            ],
            collab=[
                f"{CREATE_ROLE}`dj_collab`;\n",
                f"{GRANT_SEL}`%`.* TO `dj_collab`;\n",
            ],  # also gets own prefix below
            user=[
                f"{CREATE_ROLE}`dj_user`;\n",
                f"{GRANT_SEL}`%`.* TO `dj_user`;\n",
            ]
            + [
                f"{GRANT_ALL}`{module}`.* TO `dj_user`;\n"
                for module in self.shared_modules
            ],  # also gets own prefix below
            admin=[
                f"{CREATE_ROLE}`dj_admin`;\n",
                f"{GRANT_ALL}`%`.* TO `dj_admin`;\n",
            ],
        )

    @cached_property
    def _create_roles_sql(self):
        return sum(self._create_roles_dict.values(), [])

    def _create_user_sql(self, role):
        """Create user and grant role"""
        return [
            f"{CREATE_USR}'{self.user}'@'%'{TEMP_PASS}\n",  # create user
            f"GRANT {role} TO '{self.user}'@'%';\n",  # grant role
        ]

    @property
    def _user_prefix_sql(self):
        """Grant user all permissions for user prefix"""
        return [
            f"{GRANT_ALL}`{self.user}{ESC}`.* TO '{self.user}'@'%';\n",
        ]

    @property
    def _add_guest_sql(self):
        return self._create_user_sql("dj_guest")

    @property
    def _add_collab_sql(self):
        return self._create_user_sql("dj_collab") + self._user_prefix_sql

    @property
    def _add_user_sql(self):
        return self._create_user_sql("dj_user") + self._user_prefix_sql

    @property
    def _add_admin_sql(self):
        return self._create_user_sql("dj_admin") + self._user_prefix_sql

    def _add_module_sql(self, module_name):
        return [f"{GRANT_ALL}`{module_name}{ESC}`.* TO dj_user;\n"]

    def add_guest(self, *args, **kwargs):
        """Add guest user with select permissions to shared modules"""
        file = self.write_temp_file(self._add_guest_sql)
        self.exec(file)

    def add_collab(self, *args, **kwargs):
        """Add collaborator user with full permissions to shared modules"""
        file = self.write_temp_file(self._add_collab_sql)
        self.exec(file)

    def add_user(self, check_exists=False, *args, **kwargs):
        """Add user to database with permissions to shared modules"""
        if check_exists:
            self.check_user_exists()
        file = self.write_temp_file(self._add_user_sql)
        self.exec(file)

    def add_admin(self, *args, **kwargs):
        """Add admin user with full permissions to all modules"""
        file = self.write_temp_file(self._add_admin_sql)
        self.exec(file)

    def add_module(self, module_name):
        """Add module to database. Grant permissions to all users in group"""
        logger.info(f"Granting everyone permissions to module {module_name}")
        file = self.write_temp_file(self._add_module_sql(module_name))
        self.exec(file)

    def check_user_exists(self):
        """Add user to database with permissions to shared modules"""
        user_home = Path.home().parent / self.user
        if user_home.exists():
            logger.info("Creating database user ", self.user)
        else:
            sys.exit(
                f"Error: couldn't find {self.user} in home dir: {user_home}"
            )

    def add_user_by_role(self, role, check_exists=False):
        """Add a user to the database with the specified role"""
        add_func = {
            "guest": self.add_guest,
            "user": self.add_user,
            "collab": self.add_collab,
            "admin": self.add_admin,
        }
        if role not in add_func:
            raise ValueError(f"Role {role} not recognized")
        add_func[role]()

    def add_roles(self):
        """Add roles to database"""
        file = self.write_temp_file(self._create_roles_sql)
        self.exec(file)

    def write_temp_file(self, content: list) -> tempfile.NamedTemporaryFile:
        """Write content to a temporary file and return the file object"""
        file = tempfile.NamedTemporaryFile(mode="w")
        for line in content:
            file.write(line)
        file.flush()

        if self.debug:
            from pprint import pprint  # noqa F401

            pprint(file.name)
            pprint(content)

        return file

    def exec(self, file):
        """Run commands saved to file in sql"""

        if self.debug:
            return

        if self.test_mode:
            prefix = "sudo mysql -h 127.0.0.1 -P 3308 -uroot -ptutorial"
        else:
            prefix = f"mysql -h {self.host} -u {self.exec_user} -p"

        cmd = (
            f"{prefix} < {file.name}"
            if self.target_database == "mysql"
            else f"docker exec -i {self.target_database} mysql -u "
            + f"{self.exec_user} --password={self.exec_pass} < {file.name}"
        )

        os.system(cmd)

__init__(user_name=None, host_name=None, debug=False, target_database=None, exec_user=None, exec_pass=None, test_mode=False)

Class to manage common database settings

Roles: - dj_guest: select for all prefix - dj_collab: select for all prefix, all for user prefix - dj_user: select for all prefix, all for user prefix, all for shared - dj_admin: all for all prefix

Note: To add dj_user role to all those with common access, run: query = "SELECT user, host FROM mysql.db WHERE Db LIKE 'common%';" users = dj.conn().query(query).fetchall() for user in users: dj.conn().query(f"GRANT dj_user TO '{user[0][]}'@'%';")

Parameters:

Name Type Description Default
user_name str

The name of the user to add to the database. Default from dj.config

 None
host_name str

The name of the host to add to the database. Default from dj.config

 None
debug bool

Default False. If True, pprint sql instead of running

 False
target_database str

Default is mysql. Can also be docker container id

 None
exec_user str

User for executing commands. If None, use dj.config

 None
exec_pass str

Password for executing commands. If None, use dj.config

 None
test_mode bool

Default False. If True, prepend sudo to commands for use in CI/CD Only true in github actions, not true in local testing.

 False
Source code in src/spyglass/utils/database_settings.py 
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def __init__(
    self,
    user_name=None,
    host_name=None,
    debug=False,
    target_database=None,
    exec_user=None,
    exec_pass=None,
    test_mode=False,
):
    """Class to manage common database settings

    Roles:
    - dj_guest:  select for all prefix
    - dj_collab: select for all prefix, all for user prefix
    - dj_user:   select for all prefix, all for user prefix, all for shared
    - dj_admin:     all for all prefix

    Note: To add dj_user role to all those with common access, run:
        query = "SELECT user, host FROM mysql.db WHERE Db LIKE 'common%';"
        users = dj.conn().query(query).fetchall()
        for user in users:
            dj.conn().query(f"GRANT dj_user TO '{user[0][0]}'@'%';")

    Parameters
    ----------
    user_name : str, optional
        The name of the user to add to the database. Default from dj.config
    host_name : str, optional
        The name of the host to add to the database. Default from dj.config
    debug : bool, optional
        Default False. If True, pprint sql instead of running
    target_database : str, optional
        Default is mysql. Can also be docker container id
    exec_user : str, optional
        User for executing commands. If None, use dj.config
    exec_pass : str, optional
        Password for executing commands. If None, use dj.config
    test_mode : bool, optional
        Default False. If True, prepend sudo to commands for use in CI/CD
        Only true in github actions, not true in local testing.
    """
    self.shared_modules = [f"{m}{ESC}" for m in SHARED_MODULES]
    self.user = user_name or dj.config["database.user"]
    self.host = (
        host_name or dj.config["database.host"] or "lmf-db.cin.ucsf.edu"
    )
    self.debug = debug
    self.target_database = target_database or "mysql"
    self.exec_user = exec_user or dj.config["database.user"]
    self.exec_pass = exec_pass or dj.config["database.password"]
    self.test_mode = test_mode

add_guest(*args, **kwargs)

Add guest user with select permissions to shared modules

Source code in src/spyglass/utils/database_settings.py 
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def add_guest(self, *args, **kwargs):
    """Add guest user with select permissions to shared modules"""
    file = self.write_temp_file(self._add_guest_sql)
    self.exec(file)

add_collab(*args, **kwargs)

Add collaborator user with full permissions to shared modules

Source code in src/spyglass/utils/database_settings.py 
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def add_collab(self, *args, **kwargs):
    """Add collaborator user with full permissions to shared modules"""
    file = self.write_temp_file(self._add_collab_sql)
    self.exec(file)

add_user(check_exists=False, *args, **kwargs)

Add user to database with permissions to shared modules

Source code in src/spyglass/utils/database_settings.py 
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def add_user(self, check_exists=False, *args, **kwargs):
    """Add user to database with permissions to shared modules"""
    if check_exists:
        self.check_user_exists()
    file = self.write_temp_file(self._add_user_sql)
    self.exec(file)

add_admin(*args, **kwargs)

Add admin user with full permissions to all modules

Source code in src/spyglass/utils/database_settings.py 
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def add_admin(self, *args, **kwargs):
    """Add admin user with full permissions to all modules"""
    file = self.write_temp_file(self._add_admin_sql)
    self.exec(file)

add_module(module_name)

Add module to database. Grant permissions to all users in group

Source code in src/spyglass/utils/database_settings.py 
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def add_module(self, module_name):
    """Add module to database. Grant permissions to all users in group"""
    logger.info(f"Granting everyone permissions to module {module_name}")
    file = self.write_temp_file(self._add_module_sql(module_name))
    self.exec(file)

check_user_exists()

Add user to database with permissions to shared modules

Source code in src/spyglass/utils/database_settings.py 
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def check_user_exists(self):
    """Add user to database with permissions to shared modules"""
    user_home = Path.home().parent / self.user
    if user_home.exists():
        logger.info("Creating database user ", self.user)
    else:
        sys.exit(
            f"Error: couldn't find {self.user} in home dir: {user_home}"
        )

add_user_by_role(role, check_exists=False)

Add a user to the database with the specified role

Source code in src/spyglass/utils/database_settings.py 
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def add_user_by_role(self, role, check_exists=False):
    """Add a user to the database with the specified role"""
    add_func = {
        "guest": self.add_guest,
        "user": self.add_user,
        "collab": self.add_collab,
        "admin": self.add_admin,
    }
    if role not in add_func:
        raise ValueError(f"Role {role} not recognized")
    add_func[role]()

add_roles()

Add roles to database

Source code in src/spyglass/utils/database_settings.py 
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def add_roles(self):
    """Add roles to database"""
    file = self.write_temp_file(self._create_roles_sql)
    self.exec(file)

write_temp_file(content)

Write content to a temporary file and return the file object

Source code in src/spyglass/utils/database_settings.py 
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def write_temp_file(self, content: list) -> tempfile.NamedTemporaryFile:
    """Write content to a temporary file and return the file object"""
    file = tempfile.NamedTemporaryFile(mode="w")
    for line in content:
        file.write(line)
    file.flush()

    if self.debug:
        from pprint import pprint  # noqa F401

        pprint(file.name)
        pprint(content)

    return file

exec(file)

Run commands saved to file in sql

Source code in src/spyglass/utils/database_settings.py 
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def exec(self, file):
    """Run commands saved to file in sql"""

    if self.debug:
        return

    if self.test_mode:
        prefix = "sudo mysql -h 127.0.0.1 -P 3308 -uroot -ptutorial"
    else:
        prefix = f"mysql -h {self.host} -u {self.exec_user} -p"

    cmd = (
        f"{prefix} < {file.name}"
        if self.target_database == "mysql"
        else f"docker exec -i {self.target_database} mysql -u "
        + f"{self.exec_user} --password={self.exec_pass} < {file.name}"
    )

    os.system(cmd)