def _create_profile_local(ctx, profile_directory, profile_name, kwds):
database_type = kwds.get("database_type", "auto")
if database_type == "auto":
if which("psql"):
database_type = "postgres"
elif which("docker"):
database_type = "postgres_docker"
else:
database_type = "sqlite"
if database_type != "sqlite":
database_source = create_database_source(**kwds)
database_identifier = _profile_to_database_identifier(profile_name)
database_source.create_database(database_identifier, )
database_connection = database_source.sqlalchemy_url(
database_identifier)
else:
database_location = os.path.join(profile_directory, "galaxy.sqlite")
database_connection = DATABASE_LOCATION_TEMPLATE % database_location
return {
"database_type": database_type,
"database_connection": database_connection,
"engine": "galaxy",
}
def _create_profile_local(ctx, profile_directory, profile_name, kwds):
database_type = kwds.get("database_type", "auto")
if database_type == "auto":
if which("psql"):
database_type = "postgres"
elif which("docker"):
database_type = "postgres_docker"
else:
database_type = "sqlite"
if database_type != "sqlite":
database_source = create_database_source(**kwds)
database_identifier = _profile_to_database_identifier(profile_name)
database_source.create_database(
database_identifier,
)
database_connection = database_source.sqlalchemy_url(database_identifier)
else:
database_location = os.path.join(profile_directory, "galaxy.sqlite")
attempt_database_preseed(ctx, None, database_location, **kwds)
database_connection = DATABASE_LOCATION_TEMPLATE % database_location
return {
"database_type": database_type,
"database_connection": database_connection,
"engine": "galaxy",
}
def delete_profile(ctx, profile_name, **kwds):
"""Delete profile with the specified name."""
profile_directory = _profile_directory(ctx, profile_name)
profile_options = _read_profile_options(profile_directory)
database_type = profile_options.get("database_type")
if database_type != "sqlite":
database_source = create_database_source(**kwds)
database_identifier = _profile_to_database_identifier(profile_name)
database_source.delete_database(database_identifier, )
shutil.rmtree(profile_directory)
def cli(ctx, identifier, **kwds):
"""Delete a *development* database.
Currently the only implementation is postgres which will be managed with
``psql``.
Planemo ``database_`` commands make it very easy to create and destroy
databases, therefore it should not be used for production data - and it
should not even be connnected to a production database server. Planemo
is intended for development purposes only.
Planemo will assume that it can manage and access postgres databases
without specifying a password. This can be accomplished by configuring
postgres to not required a password for the planemo user or by specifying
a password in a ``.pgpass`` file.
Planemo can be configured to not require a password for the planemo user in
the postgres configuration file ``pg_hba.conf`` (on Ubuntu/Debian linux
distros this file is in /etc/postgresql/<postgres_version>/main/ directory).
Adding the following lines to that file will allow planemo and Galaxy to
access the databases without a password.
\b
# "local" is for Unix domain socket connections only
local all all trust
# IPv4 local connections:
host all all 127.0.0.1/32 trust
# IPv6 local connections:
host all all ::1/128 trust
More information on the ``pg_hda.conf`` configuration file can be found at
http://www.postgresql.org/docs/9.3/static/auth-pg-hba-conf.html.
Information on ``.pgpass`` files can be found at at the following location:
http://www.postgresql.org/docs/9.4/static/libpq-pgpass.html. In Ubuntu and
Debian distros - a postgres user likely already exists and its password can
be set by setting up a file ``~/.pgpass`` file with the following contents.
\b
*:*:*:postgres:<postgres_password>
"""
create_database_source(**kwds).delete_database(identifier)
def cli(ctx, identifier, **kwds):
"""Delete a *development* database.
Currently the only implementation is postgres which will be managed with
``psql``.
Planemo ``database_`` commands make it very easy to create and destroy
databases, therefore it should not be used for production data - and it
should not even be connnected to a production database server. Planemo
is intended for development purposes only.
Planemo will assume that it can manage and access postgres databases
without specifying a password. This can be accomplished by configuring
postgres to not required a password for the planemo user or by specifying
a password in a ``.pgpass`` file.
Planemo can be configured to not require a password for the planemo user in
the postgres configuration file ``pg_hba.conf`` (on Ubuntu/Debian linux
distros this file is in /etc/postgresql/<postgres_version>/main/ directory).
Adding the following lines to that file will allow planemo and Galaxy to
access the databases without a password.::
# "local" is for Unix domain socket connections only
local all all trust
# IPv4 local connections:
host all all 127.0.0.1/32 trust
# IPv6 local connections:
host all all ::1/128 trust
More information on the ``pg_hda.conf`` configuration file can be found at
http://www.postgresql.org/docs/9.3/static/auth-pg-hba-conf.html.
Information on ``.pgpass`` files can be found at at the following location:
http://www.postgresql.org/docs/9.4/static/libpq-pgpass.html. In Ubuntu and
Debian distros - a postgres user likely already exists and its password can
be set by setting up a file ``~/.pgpass`` file with the following contents.
::
*:*:*:postgres:<postgres_password>
"""
create_database_source(**kwds).delete_database(identifier)
def delete_profile(ctx, profile_name, **kwds):
"""Delete profile with the specified name."""
profile_directory = _profile_directory(ctx, profile_name)
profile_options = _read_profile_options(profile_directory)
database_type = profile_options.get("database_type")
if database_type != "sqlite":
database_source = create_database_source(**kwds)
database_identifier = _profile_to_database_identifier(profile_name)
database_source.delete_database(
database_identifier,
)
shutil.rmtree(profile_directory)
def delete_profile(ctx, profile_name, **kwds):
"""Delete profile with the specified name."""
profile_directory = _profile_directory(ctx, profile_name)
profile_options = _read_profile_options(profile_directory)
profile_options, profile_options_path = _load_profile_to_json(
ctx, profile_name)
if profile_options["engine"] != 'external_galaxy':
database_type = profile_options.get("database_type")
kwds["database_type"] = database_type
if database_type != "sqlite":
database_source = create_database_source(**kwds)
database_identifier = _profile_to_database_identifier(profile_name)
database_source.delete_database(database_identifier, )
shutil.rmtree(profile_directory)
def _create_profile_local(profile_directory, profile_name, kwds):
database_type = kwds.get("database_type", "sqlite")
if database_type != "sqlite":
database_source = create_database_source(**kwds)
database_identifier = _profile_to_database_identifier(profile_name)
database_source.create_database(database_identifier, )
database_connection = database_source.sqlalchemy_url(
database_identifier)
else:
database_location = os.path.join(profile_directory, "galaxy.sqlite")
attempt_database_preseed(None, database_location, **kwds)
database_connection = DATABASE_LOCATION_TEMPLATE % database_location
return {
"database_type": database_type,
"database_connection": database_connection,
"engine": "galaxy",
}
