Store postgres database in profile by default

Author: mvdbeek

planemo/database/factory.py

@@ -1,5 +1,7 @@
 """Create a DatabaseSource from supplied planemo configuration."""
 
+from typing import Optional
+
 from galaxy.util.commands import which
 
 from .interface import DatabaseSource
@@ -8,7 +10,7 @@
 from .postgres_singularity import SingularityPostgresDatabaseSource
 
 
-def create_database_source(**kwds) -> DatabaseSource:
+def create_database_source(profile_directory: Optional[str] = None, **kwds) -> DatabaseSource:
     """Return a :class:`planemo.database.interface.DatabaseSource` for configuration."""
     database_type = kwds.get("database_type", "auto")
     if database_type == "auto":
@@ -26,7 +28,7 @@ def create_database_source(**kwds) -> DatabaseSource:
     elif database_type == "postgres_docker":
         return DockerPostgresDatabaseSource(**kwds)
     elif database_type == "postgres_singularity":
-        return SingularityPostgresDatabaseSource(**kwds)
+        return SingularityPostgresDatabaseSource(profile_directory=profile_directory, **kwds)
     # TODO
     # from .sqlite import SqliteDatabaseSource
     # elif database_type == "sqlite":

planemo/database/interface.py

@@ -7,13 +7,6 @@
 class DatabaseSource(metaclass=abc.ABCMeta):
     """Interface describing a source of profile databases."""
 
-    @abc.abstractmethod
-    def create_database(self, identifier):
-        """Create a database with specified short identifier.
-
-        Throw an exception if it already exists.
-        """
-
     @abc.abstractmethod
     def delete_database(self, identifier):
         """Delete a database with specified short identifier.

planemo/database/postgres_singularity.py

@@ -3,6 +3,7 @@
 import os
 import time
 from tempfile import mkdtemp
+from typing import Optional
 
 from galaxy.util.commands import shell_process
 
@@ -76,14 +77,16 @@ class SingularityPostgresDatabaseSource(ExecutesPostgresSqlMixin, DatabaseSource
     "with" statements to automatically start and stop the container.
     """
 
-    def __init__(self, **kwds):
+    def __init__(self, profile_directory: Optional[str] = None, **kwds):
         """Construct a postgres database source from planemo configuration."""
 
         self.singularity_path = "singularity"
         self.database_user = DEFAULT_POSTGRES_USER
         self.database_password = DEFAULT_POSTGRES_PASSWORD
-        if "postgres_storage_location" in kwds and kwds["postgres_storage_location"] is not None:
+        if kwds.get("postgres_storage_location") is not None:
             self.database_location = kwds["postgres_storage_location"]
+        elif profile_directory:
+            self.database_location = os.path.join(profile_directory, "postgres")
         else:
             self.database_location = os.path.join(mkdtemp(suffix="_planemo_postgres_db"))
         self.database_socket_dir = os.path.join(self.database_location, "pgrun")