--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/planemo/galaxy/profiles.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,235 @@
+"""This modules describes the abstraction of a Galaxy profile.
+
+This is a workspace with a specific default configuration and shed
+tool setup. It is meant to be used with various serve commands.
+"""
+import json
+import os
+import shutil
+
+from galaxy.util.commands import which
+
+from planemo.database import create_database_source
+from planemo.galaxy.api import test_credentials_valid
+from .config import DATABASE_LOCATION_TEMPLATE
+
+PROFILE_OPTIONS_JSON_NAME = "planemo_profile_options.json"
+ALREADY_EXISTS_EXCEPTION = "Cannot create profile with name [%s], directory [%s] already exists."
+
+
+def profile_exists(ctx, profile_name, **kwds):
+    """Return a truthy value iff the specified profile already exists."""
+    profile_directory = _profile_directory(ctx, profile_name)
+    return os.path.exists(profile_directory)
+
+
+def list_profiles(ctx, **kwds):
+    """Return a list of current profile names."""
+    return os.listdir(ctx.galaxy_profiles_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(ctx, profile_name, **kwds):
+    """Create a profile with the specified name."""
+    engine_type = kwds.get("engine", "galaxy")
+    profile_directory = _profile_directory(ctx, profile_name)
+    if profile_exists(ctx, profile_name, **kwds):
+        message = ALREADY_EXISTS_EXCEPTION % (
+            profile_name, profile_directory
+        )
+        raise Exception(message)
+
+    os.makedirs(profile_directory)
+
+    if engine_type == "docker_galaxy":
+        create_for_engine = _create_profile_docker
+    elif engine_type == "external_galaxy" or kwds.get("galaxy_url"):
+        create_for_engine = _create_profile_external
+    else:
+        create_for_engine = _create_profile_local
+
+    stored_profile_options = create_for_engine(ctx, profile_directory, profile_name, kwds)
+
+    profile_options_path = _stored_profile_options_path(profile_directory)
+    with open(profile_options_path, "w") as f:
+        json.dump(stored_profile_options, f)
+
+
+def _create_profile_docker(ctx, profile_directory, profile_name, kwds):
+    export_directory = os.path.join(profile_directory, "export")
+    os.makedirs(export_directory)
+    return {
+        "engine": "docker_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")
+        database_connection = DATABASE_LOCATION_TEMPLATE % database_location
+
+    return {
+        "database_type": database_type,
+        "database_connection": database_connection,
+        "engine": "galaxy",
+    }
+
+
+def _create_profile_external(ctx, profile_directory, profile_name, kwds):
+    url = kwds.get("galaxy_url")
+    api_key = kwds.get("galaxy_admin_key") or kwds.get("galaxy_user_key")
+    if test_credentials_valid(url=url, key=api_key, is_admin=kwds.get("galaxy_admin_key")):
+        return {
+            "galaxy_url": url,
+            "galaxy_user_key": kwds.get("galaxy_user_key"),
+            "galaxy_admin_key": kwds.get("galaxy_admin_key"),
+            "engine": "external_galaxy",
+        }
+    else:
+        raise ConnectionError('The credentials provided for an external Galaxy instance are not valid.')
+
+
+def ensure_profile(ctx, profile_name, **kwds):
+    """Ensure a Galaxy profile exists and return profile defaults."""
+    if not profile_exists(ctx, profile_name, **kwds):
+        create_profile(ctx, profile_name, **kwds)
+
+    return _profile_options(ctx, profile_name, **kwds)
+
+
+def create_alias(ctx, alias, obj, profile_name, **kwds):
+    profile_options, profile_options_path = _load_profile_to_json(ctx, profile_name)
+
+    if profile_options.get('aliases'):
+        profile_options['aliases'][alias] = obj
+    else:  # no aliases yet defined
+        profile_options['aliases'] = {alias: obj}
+
+    with open(profile_options_path, 'w') as f:
+        json.dump(profile_options, f)
+
+    return 0
+
+
+def list_alias(ctx, profile_name, **kwds):
+    profile_options, _ = _load_profile_to_json(ctx, profile_name)
+    return profile_options.get('aliases', {})
+
+
+def delete_alias(ctx, alias, profile_name, **kwds):
+    profile_options, profile_options_path = _load_profile_to_json(ctx, profile_name)
+    if alias not in profile_options.get('aliases', {}):
+        return 1
+    else:
+        del profile_options['aliases'][alias]
+
+    with open(profile_options_path, 'w') as f:
+        json.dump(profile_options, f)
+
+    return 0
+
+
+def translate_alias(ctx, alias, profile_name):
+    if not profile_name:
+        return alias
+    aliases = _load_profile_to_json(ctx, profile_name)[0].get('aliases', {})
+    return aliases.get(alias, alias)
+
+
+def _load_profile_to_json(ctx, profile_name):
+    if not profile_exists(ctx, profile_name):
+        raise Exception("That profile does not exist. Create it with `planemo profile_create`")
+    profile_directory = _profile_directory(ctx, profile_name)
+    profile_options_path = _stored_profile_options_path(profile_directory)
+    with open(profile_options_path) as f:
+        profile_options = json.load(f)
+    return profile_options, profile_options_path
+
+
+def _profile_options(ctx, profile_name, **kwds):
+    profile_directory = _profile_directory(ctx, profile_name)
+    profile_options = _read_profile_options(profile_directory)
+
+    if profile_options["engine"] == "docker_galaxy":
+        engine_options = dict(
+            export_directory=os.path.join(profile_directory, "export")
+        )
+    else:
+        file_path = os.path.join(profile_directory, "files")
+        shed_tool_path = os.path.join(profile_directory, "shed_tools")
+        shed_tool_conf = os.path.join(profile_directory, "shed_tool_conf.xml")
+        tool_dependency_dir = os.path.join(profile_directory, "deps")
+
+        engine_options = dict(
+            file_path=file_path,
+            tool_dependency_dir=tool_dependency_dir,
+            shed_tool_conf=shed_tool_conf,
+            shed_tool_path=shed_tool_path,
+            galaxy_brand=profile_name,
+        )
+    profile_options.update(engine_options)
+    profile_options["galaxy_brand"] = profile_name
+    return profile_options
+
+
+def _profile_to_database_identifier(profile_name):
+    char_lst = [c if c.isalnum() else "_" for c in profile_name]
+    return "plnmoprof_%s" % "".join(char_lst)
+
+
+def _read_profile_options(profile_directory):
+    profile_options_path = _stored_profile_options_path(profile_directory)
+    with open(profile_options_path, "r") as f:
+        profile_options = json.load(f)
+    return profile_options
+
+
+def _stored_profile_options_path(profile_directory):
+    profile_options_path = os.path.join(
+        profile_directory, PROFILE_OPTIONS_JSON_NAME
+    )
+    return profile_options_path
+
+
+def _profile_directory(ctx, profile_name):
+    return os.path.join(ctx.galaxy_profiles_directory, profile_name)
+
+
+__all__ = (
+    "create_profile",
+    "delete_profile",
+    "ensure_profile",
+    "list_profiles",
+)