Drop planemo database seed option

docs/commands/run.rst

@@ -25,7 +25,6 @@ Planemo command for running tools and jobs.
                                       execute command with.
       --galaxy_python_version [2|2.7|3|3.5|3.6|3.7|3.8]
                                       Python version to start Galaxy under
-      --galaxy_database_seed PATH     Preseeded Galaxy sqlite database to target.
       --extra_tools PATH              Extra tool sources to include in Galaxy's tool
                                       panel (file or directory). These will not be
                                       linted/tested/etc... but they will be

docs/commands/serve.rst

@@ -41,7 +41,6 @@ Galaxy instance.
                                       execute command with.
       --galaxy_python_version [2|2.7|3|3.5|3.6|3.7|3.8]
                                       Python version to start Galaxy under
-      --galaxy_database_seed PATH     Preseeded Galaxy sqlite database to target.
       --extra_tools PATH              Extra tool sources to include in Galaxy's tool
                                       panel (file or directory). These will not be
                                       linted/tested/etc... but they will be

docs/commands/shed_serve.rst

@@ -49,7 +49,6 @@ logged into and explored interactively.
                                       execute command with.
       --galaxy_python_version [2|2.7|3|3.5|3.6|3.7|3.8]
                                       Python version to start Galaxy under
-      --galaxy_database_seed PATH     Preseeded Galaxy sqlite database to target.
       --extra_tools PATH              Extra tool sources to include in Galaxy's tool
                                       panel (file or directory). These will not be
                                       linted/tested/etc... but they will be

docs/commands/shed_test.rst

@@ -50,7 +50,6 @@ This command requires the target to be version 15.07 or newer.
                                       execute command with.
       --galaxy_python_version [2|2.7|3|3.5|3.6|3.7|3.8]
                                       Python version to start Galaxy under
-      --galaxy_database_seed PATH     Preseeded Galaxy sqlite database to target.
       --extra_tools PATH              Extra tool sources to include in Galaxy's tool
                                       panel (file or directory). These will not be
                                       linted/tested/etc... but they will be

docs/commands/test.rst

@@ -57,7 +57,6 @@ please careful and do not try this against production Galaxy instances.
                                       execute command with.
       --galaxy_python_version [2|2.7|3|3.5|3.6|3.7|3.8]
                                       Python version to start Galaxy under
-      --galaxy_database_seed PATH     Preseeded Galaxy sqlite database to target.
       --extra_tools PATH              Extra tool sources to include in Galaxy's tool
                                       panel (file or directory). These will not be
                                       linted/tested/etc... but they will be

docs/commands/tool_factory.rst

@@ -26,7 +26,6 @@ http://www.ncbi.nlm.nih.gov/pubmed/23024011.
                                       execute command with.
       --galaxy_python_version [2|2.7|3|3.5|3.6|3.7|3.8]
                                       Python version to start Galaxy under
-      --galaxy_database_seed PATH     Preseeded Galaxy sqlite database to target.
       --extra_tools PATH              Extra tool sources to include in Galaxy's tool
                                       panel (file or directory). These will not be
                                       linted/tested/etc... but they will be

docs/commands/training_generate_from_wf.rst

@@ -30,7 +30,6 @@ Create tutorial skeleton from workflow.
                                       execute command with.
       --galaxy_python_version [2|2.7|3|3.5|3.6|3.7|3.8]
                                       Python version to start Galaxy under
-      --galaxy_database_seed PATH     Preseeded Galaxy sqlite database to target.
       --extra_tools PATH              Extra tool sources to include in Galaxy's tool
                                       panel (file or directory). These will not be
                                       linted/tested/etc... but they will be

docs/commands/training_init.rst

@@ -40,7 +40,6 @@ Build training template from workflow.
                                       execute command with.
       --galaxy_python_version [2|2.7|3|3.5|3.6|3.7|3.8]
                                       Python version to start Galaxy under
-      --galaxy_database_seed PATH     Preseeded Galaxy sqlite database to target.
       --extra_tools PATH              Extra tool sources to include in Galaxy's tool
                                       panel (file or directory). These will not be
                                       linted/tested/etc... but they will be

docs/commands/workflow_convert.rst

@@ -23,7 +23,6 @@ Convert Format 2 workflow to a native Galaxy workflow.
                                       execute command with.
       --galaxy_python_version [2|2.7|3|3.5|3.6|3.7|3.8]
                                       Python version to start Galaxy under
-      --galaxy_database_seed PATH     Preseeded Galaxy sqlite database to target.
       --extra_tools PATH              Extra tool sources to include in Galaxy's tool
                                       panel (file or directory). These will not be
                                       linted/tested/etc... but they will be

docs/commands/workflow_edit.rst

@@ -21,7 +21,6 @@ Open a synchronized Galaxy workflow editor.
                                       execute command with.
       --galaxy_python_version [2|2.7|3|3.5|3.6|3.7|3.8]
                                       Python version to start Galaxy under
-      --galaxy_database_seed PATH     Preseeded Galaxy sqlite database to target.
       --extra_tools PATH              Extra tool sources to include in Galaxy's tool
                                       panel (file or directory). These will not be
                                       linted/tested/etc... but they will be

planemo/galaxy/config.py

@@ -190,21 +190,6 @@ class = StreamHandler
     "wget -q https://codeload.github.com/galaxyproject/galaxy/tar.gz/"
 )
 
-DOWNLOADS_URL = ("https://raw.githubusercontent.com/"
-                 "jmchilton/galaxy-downloads/master/")
-DOWNLOADABLE_MIGRATION_VERSIONS = [141, 127, 120, 117]
-MIGRATION_PER_VERSION = {
-    "dev": 145,
-    "master": 142,
-    "18.09": 142,
-    "18.05": 141,
-    "18.01": 140,
-    "17.09": 135,
-    "17.05": 134,
-    "17.01": 133,
-}
-OLDEST_SUPPORTED_VERSION = 127
-
 DATABASE_LOCATION_TEMPLATE = "sqlite:///%s?isolation_level=IMMEDIATE"
 
 COMMAND_STARTUP_COMMAND = "./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}"
@@ -403,12 +388,6 @@ def config_join(*args):
         database_location = config_join("galaxy.sqlite")
         master_api_key = _get_master_api_key(kwds)
         dependency_dir = os.path.join(config_directory, "deps")
-        preseeded_database = attempt_database_preseed(
-            ctx,
-            galaxy_root,
-            database_location,
-            **kwds
-        )
         _ensure_directory(shed_tool_path)
         port = _get_port(kwds)
         template_args = dict(
@@ -483,10 +462,6 @@ def config_join(*args):
         _build_test_env(properties, env)
         env['GALAXY_TEST_SHED_TOOL_CONF'] = shed_tool_conf
 
-        # No need to download twice - would GALAXY_TEST_DATABASE_CONNECTION
-        # work?
-        if preseeded_database:
-            env["GALAXY_TEST_DB_TEMPLATE"] = os.path.abspath(database_location)
         env["GALAXY_TEST_UPLOAD_ASYNC"] = "false"
         env["GALAXY_TEST_LOGGING_CONFIG"] = config_join("logging.ini")
         env["GALAXY_DEVELOPMENT_ENVIRONMENT"] = "1"
@@ -1003,84 +978,6 @@ def _database_connection(database_location, **kwds):
     return database_connection
 
 
-def attempt_database_preseed(
-    ctx, effective_galaxy_root, database_location, **kwds
-):
-    """If database location is unset, attempt to seed the database."""
-    if os.path.exists(database_location):
-        # Can't seed an existing database.
-        return False
-
-    if not _database_connection(database_location, **kwds).startswith("sqlite"):
-        # Not going to use an sqlite database, don't preseed.
-        return False
-
-    preseeded_database = True
-    galaxy_sqlite_database = kwds.get("galaxy_database_seed", None)
-    galaxy_branch = kwds.get("galaxy_branch", None)
-    try:
-        _download_database_template(
-            ctx,
-            effective_galaxy_root,
-            database_location,
-            galaxy_sqlite_database=galaxy_sqlite_database,
-            galaxy_branch=galaxy_branch
-        )
-    except Exception as e:
-        print(e)
-        # No network access - just roll forward from null.
-        preseeded_database = False
-    return preseeded_database
-
-
-def _download_database_template(
-    ctx,
-    galaxy_root,
-    database_location,
-    galaxy_sqlite_database=None,
-    galaxy_branch=None,
-):
-
-    if galaxy_sqlite_database is not None:
-        shutil.copyfile(galaxy_sqlite_database, database_location)
-        return True
-
-    download_migration = None
-    newest_migration = _newest_migration_version(galaxy_root, galaxy_branch)
-    for migration in DOWNLOADABLE_MIGRATION_VERSIONS:
-        if newest_migration >= migration:
-            download_migration = migration
-            break
-
-    if download_migration:
-        download_name = "db_gx_rev_0%d.sqlite" % download_migration
-        download_url = DOWNLOADS_URL + download_name
-        ctx.cache_download(download_url, database_location)
-        return True
-    else:
-        return False
-
-
-def _newest_migration_version(galaxy_root, galaxy_branch):
-    versions_dir = galaxy_root and os.path.join(galaxy_root, "lib/galaxy/model/migrate/versions")
-    if versions_dir and os.path.exists(versions_dir):
-        version = max(map(_file_name_to_migration_version, os.listdir(versions_dir)))
-    elif galaxy_branch:
-        for branch in MIGRATION_PER_VERSION:
-            if branch in galaxy_branch:
-                version = MIGRATION_PER_VERSION[branch]
-    else:
-        version = OLDEST_SUPPORTED_VERSION
-    return version
-
-
-def _file_name_to_migration_version(name):
-    try:
-        return int(name[0:4])
-    except ValueError:
-        return -1
-
-
 def _find_galaxy_root(ctx, **kwds):
     root_prop = "galaxy_root"
     cwl = kwds.get("cwl", False)
@@ -1375,7 +1272,6 @@ def _ensure_directory(path):
 
 
 __all__ = (
-    "attempt_database_preseed",
     "DATABASE_LOCATION_TEMPLATE",
     "galaxy_config",
 )

planemo/galaxy/profiles.py

@@ -13,10 +13,7 @@
     OptionSource,
 )
 from planemo.database import create_database_source
-from .config import (
-    attempt_database_preseed,
-    DATABASE_LOCATION_TEMPLATE,
-)
+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."
@@ -93,7 +90,6 @@ def _create_profile_local(ctx, profile_directory, profile_name, kwds):
         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 {

planemo/options.py

@@ -150,17 +150,6 @@ def galaxy_root_option():
     )
 
 
-def galaxy_database_seed_option():
-    return planemo_option(
-        "--galaxy_database_seed",
-        default=None,
-        use_global_config=True,
-        use_env_var=True,
-        type=click.Path(exists=True, file_okay=True, resolve_path=True),
-        help="Preseeded Galaxy sqlite database to target.",
-    )
-
-
 def galaxy_cwl_root_option():
     return planemo_option(
         "--cwl_galaxy_root",
@@ -1070,7 +1059,6 @@ def galaxy_target_options():
     return _compose(
         galaxy_root_option(),
         galaxy_python_version(),
-        galaxy_database_seed_option(),
         extra_tools_option(),
         install_galaxy_option(),
         galaxy_branch_option(),

tests/test_training.py

@@ -70,7 +70,6 @@
     'file_path': None,
     'galaxy_api_key': None,
     'galaxy_branch': None,
-    'galaxy_database_seed': None,
     'galaxy_email': 'planemo@galaxyproject.org',
     'galaxy_root': None,
     'galaxy_single_user': True,