Merge pull request #20531 from natefoo/config-script-fixes

[25.0] Fix `galaxy-config` script, move install to `galaxy-dependencies` in app package

lib/galaxy/config/script.py

@@ -5,19 +5,12 @@ import string
 import sys
 from argparse import ArgumentParser
 
-try:
-    import pip
-except ImportError:
-    pip = None  # type: ignore[assignment]
-
-
 CONFIGURE_URL = "https://docs.galaxyproject.org/en/master/admin/"
 
 DESCRIPTION = "Initialize a directory with a minimal Galaxy config."
 HELP_CONFIG_DIR = "Directory containing the configuration files for Galaxy."
 HELP_DATA_DIR = "Directory containing Galaxy-created data."
 HELP_FORCE = "Overwrite existing files if they already exist."
-HELP_INSTALL = "Install optional dependencies required by specified configuration (e.g. drmaa, etc...)."
 HELP_HOST = (
     'Host to bind Galaxy to - defaults to localhost. Specify an IP address or "all" to listen on all interfaces.'
 )
@@ -26,41 +19,57 @@ HELP_DB_CONN = "Galaxy database connection URI."
 
 DEFAULT_HOST = "localhost"
 DEFAULT_YML = "galaxy.yml"
-DEFAULT_DB_CONN = "sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE"
 
 SAMPLES_PATH = os.path.abspath(os.path.join(os.path.dirname(__file__), "sample"))
 GALAXY_CONFIG_TEMPLATE_FILE = os.path.join(SAMPLES_PATH, "galaxy.yml.sample")
-STATIC_PATH = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "web", "framework", "static"))
-CLIENT_PATH = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, "client"))
 
 MSG_CONFIG_SUMMARY = """
-For help on configuring Galaxy, consult the documentation at: \n {}
+Perform additional configuration by editing the config file at:
+
+    {config_path}
+
+For help on configuring Galaxy, consult the documentation at:
+
+    {configure_url}
 
 Additional sample configuration files for various Galaxy components (jobs,
-datatypes, etc.) can be found in:\n {}
+datatypes, etc.) can be found in:
 
-Start Galaxy by running the command from directory [{}]:
+    {samples_path}
+
+Advanced job configurations can be generated with galaxy-job-config-init. It
+can be installed and run with:
+
+    pip install galaxy-job-config-init
+    galaxy-job-config-init --help
+
+Some Galaxy dependencies are optional based on your configuration. You can
+install them with:
+
+    galaxy-dependencies --install
+
+Start Galaxy by running the command:
+
+galaxy -c {config_path}
 """
 
 # The sample is used as the default config file for Galaxy started without a config, and we don't want to duplicate the
 # whole thing into galaxy.config for templating, so for now just substitute some lines. In the future we will build
 # configs differently.
 GALAXY_CONFIG_SUBSTITUTIONS = {
-    "  #config_dir: false": "  config_dir: ${config_dir}",
-    "  #data_dir: false": "  data_dir: ${data_dir}",
-    "  #database_connection: sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE": "  database_connection: ${database_connection}",
+    "  #config_dir: null": "  config_dir: ${config_dir}",
+    "  #data_dir: null": "  data_dir: ${data_dir}",
+    "    # bind: localhost:8080": "    bind: ${host}:${port}",
 }
 
 
 def main(argv=None):
-    dependencies = []
     arg_parser = ArgumentParser(description=DESCRIPTION)
     arg_parser.add_argument("--config-dir", default=".", help=HELP_CONFIG_DIR)
     arg_parser.add_argument("--data-dir", default="./data", help=HELP_DATA_DIR)
     arg_parser.add_argument("--host", default=DEFAULT_HOST, help=HELP_HOST)
     arg_parser.add_argument("--port", default="8080", help=HELP_PORT)
-    arg_parser.add_argument("--db-conn", default=DEFAULT_DB_CONN, help=HELP_DB_CONN)
-    arg_parser.add_argument("--install", action="store_true", help=HELP_INSTALL)
+    arg_parser.add_argument("--db-conn", help=HELP_DB_CONN)
     arg_parser.add_argument("--force", action="store_true", default=False, help=HELP_FORCE)
     args = arg_parser.parse_args(argv)
     config_dir = args.config_dir
@@ -70,33 +79,39 @@ def main(argv=None):
     data_dir = os.path.abspath(data_dir)
 
     mode = _determine_mode(args)
-    if args.db_conn.startswith("postgresql://"):
-        dependencies.append("psycopg2-binary")
+    if args.db_conn:
+        GALAXY_CONFIG_SUBSTITUTIONS["  #database_connection: null"] = "  database_connection: ${database_connection}"
 
     for directory in (config_dir, data_dir):
         if not os.path.exists(directory):
             os.makedirs(directory)
 
-    print(f"Bootstrapping Galaxy configuration into directory {relative_config_dir}")
+    print(f"* Bootstrapping Galaxy configuration into directory: {relative_config_dir}")
     _handle_galaxy_yml(args, config_dir, data_dir)
-    _handle_install(args, dependencies)
     _print_config_summary(args, mode, relative_config_dir)
 
 
 def _print_config_summary(args, mode, relative_config_dir):
     _print_galaxy_yml_info(args, mode)
-    print(MSG_CONFIG_SUMMARY.format(CONFIGURE_URL, SAMPLES_PATH, relative_config_dir))
+    config_path = os.path.join(args.config_dir, DEFAULT_YML)
+    print(
+        MSG_CONFIG_SUMMARY.format(
+            configure_url=CONFIGURE_URL,
+            samples_path=SAMPLES_PATH,
+            config_path=config_path,
+        )
+    )
 
 
 def _print_galaxy_yml_info(args, mode):
-    print(" - galaxy.yml created, update to configure Galaxy.")
-    print(f"   * Target web server {mode}")
+    print("* Configuration created")
+    print(f"  - Target web server [{mode}]")
     if args.host == DEFAULT_HOST:
-        print("   * Binding to host localhost, remote clients will not be able to connect.")
+        print(f"  - Binding to [localhost:{args.port}], remote clients will not be able to connect.")
     elif _determine_host(args) == "0.0.0.0":
-        print("   * Binding to all network interfaces.")
+        print("  - Binding to all network interfaces.")
     else:
-        print("   * Binding to host [%s].", args.host)
+        print(f"  - Binding to [{args.host}:{args.port}].")
 
 
 def _determine_mode(args):
@@ -120,8 +135,6 @@ def _handle_galaxy_yml(args, config_dir, data_dir):
         host=_determine_host(args),
         config_dir=config_dir,
         data_dir=data_dir,
-        client_dir=CLIENT_PATH,
-        static_path=STATIC_PATH,
         database_connection=args.db_conn,
     )
 
@@ -139,14 +152,6 @@ def _handle_galaxy_yml(args, config_dir, data_dir):
     open(yml_file, "w").write(galaxy_config)
 
 
-def _handle_install(args, dependencies):
-    if args.install and dependencies:
-        if pip is None:
-            raise ImportError("Bootstrapping Galaxy dependencies requires pip.")
-
-        pip.main(["install"] + dependencies)
-
-
 def _check_file(path, force):
     if os.path.exists(path) and not force:
         print(f"File {path} exists, exiting. Run with --force to replace configuration.", file=sys.stderr)

lib/galaxy/dependencies/script.py

@@ -0,0 +1,70 @@
+#!/usr/bin/env python
+
+import errno
+import os
+import shlex
+import sys
+import warnings
+from argparse import ArgumentParser
+from subprocess import check_call
+
+import galaxy.dependencies
+
+DESCRIPTION = "Install optional Galaxy dependencies based on configuration values"
+PINNED_REQUIREMENTS = os.path.join(os.path.dirname(__file__), "pinned-requirements.txt")
+
+HELP_PINNED = (
+    "Include pinned required dependencies in install command, ensures all dependencies are installed at "
+    "expected versions for the Galaxy release"
+)
+HELP_INSTALL = "Perform install, if unset then only output what would have been performed"
+HELP_FREEZE = "Instead of installing, output requirent format to stdout"
+HELP_CONFIG_FILE = "Path to Galaxy config file (galaxy.yml)"
+
+# Warnings raised by dependency imports
+warnings.filterwarnings("ignore")
+
+
+def main(argv=None):
+    dependencies = []
+    arg_parser = ArgumentParser(description=DESCRIPTION)
+    arg_parser.add_argument("--pinned", action="store_true", help=HELP_PINNED)
+    arg_parser.add_argument("--install", action="store_true", help=HELP_INSTALL)
+    arg_parser.add_argument("--freeze", action="store_true", help=HELP_FREEZE)
+    arg_parser.add_argument("--config_file", "-c", help=HELP_CONFIG_FILE)
+    args = arg_parser.parse_args(argv)
+    config_file = args.config_file
+    if config_file and not os.path.exists(config_file):
+        print(f"{arg_parser.prog}: {config_file}: {os.strerror(errno.ENOENT)}", file=sys.stderr)
+        sys.exit(1)
+    dependencies = galaxy.dependencies.optional(config_file)
+    if args.freeze:
+        _handle_freeze(args, dependencies)
+    elif dependencies or args.pinned:
+        _handle_install(args, dependencies)
+    else:
+        print("Nothing to install", file=sys.stderr)
+
+
+def _handle_freeze(args, dependencies):
+    print("# generated with galaxy-dependencies")
+    if args.pinned:
+        print(f"-r {PINNED_REQUIREMENTS}")
+    print("\n".join(dependencies))
+
+
+def _handle_install(args, dependencies):
+    req_file = []
+    if args.pinned:
+        req_file = ["-r", PINNED_REQUIREMENTS]
+    cmd = [sys.executable, "-m", "pip", "install"] + req_file + dependencies
+    print("Installing dependencies with:", file=sys.stderr)
+    print(f"> {shlex.join(cmd)}", file=sys.stderr)
+    if args.install:
+        check_call(cmd)
+    else:
+        print("Dry run, use --install to perform installation", file=sys.stderr)
+
+
+if __name__ == "__main__":
+    main()

packages/app/setup.cfg

@@ -85,6 +85,7 @@ python_requires = >=3.9
 [options.entry_points]
 console_scripts =
         galaxy-main = galaxy.main:main
+        galaxy-dependencies = galaxy.dependencies.script:main
 
 [options.packages.find]
 exclude =