Merge pull request #19050 from natefoo/installed-no-config

Run installed Galaxy with no config and a simplified entry point

doc/source/admin/galaxy_options.rst

@@ -509,8 +509,9 @@
 :Description:
     Set to true to instruct Galaxy to install Conda from the web
     automatically if it cannot find a local copy and conda_exec is not
-    configured.
-:Default: ``true``
+    configured. The default is true if running Galaxy from source, and
+    false if running from installed packages.
+:Default: ``None``
 :Type: bool
 
 
@@ -5124,7 +5125,7 @@
     'deferred' are "materialized" (or undeferred) by the workflow
     scheduler. This might be a lengthy process. Setting this to 'True'
     will place the invocation back in the queue after materialization
-    before scheduling the workflow so it is less  likely to starve
+    before scheduling the workflow so it is less likely to starve
     other workflow scheduling. Ideally, Galaxy would allow more fine
     grain control of handlers but until then, this provides a way to
     tip the balance between "doing more work" and "being more fair".

lib/galaxy/config/__init__.py

@@ -982,6 +982,9 @@ def _process_config(self, kwargs: Dict[str, Any]) -> None:
             # self, populate config_dict
             self.config_dict["conda_mapping_files"] = [self.local_conda_mapping_file, _default_mapping]
 
+        if kwargs.get("conda_auto_init") is None:
+            self.config_dict["conda_auto_init"] = running_from_source
+
         if self.container_resolvers_config_file:
             self.container_resolvers_config_file = self._in_config_dir(self.container_resolvers_config_file)
 

lib/galaxy/config/sample/galaxy.yml.sample

@@ -589,8 +589,9 @@ galaxy:
 
   # Set to true to instruct Galaxy to install Conda from the web
   # automatically if it cannot find a local copy and conda_exec is not
-  # configured.
-  #conda_auto_init: true
+  # configured. The default is true if running Galaxy from source, and
+  # false if running from installed packages.
+  #conda_auto_init: false
 
   # You must set this to true if conda_prefix and job_working_directory
   # are not on the same volume, or some conda dependencies will fail to
@@ -2752,7 +2753,7 @@ galaxy:
   # 'deferred' are "materialized" (or undeferred) by the workflow
   # scheduler. This might be a lengthy process. Setting this to 'True'
   # will place the invocation back in the queue after materialization
-  # before scheduling the workflow so it is less  likely to starve other
+  # before scheduling the workflow so it is less likely to starve other
   # workflow scheduling. Ideally, Galaxy would allow more fine grain
   # control of handlers but until then, this provides a way to tip the
   # balance between "doing more work" and "being more fair". The default

lib/galaxy/config/schemas/config_schema.yml

@@ -382,11 +382,11 @@ mapping:
 
       conda_auto_init:
         type: bool
-        default: true
         required: false
         desc: |
           Set to true to instruct Galaxy to install Conda from the web automatically
-          if it cannot find a local copy and conda_exec is not configured.
+          if it cannot find a local copy and conda_exec is not configured. The default is
+          true if running Galaxy from source, and false if running from installed packages.
 
       conda_copy_dependencies:
         type: bool

lib/galaxy/model/orm/scripts.py

@@ -28,6 +28,8 @@
 DEFAULT_CONFIG_NAMES = ["galaxy", "universe_wsgi"]
 DEFAULT_CONFIG_PREFIX = ""
 DEFAULT_DATABASE = "galaxy"
+ALEMBIC_CONFIG = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "migrations", "alembic.ini"))
+
 
 DATABASE = {
     "galaxy": {
@@ -163,6 +165,9 @@ def _insert_x_argument(key, value):
     _insert_x_argument("tsi_url", tsi_config.url)
     _insert_x_argument("gxy_url", gxy_config.url)
 
+    sys.argv.insert(1, "--config")
+    sys.argv.insert(2, ALEMBIC_CONFIG)
+
     if "heads" in sys.argv and "upgrade" in sys.argv:
         i = sys.argv.index("heads")
         sys.argv[i] = f"{GXY}@head"

lib/galaxy/util/properties.py

@@ -103,7 +103,7 @@ def load_app_properties(
         config_section = config_section or ini_section
 
     # read from file or init w/no file
-    if config_file:
+    if config_file and os.path.exists(config_file):
         properties = read_properties_from_file(config_file, config_section)
     else:
         properties = {"__file__": None}
@@ -208,6 +208,8 @@ def get_data_dir(properties):
     if data_dir is None:
         if running_from_source:
             data_dir = "./database"
+        elif properties["__file__"] is None:
+            data_dir = "./data"
         else:
             config_dir = properties.get("config_dir", os.path.dirname(properties["__file__"]))
             data_dir = os.path.join(config_dir, "data")

lib/galaxy/web/framework/middleware/static.py

@@ -18,10 +18,7 @@ def __init__(self, directory, cache_seconds=None, directory_per_host=None):
 
     def __call__(self, environ, start_response):
         path_info = environ.get("PATH_INFO", "")
-        script_name = environ.get("SCRIPT_NAME", "")
-        if script_name == "/robots.txt" or script_name == "/favicon.ico":
-            filename = script_name.replace("/", "")
-        elif not path_info:
+        if not path_info:
             # See if this is a static file hackishly mapped.
             if os.path.exists(self.directory) and os.path.isfile(self.directory):
                 app = FileApp(self.directory)

lib/galaxy/webapps/base/webapp.py

@@ -1156,19 +1156,34 @@ def build_url_map(app, global_conf, **local_conf):
     # Send to dynamic app by default
     urlmap["/"] = app
 
-    def get_static_from_config(option_name, default_path):
-        config_val = conf.get(option_name, default_url_path(default_path))
+    def get_static_from_config(option_name, default_path, sample=None):
+        config_val = conf.get(option_name)
+        default = default_url_path(default_path)
+        if not config_val:
+            if not os.path.exists(default) and sample:
+                config_val = os.path.abspath(f"{sample}")
+            else:
+                config_val = default
         per_host_config_option = f"{option_name}_by_host"
         per_host_config = conf.get(per_host_config_option)
         return Static(config_val, cache_time, directory_per_host=per_host_config)
 
     # Define static mappings from config
-    urlmap["/static"] = get_static_from_config("static_dir", "static/")
-    urlmap["/images"] = get_static_from_config("static_images_dir", "static/images")
-    urlmap["/static/scripts"] = get_static_from_config("static_scripts_dir", "static/scripts/")
-    urlmap["/static/welcome.html"] = get_static_from_config("static_welcome_html", "static/welcome.html")
-    urlmap["/favicon.ico"] = get_static_from_config("static_favicon_dir", "static/favicon.ico")
-    urlmap["/robots.txt"] = get_static_from_config("static_robots_txt", "static/robots.txt")
+    static_dir = get_static_from_config("static_dir", "static/")
+    static_dir_bare = static_dir.directory.rstrip("/")
+    urlmap["/static"] = static_dir
+    urlmap["/images"] = get_static_from_config("static_images_dir", f"{static_dir_bare}/images")
+    urlmap["/static/scripts"] = get_static_from_config("static_scripts_dir", f"{static_dir_bare}/scripts/")
+
+    urlmap["/static/welcome.html"] = get_static_from_config(
+        "static_welcome_html", f"{static_dir_bare}/welcome.html", sample=default_url_path("static/welcome.sample.html")
+    )
+    urlmap["/favicon.ico"] = get_static_from_config(
+        "static_favicon_dir", f"{static_dir_bare}/favicon.ico", sample=default_url_path("static/favicon.ico")
+    )
+    urlmap["/robots.txt"] = get_static_from_config(
+        "static_robots_txt", f"{static_dir_bare}/robots.txt", sample=default_url_path("static/robots.txt")
+    )
 
     if "static_local_dir" in conf:
         urlmap["/static_local"] = Static(conf["static_local_dir"], cache_time)

lib/galaxy/webapps/galaxy/script.py

@@ -0,0 +1,30 @@
+import os
+from argparse import ArgumentParser
+
+import uvicorn
+
+
+def main() -> None:
+    parser = ArgumentParser(
+        prog="galaxy-web",
+        description="Run Galaxy Web Server",
+    )
+    parser.add_argument("--config", "-c", help="Galaxy config file")
+    parser.add_argument("--single-user", "-s", help="Single user mode as user SINGLE_USER")
+    parser.add_argument("--bind", "-b", default="localhost:8080", help="Bind to <host>:<port>")
+    parser.add_argument(
+        "--client-path", "-n", default="node_modules/@galaxyproject/galaxy-client", help="Path to Galaxy client"
+    )
+    args = parser.parse_args()
+    if args.config:
+        os.environ["GALAXY_CONFIG_FILE"] = args.config
+    if args.single_user:
+        os.environ["GALAXY_CONFIG_SINGLE_USER"] = args.single_user
+        os.environ["GALAXY_CONFIG_ADMIN_USERS"] = args.single_user
+    os.environ["GALAXY_CONFIG_STATIC_DIR"] = args.client_path
+    uvicorn.run(
+        "galaxy.webapps.galaxy.fast_factory:factory",
+        factory=True,
+        host=args.bind.split(":")[0],
+        port=int(args.bind.split(":")[1]),
+    )

packages/app/setup.cfg

@@ -57,6 +57,7 @@ install_requires =
     Mako
     Markdown
     MarkupSafe
+    mercurial
     packaging
     paramiko!=2.9.0,!=2.9.1
     pebble

packages/package-dev-install.sh

@@ -0,0 +1,36 @@
+#!/bin/bash
+#
+# Install packages in development mode, for running installed Galaxy from the source
+#
+set -euo pipefail
+
+editable=false
+
+while getopts ':e' OPTION
+do
+    case $OPTION in
+        e)
+            editable=true
+           ;;
+    esac
+done
+shift $((OPTIND - 1))
+
+up_to="${1:-}"
+
+if [ -n "$up_to" -a ! -d "$up_to" ]; then
+    echo "ERROR: package does not exist: $up_to"
+    exit 1
+fi
+
+while read package; do
+    [ -n "$package" ] || continue
+    pushd $package
+    if $editable; then
+        pip install -e .
+    else
+        pip install .
+    fi
+    popd
+    [ "$package" != "$up_to" ] || exit
+done < packages_by_dep_dag.txt

packages/web_apps/setup.cfg

@@ -68,6 +68,10 @@ install_requires =
 packages = find:
 python_requires = >=3.8
 
+[options.entry_points]
+console_scripts =
+        galaxy-web = galaxy.webapps.galaxy.script:main
+
 [options.packages.find]
 exclude =
     tests*

scripts/common_startup.sh

@@ -34,7 +34,6 @@ done
 SAMPLES="
     tool-data/shared/ucsc/builds.txt.sample
     tool-data/shared/ucsc/manual_builds.txt.sample
-    static/welcome.html.sample
 "
 
 RMFILES="