Merge pull request #1307 from mvdbeek/fix_stopping_gravity

Fix recording of virtual_env_dir
galaxyproject · Oct 31, 2022 · b6511dd · b6511dd
2 parents b7d9761 + b3f3bd9
commit b6511dd
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Showing 2 changed files with 22 additions and 9 deletions.
diff --git a/planemo/galaxy/config.py b/planemo/galaxy/config.py
@@ -1003,11 +1003,12 @@ def __init__(
             kwds,
         )
         self.galaxy_root = galaxy_root
+        self._virtual_env_dir = None
 
     @property
     def virtual_env_dir(self):
-        virtual_env = self._kwds.get("GALAXY_VIRTUAL_ENV", ".venv")
-        if virtual_env and not os.path.isabs(virtual_env):
+        virtual_env = self._virtual_env_dir or ".venv"
+        if not os.path.isabs(virtual_env):
             virtual_env = os.path.join(self.galaxy_root, virtual_env)
         return virtual_env
 
@@ -1036,7 +1037,7 @@ def startup_command(self, ctx, **kwds):
         """
         daemon = kwds.get("daemon", False)
         # TODO: Allow running dockerized Galaxy here instead.
-        setup_venv_command = setup_venv(ctx, kwds)
+        setup_venv_command = setup_venv(ctx, kwds, self)
         run_script = f"{shlex.quote(os.path.join(self.galaxy_root, 'run.sh'))} $COMMON_STARTUP_ARGS"
         if daemon:
             run_script += " --daemon"

diff --git a/planemo/galaxy/run.py b/planemo/galaxy/run.py
@@ -2,6 +2,12 @@
 import os
 import shlex
 import string
+from typing import (
+    Any,
+    Dict,
+    Optional,
+    TYPE_CHECKING,
+)
 
 from galaxy.util.commands import shell
 
@@ -14,6 +20,9 @@
     DEFAULT_PYTHON_VERSION,
 )
 
+if TYPE_CHECKING:
+    from planemo.galaxy.config import LocalGalaxyConfig
+
 # Activate galaxy's virtualenv if present (needed for tests say but not for
 # server because run.sh does this).
 ACTIVATE_COMMAND = (
@@ -38,15 +47,15 @@
 UNCACHED_VIRTUAL_ENV_COMMAND = "GALAXY_VIRTUAL_ENV=.venv"
 
 
-def setup_venv(ctx, kwds):
+def setup_venv(ctx, kwds: Dict[str, Any], config: Optional["LocalGalaxyConfig"] = None):
     if kwds.get("skip_venv", False):
         return ""
 
     create_template_params = {
         "create_virtualenv": create_command("$GALAXY_VIRTUAL_ENV", kwds.get("galaxy_python_version"))
     }
     return shell_join(
-        locate_galaxy_virtualenv(ctx, kwds),
+        locate_galaxy_virtualenv(ctx, kwds, config),
         PRINT_VENV_COMMAND if ctx.verbose else None,
         CREATE_COMMAND_TEMPLATE.safe_substitute(create_template_params),
         PRINT_VENV_COMMAND if ctx.verbose else None,
@@ -60,10 +69,10 @@ def setup_venv(ctx, kwds):
     )
 
 
-def locate_galaxy_virtualenv(ctx, kwds):
+def locate_galaxy_virtualenv(ctx, kwds: Dict[str, Any], config: Optional["LocalGalaxyConfig"] = None):
     if os.environ.get("GALAXY_VIRTUAL_ENV"):
         venv_command = ""
-        kwds["GALAXY_VIRTUAL_ENV"] = os.environ["GALAXY_VIRTUAL_ENV"]
+        virtual_env_dir = os.environ["GALAXY_VIRTUAL_ENV"]
     elif not kwds.get("no_cache_galaxy", False):
         workspace = ctx.workspace
         galaxy_branch = kwds.get("galaxy_branch") or "master"
@@ -72,11 +81,14 @@ def locate_galaxy_virtualenv(ctx, kwds):
         shared_venv_path = f"{shared_venv_path}_{galaxy_python_version}"
         if galaxy_branch != "master":
             shared_venv_path = f"{shared_venv_path}_{galaxy_branch}"
-        kwds["GALAXY_VIRTUAL_ENV"] = shared_venv_path
+
+        virtual_env_dir = shared_venv_path
         venv_command = CACHED_VIRTUAL_ENV_COMMAND % shlex.quote(shared_venv_path)
     else:
-        kwds["GALAXY_VIRTUAL_ENV"] = ".venv"
+        virtual_env_dir = ".venv"
         venv_command = UNCACHED_VIRTUAL_ENV_COMMAND
+    if config:
+        config._virtual_env_dir = virtual_env_dir
     return shell_join(
         venv_command,
         "export GALAXY_VIRTUAL_ENV",