Random fixes

planemo/cli.py

@@ -65,7 +65,7 @@ def global_config(self):
         """
         if self._global_config is None:
             self._global_config = read_global_config(self.planemo_config)
-        return self._global_config
+        return self._global_config or {}
 
     def log(self, msg, *args):
         """Log a message to stderr."""

planemo/commands/cmd_shed_serve.py

@@ -14,6 +14,7 @@
 @options.shed_read_options()
 @options.galaxy_run_options()
 @options.galaxy_config_options()
+@options.pid_file_option()
 @click.option(
     "--skip_dependencies",
     is_flag=True,

planemo/galaxy/config.py

@@ -498,6 +498,7 @@ def config_join(*args):
         env["GALAXY_TEST_UPLOAD_ASYNC"] = "false"
         env["GALAXY_TEST_LOGGING_CONFIG"] = config_join("logging.ini")
         env["GALAXY_DEVELOPMENT_ENVIRONMENT"] = "1"
+        env["GALAXY_SKIP_CLIENT_BUILD"] = "1"
         web_config = _sub(WEB_SERVER_CONFIG_TEMPLATE, template_args)
         write_file(config_join("galaxy.ini"), web_config)
         tool_conf_contents = _sub(TOOL_CONF_TEMPLATE, template_args)
@@ -850,7 +851,7 @@ def startup_command(self, ctx, **kwds):
             run_script += " --daemon"
             self.env["GALAXY_RUN_ALL"] = "1"
         else:
-            run_script += " --server-name '%s' --reload" % self.server_name
+            run_script += " --server-name '%s'" % self.server_name
         server_ini = os.path.join(self.config_directory, "galaxy.ini")
         self.env["GALAXY_CONFIG_FILE"] = server_ini
         cd_to_galaxy_command = "cd %s" % self.galaxy_root

planemo/galaxy/serve.py

@@ -2,6 +2,7 @@
 from __future__ import print_function
 
 import contextlib
+import os
 import time
 
 from planemo import io
@@ -59,6 +60,12 @@ def _serve(ctx, runnables, **kwds):
         ctx.vlog("Waiting for service on (%s, %s)" % (host, port))
         assert network_util.wait_http_service(galaxy_url)
         config.install_workflows()
+        if kwds.get("pid_file"):
+            real_pid_file = config.pid_file
+            if os.path.exists(config.pid_file):
+                os.symlink(real_pid_file, kwds["pid_file"])
+            else:
+                io.warn("Can't find Galaxy pid file [%s] to link" % real_pid_file)
         return config
 
 

planemo/io.py

@@ -2,6 +2,7 @@
 from __future__ import print_function
 
 import contextlib
+import errno
 import fnmatch
 import os
 import shutil
@@ -171,13 +172,14 @@ def ps1_for_path(path, base="PS1"):
 
 
 def kill_pid_file(pid_file):
-    if not os.path.exists(pid_file):
-        print("No pid file...")
-        return
+    try:
+        os.stat(pid_file)
+    except OSError as e:
+        if e.errno == errno.ENOENT:
+            return False
 
     pid = int(open(pid_file, "r").read())
-    killed = kill_posix(pid)
-    print("killed? %s" % killed)
+    kill_posix(pid)
 
 
 def kill_posix(pid):

planemo/network_util.py

@@ -44,14 +44,14 @@ def wait_net_service(server, port, timeout=None):
 
     port = int(port)
 
-    s = socket.socket()
-    # Following line prevents this method from interfering with process
-    # it is waiting for on localhost.
-    s.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEADDR, 1)
     if timeout:
         end = now() + timeout
 
     while True:
+        s = socket.socket()
+        # Following line prevents this method from interfering with process
+        # it is waiting for on localhost.
+        s.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEADDR, 1)
         try:
             if timeout:
                 next_timeout = end - now()
@@ -68,7 +68,9 @@ def wait_net_service(server, port, timeout=None):
                 return False
 
         except socket.error:
-            pass
+            # if getattr(e, "errno") == 61:
+            #    refused_connections += 1
+            s.close()
         else:
             s.close()
             return True

planemo/options.py

@@ -968,6 +968,20 @@ def galaxy_target_options():
     )
 
 
+def pid_file_option():
+    pid_file_type = click.Path(
+        file_okay=True,
+        dir_okay=False,
+        resolve_path=True,
+    )
+    return planemo_option(
+        "--pid_file",
+        type=pid_file_type,
+        default=None,
+        help="Location of pid file is executed with --daemon."
+    )
+
+
 def daemon_option():
     return planemo_option(
         "--daemon",
@@ -993,6 +1007,7 @@ def galaxy_serve_options():
         docker_galaxy_image_option(),
         galaxy_config_options(),
         daemon_option(),
+        pid_file_option(),
     )
 
 

tests/test_cmd_serve.py

@@ -32,6 +32,7 @@ def test_serve_daemon(self):
         user_gi = self._user_gi
         assert len(user_gi.histories.get_histories(name=TEST_HISTORY_NAME)) == 0
         user_gi.histories.create_history(TEST_HISTORY_NAME)
+        kill_pid_file(self._pid_file)
 
     @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
     def test_serve_workflow(self):
@@ -97,12 +98,12 @@ def _launch_thread_and_wait(self, func, args=[]):
         t = threading.Thread(target=target)
         t.daemon = True
         t.start()
-        time.sleep(10)
-        assert network_util.wait_net_service("127.0.0.1", port)
+        time.sleep(5)
+        assert network_util.wait_net_service("127.0.0.1", port, timeout=600)
         time.sleep(1)
-        assert network_util.wait_net_service("127.0.0.1", port)
+        assert network_util.wait_net_service("127.0.0.1", port, timeout=600)
         time.sleep(1)
-        assert network_util.wait_net_service("127.0.0.1", port)
+        assert network_util.wait_net_service("127.0.0.1", port, timeout=600)
 
     def _run(self, serve_args=[]):
         test_cmd = [

tests/test_galaxy_config.py

@@ -3,9 +3,14 @@
 import os
 
 from planemo.galaxy.config import galaxy_config
-from .test_utils import TempDirectoryContext, test_context
+from .test_utils import (
+    skip_if_environ,
+    TempDirectoryContext,
+    test_context,
+)
 
 
+@skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
 def test_defaults():
     """Test by default Galaxy files are stored in temp ``config_directory``."""
     with _test_galaxy_config() as config:
@@ -15,13 +20,15 @@ def test_defaults():
         _assert_property_is(config, "database_connection", conn)
 
 
+@skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
 def test_database_connection_override_path():
     """Test by default Galaxy files are stored in temp ``config_directory``."""
     conn = "postgresql://username:password@localhost/mydatabase"
     with _test_galaxy_config(database_connection=conn) as config:
         _assert_property_is(config, "database_connection", conn)
 
 
+@skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
 def test_override_files_path():
     """Test Galaxy file path overrideable with --file_path."""
     with TempDirectoryContext() as tdc: