Fix planemo test when TEMP env variable contain spaces

Reported by @pvanheus.

Author: nsoranzo

planemo/galaxy/config.py

@@ -17,6 +17,7 @@
     add_metaclass,
     iteritems
 )
+from six.moves import shlex_quote
 
 from planemo import git
 from planemo.config import OptionSource
@@ -198,8 +199,6 @@ class = StreamHandler
 
 DATABASE_LOCATION_TEMPLATE = "sqlite:///%s?isolation_level=IMMEDIATE"
 
-PIP_INSTALL_CMD = "pip install %s"
-
 COMMAND_STARTUP_COMMAND = "./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}"
 
 FAILED_TO_FIND_GALAXY_EXCEPTION = (
@@ -934,16 +933,15 @@ 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)
-        run_script = os.path.join(self.galaxy_root, "run.sh")
-        run_script += " $COMMON_STARTUP_ARGS"
+        run_script = "%s $COMMON_STARTUP_ARGS" % shlex_quote(os.path.join(self.galaxy_root, "run.sh"))
         if daemon:
             run_script += " --daemon"
             self.env["GALAXY_RUN_ALL"] = "1"
         else:
-            run_script += " --server-name '%s'" % self.server_name
+            run_script += " --server-name %s" % shlex_quote(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
+        cd_to_galaxy_command = ['cd', self.galaxy_root]
         return shell_join(
             cd_to_galaxy_command,
             setup_venv_command,
@@ -1238,14 +1236,14 @@ def _install_with_command(ctx, config_directory, command, env, kwds):
     # TODO: --watchdog
     pip_installs = []
     if pip_installs:
-        pip_install_command = PIP_INSTALL_CMD % " ".join(pip_installs)
+        pip_install_command = ['pip', 'install'] + pip_installs
     else:
         pip_install_command = ""
     setup_venv_command = setup_venv(ctx, kwds)
     install_cmd = shell_join(
-        "cd %s" % config_directory,
+        ['cd', config_directory],
         command,
-        "cd galaxy-dev",
+        ['cd', 'galaxy-dev'],
         setup_venv_command,
         pip_install_command,
         setup_common_startup_args(),

planemo/galaxy/run.py

@@ -3,23 +3,23 @@
 import string
 
 from galaxy.tools.deps.commands import shell
+from six.moves import shlex_quote
 
 from planemo.io import info, shell_join
 from planemo.virtualenv import create_command
 
 
 # Activate galaxy's virtualenv if present (needed for tests say but not for
 # server because run.sh does this).
-ACTIVATE_COMMAND = "[ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate"
+ACTIVATE_COMMAND = '[ -e "$GALAXY_VIRTUAL_ENV" ] && . "$GALAXY_VIRTUAL_ENV"/bin/activate'
 CREATE_COMMAND_TEMPLATE = string.Template(
-    'if [ ! -e $GALAXY_VIRTUAL_ENV ]; then $create_virtualenv; fi',
+    'if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then $create_virtualenv; fi',
 )
 PRINT_VENV_COMMAND = shell_join(
     'echo "Set \$GALAXY_VIRTUAL_ENV to $GALAXY_VIRTUAL_ENV"',
-    'if [ -e $GALAXY_VIRTUAL_ENV ]',
-    'then echo "Virtual environment directory exists."',
-    'else echo "Virtual environment directory does not exist."',
-    'fi',
+    ('if [ -e "$GALAXY_VIRTUAL_ENV" ]; ',
+     'then echo "Virtual environment directory exists."; ',
+     'else echo "Virtual environment directory does not exist."; fi'),
 )
 
 
@@ -28,9 +28,9 @@
     "wget https://codeload.github.com/galaxyproject/galaxy/tar.gz/"
 )
 
-CACHED_VIRTUAL_ENV_COMMAND = ("if [ -d .venv ] || [ -f dist-eggs.ini ];"
-                              " then GALAXY_VIRTUAL_ENV=.venv; "
-                              " else GALAXY_VIRTUAL_ENV=%s; fi")
+CACHED_VIRTUAL_ENV_COMMAND = ("if [ -d .venv ] || [ -f dist-eggs.ini ]; "
+                              "then GALAXY_VIRTUAL_ENV=.venv; "
+                              "else GALAXY_VIRTUAL_ENV=%s; fi")
 UNCACHED_VIRTUAL_ENV_COMMAND = "GALAXY_VIRTUAL_ENV=.venv"
 
 
@@ -57,7 +57,7 @@ def locate_galaxy_virtualenv(ctx, kwds):
         shared_venv_path = os.path.join(workspace, "gx_venv")
         if galaxy_branch != "master":
             shared_venv_path = "%s_%s" % (shared_venv_path, galaxy_branch)
-        venv_command = CACHED_VIRTUAL_ENV_COMMAND % shared_venv_path
+        venv_command = CACHED_VIRTUAL_ENV_COMMAND % shlex_quote(shared_venv_path)
     else:
         venv_command = UNCACHED_VIRTUAL_ENV_COMMAND
     return shell_join(

planemo/galaxy/test/actions.py

@@ -64,7 +64,7 @@ def run_in_config(ctx, config, run=run_galaxy_command, **kwds):
     config.env["GALAXY_TEST_VERBOSE_ERRORS"] = "true"
     config.env["GALAXY_TEST_SAVE"] = job_output_files
 
-    cd_to_galaxy_command = "cd %s" % config.galaxy_root
+    cd_to_galaxy_command = ['cd', config.galaxy_root]
     test_cmd = test_structures.GalaxyTestCommand(
         html_report_file,
         xunit_report_file,
@@ -74,9 +74,9 @@ def run_in_config(ctx, config, run=run_galaxy_command, **kwds):
     ).build()
     setup_common_startup_args = ""
     if kwds.get("skip_venv", False):
-        setup_common_startup_args = (
-            'COMMON_STARTUP_ARGS=--skip-venv; '
-            'export COMMON_STARTUP_ARGS; '
+        setup_common_startup_args = shell_join(
+            'COMMON_STARTUP_ARGS=--skip-venv'
+            'export COMMON_STARTUP_ARGS'
             'echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}"'
         )
     setup_venv_command = setup_venv(ctx, kwds)

planemo/galaxy/test/structures.py

@@ -6,14 +6,12 @@
 from collections import namedtuple
 from xml.etree import ElementTree as ET
 
+from six.moves import shlex_quote
+
 from planemo.io import error
 from planemo.test.results import StructuredData as BaseStructuredData
 
 
-RUN_TESTS_CMD = (
-    "sh run_tests.sh $COMMON_STARTUP_ARGS --report_file %s %s %s %s"
-)
-
 NO_STRUCTURED_FILE = (
     "Warning: Problem with target Galaxy, it did not "
     "produce a structured test results file [%s] - summary "
@@ -41,24 +39,20 @@ def __init__(
     def build(self):
         xunit_report_file = self.xunit_report_file
         sd_report_file = self.structured_report_file
-        html_report_file = self.html_report_file
+        cmd = "sh run_tests.sh $COMMON_STARTUP_ARGS --report_file %s" % shlex_quote(self.html_report_file)
         if xunit_report_file:
-            xunit_arg = "--xunit_report_file %s" % xunit_report_file
-        else:
-            xunit_arg = ""
+            cmd += " --xunit_report_file %s" % shlex_quote(xunit_report_file)
         if sd_report_file:
-            sd_arg = "--structured_data_report_file %s" % sd_report_file
-        else:
-            sd_arg = ""
+            cmd += " --structured_data_report_file %s" % shlex_quote(sd_report_file)
         if self.installed:
-            tests = "-installed"
+            cmd += ' -installed'
+        elif self.failed:
+            sd = StructuredData(sd_report_file)
+            tests = " ".join(sd.failed_ids)
+            cmd += " %s" % tests
         else:
-            tests = "functional.test_toolbox"
-            if self.failed:
-                sd = StructuredData(self.structured_report_file)
-                failed_ids = sd.failed_ids
-                tests = " ".join(failed_ids)
-        return RUN_TESTS_CMD % (html_report_file, xunit_arg, sd_arg, tests)
+            cmd += ' functional.test_toolbox'
+        return cmd
 
 
 class StructuredData(BaseStructuredData):

planemo/io.py

@@ -15,7 +15,10 @@
 import click
 from galaxy.tools.deps import commands
 from galaxy.tools.deps.commands import download_command
-from six import StringIO
+from six import (
+    string_types,
+    StringIO
+)
 
 from .exit_codes import (
     EXIT_CODE_NO_SUCH_TARGET,
@@ -26,11 +29,15 @@
 IS_OS_X = _platform == "darwin"
 
 
-def communicate(cmds, **kwds):
-    if isinstance(cmds, list):
-        cmd_string = commands.argv_to_str(cmds)
+def args_to_str(args):
+    if args is None or isinstance(args, string_types):
+        return args
     else:
-        cmd_string = cmds
+        return commands.argv_to_str(args)
+
+
+def communicate(cmds, **kwds):
+    cmd_string = args_to_str(cmds)
     info(cmd_string)
     p = commands.shell_process(cmds, **kwds)
     if kwds.get("stdout", None) is None and commands.redirecting_io(sys=sys):
@@ -46,10 +53,7 @@ def communicate(cmds, **kwds):
 
 
 def shell(cmds, **kwds):
-    if isinstance(cmds, list):
-        cmd_string = commands.argv_to_str(cmds)
-    else:
-        cmd_string = cmds
+    cmd_string = args_to_str(cmds)
     info(cmd_string)
     return commands.shell(cmds, **kwds)
 
@@ -81,7 +85,7 @@ def warn(message, *args):
 
 def shell_join(*args):
     """Join potentially empty commands together with ;."""
-    return "; ".join([c for c in args if c])
+    return "; ".join(args_to_str(_) for _ in args if _)
 
 
 def write_file(path, content, force=True):