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comparison env/lib/python3.7/site-packages/planemo/galaxy/run.py @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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-1:000000000000 0:26e78fe6e8c4
1 """Utilities for calling Galaxy scripts."""
2 import os
3 import string
4
5 from galaxy.tool_util.deps.commands import shell
6 from six.moves import shlex_quote
7
8 from planemo.io import info, shell_join
9 from planemo.virtualenv import (
10 create_command,
11 DEFAULT_PYTHON_VERSION,
12 )
13
14
15 # Activate galaxy's virtualenv if present (needed for tests say but not for
16 # server because run.sh does this).
17 ACTIVATE_COMMAND = 'if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; fi'
18 CREATE_COMMAND_TEMPLATE = string.Template(
19 'if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then $create_virtualenv; fi',
20 )
21 PRINT_VENV_COMMAND = shell_join(
22 r'echo "Set \$GALAXY_VIRTUAL_ENV to $GALAXY_VIRTUAL_ENV"',
23 ('if [ -e "$GALAXY_VIRTUAL_ENV" ]; '
24 'then echo "Virtual environment directory exists."; '
25 'else echo "Virtual environment directory does not exist."; fi'),
26 )
27
28
29 CACHED_VIRTUAL_ENV_COMMAND = ("if [ -d .venv ] || [ -f dist-eggs.ini ]; "
30 "then GALAXY_VIRTUAL_ENV=.venv; "
31 "else GALAXY_VIRTUAL_ENV=%s; fi")
32 UNCACHED_VIRTUAL_ENV_COMMAND = "GALAXY_VIRTUAL_ENV=.venv"
33
34
35 def setup_venv(ctx, kwds):
36 if kwds.get("skip_venv", False):
37 return ""
38
39 create_template_params = {
40 'create_virtualenv': create_command("$GALAXY_VIRTUAL_ENV", kwds.get('galaxy_python_version'))
41 }
42 return shell_join(
43 locate_galaxy_virtualenv(ctx, kwds),
44 PRINT_VENV_COMMAND if ctx.verbose else None,
45 CREATE_COMMAND_TEMPLATE.safe_substitute(create_template_params),
46 PRINT_VENV_COMMAND if ctx.verbose else None,
47 ACTIVATE_COMMAND,
48 )
49
50
51 def locate_galaxy_virtualenv(ctx, kwds):
52 if os.environ.get("GALAXY_VIRTUAL_ENV"):
53 venv_command = ""
54 elif not kwds.get("no_cache_galaxy", False):
55 workspace = ctx.workspace
56 galaxy_branch = kwds.get("galaxy_branch") or "master"
57 shared_venv_path = os.path.join(workspace, "gx_venv")
58 galaxy_python_version = kwds.get('galaxy_python_version') or DEFAULT_PYTHON_VERSION
59 if galaxy_python_version != DEFAULT_PYTHON_VERSION:
60 shared_venv_path = "%s_%s" % (shared_venv_path, galaxy_python_version)
61 if galaxy_branch != "master":
62 shared_venv_path = "%s_%s" % (shared_venv_path, galaxy_branch)
63 venv_command = CACHED_VIRTUAL_ENV_COMMAND % shlex_quote(shared_venv_path)
64 else:
65 venv_command = UNCACHED_VIRTUAL_ENV_COMMAND
66 return shell_join(
67 venv_command,
68 "export GALAXY_VIRTUAL_ENV",
69 )
70
71
72 def shell_if_wheels(command):
73 """ Take a shell command and convert it to shell command that runs
74 only if Galaxy is new enough to use wheels.
75 """
76 return "$(grep -q 'skip-venv' run_tests.sh) && %s" % command
77
78
79 def setup_common_startup_args():
80 return _set_variable_if_wheels(
81 "COMMON_STARTUP_ARGS", "--dev-wheels"
82 )
83
84
85 def _set_variable_if_wheels(var, if_wheels_val, else_val=""):
86 var_command = '${var}=${else_val}; '
87 var_command += shell_if_wheels(
88 '${var}="${if_wheels_val}"; '
89 )
90 var_command += "export ${var}"
91 var_command += '; echo "Set ${var} to ${${var}}"'
92 return string.Template(var_command).safe_substitute(
93 var=var,
94 if_wheels_val=if_wheels_val,
95 else_val=else_val,
96 )
97
98
99 def run_galaxy_command(ctx, command, env, action):
100 """Run Galaxy command with informative verbose logging."""
101 message = "%s with command [%s]" % (action, command)
102 info(message)
103 ctx.vlog("With environment variables:")
104 ctx.vlog("============================")
105 for key, value in env.items():
106 ctx.vlog('%s="%s"' % (key, value))
107 ctx.vlog("============================")
108 exit_code = shell(command, env=env)
109 ctx.vlog("run command exited with return code %s" % exit_code)
110 return exit_code
111
112
113 __all__ = (
114 "setup_venv",
115 "run_galaxy_command",
116 "setup_common_startup_args",
117 )