Mercurial > repos > shellac > guppy_basecaller

comparison env/lib/python3.7/site-packages/planemo/galaxy/serve.py @ 5:9b1c78e6ba9c draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"
author shellac
date Mon, 01 Jun 2020 08:59:25 -0400
parents 79f47841a781
children
comparison
equal deleted inserted replaced
4:79f47841a781 5:9b1c78e6ba9c
1 """Abstractions for serving out development Galaxy servers."""
2 from __future__ import print_function
3
4 import contextlib
5 import os
6 import time
7
8 from planemo import (
9 io,
10 network_util
11 )
12 from .config import galaxy_config
13 from .ephemeris_sleep import sleep
14 from .run import (
15 run_galaxy_command,
16 )
17
18
19 def serve(ctx, runnables=[], **kwds):
20 """Serve a Galaxy instance with artifacts defined by paths."""
21 try:
22 return _serve(ctx, runnables, **kwds)
23 except Exception as e:
24 ctx.vlog("Problem serving Galaxy", exception=e)
25 raise
26
27
28 def _serve(ctx, runnables, **kwds):
29 engine = kwds.get("engine", "galaxy")
30 if engine == "docker_galaxy":
31 kwds["dockerize"] = True
32
33 daemon = kwds.get("daemon", False)
34 if daemon:
35 kwds["no_cleanup"] = True
36
37 port = kwds.get("port", None)
38 if port is None:
39 port = network_util.get_free_port()
40 kwds["port"] = port
41
42 with galaxy_config(ctx, runnables, **kwds) as config:
43 cmd = config.startup_command(ctx, **kwds)
44 action = "Starting Galaxy"
45 exit_code = run_galaxy_command(
46 ctx,
47 cmd,
48 config.env,
49 action,
50 )
51 if exit_code:
52 message = "Problem running Galaxy command [%s]." % config.log_contents
53 io.warn(message)
54 raise Exception(message)
55 host = kwds.get("host", "127.0.0.1")
56
57 timeout = 500
58 galaxy_url = "http://%s:%s" % (host, port)
59 galaxy_alive = sleep(galaxy_url, verbose=ctx.verbose, timeout=timeout)
60 if not galaxy_alive:
61 raise Exception("Attempted to serve Galaxy at %s, but it failed to start in %d seconds." % (galaxy_url, timeout))
62 config.install_workflows()
63 if kwds.get("pid_file"):
64 real_pid_file = config.pid_file
65 if os.path.exists(config.pid_file):
66 os.symlink(real_pid_file, kwds["pid_file"])
67 else:
68 io.warn("Can't find Galaxy pid file [%s] to link" % real_pid_file)
69 return config
70
71
72 @contextlib.contextmanager
73 def shed_serve(ctx, install_args_list, **kwds):
74 """Serve a daemon instance of Galaxy with specified repositories installed."""
75 with serve_daemon(ctx, **kwds) as config:
76 install_deps = not kwds.get("skip_dependencies", False)
77 io.info("Installing repositories - this may take some time...")
78 for install_args in install_args_list:
79 install_args["install_tool_dependencies"] = install_deps
80 install_args["install_repository_dependencies"] = True
81 install_args["new_tool_panel_section_label"] = "Shed Installs"
82 config.install_repo(
83 **install_args
84 )
85 config.wait_for_all_installed()
86 yield config
87
88
89 @contextlib.contextmanager
90 def serve_daemon(ctx, runnables=[], **kwds):
91 """Serve a daemonized Galaxy instance with artifacts defined by paths."""
92 config = None
93 try:
94 kwds["daemon"] = True
95 config = serve(ctx, runnables, **kwds)
96 yield config
97 finally:
98 if config:
99 if ctx.verbose:
100 print("Galaxy Log:")
101 print(config.log_contents)
102 config.kill()
103 if not kwds.get("no_cleanup", False):
104 config.cleanup()
105
106
107 def sleep_for_serve():
108 # This is bad, do something better...
109 time.sleep(1000000)
110
111
112 __all__ = (
113 "serve",
114 "serve_daemon",
115 "shed_serve",
116 )