Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/planemo/galaxy/serve.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 """Abstractions for serving out development Galaxy servers."""
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2 from __future__ import print_function
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3
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4 import contextlib
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5 import os
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6 import time
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7
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8 from planemo import (
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9 io,
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10 network_util
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11 )
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12 from .config import galaxy_config
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13 from .ephemeris_sleep import sleep
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14 from .run import (
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15 run_galaxy_command,
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16 )
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17
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18
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19 def serve(ctx, runnables=[], **kwds):
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20 """Serve a Galaxy instance with artifacts defined by paths."""
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21 try:
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22 return _serve(ctx, runnables, **kwds)
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23 except Exception as e:
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24 ctx.vlog("Problem serving Galaxy", exception=e)
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25 raise
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26
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27
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28 def _serve(ctx, runnables, **kwds):
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29 engine = kwds.get("engine", "galaxy")
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30 if engine == "docker_galaxy":
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31 kwds["dockerize"] = True
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32
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33 daemon = kwds.get("daemon", False)
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34 if daemon:
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35 kwds["no_cleanup"] = True
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36
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37 port = kwds.get("port", None)
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38 if port is None:
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39 port = network_util.get_free_port()
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40 kwds["port"] = port
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41
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42 with galaxy_config(ctx, runnables, **kwds) as config:
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43 cmd = config.startup_command(ctx, **kwds)
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44 action = "Starting Galaxy"
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45 exit_code = run_galaxy_command(
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46 ctx,
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47 cmd,
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48 config.env,
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49 action,
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50 )
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51 if exit_code:
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52 message = "Problem running Galaxy command [%s]." % config.log_contents
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53 io.warn(message)
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54 raise Exception(message)
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55 host = kwds.get("host", "127.0.0.1")
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56
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57 timeout = 500
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58 galaxy_url = "http://%s:%s" % (host, port)
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59 galaxy_alive = sleep(galaxy_url, verbose=ctx.verbose, timeout=timeout)
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60 if not galaxy_alive:
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61 raise Exception("Attempted to serve Galaxy at %s, but it failed to start in %d seconds." % (galaxy_url, timeout))
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62 config.install_workflows()
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63 if kwds.get("pid_file"):
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64 real_pid_file = config.pid_file
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65 if os.path.exists(config.pid_file):
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66 os.symlink(real_pid_file, kwds["pid_file"])
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67 else:
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68 io.warn("Can't find Galaxy pid file [%s] to link" % real_pid_file)
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69 return config
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70
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71
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72 @contextlib.contextmanager
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73 def shed_serve(ctx, install_args_list, **kwds):
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74 """Serve a daemon instance of Galaxy with specified repositories installed."""
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75 with serve_daemon(ctx, **kwds) as config:
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76 install_deps = not kwds.get("skip_dependencies", False)
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77 io.info("Installing repositories - this may take some time...")
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78 for install_args in install_args_list:
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79 install_args["install_tool_dependencies"] = install_deps
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80 install_args["install_repository_dependencies"] = True
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81 install_args["new_tool_panel_section_label"] = "Shed Installs"
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82 config.install_repo(
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83 **install_args
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84 )
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85 config.wait_for_all_installed()
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86 yield config
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87
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88
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89 @contextlib.contextmanager
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90 def serve_daemon(ctx, runnables=[], **kwds):
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91 """Serve a daemonized Galaxy instance with artifacts defined by paths."""
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92 config = None
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93 try:
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94 kwds["daemon"] = True
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95 config = serve(ctx, runnables, **kwds)
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96 yield config
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97 finally:
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98 if config:
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99 if ctx.verbose:
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100 print("Galaxy Log:")
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101 print(config.log_contents)
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102 config.kill()
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103 if not kwds.get("no_cleanup", False):
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104 config.cleanup()
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105
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106
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107 def sleep_for_serve():
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108 # This is bad, do something better...
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109 time.sleep(1000000)
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110
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111
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112 __all__ = (
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113 "serve",
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114 "serve_daemon",
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115 "shed_serve",
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116 )