Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/planemo/galaxy/serve.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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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 INSTALLING_MESSAGE = "Installing repositories - this may take some time..." |
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18 |
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19 |
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20 def serve(ctx, runnables=None, **kwds): |
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21 if runnables is None: |
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22 runnables = [] |
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23 """Serve a Galaxy instance with artifacts defined by paths.""" |
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24 try: |
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25 return _serve(ctx, runnables, **kwds) |
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26 except Exception as e: |
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27 ctx.vlog("Problem serving Galaxy", exception=e) |
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28 raise |
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29 |
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30 |
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31 def _serve(ctx, runnables, **kwds): |
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32 engine = kwds.get("engine", "galaxy") |
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33 if engine == "docker_galaxy": |
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34 kwds["dockerize"] = True |
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35 |
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36 daemon = kwds.get("daemon", False) |
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37 if daemon: |
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38 kwds["no_cleanup"] = True |
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39 |
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40 port = kwds.get("port", None) |
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41 if port is None: |
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42 port = network_util.get_free_port() |
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43 kwds["port"] = port |
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44 |
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45 with galaxy_config(ctx, runnables, **kwds) as config: |
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46 cmd = config.startup_command(ctx, **kwds) |
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47 action = "Starting Galaxy" |
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48 exit_code = run_galaxy_command( |
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49 ctx, |
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50 cmd, |
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51 config.env, |
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52 action, |
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53 ) |
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54 if exit_code: |
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55 message = "Problem running Galaxy command [%s]." % config.log_contents |
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56 io.warn(message) |
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57 raise Exception(message) |
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58 host = kwds.get("host", "127.0.0.1") |
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59 |
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60 timeout = 500 |
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61 galaxy_url = "http://%s:%s" % (host, port) |
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62 galaxy_alive = sleep(galaxy_url, verbose=ctx.verbose, timeout=timeout) |
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63 if not galaxy_alive: |
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64 raise Exception("Attempted to serve Galaxy at %s, but it failed to start in %d seconds." % (galaxy_url, timeout)) |
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65 config.install_workflows() |
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66 if kwds.get("pid_file"): |
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67 real_pid_file = config.pid_file |
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68 if os.path.exists(config.pid_file): |
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69 os.symlink(real_pid_file, kwds["pid_file"]) |
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70 else: |
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71 io.warn("Can't find Galaxy pid file [%s] to link" % real_pid_file) |
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72 return config |
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73 |
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74 |
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75 @contextlib.contextmanager |
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76 def shed_serve(ctx, install_args_list, **kwds): |
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77 """Serve a daemon instance of Galaxy with specified repositories installed.""" |
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78 with serve_daemon(ctx, **kwds) as config: |
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79 install_deps = not kwds.get("skip_dependencies", False) |
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80 print(INSTALLING_MESSAGE) |
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81 io.info(INSTALLING_MESSAGE) |
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82 for install_args in install_args_list: |
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83 install_args["install_tool_dependencies"] = install_deps |
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84 install_args["install_repository_dependencies"] = True |
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85 install_args["new_tool_panel_section_label"] = "Shed Installs" |
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86 config.install_repo( |
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87 **install_args |
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88 ) |
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89 try: |
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90 config.wait_for_all_installed() |
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91 except Exception: |
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92 if ctx.verbose: |
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93 print("Failed to install tool repositories, Galaxy log:") |
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94 print(config.log_contents) |
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95 print("Galaxy root:") |
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96 io.shell(['ls', config.galaxy_root]) |
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97 raise |
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98 yield config |
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99 |
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100 |
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101 @contextlib.contextmanager |
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102 def serve_daemon(ctx, runnables=None, **kwds): |
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103 """Serve a daemonized Galaxy instance with artifacts defined by paths.""" |
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104 if runnables is None: |
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105 runnables = [] |
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106 config = None |
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107 try: |
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108 kwds["daemon"] = True |
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109 config = serve(ctx, runnables, **kwds) |
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110 yield config |
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111 finally: |
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112 if config: |
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113 if ctx.verbose: |
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114 print("Galaxy Log:") |
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115 print(config.log_contents) |
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116 config.kill() |
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117 if not kwds.get("no_cleanup", False): |
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118 config.cleanup() |
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119 |
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120 |
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121 def sleep_for_serve(): |
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122 # This is bad, do something better... |
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123 time.sleep(1000000) |
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124 |
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125 |
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126 __all__ = ( |
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127 "serve", |
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128 "serve_daemon", |
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129 "shed_serve", |
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130 ) |