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annotate env/lib/python3.7/site-packages/planemo/database/postgres_docker.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 """Module describes a :class:`DatabaseSource` for managed, dockerized postgres databases."""
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2 import time
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3
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4 from galaxy.tool_util.deps import (
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5 docker_util,
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6 dockerfiles,
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7 )
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8 from galaxy.tool_util.deps.commands import execute
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9 from galaxy.util import unicodify
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10
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11 from .interface import DatabaseSource
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12 from .postgres import _CommandBuilder, ExecutesPostgresSqlMixin
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13
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14 DEFAULT_CONTAINER_NAME = "planemopostgres"
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15 DEFAULT_POSTGRES_PASSWORD = "mysecretpassword"
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16 DEFAULT_POSTGRES_PORT_EXPOSE = 15432
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17
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18
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19 def docker_ps(args, **kwds):
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20 return docker_util.command_list("ps", args, **kwds)
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21
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22
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23 def docker_exec(name, commands=[], **kwds):
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24 return docker_util.command_list("exec", [name] + commands, **kwds)
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25
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26
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27 def is_running_container(name=DEFAULT_CONTAINER_NAME, **kwds):
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28 ps_command = docker_ps(["--format", "{{.Names}}"], **kwds)
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29 running_containers = unicodify(execute(ps_command))
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30 containers = running_containers.splitlines()
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31 return name in containers
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32
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33
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34 def start_postgres_docker(name=DEFAULT_CONTAINER_NAME, password=DEFAULT_POSTGRES_PASSWORD, port=DEFAULT_POSTGRES_PORT_EXPOSE, **kwds):
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35 run_command = docker_util.command_list(
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36 "run",
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37 ["-p", "%d:5432" % port, "--name", name, "-e", "POSTGRES_PASSWORD=%s" % password, "--rm", "-d", "postgres"],
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38 **kwds
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39 )
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40 execute(run_command)
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41
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42
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43 def stop_postgres_docker(name=DEFAULT_CONTAINER_NAME, **kwds):
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44 stop_command = docker_util.command_list(
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45 "stop",
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46 [name],
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47 **kwds
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48 )
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49 execute(stop_command)
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50
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51
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52 class DockerPostgresDatabaseSource(ExecutesPostgresSqlMixin, DatabaseSource):
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53 """Postgres database running inside a Docker container."""
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54
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55 def __init__(self, **kwds):
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56 """Construct a postgres database source from planemo configuration."""
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57 self.psql_path = 'psql'
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58 self.database_user = 'postgres'
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59 self.database_password = DEFAULT_POSTGRES_PASSWORD
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60 self.database_host = 'localhost' # TODO: Make docker host
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61 self.database_port = DEFAULT_POSTGRES_PORT_EXPOSE
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62 self._kwds = kwds
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63 self._docker_host_kwds = dockerfiles.docker_host_args(**kwds)
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64 if not is_running_container(**self._docker_host_kwds):
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65 start_postgres_docker(**self._docker_host_kwds)
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66 # Hack to give docker a bit of time to boot up and allow psql to start.
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67 time.sleep(30)
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68
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69 def sqlalchemy_url(self, identifier):
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70 """Return URL or form postgresql://username:password@localhost/mydatabase."""
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71 return "postgresql://%s:%s@%s:%d/%s" % (
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72 self.database_user,
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73 self.database_password,
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74 self.database_host,
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75 self.database_port,
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76 identifier
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77 )
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78
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79 def _psql_command_builder(self, *args):
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80 base_command = docker_exec(DEFAULT_CONTAINER_NAME, [self.psql_path], **self._docker_host_kwds)
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81 command_builder = _CommandBuilder(*base_command)
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82 # Print only tuples so output is easier to parse
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83 command_builder.append_command("--tuples-only")
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84 command_builder.append_command("--username", self.database_user)
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85 command_builder.append_command("-P", "pager=off")
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86 command_builder.extend_command(args)
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87 return command_builder
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88
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89
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90 __all__ = (
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91 'DockerPostgresDatabaseSource',
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92 )