Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/planemo/database/postgres.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 local postgres databases."""
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2
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3 import subprocess
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4
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5 from galaxy.util import unicodify
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6
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7 from planemo.io import communicate
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8 from .interface import DatabaseSource
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9
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10
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11 class ExecutesPostgresSqlMixin:
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12
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13 def list_databases(self):
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14 """Use `psql --list` to generate a list of identifiers."""
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15 command_builder = self._psql_command_builder("--list")
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16 stdout = unicodify(self._communicate(command_builder))
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17 output_lines = stdout.splitlines()
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18 identifiers = []
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19 for line in output_lines:
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20 identifiers.append(line.split("|")[0].strip())
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21 return [i for i in identifiers if i]
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22
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23 def create_database(self, identifier):
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24 """Use `psql -c "create database"` to create a database."""
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25 sql = "create database %s;" % identifier
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26 self._run_sql_command(sql)
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27
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28 def delete_database(self, identifier):
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29 """Use `psql -c "drop database"` to delete a database."""
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30 sql = "drop database %s;" % identifier
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31 self._run_sql_command(sql)
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32
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33 def _run_sql_command(self, sql):
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34 # communicate is just joining commands so we need to modify the
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35 # sql as an argument - it shouldn't do this.
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36 sql_arg = '%s' % sql
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37 command_builder = self._psql_command_builder("--command", sql_arg)
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38 self._communicate(command_builder)
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39
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40 def _communicate(self, command_builder):
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41 stdout, _ = communicate(
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42 command_builder.command,
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43 stdout=subprocess.PIPE,
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44 stderr=subprocess.PIPE,
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45 )
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46 return stdout
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47
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48
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49 class LocalPostgresDatabaseSource(ExecutesPostgresSqlMixin, DatabaseSource):
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50 """Local postgres database source managed through psql application."""
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51
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52 def __init__(self, **kwds):
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53 """Construct a postgres database source from planemo configuration."""
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54 self.psql_path = kwds.get("postgres_psql_path", None) or 'psql'
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55 self.database_user = kwds.get("postgres_database_user", None)
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56 self.database_host = kwds.get("postgres_database_host", None)
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57 self.database_port = kwds.get("postgres_database_port", None)
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58 self._kwds = kwds
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59
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60 def sqlalchemy_url(self, identifier):
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61 """Return URL or form postgresql://username:password@localhost/mydatabase."""
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62 hostname = self.database_host or "localhost"
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63 if self.database_port:
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64 hostname += ":%s" % self.database_port
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65 return "postgresql://%s@%s/%s" % (
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66 self.database_user,
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67 hostname,
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68 identifier
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69 )
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70
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71 def _psql_command_builder(self, *args):
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72 command_builder = _CommandBuilder(self.psql_path)
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73 # Print only tuples so output is easier to parse
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74 command_builder.append_command("--tuples-only")
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75
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76 # Specify connection information
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77 if self.database_user:
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78 command_builder.append_command("--username", self.database_user)
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79 if self.database_host:
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80 command_builder.append_command("--host", self.database_host)
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81 if self.database_port:
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82 command_builder.append_command("--port", self.database_port)
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83 command_builder.append_command("-P", "pager=off")
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84 command_builder.extend_command(args)
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85 return command_builder
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86
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87
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88 class _CommandBuilder(object):
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89
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90 def __init__(self, *args):
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91 self.command = list(args)
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92
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93 def append_command(self, *args_or_none):
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94 args_or_none = args_or_none or []
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95 for arg_or_none in args_or_none:
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96 if arg_or_none is not None:
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97 self.command.append(arg_or_none)
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98
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99 def extend_command(self, args):
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100 for arg in (args or []):
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101 self.append_command(arg)
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102
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103
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104 __all__ = (
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105 "LocalPostgresDatabaseSource",
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106 )