Mercurial > repos > shellac > guppy_basecaller
annotate env/lib/python3.7/site-packages/planemo/database/postgres.py @ 0:26e78fe6e8c4 draft
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author | shellac |
---|---|
date | Sat, 02 May 2020 07:14:21 -0400 |
parents | |
children |
rev | line source |
---|---|
0
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
1 """Module describes a :class:`DatabaseSource` for local postgres databases.""" |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
2 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
3 import subprocess |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
4 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
5 from galaxy.util import unicodify |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
6 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
7 from planemo.io import communicate |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
8 from .interface import DatabaseSource |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
9 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
10 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
11 class ExecutesPostgresSqlMixin: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
12 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
13 def list_databases(self): |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
14 """Use `psql --list` to generate a list of identifiers.""" |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
15 command_builder = self._psql_command_builder("--list") |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
16 stdout = unicodify(self._communicate(command_builder)) |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
17 output_lines = stdout.splitlines() |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
18 identifiers = [] |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
19 for line in output_lines: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
20 identifiers.append(line.split("|")[0].strip()) |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
21 return [i for i in identifiers if i] |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
22 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
23 def create_database(self, identifier): |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
24 """Use `psql -c "create database"` to create a database.""" |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
25 sql = "create database %s;" % identifier |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
26 self._run_sql_command(sql) |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
27 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
28 def delete_database(self, identifier): |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
29 """Use `psql -c "drop database"` to delete a database.""" |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
30 sql = "drop database %s;" % identifier |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
31 self._run_sql_command(sql) |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
32 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
33 def _run_sql_command(self, sql): |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
34 # communicate is just joining commands so we need to modify the |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
35 # sql as an argument - it shouldn't do this. |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
36 sql_arg = '%s' % sql |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
37 command_builder = self._psql_command_builder("--command", sql_arg) |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
38 self._communicate(command_builder) |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
39 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
40 def _communicate(self, command_builder): |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
41 stdout, _ = communicate( |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
42 command_builder.command, |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
43 stdout=subprocess.PIPE, |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
44 stderr=subprocess.PIPE, |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
45 ) |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
46 return stdout |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
47 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
48 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
49 class LocalPostgresDatabaseSource(ExecutesPostgresSqlMixin, DatabaseSource): |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
50 """Local postgres database source managed through psql application.""" |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
51 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
52 def __init__(self, **kwds): |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
53 """Construct a postgres database source from planemo configuration.""" |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
54 self.psql_path = kwds.get("postgres_psql_path", None) or 'psql' |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
55 self.database_user = kwds.get("postgres_database_user", None) |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
56 self.database_host = kwds.get("postgres_database_host", None) |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
57 self.database_port = kwds.get("postgres_database_port", None) |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
58 self._kwds = kwds |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
59 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
60 def sqlalchemy_url(self, identifier): |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
61 """Return URL or form postgresql://username:password@localhost/mydatabase.""" |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
62 hostname = self.database_host or "localhost" |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
63 if self.database_port: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
64 hostname += ":%s" % self.database_port |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
65 return "postgresql://%s@%s/%s" % ( |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
66 self.database_user, |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
67 hostname, |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
68 identifier |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
69 ) |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
70 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
71 def _psql_command_builder(self, *args): |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
72 command_builder = _CommandBuilder(self.psql_path) |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
73 # Print only tuples so output is easier to parse |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
74 command_builder.append_command("--tuples-only") |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
75 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
76 # Specify connection information |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
77 if self.database_user: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
78 command_builder.append_command("--username", self.database_user) |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
79 if self.database_host: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
80 command_builder.append_command("--host", self.database_host) |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
81 if self.database_port: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
82 command_builder.append_command("--port", self.database_port) |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
83 command_builder.append_command("-P", "pager=off") |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
84 command_builder.extend_command(args) |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
85 return command_builder |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
86 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
87 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
88 class _CommandBuilder(object): |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
89 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
90 def __init__(self, *args): |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
91 self.command = list(args) |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
92 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
93 def append_command(self, *args_or_none): |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
94 args_or_none = args_or_none or [] |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
95 for arg_or_none in args_or_none: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
96 if arg_or_none is not None: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
97 self.command.append(arg_or_none) |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
98 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
99 def extend_command(self, args): |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
100 for arg in (args or []): |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
101 self.append_command(arg) |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
102 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
103 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
104 __all__ = ( |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
105 "LocalPostgresDatabaseSource", |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
106 ) |