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comparison env/lib/python3.7/site-packages/planemo/galaxy/profiles.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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-1:000000000000 0:26e78fe6e8c4
1 """This modules describes the abstraction of a Galaxy profile.
2
3 This is a workspace with a specific default configuration and shed
4 tool setup. It is meant to be used with various serve commands.
5 """
6 import json
7 import os
8 import shutil
9
10 from galaxy.tool_util.deps.commands import which
11
12 from planemo.config import (
13 OptionSource,
14 )
15 from planemo.database import create_database_source
16 from .config import DATABASE_LOCATION_TEMPLATE
17
18 PROFILE_OPTIONS_JSON_NAME = "planemo_profile_options.json"
19 ALREADY_EXISTS_EXCEPTION = "Cannot create profile with name [%s], directory [%s] already exists."
20
21
22 def profile_exists(ctx, profile_name, **kwds):
23 """Return a truthy value iff the specified profile already exists."""
24 profile_directory = _profile_directory(ctx, profile_name)
25 return os.path.exists(profile_directory)
26
27
28 def list_profiles(ctx, **kwds):
29 """Return a list of current profile names."""
30 return os.listdir(ctx.galaxy_profiles_directory)
31
32
33 def delete_profile(ctx, profile_name, **kwds):
34 """Delete profile with the specified name."""
35 profile_directory = _profile_directory(ctx, profile_name)
36 profile_options = _read_profile_options(profile_directory)
37 database_type = profile_options.get("database_type")
38 if database_type != "sqlite":
39 database_source = create_database_source(**kwds)
40 database_identifier = _profile_to_database_identifier(profile_name)
41 database_source.delete_database(
42 database_identifier,
43 )
44 shutil.rmtree(profile_directory)
45
46
47 def create_profile(ctx, profile_name, **kwds):
48 """Create a profile with the specified name."""
49 engine_type = kwds.get("engine", "galaxy")
50 profile_directory = _profile_directory(ctx, profile_name)
51 if profile_exists(ctx, profile_name, **kwds):
52 message = ALREADY_EXISTS_EXCEPTION % (
53 profile_name, profile_directory
54 )
55 raise Exception(message)
56
57 os.makedirs(profile_directory)
58 create_for_engine = _create_profile_docker if engine_type == "docker_galaxy" else _create_profile_local
59 stored_profile_options = create_for_engine(ctx, profile_directory, profile_name, kwds)
60
61 profile_options_path = _stored_profile_options_path(profile_directory)
62 with open(profile_options_path, "w") as f:
63 json.dump(stored_profile_options, f)
64
65
66 def _create_profile_docker(ctx, profile_directory, profile_name, kwds):
67 export_directory = os.path.join(profile_directory, "export")
68 os.makedirs(export_directory)
69 return {
70 "engine": "docker_galaxy",
71 }
72
73
74 def _create_profile_local(ctx, profile_directory, profile_name, kwds):
75 database_type = kwds.get("database_type", "auto")
76 if database_type == "auto":
77 if which("psql"):
78 database_type = "postgres"
79 elif which("docker"):
80 database_type = "postgres_docker"
81 else:
82 database_type = "sqlite"
83
84 if database_type != "sqlite":
85 database_source = create_database_source(**kwds)
86 database_identifier = _profile_to_database_identifier(profile_name)
87 database_source.create_database(
88 database_identifier,
89 )
90 database_connection = database_source.sqlalchemy_url(database_identifier)
91 else:
92 database_location = os.path.join(profile_directory, "galaxy.sqlite")
93 database_connection = DATABASE_LOCATION_TEMPLATE % database_location
94
95 return {
96 "database_type": database_type,
97 "database_connection": database_connection,
98 "engine": "galaxy",
99 }
100
101
102 def ensure_profile(ctx, profile_name, **kwds):
103 """Ensure a Galaxy profile exists and return profile defaults."""
104 if not profile_exists(ctx, profile_name, **kwds):
105 create_profile(ctx, profile_name, **kwds)
106
107 return _profile_options(ctx, profile_name, **kwds)
108
109
110 def _profile_options(ctx, profile_name, **kwds):
111 profile_directory = _profile_directory(ctx, profile_name)
112 profile_options = _read_profile_options(profile_directory)
113 specified_engine_type = kwds.get("engine", "galaxy")
114 profile_engine_type = profile_options["engine"]
115 if specified_engine_type != profile_engine_type:
116 if ctx.get_option_source("engine") == OptionSource.cli:
117 raise Exception("Configured profile engine type [%s] does not match specified engine type [%s].")
118
119 if profile_engine_type == "docker_galaxy":
120 engine_options = dict(
121 export_directory=os.path.join(profile_directory, "export")
122 )
123 else:
124 file_path = os.path.join(profile_directory, "files")
125 shed_tool_path = os.path.join(profile_directory, "shed_tools")
126 shed_tool_conf = os.path.join(profile_directory, "shed_tool_conf.xml")
127 tool_dependency_dir = os.path.join(profile_directory, "deps")
128
129 engine_options = dict(
130 file_path=file_path,
131 tool_dependency_dir=tool_dependency_dir,
132 shed_tool_conf=shed_tool_conf,
133 shed_tool_path=shed_tool_path,
134 galaxy_brand=profile_name,
135 )
136 profile_options.update(engine_options)
137 profile_options["galaxy_brand"] = profile_name
138 return profile_options
139
140
141 def _profile_to_database_identifier(profile_name):
142 char_lst = [c if c.isalnum() else "_" for c in profile_name]
143 return "plnmoprof_%s" % "".join(char_lst)
144
145
146 def _read_profile_options(profile_directory):
147 profile_options_path = _stored_profile_options_path(profile_directory)
148 with open(profile_options_path, "r") as f:
149 profile_options = json.load(f)
150 return profile_options
151
152
153 def _stored_profile_options_path(profile_directory):
154 profile_options_path = os.path.join(
155 profile_directory, PROFILE_OPTIONS_JSON_NAME
156 )
157 return profile_options_path
158
159
160 def _profile_directory(ctx, profile_name):
161 return os.path.join(ctx.galaxy_profiles_directory, profile_name)
162
163
164 __all__ = (
165 "create_profile",
166 "delete_profile",
167 "ensure_profile",
168 "list_profiles",
169 )