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comparison planemo/lib/python3.7/site-packages/galaxy/tool_util/deps/dockerfiles.py @ 0:d30785e31577 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:18:57 -0400
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-1:000000000000 0:d30785e31577
1 import logging
2 import os
3
4 from galaxy.tool_util.deps import docker_util
5 from galaxy.tool_util.deps.container_classes import docker_cache_path
6 from galaxy.tool_util.deps.requirements import parse_requirements_from_xml
7 from galaxy.tool_util.loader_directory import load_tool_elements_from_path
8 from galaxy.util import commands
9
10 log = logging.getLogger(__name__)
11
12
13 def docker_host_args(**kwds):
14 return dict(
15 docker_cmd=kwds["docker_cmd"],
16 sudo=kwds["docker_sudo"],
17 sudo_cmd=kwds["docker_sudo_cmd"],
18 host=kwds["docker_host"]
19 )
20
21
22 def dockerfile_build(path, dockerfile=None, error=log.error, **kwds):
23 expected_container_names = set()
24 tool_directories = set()
25 for (tool_path, tool_xml) in load_tool_elements_from_path(path):
26 requirements, containers = parse_requirements_from_xml(tool_xml)
27 for container in containers:
28 if container.type == "docker":
29 expected_container_names.add(container.identifier)
30 tool_directories.add(os.path.dirname(tool_path))
31 break
32
33 if len(expected_container_names) == 0:
34 error("Could not find any docker identifiers to generate.")
35
36 if len(expected_container_names) > 1:
37 error("Multiple different docker identifiers found for selected tools [%s]", expected_container_names)
38
39 image_identifier = expected_container_names.pop()
40
41 dockerfile = __find_dockerfile(dockerfile, tool_directories)
42 if dockerfile is not None:
43 docker_command_parts = docker_util.build_command(
44 image_identifier,
45 dockerfile,
46 **docker_host_args(**kwds)
47 )
48 else:
49 docker_command_parts = docker_util.build_pull_command(image_identifier, **docker_host_args(**kwds))
50 commands.execute(docker_command_parts)
51
52 commands.execute(docker_command_parts)
53 docker_image_cache = kwds['docker_image_cache']
54 if docker_image_cache:
55 destination = docker_cache_path(docker_image_cache, image_identifier)
56 save_image_command_parts = docker_util.build_save_image_command(
57 image_identifier,
58 destination,
59 **docker_host_args(**kwds)
60 )
61 commands.execute(save_image_command_parts)
62
63
64 def __find_dockerfile(dockerfile, tool_directories):
65 if dockerfile is not None:
66 return dockerfile
67 search_directories = ["."]
68 if len(tool_directories) == 1:
69 tool_directory = tool_directories.pop()
70 search_directories.insert(0, tool_directory)
71 for directory in search_directories:
72 potential_dockerfile = os.path.join(directory, "Dockerfile")
73 if os.path.exists(potential_dockerfile):
74 return potential_dockerfile
75 return None