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