Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/tool_util/deps/container_resolvers/mulled.py @ 0:4f3585e2f14b draft default tip
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author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 """This module describes the :class:`MulledContainerResolver` ContainerResolver plugin.""" |
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2 |
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3 import logging |
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4 import os |
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5 import subprocess |
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6 from typing import NamedTuple, Optional |
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7 |
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8 from galaxy.util import ( |
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9 safe_makedirs, |
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10 string_as_bool, |
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11 unicodify, |
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12 which, |
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13 ) |
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14 from galaxy.util.commands import shell |
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15 from ..container_classes import CONTAINER_CLASSES |
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16 from ..container_resolvers import ( |
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17 ContainerResolver, |
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18 ) |
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19 from ..docker_util import build_docker_images_command |
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20 from ..mulled.mulled_build import ( |
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21 DEFAULT_CHANNELS, |
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22 ensure_installed, |
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23 InvolucroContext, |
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24 mull_targets, |
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25 ) |
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26 from ..mulled.mulled_build_tool import requirements_to_mulled_targets |
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27 from ..mulled.util import ( |
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28 mulled_tags_for, |
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29 split_tag, |
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30 v1_image_name, |
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31 v2_image_name, |
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32 version_sorted, |
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33 ) |
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34 from ..requirements import ( |
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35 ContainerDescription, |
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36 DEFAULT_CONTAINER_SHELL, |
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37 ) |
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38 |
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39 log = logging.getLogger(__name__) |
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40 |
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41 |
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42 class CachedMulledImageSingleTarget(NamedTuple): |
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43 package_name: str |
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44 version: str |
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45 build: str |
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46 image_identifier: str |
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47 |
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48 multi_target: bool = False |
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49 |
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50 |
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51 class CachedV1MulledImageMultiTarget(NamedTuple): |
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52 hash: str |
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53 build: str |
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54 image_identifier: str |
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55 |
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56 multi_target: str = "v1" |
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57 |
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58 |
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59 class CachedV2MulledImageMultiTarget(NamedTuple): |
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60 image_name: str |
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61 version_hash: str |
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62 build: str |
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63 image_identifier: str |
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64 |
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65 multi_target: str = "v2" |
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66 |
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67 @property |
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68 def package_hash(target): |
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69 # Make this work for Singularity file name or fully qualified Docker repository |
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70 # image names. |
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71 image_name = target.image_name |
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72 if "/" not in image_name: |
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73 return image_name |
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74 else: |
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75 return image_name.rsplit("/")[-1] |
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76 |
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77 |
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78 def list_docker_cached_mulled_images(namespace=None, hash_func="v2", resolution_cache=None): |
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79 cache_key = "galaxy.tool_util.deps.container_resolvers.mulled:cached_images" |
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80 if resolution_cache is not None and cache_key in resolution_cache: |
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81 images_and_versions = resolution_cache.get(cache_key) |
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82 else: |
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83 command = build_docker_images_command(truncate=True, sudo=False, to_str=False) |
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84 try: |
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85 images_and_versions = unicodify(subprocess.check_output(command)).strip().splitlines() |
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86 except subprocess.CalledProcessError: |
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87 log.info("Call to `docker images` failed, configured container resolution may be broken") |
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88 return [] |
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89 images_and_versions = [":".join(l.split()[0:2]) for l in images_and_versions[1:]] |
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90 if resolution_cache is not None: |
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91 resolution_cache[cache_key] = images_and_versions |
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92 |
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93 def output_line_to_image(line): |
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94 image = identifier_to_cached_target(line, hash_func, namespace=namespace) |
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95 return image |
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96 |
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97 name_filter = get_filter(namespace) |
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98 sorted_images = version_sorted([_ for _ in filter(name_filter, images_and_versions)]) |
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99 raw_images = (output_line_to_image(_) for _ in sorted_images) |
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100 return [i for i in raw_images if i is not None] |
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101 |
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102 |
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103 def identifier_to_cached_target(identifier, hash_func, namespace=None): |
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104 if ":" in identifier: |
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105 image_name, version = identifier.rsplit(":", 1) |
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106 else: |
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107 image_name = identifier |
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108 version = None |
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109 |
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110 if not version or version == "latest": |
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111 version = None |
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112 |
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113 image = None |
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114 prefix = "" |
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115 if namespace is not None: |
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116 prefix = "quay.io/%s/" % namespace |
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117 if image_name.startswith(prefix + "mulled-v1-"): |
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118 if hash_func == "v2": |
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119 return None |
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120 |
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121 hash = image_name |
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122 build = None |
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123 if version and version.isdigit(): |
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124 build = version |
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125 image = CachedV1MulledImageMultiTarget(hash, build, identifier) |
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126 elif image_name.startswith(prefix + "mulled-v2-"): |
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127 if hash_func == "v1": |
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128 return None |
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129 |
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130 version_hash = None |
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131 build = None |
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132 |
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133 if version and "-" in version: |
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134 version_hash, build = version.rsplit("-", 1) |
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135 elif version.isdigit(): |
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136 version_hash, build = None, version |
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137 elif version: |
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138 log.debug("Unparsable mulled image tag encountered [%s]" % version) |
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139 |
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140 image = CachedV2MulledImageMultiTarget(image_name, version_hash, build, identifier) |
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141 else: |
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142 build = None |
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143 if version and "--" in version: |
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144 version, build = split_tag(version) |
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145 if prefix and image_name.startswith(prefix): |
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146 image_name = image_name[len(prefix):] |
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147 image = CachedMulledImageSingleTarget(image_name, version, build, identifier) |
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148 return image |
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149 |
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150 |
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151 def list_cached_mulled_images_from_path(directory, hash_func="v2"): |
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152 contents = os.listdir(directory) |
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153 sorted_images = version_sorted(contents) |
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154 raw_images = map(lambda name: identifier_to_cached_target(name, hash_func), sorted_images) |
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155 return [i for i in raw_images if i is not None] |
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156 |
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157 |
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158 def get_filter(namespace): |
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159 prefix = "quay.io/" if namespace is None else "quay.io/%s" % namespace |
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160 return lambda name: name.startswith(prefix) and name.count("/") == 2 |
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161 |
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162 |
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163 def find_best_matching_cached_image(targets, cached_images, hash_func): |
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164 if len(targets) == 0: |
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165 return None |
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166 |
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167 image = None |
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168 if len(targets) == 1: |
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169 target = targets[0] |
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170 for cached_image in cached_images: |
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171 if cached_image.multi_target: |
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172 continue |
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173 if not cached_image.package_name == target.package_name: |
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174 continue |
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175 if not target.version or target.version == cached_image.version: |
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176 image = cached_image |
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177 break |
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178 elif hash_func == "v2": |
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179 name = v2_image_name(targets) |
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180 if ":" in name: |
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181 package_hash, version_hash = name.split(":", 2) |
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182 else: |
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183 package_hash, version_hash = name, None |
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184 |
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185 for cached_image in cached_images: |
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186 if cached_image.multi_target != "v2": |
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187 continue |
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188 |
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189 if version_hash is None: |
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190 # Just match on package hash... |
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191 if package_hash == cached_image.package_hash: |
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192 image = cached_image |
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193 break |
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194 else: |
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195 # Match on package and version hash... |
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196 if package_hash == cached_image.package_hash and version_hash == cached_image.version_hash: |
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197 image = cached_image |
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198 break |
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199 |
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200 elif hash_func == "v1": |
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201 name = v1_image_name(targets) |
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202 for cached_image in cached_images: |
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203 if cached_image.multi_target != "v1": |
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204 continue |
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205 |
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206 if name == cached_image.hash: |
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207 image = cached_image |
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208 break |
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209 return image |
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210 |
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211 |
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212 def docker_cached_container_description(targets, namespace, hash_func="v2", shell=DEFAULT_CONTAINER_SHELL, resolution_cache=None): |
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213 if len(targets) == 0: |
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214 return None |
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215 |
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216 cached_images = list_docker_cached_mulled_images(namespace, hash_func=hash_func, resolution_cache=resolution_cache) |
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217 image = find_best_matching_cached_image(targets, cached_images, hash_func) |
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218 |
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219 container = None |
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220 if image: |
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221 container = ContainerDescription( |
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222 image.image_identifier, |
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223 type="docker", |
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224 shell=shell, |
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225 ) |
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226 |
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227 return container |
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228 |
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229 |
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230 def singularity_cached_container_description(targets, cache_directory, hash_func="v2", shell=DEFAULT_CONTAINER_SHELL): |
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231 if len(targets) == 0: |
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232 return None |
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233 |
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234 if not os.path.exists(cache_directory): |
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235 return None |
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236 |
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237 cached_images = list_cached_mulled_images_from_path(cache_directory, hash_func=hash_func) |
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238 image = find_best_matching_cached_image(targets, cached_images, hash_func) |
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239 |
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240 container = None |
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241 if image: |
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242 container = ContainerDescription( |
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243 os.path.abspath(os.path.join(cache_directory, image.image_identifier)), |
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244 type="singularity", |
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245 shell=shell, |
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246 ) |
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247 |
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248 return container |
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249 |
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250 |
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251 def targets_to_mulled_name(targets, hash_func, namespace, resolution_cache=None, session=None): |
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252 unresolved_cache_key = "galaxy.tool_util.deps.container_resolvers.mulled:unresolved" |
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253 if resolution_cache is not None: |
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254 if unresolved_cache_key not in resolution_cache: |
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255 resolution_cache[unresolved_cache_key] = set() |
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256 unresolved_cache = resolution_cache.get(unresolved_cache_key) |
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257 else: |
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258 unresolved_cache = set() |
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259 |
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260 mulled_resolution_cache = None |
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261 if resolution_cache and hasattr(resolution_cache, 'mulled_resolution_cache'): |
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262 mulled_resolution_cache = resolution_cache.mulled_resolution_cache |
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263 |
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264 name = None |
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265 |
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266 def cached_name(cache_key): |
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267 if mulled_resolution_cache: |
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268 if cache_key in mulled_resolution_cache: |
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269 return resolution_cache.get(cache_key) |
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270 return None |
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271 |
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272 if len(targets) == 1: |
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273 target = targets[0] |
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274 target_version = target.version |
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275 cache_key = f"ns[{namespace}]__single__{target.package_name}__@__{target_version}" |
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276 if cache_key in unresolved_cache: |
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277 return None |
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278 name = cached_name(cache_key) |
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279 if name: |
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280 return name |
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281 |
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282 tags = mulled_tags_for(namespace, target.package_name, resolution_cache=resolution_cache, session=session) |
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283 |
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284 if tags: |
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285 for tag in tags: |
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286 if '--' in tag: |
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287 version, _ = split_tag(tag) |
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288 else: |
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289 version = tag |
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290 if target_version and version == target_version: |
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291 name = f"{target.package_name}:{tag}" |
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292 break |
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293 |
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294 else: |
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295 def first_tag_if_available(image_name): |
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296 if ":" in image_name: |
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297 repo_name, tag_prefix = image_name.split(":", 2) |
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298 else: |
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299 repo_name = image_name |
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300 tag_prefix = None |
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301 tags = mulled_tags_for(namespace, repo_name, tag_prefix=tag_prefix, resolution_cache=resolution_cache, session=session) |
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302 return tags[0] if tags else None |
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303 |
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304 if hash_func == "v2": |
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305 base_image_name = v2_image_name(targets) |
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306 elif hash_func == "v1": |
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307 base_image_name = v1_image_name(targets) |
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308 else: |
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309 raise Exception("Unimplemented mulled hash_func [%s]" % hash_func) |
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310 |
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311 cache_key = f"ns[{namespace}]__{hash_func}__{base_image_name}" |
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312 if cache_key in unresolved_cache: |
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313 return None |
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314 name = cached_name(cache_key) |
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315 if name: |
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316 return name |
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317 |
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318 tag = first_tag_if_available(base_image_name) |
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319 if tag: |
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320 if ":" in base_image_name: |
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321 assert hash_func != "v1" |
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322 # base_image_name of form <package_hash>:<version_hash>, expand tag |
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323 # to include build number in tag. |
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324 name = "{}:{}".format(base_image_name.split(":")[0], tag) |
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325 else: |
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326 # base_image_name of form <package_hash>, simply add build number |
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327 # as tag to fully qualify image. |
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328 name = f"{base_image_name}:{tag}" |
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329 |
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330 if name and mulled_resolution_cache: |
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331 mulled_resolution_cache.put(cache_key, name) |
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332 |
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333 if name is None: |
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334 unresolved_cache.add(name) |
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335 |
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336 return name |
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337 |
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338 |
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339 class CliContainerResolver(ContainerResolver): |
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340 |
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341 container_type = 'docker' |
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342 cli = 'docker' |
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343 |
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344 def __init__(self, *args, **kwargs): |
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345 self._cli_available = bool(which(self.cli)) |
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346 super().__init__(*args, **kwargs) |
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347 |
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348 @property |
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349 def cli_available(self): |
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350 return self._cli_available |
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351 |
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352 @cli_available.setter |
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353 def cli_available(self, value): |
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354 if not value: |
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355 log.info('{} CLI not available, cannot list or pull images in Galaxy process. Does not impact kubernetes.'.format(self.cli)) |
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356 self._cli_available = value |
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357 |
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358 |
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359 class SingularityCliContainerResolver(CliContainerResolver): |
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360 |
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361 container_type = 'singularity' |
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362 cli = 'singularity' |
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363 |
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364 def __init__(self, *args, **kwargs): |
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365 super().__init__(*args, **kwargs) |
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366 self.cache_directory = kwargs.get("cache_directory", os.path.join(kwargs['app_info'].container_image_cache_path, "singularity", "mulled")) |
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367 safe_makedirs(self.cache_directory) |
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368 |
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369 |
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370 class CachedMulledDockerContainerResolver(CliContainerResolver): |
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371 |
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372 resolver_type = "cached_mulled" |
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373 shell = '/bin/bash' |
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374 |
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375 def __init__(self, app_info=None, namespace="biocontainers", hash_func="v2", **kwds): |
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376 super().__init__(app_info=app_info, **kwds) |
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377 self.namespace = namespace |
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378 self.hash_func = hash_func |
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379 |
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380 def resolve(self, enabled_container_types, tool_info, **kwds): |
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381 if not self.cli_available or tool_info.requires_galaxy_python_environment or self.container_type not in enabled_container_types: |
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382 return None |
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383 |
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384 targets = mulled_targets(tool_info) |
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385 resolution_cache = kwds.get("resolution_cache") |
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386 return docker_cached_container_description(targets, self.namespace, hash_func=self.hash_func, shell=self.shell, resolution_cache=resolution_cache) |
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387 |
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388 def __str__(self): |
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389 return "CachedMulledDockerContainerResolver[namespace=%s]" % self.namespace |
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390 |
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391 |
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392 class CachedMulledSingularityContainerResolver(SingularityCliContainerResolver): |
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393 |
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394 resolver_type = "cached_mulled_singularity" |
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395 shell = '/bin/bash' |
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396 |
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397 def __init__(self, app_info=None, hash_func="v2", **kwds): |
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398 super().__init__(app_info=app_info, **kwds) |
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399 self.hash_func = hash_func |
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400 |
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401 def resolve(self, enabled_container_types, tool_info, **kwds): |
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402 if tool_info.requires_galaxy_python_environment or self.container_type not in enabled_container_types: |
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403 return None |
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404 |
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405 targets = mulled_targets(tool_info) |
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406 return singularity_cached_container_description(targets, self.cache_directory, hash_func=self.hash_func, shell=self.shell) |
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407 |
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408 def __str__(self): |
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409 return "CachedMulledSingularityContainerResolver[cache_directory=%s]" % self.cache_directory |
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410 |
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411 |
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412 class MulledDockerContainerResolver(CliContainerResolver): |
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413 """Look for mulled images matching tool dependencies.""" |
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414 |
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415 resolver_type = "mulled" |
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416 shell = '/bin/bash' |
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417 protocol: Optional[str] = None |
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418 |
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419 def __init__(self, app_info=None, namespace="biocontainers", hash_func="v2", auto_install=True, **kwds): |
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420 super().__init__(app_info=app_info, **kwds) |
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421 self.namespace = namespace |
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422 self.hash_func = hash_func |
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423 self.auto_install = string_as_bool(auto_install) |
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424 |
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425 def cached_container_description(self, targets, namespace, hash_func, resolution_cache): |
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426 try: |
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427 return docker_cached_container_description(targets, namespace, hash_func, resolution_cache) |
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428 except subprocess.CalledProcessError: |
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429 # We should only get here if a docker binary is available, but command quits with a non-zero exit code, |
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430 # e.g if the docker daemon is not available |
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431 log.exception('An error occured while listing cached docker image. Docker daemon may need to be restarted.') |
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432 return None |
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433 |
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434 def pull(self, container): |
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435 if self.cli_available: |
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436 command = container.build_pull_command() |
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437 shell(command) |
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438 |
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439 @property |
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440 def can_list_containers(self): |
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441 return self.cli_available |
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442 |
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443 def resolve(self, enabled_container_types, tool_info, install=False, session=None, **kwds): |
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444 resolution_cache = kwds.get("resolution_cache") |
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445 if tool_info.requires_galaxy_python_environment or self.container_type not in enabled_container_types: |
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446 return None |
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447 |
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448 targets = mulled_targets(tool_info) |
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449 if len(targets) == 0: |
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450 return None |
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451 |
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452 name = targets_to_mulled_name(targets=targets, hash_func=self.hash_func, namespace=self.namespace, resolution_cache=resolution_cache, session=session) |
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453 if name: |
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454 container_id = f"quay.io/{self.namespace}/{name}" |
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455 if self.protocol: |
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456 container_id = f"{self.protocol}{container_id}" |
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457 container_description = ContainerDescription( |
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458 container_id, |
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459 type=self.container_type, |
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460 shell=self.shell, |
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461 ) |
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462 if self.can_list_containers: |
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463 if install and not self.cached_container_description( |
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464 targets, |
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465 namespace=self.namespace, |
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466 hash_func=self.hash_func, |
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467 resolution_cache=resolution_cache, |
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468 ): |
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469 destination_info = {} |
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470 destination_for_container_type = kwds.get('destination_for_container_type') |
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471 if destination_for_container_type: |
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472 destination_info = destination_for_container_type(self.container_type) |
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473 container = CONTAINER_CLASSES[self.container_type](container_description.identifier, |
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474 self.app_info, |
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475 tool_info, |
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476 destination_info, |
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477 {}, |
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478 container_description) |
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479 self.pull(container) |
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480 if not self.auto_install: |
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481 container_description = self.cached_container_description( |
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482 targets, |
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483 namespace=self.namespace, |
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484 hash_func=self.hash_func, |
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485 resolution_cache=resolution_cache, |
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486 ) or container_description |
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487 return container_description |
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488 |
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489 def __str__(self): |
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490 return "MulledDockerContainerResolver[namespace=%s]" % self.namespace |
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491 |
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492 |
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493 class MulledSingularityContainerResolver(SingularityCliContainerResolver, MulledDockerContainerResolver): |
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494 |
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495 resolver_type = "mulled_singularity" |
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496 protocol = 'docker://' |
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497 |
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498 def __init__(self, app_info=None, namespace="biocontainers", hash_func="v2", auto_install=True, **kwds): |
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499 super().__init__(app_info=app_info, **kwds) |
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500 self.namespace = namespace |
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501 self.hash_func = hash_func |
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502 self.auto_install = string_as_bool(auto_install) |
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503 |
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504 def cached_container_description(self, targets, namespace, hash_func, resolution_cache): |
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505 return singularity_cached_container_description(targets, |
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506 cache_directory=self.cache_directory, |
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507 hash_func=hash_func) |
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508 |
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509 @property |
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510 def can_list_containers(self): |
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511 # Only needs access to path, doesn't require CLI |
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512 return True |
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513 |
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514 def pull(self, container): |
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515 if self.cli_available: |
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516 cmds = container.build_mulled_singularity_pull_command(cache_directory=self.cache_directory, namespace=self.namespace) |
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517 shell(cmds=cmds) |
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518 |
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519 def __str__(self): |
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520 return "MulledSingularityContainerResolver[namespace=%s]" % self.namespace |
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521 |
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522 |
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523 class BuildMulledDockerContainerResolver(CliContainerResolver): |
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524 """Build for Docker mulled images matching tool dependencies.""" |
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525 |
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526 resolver_type = "build_mulled" |
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527 shell = '/bin/bash' |
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528 builds_on_resolution = True |
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529 |
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530 def __init__(self, app_info=None, namespace="local", hash_func="v2", auto_install=True, **kwds): |
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531 super().__init__(app_info=app_info, **kwds) |
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532 self._involucro_context_kwds = { |
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533 'involucro_bin': self._get_config_option("involucro_path", None) |
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534 } |
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535 self.namespace = namespace |
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536 self.hash_func = hash_func |
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537 self.auto_install = string_as_bool(auto_install) |
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538 self._mulled_kwds = { |
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539 'namespace': namespace, |
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540 'channels': self._get_config_option("mulled_channels", DEFAULT_CHANNELS), |
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541 'hash_func': self.hash_func, |
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542 'command': 'build-and-test', |
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543 } |
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544 self.auto_init = self._get_config_option("involucro_auto_init", True) |
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545 |
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546 def resolve(self, enabled_container_types, tool_info, install=False, **kwds): |
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547 if tool_info.requires_galaxy_python_environment or self.container_type not in enabled_container_types: |
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548 return None |
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549 |
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550 targets = mulled_targets(tool_info) |
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551 if len(targets) == 0: |
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552 return None |
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553 if self.auto_install or install: |
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554 mull_targets( |
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555 targets, |
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556 involucro_context=self._get_involucro_context(), |
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557 **self._mulled_kwds |
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558 ) |
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559 return docker_cached_container_description(targets, self.namespace, hash_func=self.hash_func, shell=self.shell) |
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560 |
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561 def _get_involucro_context(self): |
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562 involucro_context = InvolucroContext(**self._involucro_context_kwds) |
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563 self.enabled = ensure_installed(involucro_context, self.auto_init) |
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564 return involucro_context |
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565 |
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566 def __str__(self): |
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567 return "BuildDockerContainerResolver[namespace=%s]" % self.namespace |
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568 |
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569 |
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570 class BuildMulledSingularityContainerResolver(SingularityCliContainerResolver): |
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571 """Build for Singularity mulled images matching tool dependencies.""" |
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572 |
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573 resolver_type = "build_mulled_singularity" |
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574 shell = '/bin/bash' |
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575 builds_on_resolution = True |
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576 |
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577 def __init__(self, app_info=None, hash_func="v2", auto_install=True, **kwds): |
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578 super().__init__(app_info=app_info, **kwds) |
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579 self._involucro_context_kwds = { |
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580 'involucro_bin': self._get_config_option("involucro_path", None) |
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581 } |
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582 self.hash_func = hash_func |
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583 self.auto_install = string_as_bool(auto_install) |
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584 self._mulled_kwds = { |
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585 'channels': self._get_config_option("mulled_channels", DEFAULT_CHANNELS), |
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586 'hash_func': self.hash_func, |
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587 'command': 'build-and-test', |
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588 'singularity': True, |
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589 'singularity_image_dir': self.cache_directory, |
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590 } |
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591 self.auto_init = self._get_config_option("involucro_auto_init", True) |
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592 |
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593 def resolve(self, enabled_container_types, tool_info, install=False, **kwds): |
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594 if tool_info.requires_galaxy_python_environment or self.container_type not in enabled_container_types: |
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595 return None |
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596 |
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597 targets = mulled_targets(tool_info) |
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598 if len(targets) == 0: |
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599 return None |
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600 |
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601 if self.auto_install or install: |
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602 mull_targets( |
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603 targets, |
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604 involucro_context=self._get_involucro_context(), |
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605 **self._mulled_kwds |
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606 ) |
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607 return singularity_cached_container_description(targets, self.cache_directory, hash_func=self.hash_func, shell=self.shell) |
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608 |
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609 def _get_involucro_context(self): |
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610 involucro_context = InvolucroContext(**self._involucro_context_kwds) |
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611 self.enabled = ensure_installed(involucro_context, self.auto_init) |
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612 return involucro_context |
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613 |
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614 def __str__(self): |
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615 return "BuildSingularityContainerResolver[cache_directory=%s]" % self.cache_directory |
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616 |
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617 |
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618 def mulled_targets(tool_info): |
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619 return requirements_to_mulled_targets(tool_info.requirements) |
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620 |
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621 |
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622 __all__ = ( |
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623 "CachedMulledDockerContainerResolver", |
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624 "CachedMulledSingularityContainerResolver", |
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625 "MulledDockerContainerResolver", |
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626 "MulledSingularityContainerResolver", |
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627 "BuildMulledDockerContainerResolver", |
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628 "BuildMulledSingularityContainerResolver", |
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629 ) |