Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/planemo/training/topic.py @ 4:79f47841a781 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:47:39 -0400
parents 26e78fe6e8c4
children
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1 """Module contains code for the Topic class, dealing with the creation of a training topic."""
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2
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3 import collections
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4 import os
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5
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6 from planemo import templates
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7 from .utils import (
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8 load_yaml,
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9 Requirement,
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10 save_to_yaml
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11 )
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12
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13
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14 INDEX_FILE_TEMPLATE = """---
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15 layout: topic
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16 topic_name: {{ topic }}
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17 ---
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18 """
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19
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20 README_FILE_TEMPLATE = """
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21 {{ topic }}
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22 ==========
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23
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24 Please refer to the [CONTRIBUTING.md](../../CONTRIBUTING.md) before adding or updating any material
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25 """
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26
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27
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28 DOCKER_FILE_TEMPLATE = """
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29 # Galaxy - {{ topic_title }}
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30 #
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31 # to build the docker image, go to root of training repo and
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32 # docker build -t {{ topic_name }} -f topics/{{ topic_name }}/docker/Dockerfile .
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33 #
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34 # to run image:
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35 # docker run -p "8080:80" -t {{ topic_name }}
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36 # use -d to automatically dowload the datalibraries in the container
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37
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38 FROM bgruening/galaxy-stable:latest
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39
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40 MAINTAINER Galaxy Training Material
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41
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42 ENV GALAXY_CONFIG_BRAND "GTN: {{ topic_title }}"
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43
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44 # copy the tutorials directory for your topic
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45 ADD topics/{{ topic_name }}/tutorials/ /tutorials/
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46
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47 # install everything for tutorials
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48 ADD bin/docker-install-tutorials.sh /setup-tutorials.sh
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49 ADD bin/mergeyaml.py /mergeyaml.py
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50 ADD bin/data_libarary_download.sh /data_libarary_download.sh
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51 RUN /setup-tutorials.sh
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52
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53 ENTRYPOINT ["/data_libarary_download.sh"]
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54 """
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55
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56
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57 INTRO_SLIDES_FILE_TEMPLATE = """---
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58 layout: introduction_slides
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59 logo: "GTN"
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60
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61 title: {{ title }}
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62 type: {{ type }}
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63 contributors:
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64 - contributor
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65 ---
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66
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67 ### How to fill the slide decks?
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68
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69 Please follow our
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70 [tutorial to learn how to fill the slides]({{ '{{' }} site.baseurl {{ '}}' }}/topics/contributing/tutorials/create-new-tutorial-slides/slides.html)
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71 """
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72
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73
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74 class Topic(object):
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75 """Class to describe a training topic."""
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76
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77 def __init__(self, name="new_topic", target="use", title="The new topic", summary="Summary", parent_dir="topics"):
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78 """Init a topic instance."""
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79 self.name = name
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80 self.type = target
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81 self.title = title
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82 self.summary = summary
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83 self.docker_image = ""
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84 self.maintainers = ["maintainers"]
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85 self.parent_dir = parent_dir
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86 self.set_default_requirement()
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87 self.set_paths()
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88
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89 def init_from_kwds(self, kwds):
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90 """Init a topic instance from a kwds dictionary."""
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91 self.name = kwds["topic_name"]
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92 self.type = kwds["topic_target"]
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93 self.title = kwds["topic_title"]
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94 self.summary = kwds["topic_summary"]
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95 self.set_default_requirement()
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96 self.set_paths()
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97
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98 def init_from_metadata(self):
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99 """Init a topic instance from the metadata file."""
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100 metadata = load_yaml(self.metadata_fp)
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101 self.name = metadata['name']
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102 self.type = metadata['type']
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103 self.title = metadata['title']
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104 self.summary = metadata['summary']
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105 self.requirements = []
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106 if 'requirements' in metadata:
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107 for r in metadata['requirements']:
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108 req = Requirement()
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109 req.init_from_dict(r)
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110 self.requirements.append(req)
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111 if 'docker_image' in metadata:
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112 self.docker_image = metadata['docker_image']
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113 self.maintainers = metadata['maintainers']
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114 self.set_paths()
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115
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116 # GETTERS
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117 def get_requirements(self):
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118 """Get the requirements as a list of ordered dictionaries."""
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119 reqs = []
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120 for req in self.requirements:
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121 reqs.append(req.export_to_ordered_dict())
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122 return reqs
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123
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124 def export_metadata_to_ordered_dict(self):
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125 """Export the topic metadata into an ordered dictionary."""
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126 metadata = collections.OrderedDict()
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127 metadata['name'] = self.name
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128 metadata['type'] = self.type
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129 metadata['title'] = self.title
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130 metadata['summary'] = self.summary
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131 metadata['requirements'] = self.get_requirements()
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132 metadata['docker_image'] = self.docker_image
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133 metadata['maintainers'] = self.maintainers
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134 return metadata
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135
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136 # SETTERS
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137 def set_default_requirement(self):
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138 """Set default requirement: Galaxy introduction."""
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139 self.requirements = []
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140 if self.type == 'use':
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141 self.requirements.append(Requirement())
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142
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143 def set_paths(self):
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144 """Set the paths to folder and files."""
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145 self.dir = os.path.join(self.parent_dir, self.name)
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146 self.img_folder = os.path.join(self.dir, "images")
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147 self.tuto_folder = os.path.join(self.dir, "tutorials")
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148 self.index_fp = os.path.join(self.dir, "index.md")
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149 self.readme_fp = os.path.join(self.dir, "README.md")
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150 self.metadata_fp = os.path.join(self.dir, "metadata.yaml")
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151 self.docker_folder = os.path.join(self.dir, "docker")
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152 self.dockerfile_fp = os.path.join(self.docker_folder, "Dockerfile")
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153 self.slides_folder = os.path.join(self.dir, "slides")
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154
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155 # TESTS
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156 def exists(self):
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157 """Test if the topic exists."""
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158 return os.path.isdir(self.dir)
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159
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160 # OTHER METHODS
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161 def create_topic_structure(self):
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162 """Create the skeleton of a new topic.
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163
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164 1. create the folder and its structure
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165 2. update the index.md to match your topic's name
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166 3. fill the metadata
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167 4. add a symbolic link to the metadata.yaml from the metadata folder
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168 """
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169 # create the folder and its structure
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170 os.makedirs(self.dir)
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171 self.img_folder = os.path.join(self.dir, "images")
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172 os.makedirs(self.img_folder)
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173 self.tuto_folder = os.path.join(self.dir, "tutorials")
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174 os.makedirs(self.tuto_folder)
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175
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176 # create the index.md and add the topic name
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177 self.index_fp = os.path.join(self.dir, "index.md")
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178 with open(self.index_fp, 'w') as index_f:
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179 index_f.write(
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180 templates.render(INDEX_FILE_TEMPLATE, **{'topic': self.name}))
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181
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182 # create the README file
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183 self.readme_fp = os.path.join(self.dir, "README.md")
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184 with open(self.readme_fp, 'w') as readme_f:
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185 readme_f.write(
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186 templates.render(README_FILE_TEMPLATE, **{'topic': self.title}))
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187
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188 # create the metadata file
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189 self.metadata_fp = os.path.join(self.dir, "metadata.yaml")
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190 save_to_yaml(self.export_metadata_to_ordered_dict(), self.metadata_fp)
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191
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192 # create Dockerfile
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193 self.docker_folder = os.path.join(self.dir, "docker")
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194 os.makedirs(self.docker_folder)
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195 self.dockerfile_fp = os.path.join(self.docker_folder, "Dockerfile")
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196 with open(self.dockerfile_fp, 'w') as dockerfile:
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197 dockerfile.write(
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198 templates.render(
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199 DOCKER_FILE_TEMPLATE,
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200 **{'topic_name': self.name, 'topic_title': self.title}))
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201
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202 # create empty introduction slides
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203 self.slides_folder = os.path.join(self.dir, "slides")
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204 os.makedirs(self.slides_folder)
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205 self.intro_slide_fp = os.path.join(self.slides_folder, "introduction.html")
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206 with open(self.intro_slide_fp, 'w') as intro_slide_f:
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207 intro_slide_f.write(
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208 templates.render(
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209 INTRO_SLIDES_FILE_TEMPLATE,
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210 **{'title': "Introduction to %s" % self.title, 'type': "introduction"}))
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211
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212 # add a symbolic link to the metadata.yaml
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213 metadata_dir = "metadata"
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214 if not os.path.isdir(metadata_dir):
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215 os.makedirs(metadata_dir)
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216 os.chdir(metadata_dir)
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217 os.symlink(os.path.join("..", self.metadata_fp), "%s.yaml" % self.name)
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218 os.chdir("..")