Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/planemo/training/tutorial.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 Tutorial class, dealing with the creation of a training tutorial."""
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2
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3 import collections
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4 import json
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5 import os
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6 import re
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7 import shutil
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8
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9 import oyaml as yaml
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10 import requests
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11 import six
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12
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13 from planemo import templates
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14 from planemo.bioblend import galaxy
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15 from planemo.engine import (
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16 engine_context,
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17 is_galaxy_engine,
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18 )
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19 from planemo.io import info
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20 from planemo.runnable import for_path
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21 from .tool_input import (
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22 get_empty_input,
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23 get_empty_param,
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24 ToolInput
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25 )
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26 from .utils import (
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27 load_yaml,
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28 save_to_yaml
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29 )
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30
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31 TUTO_HAND_ON_TEMPLATE = """---
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32 layout: tutorial_hands_on
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33
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34 {{ metadata }}
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35 ---
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36
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37 {{ body }}
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38 """
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39
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40 TUTO_SLIDES_TEMPLATE = """---
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41 layout: tutorial_slides
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42 logo: "GTN"
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43
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44 {{ metadata }}
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45 ---
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46
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47 ### How to fill the slide decks?
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48
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49 Please follow our
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50 [tutorial to learn how to fill the slides]({{ '{{' }} site.baseurl {{ '}}' }}/topics/contributing/tutorials/create-new-tutorial-slides/slides.html)
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51 """
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52
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53
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54 HANDS_ON_TOOL_BOX_TEMPLATE = """
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55 ## Sub-step with **{{tool_name}}**
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56
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57 > ### {{ '{%' }} icon hands_on {{ '%}' }} Hands-on: Task description
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58 >
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59 > 1. **{{tool_name}}** {{ '{%' }} icon tool {{ '%}' }} with the following parameters:{{inputlist}}{{paramlist}}
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60 >
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61 > ***TODO***: *Check parameter descriptions*
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62 >
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63 > ***TODO***: *Consider adding a comment or tip box*
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64 >
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65 > > ### {{ '{%' }} icon comment {{ '%}' }} Comment
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66 > >
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67 > > A comment about the tool or something else. This box can also be in the main text
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68 > {: .comment}
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69 >
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70 {: .hands_on}
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71
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72 ***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
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73
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74 > ### {{ '{%' }} icon question {{ '%}' }} Questions
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75 >
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76 > 1. Question1?
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77 > 2. Question2?
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78 >
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79 > > ### {{ '{%' }} icon solution {{ '%}' }} Solution
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80 > >
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81 > > 1. Answer for question1
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82 > > 2. Answer for question2
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83 > >
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84 > {: .solution}
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85 >
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86 {: .question}
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87
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88 """
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89
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90 TUTO_BIBLIOGRAPHY_TEMPLATE = """
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91 # This is the bibliography file for your tutorial.
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92 #
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93 # To add bibliography (bibtex) entries here, follow these steps:
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94 # 1) Find the DOI for the article you want to cite
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95 # 2) Go to https://doi2bib.org and fill in the DOI
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96 # 3) Copy the resulting bibtex entry into this file
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97 #
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98 # To cite the example below, in your tutorial.md file
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99 # use {{ '{%' }} Batut2018 {{ '%}' }}
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100
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101 @article{Batut2018,
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102 doi = {10.1016/j.cels.2018.05.012},
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103 url = {https://doi.org/10.1016/j.cels.2018.05.012},
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104 year = {2018},
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105 month = jun,
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106 publisher = {Elsevier {BV}},
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107 volume = {6},
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108 number = {6},
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109 pages = {752--758.e1},
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110 author = {B{\\'{e}}r{\\'{e}}nice Batut and Saskia Hiltemann and Andrea Bagnacani and Dannon Baker and Vivek Bhardwaj and
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111 Clemens Blank and Anthony Bretaudeau and Loraine Brillet-Gu{\\'{e}}guen and Martin {\\v{C}}ech and John Chilton
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112 and Dave Clements and Olivia Doppelt-Azeroual and Anika Erxleben and Mallory Ann Freeberg and Simon Gladman and
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113 Youri Hoogstrate and Hans-Rudolf Hotz and Torsten Houwaart and Pratik Jagtap and Delphine Larivi{\\`{e}}re and
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114 Gildas Le Corguill{\\'{e}} and Thomas Manke and Fabien Mareuil and Fidel Ram{\\'{i}}rez and Devon Ryan and
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115 Florian Christoph Sigloch and Nicola Soranzo and Joachim Wolff and Pavankumar Videm and Markus Wolfien and
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116 Aisanjiang Wubuli and Dilmurat Yusuf and James Taylor and Rolf Backofen and Anton Nekrutenko and Bj\\"{o}rn Gr\\"{u}ning},
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117 title = {Community-Driven Data Analysis Training for Biology},
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118 journal = {Cell Systems}
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119 }
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120 """
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121
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122 TUTO_HAND_ON_BODY_TEMPLATE = """
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123 # Introduction
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124 {:.no_toc}
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125
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126 <!-- This is a comment. -->
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127
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128 General introduction about the topic and then an introduction of the
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129 tutorial (the questions and the objectives). It is nice also to have a
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130 scheme to sum up the pipeline used during the tutorial. The idea is to
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131 give to trainees insight into the content of the tutorial and the (theoretical
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132 and technical) key concepts they will learn.
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133
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134 You may want to cite some publications; this can be done by adding citations to the
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135 bibliography file (`tutorial.bib` file next to your `tutorial.md` file). These citations
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136 must be in bibtex format. If you have the DOI for the paper you wish to cite, you can
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137 get the corresponding bibtex entry using [doi2bib.org](https://doi2bib.org).
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138
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139 With the example you will find in the `tutorial.bib` file, you can add a citation to
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140 this article here in your tutorial like this:
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141 {{ '{%' }} raw {{ '%}' }} `{{ '{%' }} cite Batut2018 {{ '%}' }}`{{ '{%' }} endraw {{ '%}' }}.
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142 This will be rendered like this: {{ '{%' }} cite Batut2018 {{ '%}' }}, and links to a
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143 [bibliography section](#bibliography) which will automatically be created at the end of the
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144 tutorial.
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145
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146
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147 **Please follow our
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148 [tutorial to learn how to fill the Markdown]({{ '{{' }} site.baseurl {{ '}}' }}/topics/contributing/tutorials/\
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149 create-new-tutorial-content/tutorial.html)**
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150
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151 > ### Agenda
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152 >
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153 > In this tutorial, we will cover:
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154 >
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155 > 1. TOC
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156 > {:toc}
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157 >
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158 {: .agenda}
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159
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160 # Title for your first section
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161
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162 Give some background about what the trainees will be doing in the section.
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163 Remember that many people reading your materials will likely be novices,
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164 so make sure to explain all the relevant concepts.
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165
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166 ## Title for a subsection
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167 Section and subsection titles will be displayed in the tutorial index on the left side of
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168 the page, so try to make them informative and concise!
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169
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170 # Hands-on Sections
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171 Below are a series of hand-on boxes, one for each tool in your workflow file.
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172 Often you may wish to combine several boxes into one or make other adjustments such
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173 as breaking the tutorial into sections, we encourage you to make such changes as you
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174 see fit, this is just a starting point :)
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175
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176 Anywhere you find the word "***TODO***", there is something that needs to be changed
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177 depending on the specifics of your tutorial.
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178
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179 have fun!
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180
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181 ## Get data
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182
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183 > ### {{ '{%' }} icon hands_on {{ '%}' }} Hands-on: Data upload
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184 >
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185 > 1. Create a new history for this tutorial
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186 > 2. Import the files from [Zenodo]({{ zenodo_link }}) or from the shared data library
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187 >
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188 > ```
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189 > {{ z_file_links }}
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190 > ```
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191 > ***TODO***: *Add the files by the ones on Zenodo here (if not added)*
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192 >
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193 > ***TODO***: *Remove the useless files (if added)*
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194 >
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195 > {{ '{%' }} include snippets/import_via_link.md {{ '%}' }}
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196 > {{ '{%' }} include snippets/import_from_data_library.md {{ '%}' }}
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197 >
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198 > 3. Rename the datasets
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199 > 4. Check that the datatype
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200 >
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201 > {{ '{%' }} include snippets/change_datatype.md datatype="datatypes" {{ '%}' }}
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202 >
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203 > 5. Add to each database a tag corresponding to ...
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204 >
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205 > {{ '{%' }} include snippets/add_tag.md {{ '%}' }}
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206 >
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207 {: .hands_on}
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208
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209 # Title of the section usually corresponding to a big step in the analysis
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210
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211 It comes first a description of the step: some background and some theory.
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212 Some image can be added there to support the theory explanation:
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213
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214 ![Alternative text](../../images/image_name "Legend of the image")
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215
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216 The idea is to keep the theory description before quite simple to focus more on the practical part.
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217
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218 ***TODO***: *Consider adding a detail box to expand the theory*
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219
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220 > ### {{ '{%' }} icon details {{ '%}' }} More details about the theory
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221 >
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222 > But to describe more details, it is possible to use the detail boxes which are expandable
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223 >
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224 {: .details}
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225
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226 A big step can have several subsections or sub steps:
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227
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228 {{ body }}
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229
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230 ## Re-arrange
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231
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232 To create the template, each step of the workflow had its own subsection.
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233
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234 ***TODO***: *Re-arrange the generated subsections into sections or other subsections.
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235 Consider merging some hands-on boxes to have a meaningful flow of the analyses*
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236
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237 # Conclusion
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238 {:.no_toc}
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239
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240 Sum up the tutorial and the key takeaways here. We encourage adding an overview image of the
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241 pipeline used.
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242 """
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243
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244
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245 class Tutorial(object):
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246 """Class to describe a training tutorial."""
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247
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248 def __init__(self, training, topic, name="new_tuto", title="The new tutorial", zenodo_link=""):
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249 """Init a tutorial instance."""
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250 self.training = training
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251 self.topic = topic
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252 self.name = name
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253 self.title = title
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254 self.zenodo_link = zenodo_link
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255 self.zenodo_file_links = []
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256 self.questions = []
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257 self.objectives = []
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258 self.time = ""
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259 self.key_points = []
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260 self.contributors = []
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261 self.body = ""
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262 self.init_wf_fp = None
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263 self.init_wf_id = None
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264 self.hands_on = True
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265 self.slides = False
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266 self.datatype_fp = ""
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267 self.set_dir_name()
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268 self.init_data_lib()
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269 self.body = templates.render(HANDS_ON_TOOL_BOX_TEMPLATE, **{
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270 'tool_name': "My Tool",
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271 'inputlist': get_empty_input(),
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272 'paramlist': get_empty_param()
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273 })
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274
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275 def init_from_kwds(self, kwds):
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276 """Init a tutorial instance from a kwds dictionary."""
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277 self.name = kwds["tutorial_name"]
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278 self.title = kwds["tutorial_title"]
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279 self.zenodo_link = kwds["zenodo_link"] if kwds["zenodo_link"] else ''
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280 self.questions = [
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281 "Which biological questions are addressed by the tutorial?",
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282 "Which bioinformatics techniques are important to know for this type of data?"]
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283 self.objectives = [
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284 "The learning objectives are the goals of the tutorial",
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285 "They will be informed by your audience and will communicate to them and to yourself what you should focus on during the course",
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286 "They are single sentences describing what a learner should be able to do once they have completed the tutorial",
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287 "You can use Bloom's Taxonomy to write effective learning objectives"]
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288 self.time = "3H"
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289 self.key_points = [
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290 "The take-home messages",
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291 "They will appear at the end of the tutorial"]
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292 self.contributors = ["contributor1", "contributor2"]
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293 self.init_wf_fp = kwds['workflow']
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294 self.init_wf_id = kwds['workflow_id']
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295 self.hands_on = kwds['hands_on']
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296 self.slides = kwds['slides']
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297 self.datatype_fp = kwds['datatypes']
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298 self.set_dir_name()
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299 self.init_data_lib()
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300
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301 def init_from_existing_tutorial(self, tuto_name):
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302 """Init a tutorial instance from an existing tutorial (data library and tutorial.md)."""
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303 self.name = tuto_name
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304 self.set_dir_name()
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305
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306 if not self.exists():
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307 raise Exception("The tutorial %s does not exists. It should be created" % self.name)
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308
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309 # get the metadata information of the tutorial (from the top of the tutorial.md)
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310 with open(self.tuto_fp, "r") as tuto_f:
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311 tuto_content = tuto_f.read()
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312 regex = r'^---\n(?P<metadata>[\s\S]*)\n---(?P<body>[\s\S]*)'
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313 tuto_split_regex = re.search(regex, tuto_content)
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314 if not tuto_split_regex:
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315 raise Exception("No metadata found at the top of the tutorial")
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316 metadata = yaml.safe_load(tuto_split_regex.group("metadata"))
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317 self.title = metadata["title"]
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318 self.zenodo_link = metadata["zenodo_link"]
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319 self.questions = metadata["questions"]
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320 self.objectives = metadata["objectives"]
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321 self.time_estimation = metadata["time_estimation"]
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322 self.key_points = metadata["key_points"]
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323 self.contributors = metadata["contributors"]
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324
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325 # the tutorial content
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326 self.body = tuto_split_regex.group("body")
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327
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328 # get the data library
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329 self.init_data_lib()
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330
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331 def init_data_lib(self):
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332 """Init the data library dictionary."""
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333 if os.path.exists(self.data_lib_fp):
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334 self.data_lib = load_yaml(self.data_lib_fp)
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335 else:
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336 self.data_lib = collections.OrderedDict()
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337 # set default information
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338 self.data_lib.setdefault('destination', collections.OrderedDict())
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339 self.data_lib['destination']['type'] = 'library'
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340 self.data_lib['destination']['name'] = 'GTN - Material'
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341 self.data_lib['destination']['description'] = 'Galaxy Training Network Material'
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342 self.data_lib['destination']['synopsis'] = 'Galaxy Training Network Material. See https://training.galaxyproject.org'
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343 self.data_lib.setdefault('items', [])
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344 self.data_lib.pop('libraries', None)
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345 # get topic or create new one
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346 topic = collections.OrderedDict()
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347 for item in self.data_lib['items']:
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348 if item['name'] == self.topic.title:
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349 topic = item
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350 if not topic:
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351 self.data_lib['items'].append(topic)
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352 topic['name'] = self.topic.title
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353 topic['description'] = self.topic.summary
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354 topic['items'] = []
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355 # get tutorial or create new one
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356 self.tuto_data_lib = collections.OrderedDict()
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357 for item in topic['items']:
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358 if item['name'] == self.title:
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359 self.tuto_data_lib = item
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360 if not self.tuto_data_lib:
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361 topic['items'].append(self.tuto_data_lib)
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362 self.tuto_data_lib['name'] = self.title
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363 self.tuto_data_lib['items'] = []
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364
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365 # GETTERS
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366 def get_tuto_metata(self):
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367 """Return the string corresponding to the tutorial metadata."""
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368 metadata = collections.OrderedDict()
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369 metadata['title'] = self.title
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370 metadata['zenodo_link'] = self.zenodo_link
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371 metadata['questions'] = self.questions
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372 metadata['objectives'] = self.objectives
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373 metadata['time_estimation'] = self.time
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374 metadata['key_points'] = self.key_points
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375 metadata['contributors'] = self.contributors
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376 return yaml.safe_dump(
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377 metadata,
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378 indent=2,
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379 default_flow_style=False,
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380 default_style='',
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381 explicit_start=False)
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382
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383 # SETTERS
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384 def set_dir_name(self):
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385 """Set the path to dir and files of a tutorial."""
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386 self.dir = os.path.join(self.topic.dir, "tutorials", self.name)
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387 self.tuto_fp = os.path.join(self.dir, "tutorial.md")
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388 self.bib_fp = os.path.join(self.dir, "tutorial.bib")
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389 self.slide_fp = os.path.join(self.dir, 'slides.html')
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390 self.data_lib_fp = os.path.join(self.dir, "data-library.yaml")
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391 self.wf_dir = os.path.join(self.dir, "workflows")
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392 self.wf_fp = os.path.join(self.wf_dir, "main_workflow.ga")
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393 self.tour_dir = os.path.join(self.dir, "tours")
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394 # remove empty workflow file if there
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395 empty_wf_filepath = os.path.join(self.wf_dir, "empty_workflow.ga")
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396 if os.path.exists(empty_wf_filepath):
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397 os.remove(empty_wf_filepath)
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398
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399 # TEST METHODS
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400 def exists(self):
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401 """Test if the tutorial exists."""
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402 return os.path.isdir(self.dir)
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403
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404 def has_workflow(self):
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405 """Test if a workflow is provided for the tutorial."""
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406 return self.init_wf_fp or self.init_wf_id
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407
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408 # EXPORT METHODS
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409 def export_workflow_file(self):
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410 """Copy or extract workflow file and add it to the tutorial directory."""
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411 if not os.path.exists(self.wf_dir):
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412 os.makedirs(self.wf_dir)
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413 if not os.path.exists(os.path.join(self.wf_dir, 'index.md')):
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414 with open(os.path.join(self.wf_dir, 'index.md'), 'w') as handle:
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415 handle.write('---\nlayout: workflow-list\n---\n')
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416 if self.init_wf_fp:
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417 shutil.copy(self.init_wf_fp, self.wf_fp)
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418 elif self.init_wf_id:
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419 gi = galaxy.GalaxyInstance(self.training.galaxy_url, key=self.training.galaxy_api_key)
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420 gi.workflows.export_workflow_to_local_path(
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421 self.init_wf_id,
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422 self.wf_fp,
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423 use_default_filename=False)
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424
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425 # OTHER METHODS
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426 def get_files_from_zenodo(self):
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427 """Extract a list of URLs and dictionary describing the files from the JSON output of the Zenodo API."""
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428 z_record, req_res = get_zenodo_record(self.zenodo_link)
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429
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430 self.zenodo_file_links = []
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431 if 'files' not in req_res:
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432 raise ValueError("No files in the Zenodo record")
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433
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434 files = []
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435 for f in req_res['files']:
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436 file_dict = {'url': '', 'src': 'url', 'ext': '', 'info': self.zenodo_link}
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437 if 'type' in f:
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438 file_dict['ext'] = get_galaxy_datatype(f['type'], self.datatype_fp)
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439 if 'links' not in f and 'self' not in f['links']:
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440 raise ValueError("No link for file %s" % f)
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441 file_dict['url'] = f['links']['self']
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442 self.zenodo_file_links.append(f['links']['self'])
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443 files.append(file_dict)
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444
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445 return (files, z_record)
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446
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447 def prepare_data_library_from_zenodo(self):
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448 """Get the list of URLs of the files on Zenodo, fill the data library, save it into the file."""
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449 self.zenodo_file_links = []
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450 if self.zenodo_link != '':
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451 files, z_record = self.get_files_from_zenodo()
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452 if z_record:
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453 # get current data library and/or previous data library for the tutorial
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454 # remove the latest tag of any existing library
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455 # remove the any other existing library
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456 current_data_lib = collections.OrderedDict()
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457 previous_data_lib = collections.OrderedDict()
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458 for item in self.tuto_data_lib['items']:
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459 if item['name'] == "DOI: 10.5281/zenodo.%s" % z_record:
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460 current_data_lib = item
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461 elif item['description'] == 'latest':
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462 previous_data_lib = item
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463 previous_data_lib['description'] = ''
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464 if not current_data_lib:
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465 current_data_lib['name'] = "DOI: 10.5281/zenodo.%s" % z_record
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466 current_data_lib['description'] = 'latest'
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467 current_data_lib['items'] = []
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468 current_data_lib['items'] = files
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469
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470 self.tuto_data_lib['items'] = [current_data_lib]
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471 if previous_data_lib:
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472 self.tuto_data_lib['items'].append(previous_data_lib)
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473 save_to_yaml(self.data_lib, self.data_lib_fp)
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474
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475 def write_hands_on_tutorial(self, add_z_file_links=True):
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476 """Write the content of the hands-on tutorial in the corresponding file."""
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477 if add_z_file_links:
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478 self.body = templates.render(TUTO_HAND_ON_BODY_TEMPLATE, **{
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479 "z_file_links": "\n> ".join(self.zenodo_file_links),
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480 "body": self.body
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481 })
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482 # write in the tutorial file with the metadata on the top
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483 metadata = self.get_tuto_metata()
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484 with open(self.tuto_fp, 'w') as md:
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485 md.write(templates.render(TUTO_HAND_ON_TEMPLATE, **{
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486 "metadata": metadata,
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487 "body": self.body
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488 }))
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489
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490 # create the bibliography file
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491 self.write_bibliography()
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492
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493 def write_bibliography(self):
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494 """Write the content of the bibliography file for the tutorial."""
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495 with open(self.bib_fp, 'w') as bib:
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496 bib.write(templates.render(TUTO_BIBLIOGRAPHY_TEMPLATE, **{
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497 "body": self.body
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498 }))
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499
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500 def create_hands_on_tutorial(self, ctx):
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501 """Create tutorial structure from the workflow file (if it is provided)."""
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diff changeset
502 # load workflow and get hands-on body from the workflow
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parents:
diff changeset
503 if self.init_wf_id:
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parents:
diff changeset
504 if not self.training.galaxy_url:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
505 raise ValueError("No Galaxy URL given")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
506 if not self.training.galaxy_api_key:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
507 raise ValueError("No API key to access the given Galaxy instance")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
508 self.body = get_hands_on_boxes_from_running_galaxy(self.init_wf_id, self.training.galaxy_url, self.training.galaxy_api_key)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
509 elif self.init_wf_fp:
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parents:
diff changeset
510 self.body = get_hands_on_boxes_from_local_galaxy(self.training.kwds, self.init_wf_fp, ctx)
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parents:
diff changeset
511 # write tutorial body
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parents:
diff changeset
512 self.write_hands_on_tutorial()
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parents:
diff changeset
513
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parents:
diff changeset
514 def create_tutorial(self, ctx):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
515 """Create the skeleton of a new tutorial."""
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parents:
diff changeset
516 # create tuto folder and empty files
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parents:
diff changeset
517 os.makedirs(self.dir)
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parents:
diff changeset
518 os.makedirs(self.tour_dir)
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parents:
diff changeset
519 os.makedirs(self.wf_dir)
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parents:
diff changeset
520
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parents:
diff changeset
521 # extract the data library from Zenodo and the links for the tutorial
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
522 if self.zenodo_link != '':
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parents:
diff changeset
523 info("Create the data library from Zenodo")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
524 self.prepare_data_library_from_zenodo()
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parents:
diff changeset
525
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parents:
diff changeset
526 # create tutorial skeleton from workflow and copy workflow file
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
527 if self.hands_on:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
528 info("Create tutorial skeleton from workflow (if it is provided)")
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parents:
diff changeset
529 self.create_hands_on_tutorial(ctx)
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parents:
diff changeset
530 self.export_workflow_file()
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parents:
diff changeset
531
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parents:
diff changeset
532 # create slide skeleton
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parents:
diff changeset
533 if self.slides:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
534 with open(self.slide_fp, 'w') as slide_f:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
535 slide_f.write(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
536 templates.render(TUTO_SLIDES_TEMPLATE, **{"metadata": self.get_tuto_metata()}))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
537
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
538
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parents:
diff changeset
539 def get_galaxy_datatype(z_ext, datatype_fp):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
540 """Get the Galaxy datatype corresponding to a Zenodo file type."""
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
541 g_datatype = ''
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
542 datatypes = load_yaml(datatype_fp)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
543 if z_ext in datatypes:
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parents:
diff changeset
544 g_datatype = datatypes[z_ext]
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parents:
diff changeset
545 if g_datatype == '':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
546 g_datatype = '# Please add a Galaxy datatype or update the shared/datatypes.yaml file'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
547 info("Get Galaxy datatypes: %s --> %s" % (z_ext, g_datatype))
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parents:
diff changeset
548 return g_datatype
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parents:
diff changeset
549
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parents:
diff changeset
550
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parents:
diff changeset
551 def get_zenodo_record(zenodo_link):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
552 """Get the content of a Zenodo record."""
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parents:
diff changeset
553 # get the record in the Zenodo link
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parents:
diff changeset
554 if 'doi' in zenodo_link:
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parents:
diff changeset
555 z_record = zenodo_link.split('.')[-1]
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parents:
diff changeset
556 else:
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parents:
diff changeset
557 z_record = zenodo_link.split('/')[-1]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
558 # get JSON corresponding to the record from Zenodo API
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parents:
diff changeset
559 req = "https://zenodo.org/api/records/%s" % (z_record)
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parents:
diff changeset
560 r = requests.get(req)
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parents:
diff changeset
561 if r:
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parents:
diff changeset
562 req_res = r.json()
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parents:
diff changeset
563 else:
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parents:
diff changeset
564 info("The Zenodo link (%s) seems invalid" % (zenodo_link))
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parents:
diff changeset
565 req_res = {'files': []}
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parents:
diff changeset
566 z_record = None
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parents:
diff changeset
567 return(z_record, req_res)
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parents:
diff changeset
568
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
569
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
570 def get_wf_inputs(step_inp):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
571 """Get the inputs from a workflow step and format them into a hierarchical dictionary."""
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
572 inputs = {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
573 for inp_n, inp in step_inp.items():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
574 if '|' in inp_n:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
575 repeat_regex = r'(?P<prefix>[^\|]*)_(?P<nb>\d+)\|(?P<suffix>.+).+'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
576 repeat_search = re.search(repeat_regex, inp_n)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
577 hier_regex = r'(?P<prefix>[^\|]*)\|(?P<suffix>.+)'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
578 hier_regex = re.search(hier_regex, inp_n)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
579 if repeat_search and repeat_search.start(0) <= hier_regex.start(0):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
580 inputs.setdefault(repeat_search.group('prefix'), {})
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
581 inputs[repeat_search.group('prefix')].setdefault(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
582 repeat_search.group('nb'),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
583 get_wf_inputs({hier_regex.group('suffix'): inp}))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
584 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
585 inputs.setdefault(hier_regex.group('prefix'), {})
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
586 inputs[hier_regex.group('prefix')].update(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
587 get_wf_inputs({hier_regex.group('suffix'): inp}))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
588 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
589 inputs.setdefault(inp_n, inp)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
590 return inputs
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
591
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
592
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
593 def get_wf_param_values(init_params, inp_connections):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
594 """Get the param values from a workflow step and format them into a hierarchical dictionary."""
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
595 if not isinstance(init_params, six.string_types) or '": ' not in init_params:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
596 form_params = init_params
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
597 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
598 form_params = json.loads(init_params)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
599 if isinstance(form_params, dict):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
600 if '__class__' in form_params and (form_params['__class__'] == 'RuntimeValue' or form_params['__class__'] == 'ConnectedValue'):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
601 form_params = inp_connections
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
602 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
603 for p in form_params:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
604 inp = inp_connections[p] if p in inp_connections else {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
605 form_params[p] = get_wf_param_values(form_params[p], inp)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
606 elif isinstance(form_params, list):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
607 json_params = form_params
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
608 form_params = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
609 for i, p in enumerate(json_params):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
610 inp = inp_connections[str(i)] if str(i) in inp_connections else {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
611 form_params.append(get_wf_param_values(p, inp))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
612 elif isinstance(form_params, six.string_types) and '"' in form_params:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
613 form_params = form_params.replace('"', '')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
614 return form_params
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
615
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
616
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
617 def format_wf_steps(wf, gi):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
618 """Get a string with the hands-on boxes describing the different steps of the worklow."""
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
619 body = ''
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
620 steps = wf['steps']
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
621
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parents:
diff changeset
622 for s in range(len(steps)):
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parents:
diff changeset
623 wf_step = steps[str(s)]
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shellac
parents:
diff changeset
624 # get params in workflow
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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625 wf_param_values = {}
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626 if wf_step['tool_state'] and wf_step['input_connections']:
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627 wf_param_values = get_wf_param_values(wf_step['tool_state'], get_wf_inputs(wf_step['input_connections']))
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628 if not wf_param_values:
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629 continue
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630 # get tool description
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631 try:
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632 tool_desc = gi.tools.show_tool(wf_step['tool_id'], io_details=True)
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633 except Exception:
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634 tool_desc = {'inputs': []}
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635 # get formatted param description
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636 paramlist = ''
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637 for inp in tool_desc["inputs"]:
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638 tool_inp = ToolInput(inp, wf_param_values, steps, 1, should_be_there=True)
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639 paramlist += tool_inp.get_formatted_desc()
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640 # format the hands-on box
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641 body += templates.render(HANDS_ON_TOOL_BOX_TEMPLATE, **{
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642 "tool_name": wf_step['name'],
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643 "paramlist": paramlist})
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644 return body
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645
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646
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647 def get_hands_on_boxes_from_local_galaxy(kwds, wf_filepath, ctx):
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648 """Server local Galaxy and get the workflow dictionary."""
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649 assert is_galaxy_engine(**kwds)
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650 runnable = for_path(wf_filepath)
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651 tuto_body = ''
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652 with engine_context(ctx, **kwds) as galaxy_engine:
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653 with galaxy_engine.ensure_runnables_served([runnable]) as config:
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654 workflow_id = config.workflow_id(wf_filepath)
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655 wf = config.gi.workflows.export_workflow_dict(workflow_id)
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656 tuto_body = format_wf_steps(wf, config.gi)
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657 return tuto_body
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658
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659
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660 def get_hands_on_boxes_from_running_galaxy(wf_id, galaxy_url, galaxy_api_key):
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661 """Get the workflow dictionary from a running Galaxy instance with the workflow installed on it."""
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662 gi = galaxy.GalaxyInstance(galaxy_url, key=galaxy_api_key)
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663 wf = gi.workflows.export_workflow_dict(wf_id)
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664 tuto_body = format_wf_steps(wf, gi)
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665 return tuto_body