Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/planemo/training/__init__.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 """Module contains code for gtdk: Galaxy training development kit.""" |
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2 |
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3 from planemo.io import info |
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4 from .topic import Topic |
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5 from .tutorial import Tutorial |
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6 |
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7 |
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8 class Training(object): |
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9 """Class to describe a training.""" |
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10 |
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11 def __init__(self, kwds): |
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12 """Init an instance of Training.""" |
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13 self.kwds = kwds |
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14 self.topics_dir = "topics" |
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15 self.topic = Topic(parent_dir=self.topics_dir, name=kwds['topic_name']) |
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16 self.galaxy_url = kwds['galaxy_url'] if 'galaxy_url' in kwds else '' |
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17 self.galaxy_api_key = kwds['galaxy_api_key'] if 'galaxy_api_key' in kwds else '' |
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18 self.tuto = None |
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19 |
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20 def init_training(self, ctx): |
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21 """Create/update a topic/tutorial.""" |
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22 if not self.topic.exists(): |
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23 info("The topic %s does not exist. It will be created" % self.topic.name) |
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24 self.topic.init_from_kwds(self.kwds) |
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25 self.topic.create_topic_structure() |
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26 |
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27 if not self.kwds['tutorial_name']: |
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28 if self.kwds["slides"]: |
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29 raise Exception("A tutorial name is needed to create the skeleton of a tutorial slide deck") |
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30 if self.kwds['workflow'] or self.kwds['workflow_id']: |
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31 raise Exception("A tutorial name is needed to create the skeleton of the tutorial from a workflow") |
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32 if self.kwds['zenodo_link']: |
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33 raise Exception("A tutorial name is needed to add Zenodo information") |
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34 else: |
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35 self.tuto = Tutorial(training=self, topic=self.topic) |
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36 self.tuto.init_from_kwds(self.kwds) |
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37 if not self.tuto.exists(): |
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38 info("The tutorial %s in topic %s does not exist. It will be created." % (self.tuto.name, self.topic.name)) |
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39 self.tuto.create_tutorial(ctx) |
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40 info("WARNING: Change the contributors/maintainers listed in the metadata of the new training ") |
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41 info("before serving the website to fit the one listed in the CONTRIBUTORS.yaml file") |
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42 |
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43 def check_topic_init_tuto(self): |
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44 """Check that the topic and tutorial are already there and retrieve them.""" |
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45 # check topic |
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46 if not self.topic.exists(): |
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47 raise Exception("The topic %s does not exists. It should be created" % self.topic.name) |
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48 self.topic.init_from_metadata() |
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49 # initiate the tutorial |
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50 self.tuto = Tutorial(training=self, topic=self.topic) |
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51 self.tuto.init_from_existing_tutorial(self.kwds['tutorial_name']) |
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52 if 'datatypes' in self.kwds: |
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53 self.tuto.datatype_fp = self.kwds['datatypes'] |
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54 if 'workflow' in self.kwds: |
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55 self.tuto.init_wf_fp = self.kwds['workflow'] |
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56 if 'workflow_id' in self.kwds: |
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57 self.tuto.init_wf_id = self.kwds['workflow_id'] |
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58 |
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59 def fill_data_library(self, ctx): |
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60 """Fill a data library for a tutorial.""" |
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61 self.check_topic_init_tuto() |
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62 # get the zenodo link |
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63 z_link = '' |
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64 update_metadata = False |
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65 if self.tuto.zenodo_link != '': |
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66 if self.kwds['zenodo_link']: |
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67 info("The data library and the metadata will be updated with the new Zenodo link") |
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68 z_link = self.kwds['zenodo_link'] |
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69 self.tuto.zenodo_link = z_link |
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70 update_metadata = True |
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71 else: |
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72 info("The data library will be extracted using the Zenodo link in the metadata of the tutorial") |
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73 z_link = self.tuto.zenodo_link |
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74 elif self.kwds['zenodo_link']: |
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75 info("The data library will be created and the metadata will be filled with the new Zenodo link") |
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76 z_link = self.kwds['zenodo_link'] |
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77 self.tuto.zenodo_link = z_link |
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78 update_metadata = True |
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79 |
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80 if z_link == '' or z_link is None: |
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81 raise Exception("A Zenodo link should be provided either in the metadata file or as argument of the command") |
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82 |
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83 # extract the data library from Zenodo |
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84 self.tuto.prepare_data_library_from_zenodo() |
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85 |
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86 # update the metadata |
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87 if update_metadata: |
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88 self.tuto.write_hands_on_tutorial(add_z_file_links=False) |
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89 |
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90 def generate_tuto_from_wf(self, ctx): |
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91 """Generate the skeleton of a tutorial from a workflow.""" |
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92 self.check_topic_init_tuto() |
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93 if self.tuto.has_workflow(): |
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94 info("Create tutorial skeleton from workflow") |
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95 self.tuto.create_hands_on_tutorial(ctx) |
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96 self.tuto.export_workflow_file() |
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97 else: |
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98 raise Exception( |
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99 "A path to a local workflow or the id of a workflow on a running Galaxy instance should be provided" |
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100 ) |