diff env/lib/python3.9/site-packages/planemo/training/__init__.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/planemo/training/__init__.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,100 @@
+"""Module contains code for gtdk: Galaxy training development kit."""
+
+from planemo.io import info
+from .topic import Topic
+from .tutorial import Tutorial
+
+
+class Training(object):
+    """Class to describe a training."""
+
+    def __init__(self, kwds):
+        """Init an instance of Training."""
+        self.kwds = kwds
+        self.topics_dir = "topics"
+        self.topic = Topic(parent_dir=self.topics_dir, name=kwds['topic_name'])
+        self.galaxy_url = kwds['galaxy_url'] if 'galaxy_url' in kwds else ''
+        self.galaxy_api_key = kwds['galaxy_api_key'] if 'galaxy_api_key' in kwds else ''
+        self.tuto = None
+
+    def init_training(self, ctx):
+        """Create/update a topic/tutorial."""
+        if not self.topic.exists():
+            info("The topic %s does not exist. It will be created" % self.topic.name)
+            self.topic.init_from_kwds(self.kwds)
+            self.topic.create_topic_structure()
+
+        if not self.kwds['tutorial_name']:
+            if self.kwds["slides"]:
+                raise Exception("A tutorial name is needed to create the skeleton of a tutorial slide deck")
+            if self.kwds['workflow'] or self.kwds['workflow_id']:
+                raise Exception("A tutorial name is needed to create the skeleton of the tutorial from a workflow")
+            if self.kwds['zenodo_link']:
+                raise Exception("A tutorial name is needed to add Zenodo information")
+        else:
+            self.tuto = Tutorial(training=self, topic=self.topic)
+            self.tuto.init_from_kwds(self.kwds)
+            if not self.tuto.exists():
+                info("The tutorial %s in topic %s does not exist. It will be created." % (self.tuto.name, self.topic.name))
+                self.tuto.create_tutorial(ctx)
+        info("WARNING: Change the contributors/maintainers listed in the metadata of the new training ")
+        info("before serving the website to fit the one listed in the CONTRIBUTORS.yaml file")
+
+    def check_topic_init_tuto(self):
+        """Check that the topic and tutorial are already there and retrieve them."""
+        # check topic
+        if not self.topic.exists():
+            raise Exception("The topic %s does not exists. It should be created" % self.topic.name)
+        self.topic.init_from_metadata()
+        # initiate the tutorial
+        self.tuto = Tutorial(training=self, topic=self.topic)
+        self.tuto.init_from_existing_tutorial(self.kwds['tutorial_name'])
+        if 'datatypes' in self.kwds:
+            self.tuto.datatype_fp = self.kwds['datatypes']
+        if 'workflow' in self.kwds:
+            self.tuto.init_wf_fp = self.kwds['workflow']
+        if 'workflow_id' in self.kwds:
+            self.tuto.init_wf_id = self.kwds['workflow_id']
+
+    def fill_data_library(self, ctx):
+        """Fill a data library for a tutorial."""
+        self.check_topic_init_tuto()
+        # get the zenodo link
+        z_link = ''
+        update_metadata = False
+        if self.tuto.zenodo_link != '':
+            if self.kwds['zenodo_link']:
+                info("The data library and the metadata will be updated with the new Zenodo link")
+                z_link = self.kwds['zenodo_link']
+                self.tuto.zenodo_link = z_link
+                update_metadata = True
+            else:
+                info("The data library will be extracted using the Zenodo link in the metadata of the tutorial")
+                z_link = self.tuto.zenodo_link
+        elif self.kwds['zenodo_link']:
+            info("The data library will be created and the metadata will be filled with the new Zenodo link")
+            z_link = self.kwds['zenodo_link']
+            self.tuto.zenodo_link = z_link
+            update_metadata = True
+
+        if z_link == '' or z_link is None:
+            raise Exception("A Zenodo link should be provided either in the metadata file or as argument of the command")
+
+        # extract the data library from Zenodo
+        self.tuto.prepare_data_library_from_zenodo()
+
+        # update the metadata
+        if update_metadata:
+            self.tuto.write_hands_on_tutorial(add_z_file_links=False)
+
+    def generate_tuto_from_wf(self, ctx):
+        """Generate the skeleton of a tutorial from a workflow."""
+        self.check_topic_init_tuto()
+        if self.tuto.has_workflow():
+            info("Create tutorial skeleton from workflow")
+            self.tuto.create_hands_on_tutorial(ctx)
+            self.tuto.export_workflow_file()
+        else:
+            raise Exception(
+                "A path to a local workflow or the id of a workflow on a running Galaxy instance should be provided"
+            )