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127 lines
5.8 KiB
Python
127 lines
5.8 KiB
Python
#!/usr/bin/env python
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"""
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"""
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import unittest
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from galaxy import model
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from galaxy.managers.collections import DatasetCollectionManager
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from galaxy.managers.datasets import DatasetManager
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from galaxy.managers.hdas import HDAManager
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from galaxy.managers.histories import HistoryManager
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from .base import (
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BaseTestCase,
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CreatesCollectionsMixin,
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)
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# =============================================================================
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default_password = "123456"
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user2_data = dict(email="user2@user2.user2", username="user2", password=default_password)
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user3_data = dict(email="user3@user3.user3", username="user3", password=default_password)
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# =============================================================================
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class DatasetCollectionManagerTestCase(BaseTestCase, CreatesCollectionsMixin):
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def set_up_managers(self):
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super().set_up_managers()
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self.dataset_manager = self.app[DatasetManager]
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self.hda_manager = self.app[HDAManager]
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self.history_manager = self.app[HistoryManager]
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self.collection_manager = self.app[DatasetCollectionManager]
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def test_create_simple_list(self):
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owner = self.user_manager.create(**user2_data)
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history = self.history_manager.create(name="history1", user=owner)
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hda1 = self.hda_manager.create(name="one", history=history, dataset=self.dataset_manager.create())
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hda2 = self.hda_manager.create(name="two", history=history, dataset=self.dataset_manager.create())
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hda3 = self.hda_manager.create(name="three", history=history, dataset=self.dataset_manager.create())
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self.log("should be able to create a new Collection via ids")
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element_identifiers = self.build_element_identifiers([hda1, hda2, hda3])
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hdca = self.collection_manager.create(
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self.trans, history, "test collection", "list", element_identifiers=element_identifiers
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)
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self.assertIsInstance(hdca, model.HistoryDatasetCollectionAssociation)
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self.assertEqual(hdca.name, "test collection")
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self.assertEqual(hdca.hid, 4)
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self.assertFalse(hdca.deleted)
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self.assertTrue(hdca.visible)
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self.log("should contain an underlying, well-formed DatasetCollection")
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self.assertIsInstance(hdca.collection, model.DatasetCollection)
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collection = hdca.collection
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self.assertEqual(collection.collection_type, "list")
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self.assertEqual(collection.state, "ok")
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self.assertEqual(len(collection.dataset_instances), 3)
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self.assertEqual(len(collection.elements), 3)
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self.log("and that collection should have three well-formed Elements")
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self.assertIsInstance(collection.elements[0], model.DatasetCollectionElement)
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self.assertEqual(collection.elements[0].element_identifier, "one")
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self.assertEqual(collection.elements[0].element_index, 0)
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self.assertEqual(collection.elements[0].element_type, "hda")
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self.assertEqual(collection.elements[0].element_object, hda1)
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self.assertIsInstance(collection.elements[1], model.DatasetCollectionElement)
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self.assertEqual(collection.elements[1].element_identifier, "two")
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self.assertEqual(collection.elements[1].element_index, 1)
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self.assertEqual(collection.elements[1].element_type, "hda")
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self.assertEqual(collection.elements[1].element_object, hda2)
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self.assertIsInstance(collection.elements[2], model.DatasetCollectionElement)
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self.assertEqual(collection.elements[2].element_identifier, "three")
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self.assertEqual(collection.elements[2].element_index, 2)
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self.assertEqual(collection.elements[2].element_type, "hda")
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self.assertEqual(collection.elements[2].element_object, hda3)
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self.log("should be able to create a new Collection via objects")
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elements = dict(one=hda1, two=hda2, three=hda3)
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hdca2 = self.collection_manager.create(self.trans, history, "test collection 2", "list", elements=elements)
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self.assertIsInstance(hdca2, model.HistoryDatasetCollectionAssociation)
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def test_update_from_dict(self):
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owner = self.user_manager.create(**user2_data)
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history = self.history_manager.create(name="history1", user=owner)
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hda1 = self.hda_manager.create(name="one", history=history, dataset=self.dataset_manager.create())
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hda2 = self.hda_manager.create(name="two", history=history, dataset=self.dataset_manager.create())
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hda3 = self.hda_manager.create(name="three", history=history, dataset=self.dataset_manager.create())
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elements = dict(one=hda1, two=hda2, three=hda3)
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hdca = self.collection_manager.create(self.trans, history, "test collection", "list", elements=elements)
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self.log("should be set from a dictionary")
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self.collection_manager._set_from_dict(
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self.trans,
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hdca,
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{
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"deleted": True,
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"visible": False,
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"name": "New Name",
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"tags": ["name:one", "group:two", "three"]
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# TODO: doesn't work
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# 'annotations' : [?]
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},
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)
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self.assertEqual(hdca.name, "New Name")
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self.assertTrue(hdca.deleted)
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self.assertFalse(hdca.visible)
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tag_names = hdca.make_tag_string_list()
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self.assertEqual(tag_names, ["name:one", "group:two", "three"])
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# self.assertEqual( hdca.annotations, [ 'one', 'two', 'three' ] )
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# def test_validation( self ):
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# self.log( "should be able to change the name" )
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# self.log( "should be able to set deleted" )
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# self.log( "should be able to set visible" )
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# self.log( "should be able to set tags" )
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# =============================================================================
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if __name__ == "__main__":
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# or more generally, nosetests test_resourcemanagers.py -s -v
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unittest.main()
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