How to use the bioblend.galaxy.dataset_collections.CollectionDescription function in bioblend

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github galaxyproject / bioblend / bioblend / _tests / TestGalaxyObjects.py View on Github external
def _create_collection_description(self):
        self.dataset1 = self.hist.paste_content(FOO_DATA)
        self.dataset2 = self.hist.paste_content(FOO_DATA_2)
        self.collection_description = dataset_collections.CollectionDescription(
            name="MyDatasetList",
            elements=[
                dataset_collections.HistoryDatasetElement(name="sample1", id=self.dataset1.id),
                dataset_collections.HistoryDatasetElement(name="sample2", id=self.dataset2.id),
            ]
github galaxyproject / bioblend / bioblend / _tests / TestGalaxyDatasetCollections.py View on Github external
def test_create_list_of_paired_datasets_in_history(self):
        history_id = self.gi.histories.create_history(name="TestDSListCreate")["id"]
        dataset1_id = self._test_dataset(history_id)
        dataset2_id = self._test_dataset(history_id)
        dataset3_id = self._test_dataset(history_id)
        dataset4_id = self._test_dataset(history_id)
        collection_response = self.gi.histories.create_dataset_collection(
            history_id=history_id,
            collection_description=collections.CollectionDescription(
                name="MyListOfPairedDatasets",
                type="list:paired",
                elements=[
                    collections.CollectionElement(
                        name="sample1",
                        type="paired",
                        elements=[
                            collections.HistoryDatasetElement(name="forward", id=dataset1_id),
                            collections.HistoryDatasetElement(name="reverse", id=dataset2_id),
                        ]
                    ),
                    collections.CollectionElement(
                        name="sample2",
                        type="paired",
                        elements=[
                            collections.HistoryDatasetElement(name="forward", id=dataset3_id),
github refinery-platform / refinery-platform / refinery / tool_manager / models.py View on Github external
def _associate_collection_elements(self, galaxy_element_data):
        """
        Handles the association of Galaxy objects with their parent elements
        :param galaxy_element_data: list of bioblend objects to associate
        with each other
        :return: 
        """
        if not len(galaxy_element_data) == 1:
            for index, galaxy_element in enumerate(galaxy_element_data):
                if type(galaxy_element) == CollectionDescription:
                    for prev_galaxy_element in galaxy_element_data[:index]:
                        if (type(prev_galaxy_element) ==
                                HistoryDatasetElement or
                                type(prev_galaxy_element) ==
                                CollectionElement):
                            galaxy_element.add(prev_galaxy_element)
                            galaxy_element_data.remove(prev_galaxy_element)
                            return self._associate_collection_elements(
                                galaxy_element_data
                            )
                if type(galaxy_element) == CollectionElement:
                    for prev_galaxy_element in galaxy_element_data[:index]:
                        if type(prev_galaxy_element) == HistoryDatasetElement:
                            galaxy_element.add(prev_galaxy_element)
                            galaxy_element_data.remove(prev_galaxy_element)
                            return self._associate_collection_elements(