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

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github galaxyproject / bioblend / bioblend / _tests / TestGalaxyDatasetCollections.py View on Github external
def _create_pair_in_history(self, history_id):
        dataset1_id = self._test_dataset(history_id)
        dataset2_id = self._test_dataset(history_id)
        collection_response = self.gi.histories.create_dataset_collection(
            history_id=history_id,
            collection_description=dataset_collections.CollectionDescription(
                name="MyTestPair",
                type="paired",
                elements=[
                    dataset_collections.HistoryDatasetElement(name="forward", id=dataset1_id),
                    dataset_collections.HistoryDatasetElement(name="reverse", id=dataset2_id),
                ]
            )
        )
        return collection_response
github galaxyproject / bioblend / bioblend / _tests / TestGalaxyDatasetCollections.py View on Github external
def _create_pair_in_history(self, history_id):
        dataset1_id = self._test_dataset(history_id)
        dataset2_id = self._test_dataset(history_id)
        collection_response = self.gi.histories.create_dataset_collection(
            history_id=history_id,
            collection_description=dataset_collections.CollectionDescription(
                name="MyTestPair",
                type="paired",
                elements=[
                    dataset_collections.HistoryDatasetElement(name="forward", id=dataset1_id),
                    dataset_collections.HistoryDatasetElement(name="reverse", id=dataset2_id),
                ]
            )
        )
        return collection_response
github galaxyproject / bioblend / bioblend / _tests / TestGalaxyDatasetCollections.py View on Github external
def _create_pair_in_history(self, history_id):
        dataset1_id = self._test_dataset(history_id)
        dataset2_id = self._test_dataset(history_id)
        collection_response = self.gi.histories.create_dataset_collection(
            history_id=history_id,
            collection_description=collections.CollectionDescription(
                name="MyTestPair",
                type="paired",
                elements=[
                    collections.HistoryDatasetElement(name="forward", id=dataset1_id),
                    collections.HistoryDatasetElement(name="reverse", id=dataset2_id),
                ]
            )
        )
        return collection_response
github galaxyproject / bioblend / bioblend / _tests / TestGalaxyDatasetCollections.py View on Github external
def _create_pair_in_history(self, history_id):
        dataset1_id = self._test_dataset(history_id)
        dataset2_id = self._test_dataset(history_id)
        collection_response = self.gi.histories.create_dataset_collection(
            history_id=history_id,
            collection_description=collections.CollectionDescription(
                name="MyTestPair",
                type="paired",
                elements=[
                    collections.HistoryDatasetElement(name="forward", id=dataset1_id),
                    collections.HistoryDatasetElement(name="reverse", id=dataset2_id),
                ]
            )
        )
        return collection_response
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=dataset_collections.CollectionDescription(
                name="MyListOfPairedDatasets",
                type="list:paired",
                elements=[
                    dataset_collections.CollectionElement(
                        name="sample1",
                        type="paired",
                        elements=[
                            dataset_collections.HistoryDatasetElement(name="forward", id=dataset1_id),
                            dataset_collections.HistoryDatasetElement(name="reverse", id=dataset2_id),
                        ]
                    ),
                    dataset_collections.CollectionElement(
                        name="sample2",
                        type="paired",
                        elements=[
                            dataset_collections.HistoryDatasetElement(name="forward", id=dataset3_id),
github galaxyproject / bioblend / bioblend / _tests / TestGalaxyDatasetCollections.py View on Github external
def test_create_list_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)
        collection_response = self.gi.histories.create_dataset_collection(
            history_id=history_id,
            collection_description=collections.CollectionDescription(
                name="MyDatasetList",
                elements=[
                    collections.HistoryDatasetElement(name="sample1", id=dataset1_id),
                    collections.HistoryDatasetElement(name="sample2", id=dataset2_id),
                    collections.HistoryDatasetElement(name="sample3", id=dataset3_id),
                ]
            )
        )
        self.assertEqual(collection_response["name"], "MyDatasetList")
        self.assertEqual(collection_response["collection_type"], "list")
        elements = collection_response["elements"]
        self.assertEqual(len(elements), 3)
        self.assertEqual(elements[0]["element_index"], 0)
        self.assertEqual(elements[0]["object"]["id"], dataset1_id)
        self.assertEqual(elements[1]["object"]["id"], dataset2_id)
        self.assertEqual(elements[2]["object"]["id"], dataset3_id)
        self.assertEqual(elements[2]["element_identifier"], "sample3")
github galaxyproject / bioblend / bioblend / _tests / TestGalaxyObjects.py View on Github external
def test_run_workflow_with_dataset_collection(self):
        dataset1 = self.hist.paste_content(FOO_DATA)
        dataset2 = self.hist.paste_content(FOO_DATA_2)
        collection_description = dataset_collections.CollectionDescription(
            name="MyDatasetList",
            elements=[
                dataset_collections.HistoryDatasetElement(name="sample1", id=dataset1.id),
                dataset_collections.HistoryDatasetElement(name="sample2", id=dataset2.id),
            ]
        )
        dataset_collection = self.hist.create_dataset_collection(collection_description)
        input_map = {"Input Dataset Collection": dataset_collection,
                     "Input 2": dataset1}
        outputs, out_hist = self.wf.run(input_map, self.hist, wait=True)
        self.assertEqual(len(outputs), 1)
        out_hdca = outputs[0]
        self.assertIsInstance(out_hdca, wrappers.HistoryDatasetCollectionAssociation)
        self.assertEqual(out_hdca.collection_type, 'list')
        self.assertEqual(len(out_hdca.elements), 2)
        self.assertEqual(out_hist.id, self.hist.id)
github galaxyproject / galaxy / scripts / api / filter_failed_datasets_from_collection.py View on Github external
if len(matchingCollections) > 1:
    print("Error: more than one collection matching that id found (WTF?)")
    exit(1)

collectionId = matchingCollections[0]['id']
failedCollection = gi.histories.show_dataset_collection(historyId, collectionId)
okDatasets = [d for d in failedCollection['elements'] if d['object']['state'] == 'ok' and d['object']['file_size'] > 0]
notOkDatasets = [d for d in failedCollection['elements'] if d['object']['state'] != 'ok' or d['object']['file_size'] == 0]
okCollectionName = failedCollection['name'] + " (ok)"
notOkCollectionName = failedCollection['name'] + " (not ok)"

gi.histories.create_dataset_collection(
    history_id=historyId,
    collection_description=collections.CollectionDescription(
        name=okCollectionName,
        elements=[collections.HistoryDatasetElement(d['object']['name'], d['object']['id']) for d in okDatasets]))

gi.histories.create_dataset_collection(
    history_id=historyId,
    collection_description=collections.CollectionDescription(
        name=notOkCollectionName,
        elements=[collections.HistoryDatasetElement(d['object']['name'], d['object']['id']) for d in notOkDatasets]))
github galaxyproject / galaxy / scripts / api / filter_failed_datasets_from_collection.py View on Github external
exit(1)

if len(matchingCollections) > 1:
    print("Error: more than one collection matching that id found (WTF?)")
    exit(1)

collectionId = matchingCollections[0]['id']
failedCollection = gi.histories.show_dataset_collection(historyId, collectionId)
okDatasets = [d for d in failedCollection['elements'] if d['object']['state'] == 'ok' and d['object']['file_size'] > 0]
notOkDatasets = [d for d in failedCollection['elements'] if d['object']['state'] != 'ok' or d['object']['file_size'] == 0]
okCollectionName = failedCollection['name'] + " (ok)"
notOkCollectionName = failedCollection['name'] + " (not ok)"

gi.histories.create_dataset_collection(
    history_id=historyId,
    collection_description=collections.CollectionDescription(
        name=okCollectionName,
        elements=[collections.HistoryDatasetElement(d['object']['name'], d['object']['id']) for d in okDatasets]))

gi.histories.create_dataset_collection(
    history_id=historyId,
    collection_description=collections.CollectionDescription(
        name=notOkCollectionName,
        elements=[collections.HistoryDatasetElement(d['object']['name'], d['object']['id']) for d in notOkDatasets]))
github galaxyproject / galaxy / scripts / api / filter_failed_datasets_from_collection.py View on Github external
collectionId = matchingCollections[0]['id']
failedCollection = gi.histories.show_dataset_collection(historyId, collectionId)
okDatasets = [d for d in failedCollection['elements'] if d['object']['state'] == 'ok' and d['object']['file_size'] > 0]
notOkDatasets = [d for d in failedCollection['elements'] if d['object']['state'] != 'ok' or d['object']['file_size'] == 0]
okCollectionName = failedCollection['name'] + " (ok)"
notOkCollectionName = failedCollection['name'] + " (not ok)"

gi.histories.create_dataset_collection(
    history_id=historyId,
    collection_description=collections.CollectionDescription(
        name=okCollectionName,
        elements=[collections.HistoryDatasetElement(d['object']['name'], d['object']['id']) for d in okDatasets]))

gi.histories.create_dataset_collection(
    history_id=historyId,
    collection_description=collections.CollectionDescription(
        name=notOkCollectionName,
        elements=[collections.HistoryDatasetElement(d['object']['name'], d['object']['id']) for d in notOkDatasets]))