Source code for galaxy_test.api.test_dataset_collections

import json
import tarfile

from six import BytesIO

from galaxy_test.base.populators import DatasetCollectionPopulator, DatasetPopulator, skip_if_github_down
from ._framework import ApiTestCase


[docs]class DatasetCollectionApiTestCase(ApiTestCase):

[docs]    def setUp(self):
        super(DatasetCollectionApiTestCase, self).setUp()
        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
        self.dataset_collection_populator = DatasetCollectionPopulator(self.galaxy_interactor)
        self.history_id = self.dataset_populator.new_history()

[docs]    def test_create_pair_from_history(self):
        payload = self.dataset_collection_populator.create_pair_payload(
            self.history_id,
            instance_type="history",
        )
        create_response = self._post("dataset_collections", payload)
        dataset_collection = self._check_create_response(create_response)
        returned_datasets = dataset_collection["elements"]
        assert len(returned_datasets) == 2, dataset_collection

[docs]    def test_create_list_from_history(self):
        element_identifiers = self.dataset_collection_populator.list_identifiers(self.history_id)

        payload = dict(
            instance_type="history",
            history_id=self.history_id,
            element_identifiers=json.dumps(element_identifiers),
            collection_type="list",
        )

        create_response = self._post("dataset_collections", payload)
        dataset_collection = self._check_create_response(create_response)
        returned_datasets = dataset_collection["elements"]
        assert len(returned_datasets) == 3, dataset_collection

[docs]    def test_create_list_of_existing_pairs(self):
        pair_payload = self.dataset_collection_populator.create_pair_payload(
            self.history_id,
            instance_type="history",
        )
        pair_create_response = self._post("dataset_collections", pair_payload)
        dataset_collection = self._check_create_response(pair_create_response)
        hdca_id = dataset_collection["id"]

        element_identifiers = [
            dict(name="test1", src="hdca", id=hdca_id)
        ]

        payload = dict(
            instance_type="history",
            history_id=self.history_id,
            element_identifiers=json.dumps(element_identifiers),
            collection_type="list",
        )
        create_response = self._post("dataset_collections", payload)
        dataset_collection = self._check_create_response(create_response)
        returned_collections = dataset_collection["elements"]
        assert len(returned_collections) == 1, dataset_collection

[docs]    def test_create_list_of_new_pairs(self):
        identifiers = self.dataset_collection_populator.nested_collection_identifiers(self.history_id, "list:paired")
        payload = dict(
            collection_type="list:paired",
            instance_type="history",
            history_id=self.history_id,
            name="a nested collection",
            element_identifiers=json.dumps(identifiers),
        )
        create_response = self._post("dataset_collections", payload)
        dataset_collection = self._check_create_response(create_response)
        assert dataset_collection["collection_type"] == "list:paired"
        assert dataset_collection["name"] == "a nested collection"
        returned_collections = dataset_collection["elements"]
        assert len(returned_collections) == 1, dataset_collection
        pair_1_element = returned_collections[0]
        self._assert_has_keys(pair_1_element, "element_identifier", "element_index", "object")
        assert pair_1_element["element_identifier"] == "test_level_1", pair_1_element
        assert pair_1_element["element_index"] == 0, pair_1_element
        pair_1_object = pair_1_element["object"]
        self._assert_has_keys(pair_1_object, "collection_type", "elements", "element_count")
        self.assertEqual(pair_1_object["collection_type"], "paired")
        self.assertEqual(pair_1_object["populated"], True)
        pair_elements = pair_1_object["elements"]
        assert len(pair_elements) == 2
        pair_1_element_1 = pair_elements[0]
        assert pair_1_element_1["element_index"] == 0

[docs]    def test_list_download(self):
        fetch_response = self.dataset_collection_populator.create_list_in_history(self.history_id, direct_upload=True).json()
        dataset_collection = self.dataset_collection_populator.wait_for_fetched_collection(fetch_response)
        returned_dce = dataset_collection["elements"]
        assert len(returned_dce) == 3, dataset_collection
        create_response = self._download_dataset_collection(history_id=self.history_id, hdca_id=dataset_collection['id'])
        self._assert_status_code_is(create_response, 200)
        tar_contents = tarfile.open(fileobj=BytesIO(create_response.content))
        namelist = tar_contents.getnames()
        assert len(namelist) == 3, "Expected 3 elements in [%s]" % namelist
        collection_name = dataset_collection['name']
        for element, zip_path in zip(returned_dce, namelist):
            assert "%s/%s.%s" % (collection_name, element['element_identifier'], element['object']['file_ext']) == zip_path

[docs]    def test_pair_download(self):
        fetch_response = self.dataset_collection_populator.create_pair_in_history(self.history_id, direct_upload=True).json()
        dataset_collection = self.dataset_collection_populator.wait_for_fetched_collection(fetch_response)
        returned_dce = dataset_collection["elements"]
        assert len(returned_dce) == 2, dataset_collection
        hdca_id = dataset_collection['id']
        create_response = self._download_dataset_collection(history_id=self.history_id, hdca_id=hdca_id)
        self._assert_status_code_is(create_response, 200)
        tar_contents = tarfile.open(fileobj=BytesIO(create_response.content))
        namelist = tar_contents.getnames()
        assert len(namelist) == 2, "Expected 2 elements in [%s]" % namelist
        collection_name = dataset_collection['name']
        for element, zip_path in zip(returned_dce, namelist):
            assert "%s/%s.%s" % (collection_name, element['element_identifier'], element['object']['file_ext']) == zip_path

[docs]    def test_list_pair_download(self):
        fetch_response = self.dataset_collection_populator.create_list_of_pairs_in_history(self.history_id).json()
        dataset_collection = self.dataset_collection_populator.wait_for_fetched_collection(fetch_response)
        returned_dce = dataset_collection["elements"]
        assert len(returned_dce) == 1, dataset_collection
        list_collection_name = dataset_collection['name']
        pair = returned_dce[0]
        create_response = self._download_dataset_collection(history_id=self.history_id, hdca_id=dataset_collection['id'])
        self._assert_status_code_is(create_response, 200)
        tar_contents = tarfile.open(fileobj=BytesIO(create_response.content))
        namelist = tar_contents.getnames()
        assert len(namelist) == 2, "Expected 2 elements in [%s]" % namelist
        pair_collection_name = pair['element_identifier']
        for element, zip_path in zip(pair['object']['elements'], namelist):
            assert "%s/%s/%s.%s" % (list_collection_name, pair_collection_name, element['element_identifier'], element['object']['file_ext']) == zip_path

[docs]    def test_list_list_download(self):
        dataset_collection = self.dataset_collection_populator.create_list_of_list_in_history(self.history_id).json()
        self.dataset_collection_populator.wait_for_dataset_collection(dataset_collection, assert_ok=True)
        returned_dce = dataset_collection["elements"]
        assert len(returned_dce) == 1, dataset_collection
        create_response = self._download_dataset_collection(history_id=self.history_id, hdca_id=dataset_collection['id'])
        self._assert_status_code_is(create_response, 200)
        tar_contents = tarfile.open(fileobj=BytesIO(create_response.content))
        namelist = tar_contents.getnames()
        assert len(namelist) == 3, "Expected 3 elements in [%s]" % namelist

[docs]    def test_list_list_list_download(self):
        dataset_collection = self.dataset_collection_populator.create_list_of_list_in_history(self.history_id, collection_type='list:list:list').json()
        self.dataset_collection_populator.wait_for_dataset_collection(dataset_collection, assert_ok=True)
        returned_dce = dataset_collection["elements"]
        assert len(returned_dce) == 1, dataset_collection
        create_response = self._download_dataset_collection(history_id=self.history_id, hdca_id=dataset_collection['id'])
        self._assert_status_code_is(create_response, 200)
        tar_contents = tarfile.open(fileobj=BytesIO(create_response.content))
        namelist = tar_contents.getnames()
        assert len(namelist) == 3, "Expected 3 elements in [%s]" % namelist

[docs]    def test_hda_security(self):
        element_identifiers = self.dataset_collection_populator.pair_identifiers(self.history_id)
        self.dataset_populator.make_private(self.history_id, element_identifiers[0]["id"])
        with self._different_user():
            history_id = self.dataset_populator.new_history()
            payload = dict(
                instance_type="history",
                history_id=history_id,
                element_identifiers=json.dumps(element_identifiers),
                collection_type="paired",
            )
            create_response = self._post("dataset_collections", payload)
            self._assert_status_code_is(create_response, 403)

[docs]    def test_enforces_unique_names(self):
        element_identifiers = self.dataset_collection_populator.list_identifiers(self.history_id)
        element_identifiers[2]["name"] = element_identifiers[0]["name"]
        payload = dict(
            instance_type="history",
            history_id=self.history_id,
            element_identifiers=json.dumps(element_identifiers),
            collection_type="list",
        )

        create_response = self._post("dataset_collections", payload)
        self._assert_status_code_is(create_response, 400)

[docs]    def test_upload_collection(self):
        elements = [{"src": "files", "dbkey": "hg19", "info": "my cool bed", "tags": ["name:data1", "group:condition:treated", "machine:illumina"]}]
        targets = [{
            "destination": {"type": "hdca"},
            "elements": elements,
            "collection_type": "list",
            "name": "Test upload",
            "tags": ["name:collection1"]
        }]
        payload = {
            "history_id": self.history_id,
            "targets": json.dumps(targets),
            "__files": {"files_0|file_data": open(self.test_data_resolver.get_filename("4.bed"))},
        }
        self.dataset_populator.fetch(payload)
        hdca = self._assert_one_collection_created_in_history()
        self.assertEqual(hdca["name"], "Test upload")
        hdca_tags = hdca["tags"]
        assert len(hdca_tags) == 1
        assert "name:collection1" in hdca_tags
        assert len(hdca["elements"]) == 1, hdca
        element0 = hdca["elements"][0]
        assert element0["element_identifier"] == "4.bed"
        dataset0 = element0["object"]
        assert dataset0["file_size"] == 61
        dataset_tags = dataset0["tags"]
        assert len(dataset_tags) == 3, dataset0

[docs]    def test_upload_nested(self):
        elements = [{"name": "samp1", "elements": [{"src": "files", "dbkey": "hg19", "info": "my cool bed"}]}]
        targets = [{
            "destination": {"type": "hdca"},
            "elements": elements,
            "collection_type": "list:list",
            "name": "Test upload",
        }]
        payload = {
            "history_id": self.history_id,
            "targets": json.dumps(targets),
            "__files": {"files_0|file_data": open(self.test_data_resolver.get_filename("4.bed"))},
        }
        self.dataset_populator.fetch(payload)
        hdca = self._assert_one_collection_created_in_history()
        self.assertEqual(hdca["name"], "Test upload")
        assert len(hdca["elements"]) == 1, hdca
        element0 = hdca["elements"][0]
        assert element0["element_identifier"] == "samp1"

[docs]    @skip_if_github_down
    def test_upload_collection_from_url(self):
        elements = [{"src": "url", "url": "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/4.bed", "info": "my cool bed"}]
        targets = [{
            "destination": {"type": "hdca"},
            "elements": elements,
            "collection_type": "list",
        }]
        payload = {
            "history_id": self.history_id,
            "targets": json.dumps(targets),
            "__files": {"files_0|file_data": open(self.test_data_resolver.get_filename("4.bed"))},
        }
        self.dataset_populator.fetch(payload)
        hdca = self._assert_one_collection_created_in_history()
        assert len(hdca["elements"]) == 1, hdca
        element0 = hdca["elements"][0]
        assert element0["element_identifier"] == "4.bed"
        assert element0["object"]["file_size"] == 61

    def _assert_one_collection_created_in_history(self):
        contents_response = self._get("histories/%s/contents/dataset_collections" % self.history_id)
        self._assert_status_code_is(contents_response, 200)
        contents = contents_response.json()
        assert len(contents) == 1
        hdca = contents[0]
        assert hdca["history_content_type"] == "dataset_collection"
        hdca_id = hdca["id"]
        collection_response = self._get("histories/%s/contents/dataset_collections/%s" % (self.history_id, hdca_id))
        self._assert_status_code_is(collection_response, 200)
        return collection_response.json()

    def _check_create_response(self, create_response):
        self._assert_status_code_is(create_response, 200)
        dataset_collection = create_response.json()
        self._assert_has_keys(dataset_collection, "elements", "url", "name", "collection_type", "element_count")
        return dataset_collection

    def _download_dataset_collection(self, history_id, hdca_id):
        return self._get("histories/%s/contents/dataset_collections/%s/download" % (history_id, hdca_id))