Source code for biothings.tests.web

    Biothings Test Helpers

    There are two types of test classes that provide utilities to
    three types of test cases, developed in the standalone apps.

    The two types of test classes are:
        BiothingsWebTest, which targets a running web server.
        BiothingsWebAppTest, which targets a web server config file.

    To further illustrate, for any biothings web applications, it
    typically conforms to the following architectures:

    Layer 3: A web server that implements the behaviors defined below.
    Layer 2: A config file that defines how to serve data from ES.
    Layer 1: An Elasticsearch server with data.

    And for the two types of test classes, to explain their differences
    in the context of the layered design described above:
        BiothingsWebTest targets an existing Layer 3 endpoint.
        BiothingsWebAppTest targets layer 2 and runs its own layer 3.
        Note no utility is provided to directly talk to layer 1.

    The above discussed the python structures provided as programming
    utilities, on the other hand, there are three types of use cases,
    or testing objectives:
        L3 Data test, which is aimed to test the data integrity of an API.
            It subclasses BiothingsWebTest and ensures all layers working.
            The data has to reside in elasticsearch already.
        L3 Feature test, which is aimed to test the API implementation.
            It makes sure the settings in config file is reflected.
            These tests work on production data and require constant
            updates to keep the test cases in sync with the actual data.
            These test cases subclass BiothingsWebTest as well and asl
            require existing production data in elasticsearch.
        L2 Feature test, doing basically the same things as above but uses
            a small set of data that it ingests into elasticsearch.
            This is a lightweight test for development and automated testings
            for each new commit. It comes with data it will ingest in ES
            and does not require any existing data setup to run.

    To illustrate the differences in a chart:
    | Objectives   | Class               | Test Target     | ES Has Data | Automated Testing Trigger |
    | L3 Data Test | BiothingsWebTest    | A Running API   | Yes         | Data Release              |
    | L3 Feature T.| BiothingsWebTest    | A Running API   | Yes         | Data Release & New Commit |
    | L2 Feature T.| BiothingsWebAppTest | A config module | No*         | New Commit                |
    * For L2 Feature Test, data is defined in the test cases and will be automatically ingested into
      Elasticsearch at the start of the testing and get deleted after testing finishes. The other
      two types of testing require existing production data on the corresponding ES servers.

    In development, it is certainly possible for a particular test case
    to fall under multiple test types, then the developer can use proper
    inheritance structures to avoid repeating the specific test case.

    In terms of naming conventions, sometimes the L3 tests are grouped
    together and called remote tests, as they mostly target remote servers.
    And the L2 tests are called local tests, as they starts a local server.

    L3 Envs:


    L2 Envs:

    < Config Module Override >

import glob
import inspect
import json
import os
from functools import partial
from typing import Optional, Union

import pytest
import requests
import urllib3
from requests.adapters import HTTPAdapter
from requests.packages.urllib3.util.retry import Retry

from biothings.utils.common import traverse
from biothings.web.launcher import BiothingsAPI
from biothings.web.settings import configs
from tornado.ioloop import IOLoop
from tornado.testing import AsyncHTTPTestCase

[docs]class BiothingsWebTest: # relative path parsing configuration scheme = 'http' prefix = 'v1' host = ''
[docs] def request(self, path, method='GET', expect=200, **kwargs): """ Use requests library to make an HTTP request. Ensure path is translated to an absolute path. Conveniently check if status code is as expected. """ url = self.get_url(path) res = requests.request(method, url, **kwargs) assert res.status_code == expect, res.text return res
[docs] def get_url(self, path): """ Try best effort to get a full url to make a request. Return an absolute url when class var 'host' is defined. If not, return a path relative to the host root. """ scheme = os.getenv("TEST_SCHEME", self.scheme) prefix = os.getenv("TEST_PREFIX", self.prefix).strip('/') host = os.getenv("TEST_HOST",'/') # already an absolute path if path.lower().startswith(("http://", "https://")): return path # path standardization if not path.startswith('/'): if prefix: # append prefix path = '/'.join((prefix, path)) path = '/' + path # host standardization if host: path = f"{scheme}://{host}{path}" return path
[docs] def query(self, method='GET', endpoint='query', hits=True, data=None, json=None, **kwargs): """ Make a query and assert positive hits by default. Assert zero hit when hits is set to False. """ if method == 'GET': res = self.request( endpoint, params=kwargs, data=data, json=json).json() assert bool(res.get('hits')) == hits return res if method == 'POST': res = self.request( endpoint, method=method, params=kwargs, data=data, json=json).json() for item in res: # list if "_id" not in item: _hits = False break else: _hits = bool(res) assert _hits is hits return res raise ValueError('Invalid Request Method.')
[docs] @staticmethod def msgpack_ok(packed_bytes): """ Load msgpack into a dict """ try: import msgpack except ImportError: pytest.skip('Msgpack is not installed.') try: dic = msgpack.unpackb(packed_bytes) except BaseException: # pylint: disable=bare-except assert False, 'Not a valid Msgpack binary.' return dic
[docs] @staticmethod def value_in_result(value, result: Union[dict, list], key: str, case_insensitive: bool = False) -> bool: """ Check if value is in result at specific key Elasticsearch does not care if a field has one or more values (arrays), so you may get a search with multiple values in one field. You were expecting a result of type T but now you have a List[T] which is bad. In testing, usually any one element in the list eq. to the value you're looking for, you don't really care which. This helper function checks if the value is at a key, regardless of the details of nesting, so you can just do this: assert self.value_in_result(value, result, '') Caveats: case_insensitive only calls .lower() and does not care about locale/ unicode/anything Args: value: value to look for result: dict or list of input, most likely from the APIs key: dot delimited key notation case_insensitive: for str comparisons, invoke .lower() first Returns: boolean indicating whether the value is found at the key Raises: TypeError: when case_insensitive set to true on unsupported types """ res_at_key = [] if case_insensitive: try: value = value.lower() except Exception: raise TypeError("failed to invoke method .lower()") for k, v in traverse(result, leaf_node=True): if k == key: if case_insensitive: try: v = v.lower() except Exception: raise TypeError("failed to invoke method .lower()") res_at_key.append(v) return value in res_at_key
[docs]class BiothingsWebAppTest(BiothingsWebTest, AsyncHTTPTestCase): """ Starts the tornado application to run tests locally. Need a under the test class folder. """ TEST_DATA_DIR_NAME: Optional[str] = None # set sub-dir name @pytest.fixture(scope="class", autouse=True) def _setup_elasticsearch(self): # Author: Zhongchao Qian # if not self.TEST_DATA_DIR_NAME: yield # do no setup and yield control to pytest return s = requests.Session() s.mount('http://', adapter=requests.adapters.HTTPAdapter( max_retries=urllib3.Retry(total=5, backoff_factor=3.0) )) # values seem reasonable es_host = 'http://' + self.config.ES_HOST server_info = s.get(es_host).json() version_info = tuple(int(v) for v in server_info['version']['number'].split('.')) if version_info[0] < 6 or version_info[0] == 6 and version_info[1] < 8: pytest.exit("Tests need to be running on ES6.8+") indices = [] # for cleanup later data_dir_path = os.path.dirname(inspect.getfile(type(self))) data_dir_path = os.path.join(data_dir_path, 'test_data') data_dir_path = os.path.join(data_dir_path, self.TEST_DATA_DIR_NAME) glob_json_pattern = os.path.join(data_dir_path, '*.json') # wrap around in try-finally so the index is guaranteed to be err_flag = False try: # TODO No match seems to cause illegible error for index_mapping_path in glob.glob(glob_json_pattern): index_name = os.path.basename(index_mapping_path) index_name = os.path.splitext(index_name)[0] indices.append(index_name) r = s.head(f'{es_host}/{index_name}') if r.status_code != 404: if os.environ.get('TEST_KEEPDATA'): continue raise RuntimeError(f"{index_name} already exists!") with open(index_mapping_path, 'r') as f: mapping = json.load(f) data_path = os.path.join(data_dir_path, index_name + '.ndjson') with open(data_path, 'r') as f: bulk_data = if version_info[0] == 6: r = s.put(f'{es_host}/{index_name}', json=mapping, params={'include_type_name': 'false'}) elif version_info[0] > 6: r = s.put(f'{es_host}/{index_name}', json=mapping) else: raise RuntimeError("This shouldn't have happened") r.raise_for_status() if version_info[0] < 8: r ='{es_host}/{index_name}/_doc/_bulk', data=bulk_data, headers={'Content-type': 'application/x-ndjson'}) elif version_info[0] >= 8: r ='{es_host}/{index_name}/_bulk', data=bulk_data, headers={'Content-type': 'application/x-ndjson'}) else: raise RuntimeError("This shouldn't have happened") r.raise_for_status()'{es_host}/{index_name}/_refresh') yield except Exception as e: err_msg = str(e) err_flag = True finally: if not os.environ.get('TEST_KEEPDATA'): for index_name in indices: s.delete(f'{es_host}/{index_name}') if err_flag: pytest.exit("Error setting up ES for tests:", err_msg) @property def config(self): if not hasattr(self, '_config'): conf = os.getenv("TEST_CONF", '') base = os.path.dirname(inspect.getfile(type(self))) file = os.path.join(base, conf) self._config = configs.load(file) return self._config # override
[docs] def get_new_ioloop(self): return IOLoop.current()
# override
[docs] def get_app(self): prefix = self.config.APP_PREFIX version = self.config.APP_VERSION self.prefix = f'{prefix}/{version}' return BiothingsAPI.get_app(self.config)
# override
[docs] def request(self, path, method="GET", expect=200, **kwargs): url = self.get_url(path) func = partial(requests.request, method, url, **kwargs) res = self.io_loop.run_sync( lambda: self.io_loop.run_in_executor(None, func)) assert res.status_code == expect, res.text return res
# override
[docs] def get_url(self, path): path = BiothingsWebTest.get_url(self, path) return AsyncHTTPTestCase.get_url(self, path)
# Compatibility BiothingsTestCase = BiothingsWebAppTest BiothingsDataTest = BiothingsWebTest