Merge pull request #53 from antgonza/actually-test

add nosetests

Author: charles-cowart

Diff for: .github/workflows/qiita-ci.yml

@@ -81,6 +81,12 @@ jobs:
           conda activate qiita_client
           pip --quiet install .
 
+          # Note that the qiita conda environment has installed the qiita_client "master branch"
+          # but to fully test we need to install the current branch of qiita_client
+          conda deactivate
+          conda activate qiita
+          pip --quiet install .
+
       - name: Starting Main Services
         shell: bash -l {0}
         run: |
@@ -119,6 +125,9 @@ jobs:
           conda activate qiita_client
           export QIITA_ROOTCA_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
           export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg
+          export QIITA_CLIENT_DEBUG_LEVEL=DEBUG
+          nosetests --with-doctest --with-coverage --cover-package=qiita_client
+
       - uses: codecov/codecov-action@v3
         with:
          token: ${{ secrets.CODECOV_TOKEN }}

Diff for: README.md

@@ -9,7 +9,7 @@ This package includes the Qiita Client utility library, a library to simplify th
 
 How to test this package?
 -------------------------
-In order to test the Qiita Client package, a local installation of Qiita should be running in test mode on the address `https://localhost:21174`, with the default test database created in Qiita's test suite.
+In order to test the Qiita Client package, a local installation of Qiita should be running in test mode on the address `https://localhost:8383`, with the default test database created in Qiita's test suite.
 Also, if Qiita is running with the default server SSL certificate, you need to export the variable `QIITA_ROOTCA_CERT` in your environment, so the Qiita Client can perform secure connections against the Qiita server:
 
 ```bash

Diff for: qiita_client/plugin.py

@@ -250,7 +250,7 @@ def __call__(self, server_url, job_id, output_dir):
                               # this value will prevent underlying libraries
                               # from validating the server's cert using
                               # certifi's pem cache.
-                              ca_cert=environ['QIITA_ROOTCA_CERT'])
+                              ca_cert=config.get('oauth2', 'SERVER_CERT'))
 
         if job_id == 'register':
             self._register(qclient)
@@ -379,5 +379,6 @@ def register_command(self, command):
 PUBLICATIONS = %s
 
 [oauth2]
+SERVER_CERT = %s
 CLIENT_ID = %s
 CLIENT_SECRET = %s"""

Diff for: qiita_client/qiita_client.py

@@ -28,9 +28,16 @@
 logger = logging.getLogger(__name__)
 
 JOB_COMPLETED = False
-MAX_RETRIES = 3
-MIN_TIME_SLEEP = 180
-MAX_TIME_SLEEP = 360
+# if the log level is not CRITICAL, the default, then we not expect slow
+# responses from the server so let's make the retries values small
+if logger.level != logging.CRITICAL:
+    MAX_RETRIES = 2
+    MIN_TIME_SLEEP = 2
+    MAX_TIME_SLEEP = 5
+else:
+    MAX_RETRIES = 3
+    MIN_TIME_SLEEP = 180
+    MAX_TIME_SLEEP = 360
 BLANK_FILE_THRESHOLD = 100
 
 

Diff for: qiita_client/testing.py

@@ -15,6 +15,7 @@
 import logging
 
 logger = logging.getLogger(__name__)
+URL = "https://localhost:8383"
 
 
 class PluginTestCase(TestCase):
@@ -24,12 +25,13 @@ def setUpClass(cls):
         cls.client_id = '19ndkO3oMKsoChjVVWluF7QkxHRfYhTKSFbAVt8IhK7gZgDaO4'
         cls.client_secret = ('J7FfQ7CQdOxuKhQAf1eoGgBAE81Ns8Gu3EKaWFm3IO2JKh'
                              'AmmCWZuabe0O5Mp28s1')
-        qiita_port = int(environ.get('QIITA_PORT', 21174))
+        cls.ca_cert = environ.get('QIITA_ROOTCA_CERT')
 
         # do not rely on defining ca_cert for these tests. Instead append
         # the appropriate CA cert to certifi's pem file.
-        cls.qclient = QiitaClient("https://localhost:%d" % qiita_port,
-                                  cls.client_id, cls.client_secret)
+        cls.qclient = QiitaClient(
+            URL, cls.client_id, cls.client_secret, cls.ca_cert)
+
         logger.debug(
             'PluginTestCase.setUpClass() token %s' % cls.qclient._token)
         cls.qclient.post('/apitest/reload_plugins/')

Diff for: qiita_client/tests/test_plugin.py

@@ -13,7 +13,7 @@
 from json import dumps
 from tempfile import mkdtemp
 
-from qiita_client.testing import PluginTestCase
+from qiita_client.testing import PluginTestCase, URL
 from qiita_client import (QiitaPlugin, QiitaTypePlugin, QiitaCommand,
                           QiitaArtifactType, ArtifactInfo)
 
@@ -146,7 +146,8 @@ def html_generator_func(a, b, c, d):
                      'PLUGIN_TYPE = artifact definition\n',
                      'PUBLICATIONS = \n',
                      '\n',
-                     '[oauth2]\n']
+                     '[oauth2]\n',
+                     'SERVER_CERT = \n']
         # We will test the last 2 lines independently since they're variable
         # in each test run
         self.assertEqual(conf[:-2], exp_lines)
@@ -167,12 +168,12 @@ def html_generator_func(a, b, c, d):
                                  validate_func, html_generator_func, atypes)
 
         # Generate the config file for the new plugin
-        tester.generate_config('ls', 'echo')
+        tester.generate_config('ls', 'echo', self.ca_cert)
         # Ask Qiita to reload the plugins
         self.qclient.post('/apitest/reload_plugins/')
 
         # Install the current plugin
-        tester("https://localhost:21174", 'register', 'ignored')
+        tester(URL, 'register', 'ignored')
 
         # Check that it has been installed
         obs = self.qclient.get('/qiita_db/plugins/NewPlugin/1.0.0/')
@@ -211,9 +212,9 @@ def func(qclient, job_id, job_params, working_dir):
                              {'out1': 'Demultiplexed'})
         tester.register_command(a_cmd)
 
-        tester.generate_config('ls', 'echo')
+        tester.generate_config('ls', 'echo', self.ca_cert)
         self.qclient.post('/apitest/reload_plugins/')
-        tester("https://localhost:21174", 'register', 'ignored')
+        tester(URL, 'register', 'ignored')
 
         obs = self.qclient.get('/qiita_db/plugins/NewPlugin/0.0.1/')
         self.assertEqual(obs['name'], 'NewPlugin')
@@ -229,7 +230,7 @@ def func(qclient, job_id, job_params, working_dir):
                 'status': 'queued'}
         job_id = self.qclient.post('/apitest/processing_job/',
                                    data=data)['job']
-        tester("https://localhost:21174", job_id, self.outdir)
+        tester(URL, job_id, self.outdir)
 
         status = self._wait_for_running_job(job_id)
         self.assertEqual(status, 'success')

Diff for: qiita_client/tests/test_qiita_client.py

@@ -7,15 +7,15 @@
 # -----------------------------------------------------------------------------
 
 from unittest import TestCase, main
-from os import remove, close, environ
+from os import remove, close
 from os.path import basename, exists
 from tempfile import mkstemp
 from json import dumps
 import pandas as pd
 
 from qiita_client.qiita_client import (QiitaClient, _format_payload,
                                        ArtifactInfo)
-from qiita_client.testing import PluginTestCase
+from qiita_client.testing import PluginTestCase, URL
 from qiita_client.exceptions import BadRequestError
 
 CLIENT_ID = '19ndkO3oMKsoChjVVWluF7QkxHRfYhTKSFbAVt8IhK7gZgDaO4'
@@ -97,12 +97,9 @@ def test_format_payload_error(self):
 
 class QiitaClientTests(PluginTestCase):
     def setUp(self):
-        self.tester = QiitaClient("https://localhost:21174",
+        self.tester = QiitaClient(URL,
                                   CLIENT_ID,
-                                  CLIENT_SECRET)
-        self.bad_tester = QiitaClient("https://localhost:21174",
-                                      BAD_CLIENT_ID,
-                                      CLIENT_SECRET)
+                                  CLIENT_SECRET, self.ca_cert)
         self.clean_up_files = []
 
         # making assertRaisesRegex compatible with Python 2.7 and 3.9
@@ -115,14 +112,14 @@ def tearDown(self):
                 remove(fp)
 
     def test_init(self):
-        obs = QiitaClient("https://localhost:21174",
+        obs = QiitaClient(URL,
                           CLIENT_ID,
                           CLIENT_SECRET,
-                          ca_cert=environ['QIITA_ROOT_CA'])
-        self.assertEqual(obs._server_url, "https://localhost:21174")
+                          ca_cert=self.ca_cert)
+        self.assertEqual(obs._server_url, URL)
         self.assertEqual(obs._client_id, CLIENT_ID)
         self.assertEqual(obs._client_secret, CLIENT_SECRET)
-        self.assertEqual(obs._verify, environ['QIITA_ROOT_CA'])
+        self.assertEqual(obs._verify, self.ca_cert)
 
     def test_get(self):
         obs = self.tester.get("/qiita_db/artifacts/1/")
@@ -244,9 +241,14 @@ def test_update_job_step_ignore_failure(self):
 
         # confirm that update_job_step behaves as before when ignore_error
         # parameter absent or set to False.
+        self.bad_tester = QiitaClient(URL,
+                                      BAD_CLIENT_ID,
+                                      CLIENT_SECRET,
+                                      self.ca_cert)
 
         with self.assertRaises(BaseException):
-            self.bad_tester.update_job_step(job_id, new_step)
+            self.bad_tester.update_job_step(
+                job_id, new_step, ignore_error=False)
 
         with self.assertRaises(BaseException):
             self.bad_tester.update_job_step(job_id,