testing might fail due to diff parameter names

[sjanssen2]

Hi @antgonza ,
in my local setup, one test for qp-target-gene fails. Namely

qp-target-gene/qp_target_gene/tests/test_pick_otus.py

Lines 100 to 139 in 858436e

	def test_pick_closed_reference_otus(self):
	# Create a new job
	data = {'user': 'demo@microbio.me',
	'command': dumps(['QIIMEq2', '1.9.1',
	'Pick closed-reference OTUs']),
	'status': 'running',
	'parameters': dumps(self.parameters)}
	job_id = self.qclient.post(
	'/apitest/processing_job/', data=data)['job']
	# These filepaths do not exist in Qiita - create them
	fps = self.qclient.get('/qiita_db/artifacts/2/')['files']
	fasta_fp = fps['preprocessed_fasta'][0]['filepath']
	self.parameters['reference-seq'] = '/tmp/seq.fna'
	self.parameters['reference-tax'] = '/tmp/tax.txt'
	with open(fasta_fp, 'w') as f:
	f.write(READS)
	# self._clean_up_files.append(fasta_fp)
	with open(self.parameters['reference-seq'], 'w') as f:
	f.write(REF_SEQ)
	# self._clean_up_files.append(self.parameters['reference-seq'])
	with open(self.parameters['reference-tax'], 'w') as f:
	f.write(REF_TAX)
	# self._clean_up_files.append(self.parameters['reference-tax'])
	out_dir = mkdtemp()
	self._clean_up_files.append(out_dir)
	obs_success, obs_ainfo, obs_msg = pick_closed_reference_otus(
	self.qclient, job_id, self.parameters, out_dir)
	self.assertEqual(obs_msg, "")
	self.assertTrue(obs_success)
	path_builder = partial(join, out_dir, 'cr_otus')
	log_fp = glob(path_builder("log_*.txt"))[0]
	fps = [(path_builder("otu_table.biom"), "biom"),
	(path_builder("sortmerna_picked_otus"), "directory"),
	(path_builder("sortmerna_picked_otus.tgz"), "tgz"),
	(log_fp, "log")]
	exp_ainfo = [ArtifactInfo('OTU table', 'BIOM', fps)]
	self.assertEqual(obs_ainfo, exp_ainfo)

Looking at the plugin configuration, I see parameters reference-seq and reference-tax:

qp-target-gene/qp_target_gene/__init__.py

Lines 148 to 149 in 858436e

	'reference-seq': '/databases/gg/13_8/rep_set/97_otus.fasta',
	'reference-tax': '/databases/gg/13_8/taxonomy/97_otu_taxonomy.txt',

However, the populate_test_db.sql inserts a parameter reference, but not reference-seq nor reference-tax.
https://github.com/qiita-spots/qiita/blob/a34dcebc44ea6408340d31ecaf0efd1f78e3cc6b/qiita_db/support_files/populate_test_db.sql#L1818

Updating the plugin with config file information does not change values, I figure because a plugin with same name and version number already exists in the re-populated DB.

This issue might be arising from the larger change of the patch system: qiita-spots/qiita@7b9cb33 Not sure if you ever re-executed the qp-target-gene github tests after this change.

Full error message is below:

root@363bf284c221:/qp-target-gene# pytest qp_target_gene/tests/test_pick_otus.py 
==================================== test session starts =====================================
platform linux2 -- Python 2.7.18, pytest-4.6.11, py-1.11.0, pluggy-0.13.1
rootdir: /qp-target-gene
collected 1 item                                                                             

qp_target_gene/tests/test_pick_otus.py F                                               [100%]

========================================== FAILURES ==========================================
_______________________ PickOTUsTests.test_pick_closed_reference_otus ________________________

self = <qp_target_gene.tests.test_pick_otus.PickOTUsTests testMethod=test_pick_closed_reference_otus>

    def test_pick_closed_reference_otus(self):
        # Create a new job
        data = {'user': 'demo@microbio.me',
                'command': dumps(['QIIMEq2', '1.9.1',
                                  'Pick closed-reference OTUs']),
                'status': 'running',
                'parameters': dumps(self.parameters)}
        job_id = self.qclient.post(
>           '/apitest/processing_job/', data=data)['job']

qp_target_gene/tests/test_pick_otus.py:59: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
/usr/local/lib/python2.7/dist-packages/qiita_client/qiita_client.py:450: in post
    self._session.post, url, rettype='json', **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <qiita_client.qiita_client.QiitaClient object at 0x731b17dd1fd0>
req = <bound method Session.post of <requests.sessions.Session object at 0x731b17dd1f10>>
url = 'https://tinqiita-qiita-1:21174/apitest/processing_job/', rettype = 'json'
kwargs = {'data': {'command': '["QIIMEq2", "1.9.1", "Pick closed-reference OTUs"]', 'parameters': '{"input_data": 2, "reference...overage": 0.97, "sortmerna_e_value": 1, "sortmerna_max_pos": 10000}', 'status': 'running', 'user': 'demo@microbio.me'}}
retries = 0, r = <Response [500]>

    def _request_retry(self, req, url, rettype='json', **kwargs):
        """Executes a request retrying it 2 times in case of failure
    
        Parameters
        ----------
        req : function
            The request to execute
        rettype : string
            The return type of the function, either "json" (default) or
            if e.g. files are transferred "content"
        url : str
            The url to access in the server
        kwargs : dict
            The request kwargs
    
        Returns
        -------
        dict or None or plain content IF rettype='content'
            The JSON information in the request response, if any
    
        Raises
        ------
        NotFoundError
            If the request returned a 404 error
        BadRequestError
            If the request returned a 400 error
        ForbiddenError
            If the request returned a 403 error
        RuntimeError
            If the request did not succeed due to unknown causes
    
        Notes
        -----
        After doing some research on the topic, there are multiple ways of
        engineering the number of times a request should be retried (multiple
        sources - most of them on RPC systems). A short summary of those are:
          1. Keep retrying indefinitely
          2. The probability of retrying a request is based on the number of
          retries already done, as well as the cost of a retry
          3. Retry just once
    
        Number 1 could create an infinite loop. Number 2 is too complex and
        the cost of retrying depends on the actual work that we are currently
        doing (which is unknown to the current function). We thus decided to
        implement 3, which is simple and allows to overcome simple
        communication problems.
        """
        logger.debug('Entered QiitaClient._request_retry()')
        url = self._server_url + url
        retries = MAX_RETRIES
        while retries > 0:
            retries -= 1
            r = self._request_oauth2(
                req, rettype, url, verify=self._verify, **kwargs)
            r.close()
            # There are some error codes that the specification says that they
            # shouldn't be retried
            if r.status_code == 404:
                raise NotFoundError(r.text)
            elif r.status_code == 403:
                raise ForbiddenError(r.text)
            elif r.status_code == 400:
                raise BadRequestError(r.text)
            elif r.status_code in (500, 405):
                raise RuntimeError(
                    "Request '%s %s' did not succeed. Status code: %d. "
>                   "Message: %s" % (req.__name__, url, r.status_code, r.text))
E               RuntimeError: Request 'post https://tinqiita-qiita-1:21174/apitest/processing_job/' did not succeed. Status code: 500. Message: The provided JSON string doesn't encode a parameter set for command 3. Extra parameters: reference-tax, reference-seq

/usr/local/lib/python2.7/dist-packages/qiita_client/qiita_client.py:387: RuntimeError
----------------------------------- Captured stderr setup ------------------------------------
2025-09-09 21:01:49,196 qiita_client.testing DEBUG    Entered PluginTestCase.setUpClass()
2025-09-09 21:01:49,200 qiita_client.qiita_client DEBUG    Entered QiitaClient._fetch_token()
2025-09-09 21:01:49,200 qiita_client.qiita_client DEBUG    data = {'client_secret': 'J7FfQ7CQdOxuKhQAf1eoGgBAE81Ns8Gu3EKaWFm3IO2JKhAmmCWZuabe0O5Mp28s1', 'grant_type': 'client', 'client_id': '19ndkO3oMKsoChjVVWluF7QkxHRfYhTKSFbAVt8IhK7gZgDaO4'}
2025-09-09 21:01:49,200 qiita_client.qiita_client DEBUG    authenticate_url = https://tinqiita-qiita-1:21174/qiita_db/authenticate/
2025-09-09 21:01:49,200 qiita_client.qiita_client DEBUG    verify = True
2025-09-09 21:01:49,215 qiita_client.qiita_client DEBUG    status code = 200
2025-09-09 21:01:49,215 qiita_client.qiita_client DEBUG    RESULT.JSON() = {u'access_token': u'wlOjRSuh0s8vPoM61PBUL6OfqeDHMjGheg5819hdmwEwpgbh568TLIa', u'token_type': u'Bearer', u'expires_in': 3600}
2025-09-09 21:01:49,215 qiita_client.qiita_client DEBUG    access_token = wlOjRSuh0s8vPoM61PBUL6OfqeDHMjGheg5819hdmwEwpgbh568TLIa
2025-09-09 21:01:49,215 qiita_client.testing DEBUG    PluginTestCase.setUpClass() token wlOjRSuh0s8vPoM61PBUL6OfqeDHMjGheg5819hdmwEwpgbh568TLIa
2025-09-09 21:01:49,215 qiita_client.qiita_client DEBUG    Entered QiitaClient.post(/apitest/reload_plugins/)
2025-09-09 21:01:49,215 qiita_client.qiita_client DEBUG    Entered QiitaClient._request_retry()
2025-09-09 21:01:49,215 qiita_client.qiita_client DEBUG    Entered QiitaClient._request_oauth2()
------------------------------------- Captured log setup -------------------------------------
DEBUG    qiita_client.testing:testing.py:24 Entered PluginTestCase.setUpClass()
DEBUG    qiita_client.qiita_client:qiita_client.py:235 Entered QiitaClient._fetch_token()
DEBUG    qiita_client.qiita_client:qiita_client.py:240 data = {'client_secret': 'J7FfQ7CQdOxuKhQAf1eoGgBAE81Ns8Gu3EKaWFm3IO2JKhAmmCWZuabe0O5Mp28s1', 'grant_type': 'client', 'client_id': '19ndkO3oMKsoChjVVWluF7QkxHRfYhTKSFbAVt8IhK7gZgDaO4'}
DEBUG    qiita_client.qiita_client:qiita_client.py:241 authenticate_url = https://tinqiita-qiita-1:21174/qiita_db/authenticate/
DEBUG    qiita_client.qiita_client:qiita_client.py:242 verify = True
DEBUG    qiita_client.qiita_client:qiita_client.py:248 status code = 200
DEBUG    qiita_client.qiita_client:qiita_client.py:253 RESULT.JSON() = {u'access_token': u'wlOjRSuh0s8vPoM61PBUL6OfqeDHMjGheg5819hdmwEwpgbh568TLIa', u'token_type': u'Bearer', u'expires_in': 3600}
DEBUG    qiita_client.qiita_client:qiita_client.py:255 access_token = wlOjRSuh0s8vPoM61PBUL6OfqeDHMjGheg5819hdmwEwpgbh568TLIa
DEBUG    qiita_client.testing:testing.py:37 PluginTestCase.setUpClass() token wlOjRSuh0s8vPoM61PBUL6OfqeDHMjGheg5819hdmwEwpgbh568TLIa
DEBUG    qiita_client.qiita_client:qiita_client.py:448 Entered QiitaClient.post(/apitest/reload_plugins/)
DEBUG    qiita_client.qiita_client:qiita_client.py:368 Entered QiitaClient._request_retry()
DEBUG    qiita_client.qiita_client:qiita_client.py:282 Entered QiitaClient._request_oauth2()
------------------------------------ Captured stderr call ------------------------------------
2025-09-09 21:02:55,220 qiita_client.qiita_client DEBUG    Entered QiitaClient.post(/apitest/processing_job/)
2025-09-09 21:02:55,220 qiita_client.qiita_client DEBUG    Entered QiitaClient._request_retry()
2025-09-09 21:02:55,220 qiita_client.qiita_client DEBUG    Entered QiitaClient._request_oauth2()
------------------------------------- Captured log call --------------------------------------
DEBUG    qiita_client.qiita_client:qiita_client.py:448 Entered QiitaClient.post(/apitest/processing_job/)
DEBUG    qiita_client.qiita_client:qiita_client.py:368 Entered QiitaClient._request_retry()
DEBUG    qiita_client.qiita_client:qiita_client.py:282 Entered QiitaClient._request_oauth2()
---------------------------------- Captured stderr teardown ----------------------------------
2025-09-09 21:02:55,284 qiita_client.testing DEBUG    Entered PluginTestCase.tearDownClass()
2025-09-09 21:02:55,284 qiita_client.qiita_client DEBUG    Entered QiitaClient.post(/apitest/reset/)
2025-09-09 21:02:55,284 qiita_client.qiita_client DEBUG    Entered QiitaClient._request_retry()
2025-09-09 21:02:55,284 qiita_client.qiita_client DEBUG    Entered QiitaClient._request_oauth2()
----------------------------------- Captured log teardown ------------------------------------
DEBUG    qiita_client.testing:testing.py:44 Entered PluginTestCase.tearDownClass()
DEBUG    qiita_client.qiita_client:qiita_client.py:448 Entered QiitaClient.post(/apitest/reset/)
DEBUG    qiita_client.qiita_client:qiita_client.py:368 Entered QiitaClient._request_retry()
DEBUG    qiita_client.qiita_client:qiita_client.py:282 Entered QiitaClient._request_oauth2()
====================================== warnings summary ======================================
qp_target_gene/tests/test_pick_otus.py::PickOTUsTests::test_pick_closed_reference_otus
qp_target_gene/tests/test_pick_otus.py::PickOTUsTests::test_pick_closed_reference_otus
  /usr/local/lib/python2.7/dist-packages/requests/models.py:915: DeprecationWarning: BaseException.message has been deprecated as of Python 2.6
    raise RequestsJSONDecodeError(e.message)

-- Docs: https://docs.pytest.org/en/latest/warnings.html
=========================== 1 failed, 2 warnings in 67.27 seconds ============================

[antgonza]

I think this is related to qiita-spots/qiita#3374; remember that the populate_test_db.sql & qiita needs to be strip of the reference functionality.

However, I'm confused to why it's failing in your install and not here; thus started a new build: #25.

Now, to be honest, I think the functionality on this plugin should be replaced with commands running QIIME 2.

[antgonza]

You are right: the issue is that the original command, which only exists in the qiita-test is a "copy" of the command here so the parameters are not being updated. I think the easiest would be to rename the command in Qiita (and it's tests) to something else; the plugin version or name should be sufficient; do you agree with this change? If yes, I can issue a PR.

[sjanssen2]

I @antgonza sorry for the late reply.
My "hack" is to rename the plugin name of the test database, i.e. the populate_test_db.sql into something that is different from the actual plugins name: https://github.com/jlab/qiita-keycloak/blob/a3fe62095cfce51778b3f3b9989361fbe4318c06/Images/qiita/qiita.dockerfile#L59-L60
Works fine for me, e.g. https://github.com/jlab/qiita-keycloak/actions/runs/17855484834

And yes, in principle, we should migrate the functions to proper Q2 commands - but one step at a time ;-)