make help email address configurable instead of hard coding (#3384)

* Update CHANGELOG.md

* make help email address configurable instead of hard coding

* codestyle

* don't default with email addresses but raise Errors

* set mail addresses in example configuration, which is also used for
testing

* addessing Antonios issues + switch to a non deprecated read fct.

* updating dummy help email address in tests

---------

Co-authored-by: Antonio Gonzalez <antgonza@gmail.com>

qiita_core/configuration_manager.py

@@ -117,6 +117,10 @@ class ConfigurationManager(object):
         The script used to start the plugins
     plugin_dir : str
         The path to the directory containing the plugin configuration files
+    help_email : str
+        The email address a user should write to when asking for help
+    sysadmin_email : str
+        The email address, Qiita sends internal notifications to a sys admin
 
     Raises
     ------
@@ -234,6 +238,32 @@ def _get_main(self, config):
             self.key_file = join(install_dir, 'qiita_core', 'support_files',
                                  'ci_server.key')
 
+        self.help_email = config.get('main', 'HELP_EMAIL')
+        if not self.help_email:
+            raise ValueError(
+                "You did not specify the HELP_EMAIL address in the main "
+                "section of Qiita's config file. This address is essential "
+                "for users to ask for help as it is displayed at various "
+                "location throughout Qiita's web pages.")
+        if (self.help_email == 'foo@bar.com') and \
+           (self.test_environment is False):
+            warnings.warn(
+                "Using the github fake email for HELP_EMAIL, "
+                "are you sure this is OK?")
+
+        self.sysadmin_email = config.get('main', 'SYSADMIN_EMAIL')
+        if not self.sysadmin_email:
+            raise ValueError(
+                "You did not specify the SYSADMIN_EMAIL address in the main "
+                "section of Qiita's config file. Serious issues will "
+                "automatically be reported to a sys admin, an according "
+                "address is therefore required!")
+        if (self.sysadmin_email == 'jeff@bar.com') and \
+           (self.test_environment is False):
+            warnings.warn(
+                "Using the github fake email for SYSADMIN_EMAIL, "
+                "are you sure this is OK?")
+
     def _get_job_scheduler(self, config):
         """Get the configuration of the job_scheduler section"""
         self.job_scheduler_owner = config.get(

qiita_core/support_files/config_test.cfg

@@ -68,6 +68,12 @@ COOKIE_SECRET = SECRET
 # The value used to secure JWTs for delegated permission artifact download.
 JWT_SECRET = SUPER_SECRET
 
+# Address a user should write to when asking for help
+HELP_EMAIL = foo@bar.com
+
+# The email address, Qiita sends internal notifications to a sys admin
+SYSADMIN_EMAIL = jeff@bar.com
+
 # ----------------------------- SMTP settings -----------------------------
 [smtp]
 # The hostname to connect to

qiita_core/tests/test_configuration_manager.py

@@ -29,7 +29,7 @@ def setUp(self):
 
         self.conf = ConfigParser()
         with open(self.conf_fp, newline=None) as f:
-            self.conf.readfp(f)
+            self.conf.read_file(f)
 
     def tearDown(self):
         if self.old_conf_fp is not None:
@@ -132,6 +132,8 @@ def test_get_main(self):
 
         # Warning raised if No files will be allowed to be uploaded
         # Warning raised if no cookie_secret
+        self.conf.set('main', 'HELP_EMAIL', 'ignore@me')
+        self.conf.set('main', 'SYSADMIN_EMAIL', 'ignore@me')
         with warnings.catch_warnings(record=True) as warns:
             obs._get_main(self.conf)
 
@@ -180,6 +182,35 @@ def test_get_main(self):
 
         self.assertEqual(obs.qiita_env, "")
 
+    def test_help_email(self):
+        obs = ConfigurationManager()
+
+        with warnings.catch_warnings(record=True) as warns:
+            # warning get only issued when in non test environment
+            self.conf.set('main', 'TEST_ENVIRONMENT', 'FALSE')
+
+            obs._get_main(self.conf)
+            self.assertEqual(obs.help_email, 'foo@bar.com')
+            self.assertEqual(obs.sysadmin_email, 'jeff@bar.com')
+
+            obs_warns = [str(w.message) for w in warns]
+            exp_warns = [
+                'Using the github fake email for HELP_EMAIL, '
+                'are you sure this is OK?',
+                'Using the github fake email for SYSADMIN_EMAIL, '
+                'are you sure this is OK?']
+            self.assertCountEqual(obs_warns, exp_warns)
+
+        # test if it falls back to qiita.help@gmail.com
+        self.conf.set('main', 'HELP_EMAIL', '')
+        with self.assertRaises(ValueError):
+            obs._get_main(self.conf)
+
+        # test if it falls back to qiita.help@gmail.com
+        self.conf.set('main', 'SYSADMIN_EMAIL', '')
+        with self.assertRaises(ValueError):
+            obs._get_main(self.conf)
+
     def test_get_job_scheduler(self):
         obs = ConfigurationManager()
 
@@ -274,6 +305,12 @@ def test_get_portal(self):
 # The value used to secure JWTs for delegated permission artifact download.
 JWT_SECRET = SUPER_SECRET
 
+# Address a user should write to when asking for help
+HELP_EMAIL = foo@bar.com
+
+# The email address, Qiita sends internal notifications to a sys admin
+SYSADMIN_EMAIL = jeff@bar.com
+
 # ----------------------------- SMTP settings -----------------------------
 [smtp]
 # The hostname to connect to

qiita_db/processing_job.py

@@ -493,7 +493,7 @@ def resource_allocation_info(self):
                 samples, columns, input_size = self.shape
                 parts = []
                 error_msg = ('Obvious incorrect allocation. Please '
-                             'contact qiita.help@gmail.com')
+                             'contact %s' % qiita_config.help_email)
                 for part in allocation.split('--'):
                     param = ''
                     if part.startswith('time '):
@@ -902,7 +902,7 @@ def _set_status(self, value, error_msg=None):
                 if self.user.level in {'admin', 'wet-lab admin'}:
                     if value == 'error':
                         qdb.util.send_email(
-                            'jdereus@health.ucsd.edu', msg['subject'],
+                            qiita_config.sysadmin_email, msg['subject'],
                             msg['message'])
 
             sql = """UPDATE qiita.processing_job

qiita_pet/handlers/artifact_handlers/base_handlers.py

@@ -370,7 +370,7 @@ def artifact_patch_request(user, artifact_id, req_op, req_path, req_value=None,
 
             sid = artifact.study.id
             if artifact.visibility == 'awaiting_approval':
-                email_to = 'qiita.help@gmail.com'
+                email_to = qiita_config.help_email
                 subject = ('QIITA: Artifact %s awaiting_approval. Study %d, '
                            'Prep %d' % (artifact_id, sid,
                                         artifact.prep_templates[0].id))

qiita_pet/handlers/auth_handlers.py

@@ -62,8 +62,8 @@ def post(self):
                               url_escape(username), url))
             except Exception:
                 msg = ("Unable to send verification email. Please contact the "
-                       "qiita developers at <a href='mailto:qiita.help"
-                       "@gmail.com'>qiita.help@gmail.com</a>")
+                       "qiita developers at <a href='mailto:%s'>%s</a>") % (
+                       qiita_config.help_email, qiita_config.help_email)
                 self.redirect(u"%s/?level=danger&message=%s"
                               % (qiita_config.portal_dir, url_escape(msg)))
                 return
@@ -75,8 +75,9 @@ def post(self):
                    "<p>If you don't receive your activation email within a "
                    "couple of minutes, check your spam folder. If you still "
                    "don't see it, send us an email at <a "
-                   "href=\"mailto:qiita.help@gmail.com\">qiita.help@gmail.com"
-                   "</a>.</p>")
+                   "href=\"mailto:%s\">%s"
+                   "</a>.</p>") % (qiita_config.help_email,
+                                   qiita_config.help_email)
             self.redirect(u"%s/?level=success&message=%s" %
                           (qiita_config.portal_dir, url_escape(msg)))
         else:
@@ -135,7 +136,8 @@ def post(self):
                        "the verify link. You may need to check your spam "
                        "folder to find the email.<br/>If a verification email"
                        " has not arrived in 15 minutes, please email <a href='"
-                       "mailto:qiita.help@gmail.com'>qiita.help@gmail.com</a>")
+                       "mailto:%s'>%s</a>") % (qiita_config.help_email,
+                                               qiita_config.help_email)
         except QiitaDBUnknownIDError:
             msg = "Unknown user"
         except RuntimeError:

qiita_pet/handlers/download.py

@@ -445,12 +445,12 @@ def get(self):
                 public_raw_download = study.public_raw_download
                 if study.status != 'public':
                     raise HTTPError(404, reason='Study is not public. If this '
-                                    'is a mistake contact: '
-                                    'qiita.help@gmail.com')
+                                    'is a mistake contact: %s' %
+                                    qiita_config.help_email)
                 elif data == 'raw' and not public_raw_download:
                     raise HTTPError(422, reason='No raw data access. If this '
-                                    'is a mistake contact: '
-                                    'qiita.help@gmail.com')
+                                    'is a mistake contact: %s'
+                                    % qiita_config.help_email)
                 else:
                     # raw data
                     artifacts = [a for a in study.artifacts(dtype=data_type)
@@ -466,8 +466,8 @@ def get(self):
 
                 if not to_download:
                     raise HTTPError(422, reason='Nothing to download. If '
-                                    'this is a mistake contact: '
-                                    'qiita.help@gmail.com')
+                                    'this is a mistake contact: %s'
+                                    % qiita_config.help_email)
                 else:
                     self._write_nginx_file_list(to_download)
 
@@ -496,18 +496,18 @@ def get(self):
             else:
                 if artifact.visibility != 'public':
                     raise HTTPError(404, reason='Artifact is not public. If '
-                                    'this is a mistake contact: '
-                                    'qiita.help@gmail.com')
+                                    'this is a mistake contact: %s'
+                                    % qiita_config.help_email)
                 elif artifact.has_human:
                     raise HTTPError(404, reason='Artifact has possible human '
                                     'sequences. If this is a mistake contact: '
-                                    'qiita.help@gmail.com')
+                                    '%s' % qiita_config.help_email)
                 else:
                     to_download = self._list_artifact_files_nginx(artifact)
                     if not to_download:
                         raise HTTPError(422, reason='Nothing to download. If '
-                                        'this is a mistake contact: '
-                                        'qiita.help@gmail.com')
+                                        'this is a mistake contact: %s'
+                                        % qiita_config.help_email)
                     else:
                         self._write_nginx_file_list(to_download)
 
@@ -600,8 +600,8 @@ def get(self, jti):
         to_download = self._list_artifact_files_nginx(artifact)
         if not to_download:
             raise HTTPError(422, reason='Nothing to download. If '
-                                        'this is a mistake contact: '
-                                        'qiita.help@gmail.com')
+                                        'this is a mistake contact: %s' %
+                                        qiita_config.help_email)
         else:
             self._write_nginx_file_list(to_download)
 

qiita_pet/handlers/study_handlers/sample_template.py

@@ -12,7 +12,7 @@
 
 from tornado.web import authenticated, HTTPError
 
-from qiita_core.qiita_settings import r_client
+from qiita_core.qiita_settings import r_client, qiita_config
 from qiita_pet.handlers.util import to_int
 from qiita_pet.handlers.base_handlers import BaseHandler
 from qiita_db.util import get_files_from_uploads_folders
@@ -214,8 +214,8 @@ def sample_template_handler_patch_request(user, req_op, req_path,
                 # the system
                 filepath = req_value
                 if not exists(filepath):
-                    reason = ('Upload file not found (%s), please report to '
-                              'qiita.help@gmail.com' % filepath)
+                    reason = ('Upload file not found (%s), please report to %s'
+                              % (filepath, qiita_config.help_email))
                     raise HTTPError(404, reason=reason)
             else:
                 # Check if the file exists

qiita_pet/templates/admin_processing_job.html

@@ -191,7 +191,7 @@
         $inp.attr('type', 'file');
       }
       else {
-        bootstrapAlert("Error: Parameter type (" + p_type + ") not recognized. Please, take a screenshot and <a href='mailto:qiita.help@gmail.com'>contact us</a>", "danger");
+        bootstrapAlert("Error: Parameter type (" + p_type + ") not recognized. Please, take a screenshot and <a href='mailto:{% raw qiita_config.portal_dir %}'>contact us</a>", "danger");
       }
     }
 

qiita_pet/templates/error.html

@@ -3,7 +3,7 @@
     <h1 style="text-align:center">ERROR: CODE {{status_code}}!</h1>
     <h2 style="text-align:center">{% raw escape(error) %}</h2>
     <p style="text-align:center">The error has been logged and will be looked at.</p>
-    <p style="text-align:center">Need help? Send us an <a href="mailto:qiita.help@gmail.com">email</a>.</p>
+    <p style="text-align:center">Need help? Send us an <a href="mailto:{% raw qiita_config.help_email %}">email</a>.</p>
     {% if is_admin %}
     <p style="text-align:center">Go to the <a href="{% raw qiita_config.portal_dir %}/admin/error/">error page</a> to view the logs</p>
     {% end %}

qiita_pet/templates/list_analyses.html

@@ -121,7 +121,7 @@
         message.append(' '+data[level]);
         // prepend the "Need help" message
         if (level == 'warning' || level == 'danger'){
-          message.append('<p style="text-align:center">Need help? Send us an <a href="mailto:qiita.help@gmail.com">email</a>.</p>');
+          message.append('<p style="text-align:center">Need help? Send us an <a href="mailto:{% raw qiita_config.portal_dir %}">email</a>.</p>');
         }
         analyses_all_messages.prepend(message);
       }

qiita_pet/templates/redbiom.html

@@ -163,7 +163,7 @@
     .fail(function(response, status, error) {
       var text = 'The query response is larger than is currently allowed, please try another. <a href="https://github.com/biocore/qiita/issues/2312" target="_blank">Track progress on this issue.</a>';
       if (response.status != 504) {
-        text = 'Status code: "' + response.status + '" - ' + error + '.<br/>Please send a screenshot to <a href="qiita.help@gmail.com">qiita.help@gmail.com</a>.';
+        text = 'Status code: "' + response.status + '" - ' + error + '.<br/>Please send a screenshot to <a href="mailto:{% raw qiita_config.portal_dir %}">{% raw qiita_config.portal_dir %}</a>.';
       }
       redbiom_info.html(
         `<div class="alert alert-danger alert-dismissible" role="alert">

qiita_pet/templates/sitebase.html

@@ -588,7 +588,7 @@ <h4 class="modal-title">File really big.</h4>
       <div id="footer" style="font-size: 12px; text-align: center; z-index: 1000;">
         Thank you for using Qiita. <a target="_blank" href="{% raw qiita_config.portal_dir %}/static/doc/html/faq.html#how-to-cite-qiita">Citing Qiita?</a>.
         <br/>
-        Questions? <a href="mailto:qiita.help@gmail.com">qiita.help@gmail.com</a>; don't forget to add your study or analysis id.
+        Questions? <a href="mailto:{% raw qiita_config.help_email %}">{% raw qiita_config.help_email %}</a>; don't forget to add your study or analysis id.
         <br/>
         Read our <a href="{% raw qiita_config.portal_dir %}/iframe/?iframe=qiita-terms">terms and conditions</a>.
       </div>

qiita_pet/templates/study_ajax/base_info.html

@@ -159,7 +159,7 @@
         <input id="studyTags">
         <small>
           New tags are linked to the user that created them.
-          Report <a href="mailto:qiita.help@gmail.com">abuse</a>.
+          Report <a href="mailto:{% raw qiita_config.help_email %}">abuse</a>.
         </small>
         <br/>
         <button type="submit" class="btn btn-default" onclick="tags_patch(); return false;">Save tags</button>

qiita_pet/test/test_download.py

@@ -387,15 +387,15 @@ def test_download(self):
         response = self.get('/public_download/?data=raw&study_id=1')
         self.assertEqual(response.code, 404)
         self.assertEqual(response.reason, 'Study is not public. '
-                         'If this is a mistake contact: qiita.help@gmail.com')
+                         'If this is a mistake contact: foo@bar.com')
 
         # 7 is an uploaded biom, which should now be available but as it's a
         # biom, only the prep info file will be retrieved
         Artifact(7).visibility = 'public'
         response = self.get('/public_download/?data=raw&study_id=1')
         self.assertEqual(response.code, 422)
         self.assertEqual(response.reason, 'No raw data access. '
-                         'If this is a mistake contact: qiita.help@gmail.com')
+                         'If this is a mistake contact: foo@bar.com')
 
         # check success
         response = self.get('/public_download/?data=biom&study_id=1')
@@ -426,12 +426,12 @@ def test_download(self):
             '/public_download/?data=raw&study_id=1&data_type=Genomics')
         self.assertEqual(response.code, 422)
         self.assertEqual(response.reason, 'Nothing to download. If this is a '
-                         'mistake contact: qiita.help@gmail.com')
+                         'mistake contact: foo@bar.com')
         response = self.get(
             '/public_download/?data=biom&study_id=1&data_type=Genomics')
         self.assertEqual(response.code, 422)
         self.assertEqual(response.reason, 'Nothing to download. If this is a '
-                         'mistake contact: qiita.help@gmail.com')
+                         'mistake contact: foo@bar.com')
 
         # check success
         Artifact(5).visibility = 'public'
@@ -521,7 +521,7 @@ def test_download(self):
         response = self.get('/public_artifact_download/?artifact_id=3')
         self.assertEqual(response.code, 404)
         self.assertEqual(response.reason, 'Artifact is not public. If this is '
-                         'a mistake contact: qiita.help@gmail.com')
+                         'a mistake contact: foo@bar.com')
 
         # check success
         Artifact(5).visibility = 'public'

qiita_ware/test/test_private_plugin.py

@@ -403,7 +403,7 @@ def _set_allocation(memory):
         self.assertEqual(job.resource_allocation_info, 'Not valid')
         self.assertEqual(job.status, 'error')
         self.assertEqual(job.log.msg, 'Obvious incorrect allocation. Please '
-                         'contact qiita.help@gmail.com')
+                         'contact foo@bar.com')
 
         # now let's test something that will cause not a number input_size*N
         job = self._create_job('build_analysis_files', {
@@ -412,7 +412,7 @@ def _set_allocation(memory):
         self.assertEqual(job.resource_allocation_info, 'Not valid')
         self.assertEqual(job.status, 'error')
         self.assertEqual(job.log.msg, 'Obvious incorrect allocation. Please '
-                         'contact qiita.help@gmail.com')
+                         'contact foo@bar.com')
 
         # now let's test something that will return a negative number -samples
         job = self._create_job('build_analysis_files', {
@@ -421,7 +421,7 @@ def _set_allocation(memory):
         self.assertEqual(job.resource_allocation_info, 'Not valid')
         self.assertEqual(job.status, 'error')
         self.assertEqual(job.log.msg, 'Obvious incorrect allocation. Please '
-                         'contact qiita.help@gmail.com')
+                         'contact foo@bar.com')
 
         # now let's test a full build_analysis_files job
         job = self._create_job('build_analysis_files', {