Merge pull request #15557 from jdavcs/dev_emailfrom

Handle "email_from" config option consistently, as per schema description

lib/galaxy/config/__init__.py

@@ -30,6 +30,7 @@ from typing import (
     TypeVar,
     Union,
 )
+from urllib.parse import urlparse
 
 import yaml
 
@@ -135,6 +136,7 @@ LOGGING_CONFIG_DEFAULT: Dict[str, Any] = {
 """Default value for logging configuration, passed to :func:`logging.config.dictConfig`"""
 
 VERSION_JSON_FILE = "version.json"
+DEFAULT_EMAIL_FROM_LOCAL_PART = "galaxy-no-reply"
 
 
 def configure_logging(config, facts=None):
@@ -612,16 +614,6 @@ class CommonConfigurationMixin:
 
 
 class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
-    deprecated_options = (
-        "database_file",
-        "track_jobs_in_database",
-        "blacklist_file",
-        "whitelist_file",
-        "sanitize_whitelist_file",
-        "user_library_import_symlink_whitelist",
-        "fetch_url_whitelist",
-        "containers_resolvers_config_file",
-    )
     renamed_options = {
         "blacklist_file": "email_domain_blocklist_file",
         "whitelist_file": "email_domain_allowlist_file",
@@ -629,7 +621,14 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
         "user_library_import_symlink_whitelist": "user_library_import_symlink_allowlist",
         "fetch_url_whitelist": "fetch_url_allowlist",
         "containers_resolvers_config_file": "container_resolvers_config_file",
+        "activation_email": "email_from",
     }
+
+    deprecated_options = list(renamed_options.keys()) + [
+        "database_file",
+        "track_jobs_in_database",
+    ]
+
     default_config_file_name = "galaxy.yml"
     deprecated_dirs = {"config_dir": "config", "data_dir": "database"}
 
@@ -895,8 +894,6 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
         self.nodejs_path = kwargs.get("nodejs_path")
         self.container_image_cache_path = self._in_data_dir(kwargs.get("container_image_cache_path", "container_cache"))
         self.output_size_limit = int(kwargs.get("output_size_limit", 0))
-        # activation_email was used until release_15.03
-        self.email_from = self.email_from or kwargs.get("activation_email")
 
         self.email_domain_blocklist_content = (
             self._load_list_from_file(self._in_config_dir(self.email_domain_blocklist_file))
@@ -1046,7 +1043,7 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
             if section.startswith("server:"):
                 self.server_names.append(section.replace("server:", "", 1))
 
-        self._set_galaxy_infrastructure_url(kwargs)
+        self._set_host_related_options(kwargs)
 
         # Asynchronous execution process pools - limited functionality for now, attach_to_pools is designed to allow
         # webless Galaxy server processes to attach to arbitrary message queues (e.g. as job handlers) so they do not
@@ -1209,6 +1206,12 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
         with open(filepath) as f:
             return [line.strip() for line in f]
 
+    def _set_host_related_options(self, kwargs):
+        # The following 3 method calls must be made in sequence
+        self._set_galaxy_infrastructure_url(kwargs)
+        self._set_hostname()
+        self._set_email_from()
+
     def _set_galaxy_infrastructure_url(self, kwargs):
         # indicate if this was not set explicitly, so dependending on the context a better default
         # can be used (request url in a web thread, Docker parent in IE stuff, etc.)
@@ -1227,6 +1230,16 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
         if "UWSGI_PORT" in self.galaxy_infrastructure_url:
             raise Exception("UWSGI_PORT is not supported anymore")
 
+    def _set_hostname(self):
+        if self.galaxy_infrastructure_url_set:
+            self.hostname = urlparse(self.galaxy_infrastructure_url).hostname
+        else:
+            self.hostname = socket.getfqdn()
+
+    def _set_email_from(self):
+        if not self.email_from:
+            self.email_from = f"{DEFAULT_EMAIL_FROM_LOCAL_PART}@{self.hostname}"
+
     def reload_sanitize_allowlist(self, explicit=True):
         self.sanitize_allowlist = []
         if not os.path.exists(self.sanitize_allowlist_file):

lib/galaxy/job_execution/actions/post.py

@@ -3,7 +3,6 @@ Actions to be run at job completion (or output hda creation, as in the case of
 immediate_actions listed below.
 """
 import datetime
-import socket
 
 from markupsafe import escape
 
@@ -53,7 +52,6 @@ class EmailAction(DefaultJobAction):
     @classmethod
     def execute(cls, app, sa_session, action, job, replacement_dict, final_job_state=None):
         try:
-            frm = app.config.email_from
             history_id_encoded = app.security.encode_id(job.history_id)
             link_invocation = None
             if job.workflow_invocation_step:
@@ -62,19 +60,13 @@ class EmailAction(DefaultJobAction):
                     f"{app.config.galaxy_infrastructure_url}/workflows/invocations/report?id={invocation_id_encoded}"
                 )
             link = f"{app.config.galaxy_infrastructure_url}/histories/view?id={history_id_encoded}"
-            if frm is None:
-                if action.action_arguments and "host" in action.action_arguments:
-                    host = action.action_arguments["host"]
-                else:
-                    host = socket.getfqdn()
-                frm = f"galaxy-no-reply@{host}"
             to = job.get_user_email()
             subject = f"Galaxy job completion notification from history '{job.history.name}'"
             outdata = ",\n".join(ds.dataset.display_name() for ds in job.output_datasets)
             body = f"Your Galaxy job generating dataset(s):\n\n{outdata}\n\nis complete as of {datetime.datetime.now().strftime('%I:%M')}. Click the link below to access your data: \n{link}"
             if link_invocation:
                 body += f"\n\nWorkflow Invocation Report:\n{link_invocation}"
-            send_mail(frm, to, subject, body, app.config)
+            send_mail(app.config.email_from, to, subject, body, app.config)
         except Exception as e:
             log.error("EmailAction PJA Failed, exception: %s", unicodify(e))
 

lib/galaxy/managers/users.py

@@ -5,7 +5,6 @@ import hashlib
 import logging
 import random
 import re
-import socket
 import time
 from datetime import datetime
 from typing import Optional
@@ -484,7 +483,6 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin):
         activation_link = url_for(
             controller="user", action="activate", activation_token=activation_token, email=escape(email), qualified=True
         )
-        host = self.__get_host(trans)
         template_context = {
             "name": escape(username),
             "user_email": escape(email),
@@ -500,10 +498,9 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin):
         body = templates.render(TXT_ACTIVATION_EMAIL_TEMPLATE_RELPATH, template_context, self.app.config.templates_dir)
         html = templates.render(HTML_ACTIVATION_EMAIL_TEMPLATE_RELPATH, template_context, self.app.config.templates_dir)
         to = email
-        frm = self.app.config.email_from or f"galaxy-no-reply@{host}"
         subject = "Galaxy Account Activation"
         try:
-            util.send_mail(frm, to, subject, body, self.app.config, html=html)
+            util.send_mail(self.app.config.email_from, to, subject, body, self.app.config, html=html)
             return True
         except Exception:
             log.debug(body)
@@ -536,18 +533,16 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin):
         else:
             reset_user, prt = self.get_reset_token(trans, email)
             if prt:
-                host = self.__get_host(trans)
                 reset_url = url_for(controller="login", action="start", token=prt.token)
                 body = PASSWORD_RESET_TEMPLATE % (
-                    host,
+                    trans.app.config.hostname,
                     prt.expiration_time.strftime(trans.app.config.pretty_datetime_format),
                     trans.request.host,
                     reset_url,
                 )
-                frm = trans.app.config.email_from or f"galaxy-no-reply@{host}"
                 subject = "Galaxy Password Reset"
                 try:
-                    util.send_mail(frm, email, subject, body, self.app.config)
+                    util.send_mail(trans.app.config.email_from, email, subject, body, self.app.config)
                     trans.sa_session.add(reset_user)
                     trans.sa_session.flush()
                     trans.log_event(f"User reset password: {email}")
@@ -574,12 +569,6 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin):
             return reset_user, prt
         return None, None
 
-    def __get_host(self, trans):
-        host = trans.request.host.split(":")[0]
-        if host in ["localhost", "127.0.0.1", "0.0.0.0"]:
-            host = socket.getfqdn()
-        return host
-
     def send_subscription_email(self, email):
         if self.app.config.smtp_server is None:
             return "Subscribing to the mailing list has failed because mail is not configured for this Galaxy instance. Please contact your local Galaxy administrator."

lib/galaxy/tools/errors.py

@@ -243,7 +243,6 @@ class EmailErrorReporter(ErrorReporter):
         to = self.app.config.error_email_to
         assert to, ValueError("Error reporting has been disabled for this Galaxy instance")
 
-        frm = self.app.config.email_from
         error_msg = validate_email_str(email)
         if not error_msg and self._can_access_dataset(user):
             to += f", {email.strip()}"
@@ -255,4 +254,6 @@ class EmailErrorReporter(ErrorReporter):
         except Exception:
             pass
 
-        return util.send_mail(frm, to, subject, self.report, self.app.config, html=self.html_report)
+        return util.send_mail(
+            self.app.config.email_from, to, subject, self.report, self.app.config, html=self.html_report
+        )

test/unit/config/test_config_values.py

@@ -3,6 +3,7 @@ import os
 import pytest
 
 from galaxy import config
+from galaxy.config import DEFAULT_EMAIL_FROM_LOCAL_PART
 from galaxy.util.properties import running_from_source
 
 
@@ -42,3 +43,10 @@ def test_base_config_if_running_not_from_source(monkeypatch):
     assert appconfig.config_dir == os.getcwd()
     assert appconfig.data_dir == os.path.join(appconfig.config_dir, "data")
     assert appconfig.managed_config_dir == os.path.join(appconfig.data_dir, "config")
+
+
+def test_assign_email_from(monkeypatch):
+    appconfig = config.GalaxyAppConfiguration(
+        override_tempdir=False, galaxy_infrastructure_url="http://myhost:8080/galaxy/"
+    )
+    assert appconfig.email_from == f"{DEFAULT_EMAIL_FROM_LOCAL_PART}@myhost"