Merge branch 'release_24.0' into release_24.1

lib/galaxy/managers/hdas.py

@@ -625,18 +625,19 @@ def serialize_display_apps(self, item, key, trans=None, **context):
         """
         hda = item
         display_apps: List[Dict[str, Any]] = []
-        for display_app in hda.get_display_applications(trans).values():
-            app_links = []
-            for link_app in display_app.links.values():
-                app_links.append(
-                    {
-                        "target": link_app.url.get("target_frame", "_blank"),
-                        "href": link_app.get_display_url(hda, trans),
-                        "text": gettext.gettext(link_app.name),
-                    }
-                )
-            if app_links:
-                display_apps.append(dict(label=display_app.name, links=app_links))
+        if hda.state == model.HistoryDatasetAssociation.states.OK and not hda.deleted:
+            for display_app in hda.get_display_applications(trans).values():
+                app_links = []
+                for link_app in display_app.links.values():
+                    app_links.append(
+                        {
+                            "target": link_app.url.get("target_frame", "_blank"),
+                            "href": link_app.get_display_url(hda, trans),
+                            "text": gettext.gettext(link_app.name),
+                        }
+                    )
+                if app_links:
+                    display_apps.append(dict(label=display_app.name, links=app_links))
 
         return display_apps
 
@@ -646,28 +647,30 @@ def serialize_old_display_applications(self, item, key, trans=None, **context):
         """
         hda = item
         display_apps: List[Dict[str, Any]] = []
-        if not self.app.config.enable_old_display_applications:
-            return display_apps
-
-        display_link_fn = hda.datatype.get_display_links
-        for display_app in hda.datatype.get_display_types():
-            target_frame, display_links = display_link_fn(
-                hda,
-                display_app,
-                self.app,
-                trans.request.base,
-            )
+        if (
+            self.app.config.enable_old_display_applications
+            and hda.state == model.HistoryDatasetAssociation.states.OK
+            and not hda.deleted
+        ):
+            display_link_fn = hda.datatype.get_display_links
+            for display_app in hda.datatype.get_display_types():
+                target_frame, display_links = display_link_fn(
+                    hda,
+                    display_app,
+                    self.app,
+                    trans.request.base,
+                )
 
-            if len(display_links) > 0:
-                display_label = hda.datatype.get_display_label(display_app)
+                if len(display_links) > 0:
+                    display_label = hda.datatype.get_display_label(display_app)
 
-                app_links = []
-                for display_name, display_link in display_links:
-                    app_links.append(
-                        {"target": target_frame, "href": display_link, "text": gettext.gettext(display_name)}
-                    )
-                if app_links:
-                    display_apps.append(dict(label=display_label, links=app_links))
+                    app_links = []
+                    for display_name, display_link in display_links:
+                        app_links.append(
+                            {"target": target_frame, "href": display_link, "text": gettext.gettext(display_name)}
+                        )
+                    if app_links:
+                        display_apps.append(dict(label=display_label, links=app_links))
 
         return display_apps
 

lib/galaxy/web/framework/middleware/error.py

@@ -9,6 +9,7 @@
 When an exception is thrown from the wrapper application, this logs
 the exception and displays an error page.
 """
+import logging
 import sys
 import traceback
 from io import StringIO
@@ -25,6 +26,8 @@
     reporter,
 )
 
+log = logging.getLogger(__name__)
+
 __all__ = ("ErrorMiddleware", "handle_exception")
 
 
@@ -169,10 +172,11 @@ def __call__(self, environ, start_response):
                 for expect in environ.get("paste.expected_exceptions", []):
                     if isinstance(exc_info[1], expect):
                         raise
+                log.exception("Uncaught Exception")
                 start_response("500 Internal Server Error", [("content-type", "text/html")], exc_info)
                 # @@: it would be nice to deal with bad content types here
                 response = self.exception_handler(exc_info, environ)
-                return [response]
+                return [response.encode(errors="ignore")]
             finally:
                 # clean up locals...
                 exc_info = None
@@ -183,7 +187,7 @@ def make_catching_iter(self, app_iter, environ, sr_checker):
             return app_iter
         return CatchingIter(app_iter, environ, sr_checker, self)
 
-    def exception_handler(self, exc_info, environ):
+    def exception_handler(self, exc_info, environ) -> str:
         simple_html_error = False
         if self.xmlhttp_key:
             get_vars = wsgilib.parse_querystring(environ)
@@ -192,7 +196,6 @@ def exception_handler(self, exc_info, environ):
         return handle_exception(
             exc_info,
             environ["wsgi.errors"],
-            html=True,
             debug_mode=self.debug_mode,
             error_email=self.error_email,
             error_log=self.error_log,
@@ -341,7 +344,6 @@ def extraData(self):
 def handle_exception(
     exc_info,
     error_stream,
-    html=True,
     debug_mode=False,
     error_email=None,
     error_log=None,
@@ -355,7 +357,7 @@ def handle_exception(
     error_message=None,
     simple_html_error=False,
     environ=None,
-):
+) -> str:
     """
     For exception handling outside of a web context
 
@@ -386,54 +388,51 @@ def handle_exception(
             smtp_use_tls=smtp_use_tls,
             subject_prefix=error_subject_prefix,
         )
-        rep_err = send_report(rep, exc_data, html=html)
+        rep_err = send_report(rep, exc_data, html=True)
         if rep_err:
             extra_data += rep_err
         else:
             reported = True
     if error_log:
         rep = reporter.LogReporter(filename=error_log)
-        rep_err = send_report(rep, exc_data, html=html)
+        rep_err = send_report(rep, exc_data, html=True)
         if rep_err:
             extra_data += rep_err
         else:
             reported = True
     if show_exceptions_in_wsgi_errors:
         rep = reporter.FileReporter(file=error_stream)
-        rep_err = send_report(rep, exc_data, html=html)
+        rep_err = send_report(rep, exc_data, html=True)
         if rep_err:
             extra_data += rep_err
         else:
             reported = True
     else:
         error_stream.write(f"Error - {exc_data.exception_type}: {exc_data.exception_value}\n")
-    if html:
-        if debug_mode and simple_html_error:
-            return_error = formatter.format_html(
-                exc_data, include_hidden_frames=False, include_reusable=False, show_extra_data=False
-            )
-            reported = True
-        elif debug_mode and not simple_html_error:
-            error_html = formatter.format_html(exc_data, include_hidden_frames=True, include_reusable=False)
-            head_html = formatter.error_css + formatter.hide_display_js
-            return_error = error_template(head_html, error_html, extra_data)
-            extra_data = ""
-            reported = True
-        else:
-            msg = (
-                error_message
-                or """
-            An error occurred.
-            """
-            )
-            extra = "<p><b>The error has been logged to our team.</b>"
-            if "sentry_event_id" in environ:
-                extra += " If you want to contact us about this error, please reference the following<br><br>"
-                extra += f"<b><large>GURU MEDITATION: #{environ['sentry_event_id']}</large></b>"
-            extra += "</p>"
-            return_error = error_template("", msg, extra)
+    if debug_mode and simple_html_error:
+        return_error = formatter.format_html(
+            exc_data, include_hidden_frames=False, include_reusable=False, show_extra_data=False
+        )
+        reported = True
+    elif debug_mode and not simple_html_error:
+        error_html = formatter.format_html(exc_data, include_hidden_frames=True, include_reusable=False)
+        head_html = formatter.error_css + formatter.hide_display_js
+        return_error = error_template(head_html, error_html, extra_data)
+        extra_data = ""
+        reported = True
     else:
-        return_error = None
+        msg = (
+            error_message
+            or """
+        An error occurred.
+        """
+        )
+        extra = "<p><b>The error has been logged to our team.</b>"
+        if "sentry_event_id" in environ:
+            extra += " If you want to contact us about this error, please reference the following<br><br>"
+            extra += f"<b><large>GURU MEDITATION: #{environ['sentry_event_id']}</large></b>"
+        extra += "</p>"
+        return_error = error_template("", msg, extra)
     if not reported and error_stream:
         err_report = formatter.format_text(exc_data, show_hidden_frames=True)
         err_report += f"\n{'-' * 60}\n"

lib/tool_shed/managers/repositories.py

@@ -471,7 +471,7 @@ def create_repository(trans: ProvidesUserContext, request: CreateRepositoryReque
         type=request.type_,
         description=request.synopsis,
         long_description=request.description,
-        user_id=user.id,
+        user=user,
         category_ids=category_ids,
         remote_repository_url=request.remote_repository_url,
         homepage_url=request.homepage_url,

lib/tool_shed/util/hg_util.py

@@ -71,14 +71,13 @@ def get_hgrc_path(repo_path):
     return os.path.join(repo_path, ".hg", "hgrc")
 
 
-def create_hgrc_file(app, repository):
+def create_hgrc_file(app, repository, repo_path):
     # Since we support both http and https, we set `push_ssl` to False to
     # override the default (which is True) in the Mercurial API.
     # The hg purge extension purges all files and directories not being tracked
     # by Mercurial in the current repository. It will remove unknown files and
     # empty directories. This is not currently used because it is not supported
     # in the Mercurial API.
-    repo_path = repository.repo_path(app)
     hgrc_path = get_hgrc_path(repo_path)
     with open(hgrc_path, "w") as fp:
         fp.write("[paths]\n")

lib/tool_shed/util/hgweb_config.py

@@ -5,8 +5,6 @@
 import threading
 from datetime import date
 
-from galaxy.util import unicodify
-
 log = logging.getLogger(__name__)
 
 new_hgweb_config_template = """
@@ -20,6 +18,7 @@ def __init__(self):
         self.hgweb_config_dir = None
         self.in_memory_config = None
         self.lock = threading.Lock()
+        self.hgweb_repo_prefix = None
 
     def add_entry(self, lhs, rhs):
         """Add an entry in the hgweb.config file for a new repository."""
@@ -35,8 +34,8 @@ def add_entry(self, lhs, rhs):
             self.in_memory_config.set("paths", lhs, rhs)
             # Persist our in-memory configuration.
             self.write_config()
-        except Exception as e:
-            log.debug("Exception in HgWebConfigManager.add_entry(): %s", unicodify(e))
+        except Exception:
+            log.exception("Exception in HgWebConfigManager.add_entry()")
         finally:
             self.lock.release()
 
@@ -51,8 +50,8 @@ def change_entry(self, old_lhs, new_lhs, new_rhs):
             self.in_memory_config.set("paths", new_lhs, new_rhs)
             # Persist our in-memory configuration.
             self.write_config()
-        except Exception as e:
-            log.debug("Exception in HgWebConfigManager.change_entry(): %s", unicodify(e))
+        except Exception:
+            log.exception("Exception in HgWebConfigManager.change_entry()")
         finally:
             self.lock.release()