Merge branch 'release_24.1' into dev

client/src/components/History/HistoryView.vue

@@ -22,7 +22,7 @@
         </div>
 
         <b-alert :show="copySuccess">
-            History imported and is now your active history. <b-link to="/histories/list">View here</b-link>.
+            History imported and is now your active history. <b-link :to="importedHistoryLink">View here</b-link>.
         </b-alert>
 
         <CollectionPanel
@@ -40,6 +40,7 @@
 <script>
 import { mapActions, mapState } from "pinia";
 
+import { isAnonymousUser } from "@/api";
 import { useHistoryStore } from "@/stores/historyStore";
 import { useUserStore } from "@/stores/userStore";
 
@@ -89,6 +90,9 @@ export default {
         canImportHistory() {
             return !this.userOwnsHistory && !this.history.purged;
         },
+        importedHistoryLink() {
+            return isAnonymousUser(this.currentUser) ? "/" : "/histories/list";
+        },
     },
     created() {
         this.loadHistoryById(this.id);

client/src/components/History/Modals/CopyModal.vue

@@ -78,7 +78,7 @@ async function copy(close: () => void) {
         <transition name="fade">
             <BAlert v-localize :show="isAnonymous" variant="warning">
                 As an anonymous user, unless you log in or register, you will lose your current history after copying
-                this history. You can <a href="/user/login">log in here</a> or <a href="/user/create">register here</a>.
+                this history. You can <a href="/login/start">log in or register here</a>.
             </BAlert>
         </transition>
 

lib/galaxy/visualization/data_providers/genome.py

@@ -39,6 +39,7 @@
     GFFReaderWrapper,
     parse_gff_attributes,
 )
+from galaxy.exceptions import MessageException
 from galaxy.model import DatasetInstance
 from galaxy.visualization.data_providers.basic import BaseDataProvider
 from galaxy.visualization.data_providers.cigar import get_ref_based_read_seq_and_cigar
@@ -106,43 +107,53 @@ def __init__(self, converted_dataset):
         self.converted_dataset = converted_dataset
 
     def get_data(self, query):
+        if self.converted_dataset is None or not self.converted_dataset.is_ok:
+            raise MessageException("The dataset is not available or is in an error state.")
         # Init.
-        textloc_file = open(self.converted_dataset.get_file_name())
-        line_len = int(textloc_file.readline())
-        file_len = os.path.getsize(self.converted_dataset.get_file_name())
-        query = query.lower()
-
-        # Find query in file using binary search.
-        low = 0
-        high = int(file_len / line_len)
-        while low < high:
-            mid: int = (low + high) // 2
-            position = mid * line_len
-            textloc_file.seek(position)
-
-            # Compare line with query and update low, high.
+        result = []
+        with open(self.converted_dataset.get_file_name()) as textloc_file:
             line = textloc_file.readline()
-            if line < query:
-                low = mid + 1
-            else:
-                high = mid
+            if not line:
+                raise MessageException("The dataset is empty.")
+            try:
+                line_len = int(line)
+            except ValueError:
+                raise MessageException(f"Expected an integer at first line, but found: '{line}'")
+            if line_len < 1:
+                raise MessageException(f"The first line must be a positive integer, but found: {line_len}")
+
+            file_len = os.path.getsize(self.converted_dataset.get_file_name())
+            query = query.lower()
+
+            # Find query in file using binary search.
+            low = 0
+            high = int(file_len / line_len)
+            while low < high:
+                mid: int = (low + high) // 2
+                position = mid * line_len
+                textloc_file.seek(position)
+
+                # Compare line with query and update low, high.
+                line = textloc_file.readline()
+                if line < query:
+                    low = mid + 1
+                else:
+                    high = mid
 
-        # Need to move back one line because last line read may be included in
-        # results.
-        position = low * line_len
-        textloc_file.seek(position)
+            # Need to move back one line because last line read may be included in
+            # results.
+            position = low * line_len
+            textloc_file.seek(position)
 
-        # At right point in file, generate hits.
-        result = []
-        while True:
-            line = textloc_file.readline()
-            if not line.startswith(query):
-                break
-            if line[-1:] == "\n":
-                line = line[:-1]
-            result.append(line.split()[1:])
+            # At right point in file, generate hits.
+            while True:
+                line = textloc_file.readline()
+                if not line.startswith(query):
+                    break
+                if line[-1:] == "\n":
+                    line = line[:-1]
+                result.append(line.split()[1:])
 
-        textloc_file.close()
         return result
 
 

lib/galaxy_test/driver/driver_util.py

@@ -50,8 +50,6 @@
     DEFAULT_WEB_HOST,
     target_url_parts,
 )
-from tool_shed.webapp.app import UniverseApplication as ToolshedUniverseApplication
-from tool_shed.webapp.fast_app import initialize_fast_app as init_tool_shed_fast_app
 from .test_logging import logging_config_file
 
 galaxy_root = galaxy_directory()
@@ -71,9 +69,8 @@
 log = logging.getLogger("test_driver")
 
 
-# Global variables to pass database contexts around - only needed for older
+# Global variable to pass database contexts around - only needed for older
 # Tool Shed twill tests that didn't utilize the API for such interactions.
-tool_shed_context = None
 install_context = None
 
 
@@ -583,26 +580,6 @@ def build_galaxy_app(simple_kwargs) -> GalaxyUniverseApplication:
     return app
 
 
-def build_shed_app(simple_kwargs):
-    """Build a Galaxy app object from a simple keyword arguments.
-
-    Construct paste style complex dictionary. Also setup "global" reference
-    to sqlalchemy database context for tool shed database.
-    """
-    log.info("Tool shed database connection: %s", simple_kwargs["database_connection"])
-    # TODO: Simplify global_conf to match Galaxy above...
-    simple_kwargs["__file__"] = "tool_shed_wsgi.yml.sample"
-    simple_kwargs["global_conf"] = get_webapp_global_conf()
-
-    app = ToolshedUniverseApplication(**simple_kwargs)
-    log.info("Embedded Toolshed application started")
-
-    global tool_shed_context
-    tool_shed_context = app.model.context
-
-    return app
-
-
 def explicitly_configured_host_and_port(prefix, config_object):
     host_env_key = f"{prefix}_TEST_HOST"
     port_env_key = f"{prefix}_TEST_PORT"
@@ -758,7 +735,14 @@ def launch_gravity(port, gxit_port=None, galaxy_config=None):
     )
 
 
-def launch_server(app_factory, webapp_factory, prefix=DEFAULT_CONFIG_PREFIX, galaxy_config=None, config_object=None):
+def launch_server(
+    app_factory,
+    webapp_factory,
+    prefix=DEFAULT_CONFIG_PREFIX,
+    galaxy_config=None,
+    config_object=None,
+    init_fast_app=init_galaxy_fast_app,
+):
     name = prefix.lower()
     host, port = explicitly_configured_host_and_port(prefix, config_object)
     port = attempt_ports(port)
@@ -792,12 +776,7 @@ def launch_server(app_factory, webapp_factory, prefix=DEFAULT_CONFIG_PREFIX, gal
         static_enabled=True,
         register_shutdown_at_exit=False,
     )
-    if name == "galaxy":
-        asgi_app = init_galaxy_fast_app(wsgi_webapp, app)
-    elif name == "tool_shed":
-        asgi_app = init_tool_shed_fast_app(wsgi_webapp, app)
-    else:
-        raise NotImplementedError(f"Launching {name} not implemented")
+    asgi_app = init_fast_app(wsgi_webapp, app)
 
     server, port, thread = uvicorn_serve(asgi_app, host=host, port=port)
     set_and_wait_for_http_target(prefix, host, port, url_prefix=url_prefix)

lib/tool_shed/test/base/driver.py

@@ -11,6 +11,8 @@
 from galaxy_test.driver import driver_util
 from tool_shed.test.base.api_util import get_admin_api_key
 from tool_shed.webapp import buildapp as toolshedbuildapp
+from tool_shed.webapp.app import UniverseApplication as ToolshedUniverseApplication
+from tool_shed.webapp.fast_app import initialize_fast_app as init_tool_shed_fast_app
 
 log = driver_util.build_logger()
 
@@ -36,6 +38,29 @@
 <data_managers>
 </data_managers>
 """
+# Global variable to pass database contexts around - only needed for older
+# Tool Shed twill tests that didn't utilize the API for such interactions.
+tool_shed_context = None
+
+
+def build_shed_app(simple_kwargs):
+    """Build a Galaxy app object from a simple keyword arguments.
+
+    Construct paste style complex dictionary. Also setup "global" reference
+    to sqlalchemy database context for tool shed database.
+    """
+    log.info("Tool shed database connection: %s", simple_kwargs["database_connection"])
+    # TODO: Simplify global_conf to match Galaxy above...
+    simple_kwargs["__file__"] = "tool_shed_wsgi.yml.sample"
+    simple_kwargs["global_conf"] = driver_util.get_webapp_global_conf()
+
+    app = ToolshedUniverseApplication(**simple_kwargs)
+    log.info("Embedded Toolshed application started")
+
+    global tool_shed_context
+    tool_shed_context = app.model.context
+
+    return app
 
 
 class ToolShedTestDriver(driver_util.TestDriver):
@@ -117,10 +142,11 @@ def _setup_local(self):
         # ---- Run tool shed webserver ------------------------------------------------------
         # TODO: Needed for hg middleware ('lib/galaxy/webapps/tool_shed/framework/middleware/hg.py')
         tool_shed_server_wrapper = driver_util.launch_server(
-            app_factory=lambda: driver_util.build_shed_app(kwargs),
+            app_factory=lambda: build_shed_app(kwargs),
             webapp_factory=toolshedbuildapp.app_factory,
             galaxy_config=kwargs,
             prefix="TOOL_SHED",
+            init_fast_app=init_tool_shed_fast_app,
         )
         self.server_wrappers.append(tool_shed_server_wrapper)
         tool_shed_test_host = tool_shed_server_wrapper.host

lib/tool_shed/test/base/test_db_util.py

@@ -18,7 +18,7 @@
 
 
 def sa_session():
-    from galaxy_test.driver.driver_util import tool_shed_context as sa_session
+    from .driver import tool_shed_context as sa_session
 
     return sa_session