Merge branch 'release_23.1' into dev

client/src/components/Common/DelayedInput.vue

@@ -13,7 +13,7 @@
         <b-input-group-append>
             <b-button
                 v-if="enableAdvanced"
-                v-b-tooltip.hover.noninteractive
+                v-b-tooltip.hover.bottom.noninteractive
                 aria-haspopup="true"
                 size="sm"
                 :pressed="showAdvanced"
@@ -25,7 +25,7 @@
                 <icon v-else fixed-width icon="angle-double-down" />
             </b-button>
             <b-button
-                v-b-tooltip.hover.noninteractive
+                v-b-tooltip.hover.bottom.noninteractive
                 aria-haspopup="true"
                 class="search-clear"
                 size="sm"

client/src/components/History/CurrentHistory/HistoryFilters/HistoryFilters.vue

@@ -13,7 +13,7 @@
             </DebouncedInput>
             <b-input-group-append>
                 <b-button
-                    v-b-tooltip.hover
+                    v-b-tooltip.hover.bottom.noninteractive
                     aria-haspopup="true"
                     size="sm"
                     :pressed="showAdvanced"
@@ -26,7 +26,7 @@
                     <icon v-else fixed-width icon="angle-double-down" />
                 </b-button>
                 <b-button
-                    v-b-tooltip.hover
+                    v-b-tooltip.hover.bottom.noninteractive
                     aria-haspopup="true"
                     size="sm"
                     title="Clear Filters (esc)"

client/src/components/History/CurrentHistory/HistoryNavigation.vue

@@ -7,7 +7,7 @@
             <h2 class="m-1 h-sm">History</h2>
             <b-button-group>
                 <b-button
-                    v-b-tooltip.bottom.hover
+                    v-b-tooltip.top.hover.noninteractive
                     class="create-hist-btn"
                     data-description="create new history"
                     size="sm"
@@ -19,7 +19,7 @@
                 </b-button>
 
                 <b-button
-                    v-b-tooltip.bottom.hover
+                    v-b-tooltip.top.hover.noninteractive
                     data-description="switch to another history"
                     size="sm"
                     variant="link"
@@ -30,7 +30,7 @@
                 </b-button>
 
                 <b-dropdown
-                    v-b-tooltip.bottom.hover
+                    v-b-tooltip.top.hover.noninteractive
                     size="sm"
                     variant="link"
                     toggle-class="text-decoration-none"

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

@@ -36,7 +36,7 @@
         <div slot="modal-footer" slot-scope="{ ok, cancel }">
             <div>
                 <b-button class="mr-3" @click="cancel()"> Cancel </b-button>
-                <b-button :variant="saveVariant" :disabled="!formValid" @click="copy(ok)">
+                <b-button :variant="saveVariant" :disabled="loading || !formValid" @click="copy(ok)">
                     {{ saveTitle | localize }}
                 </b-button>
             </div>

client/src/components/Panels/Buttons/FavoritesButton.vue

@@ -1,6 +1,6 @@
 <template>
     <b-button
-        v-b-tooltip.hover.noninteractive
+        v-b-tooltip.hover.top.noninteractive
         class="panel-header-button-toolbox"
         size="sm"
         variant="link"

client/src/components/Panels/Buttons/PanelViewButton.vue

@@ -1,6 +1,6 @@
 <template>
     <b-dropdown
-        v-b-tooltip.hover.noninteractive
+        v-b-tooltip.hover.top.noninteractive
         right
         title="Show panel options"
         variant="link"

lib/galaxy/managers/jobs.py

@@ -970,8 +970,6 @@ def inputs_recursive(input_params, param_values, depth=1, upgrade_messages=None)
                 # Get parameter label.
                 if input.type == "conditional":
                     label = input.test_param.label
-                elif input.type == "repeat":
-                    label = input.label()
                 else:
                     label = input.label or input.name
                 rval.append(

lib/galaxy/managers/workflows.py

@@ -1057,7 +1057,15 @@ def do_inputs(inputs, values, prefix, step, other_values=None):
                     except KeyError:
                         continue
                 else:
-                    row_for_param(input_dict, input, values[input.name], other_values, prefix, step)
+                    row_for_param(
+                        input_dict,
+                        input,
+                        # Use values.get so that unspecified param values don't blow up the display
+                        values.get(input.name),
+                        other_values,
+                        prefix,
+                        step,
+                    )
                 input_dicts.append(input_dict)
             return input_dicts
 

lib/galaxy/model/__init__.py

@@ -9544,7 +9544,7 @@ class CustosAuthnzToken(Base, RepresentById):
 
     id = Column(Integer, primary_key=True)
     user_id = Column(Integer, ForeignKey("galaxy_user.id"))
-    external_user_id = Column(String(64))
+    external_user_id = Column(String(255))
     provider = Column(String(255))
     access_token = Column(Text)
     id_token = Column(Text)

lib/galaxy/model/migrations/alembic/versions_gxy/e93c5d0b47a9_alter_column_external_user_id.py

@@ -0,0 +1,30 @@
+"""alter column CustosAuthnzToken.external_user_id to increase length
+
+Revision ID: e93c5d0b47a9
+Revises: e0561d5fc8c7
+Create Date: 2023-10-08 12:11:02.024669
+
+"""
+import sqlalchemy as sa
+
+from galaxy.model.migrations.util import alter_column
+
+# revision identifiers, used by Alembic.
+revision = "e93c5d0b47a9"
+down_revision = "e0561d5fc8c7"
+branch_labels = None
+depends_on = None
+
+table_name = "custos_authnz_token"
+column_name = "external_user_id"
+
+LONGER_LENGTH = 255
+
+
+def upgrade():
+    alter_column(table_name, column_name, type_=sa.String(LONGER_LENGTH))
+
+
+def downgrade():
+    # No need to downgrade, this is a one-way migration. Otherwise, existing data would be truncated or lost.
+    pass

lib/galaxy/model/migrations/dbscript.py

@@ -36,8 +36,8 @@
     "22.05": "186d4835587b",
     "release_23.0": "caa7742f7bca",
     "23.0": "caa7742f7bca",
-    "release_23.1": "e0561d5fc8c7",
-    "23.1": "e0561d5fc8c7",
+    "release_23.1": "e93c5d0b47a9",
+    "23.1": "e93c5d0b47a9",
 }
 
 

lib/galaxy/tool_util/deps/conda_util.py

@@ -96,7 +96,7 @@ class CondaContext(installable.InstallableContext):
     installable_description = "Conda"
     _conda_build_available: Optional[bool]
     _conda_version: Optional[Version]
-    _experimental_solver_available: Optional[bool]
+    _libmamba_solver_available: Optional[bool]
 
     def __init__(
         self,
@@ -137,7 +137,7 @@ def __init__(
     def _reset_conda_properties(self) -> None:
         self._conda_version = None
         self._conda_build_available = None
-        self._experimental_solver_available = None
+        self._libmamba_solver_available = None
 
     @property
     def conda_version(self) -> Version:
@@ -175,13 +175,17 @@ def _override_channels_args(self) -> List[str]:
         return override_channels_args
 
     @property
-    def _experimental_solver_args(self) -> List[str]:
-        if self._experimental_solver_available is None:
-            self._experimental_solver_available = self.conda_version >= Version("4.12.0") and self.is_package_installed(
+    def _solver_args(self) -> List[str]:
+        if self._libmamba_solver_available is None:
+            self._libmamba_solver_available = self.conda_version >= Version("4.12.0") and self.is_package_installed(
                 "conda-libmamba-solver"
             )
-        if self._experimental_solver_available:
-            return ["--experimental-solver", "libmamba"]
+        if self._libmamba_solver_available:
+            # The "--solver" option was introduced in conda 22.11.0, when the
+            # "--experimental-solver" option was deprecated.
+            # The "--experimental-solver" option was removed in conda 23.9.0 .
+            solver_option = "--solver" if self.conda_version >= Version("22.11.0") else "--experimental-solver"
+            return [solver_option, "libmamba"]
         else:
             return []
 
@@ -296,7 +300,7 @@ def exec_create(self, args: Iterable[str], allow_local: bool = True, stdout_path
                     continue
             if allow_local and self.use_local:
                 create_args.append("--use-local")
-            create_args.extend(self._experimental_solver_args)
+            create_args.extend(self._solver_args)
             create_args.extend(self._override_channels_args)
             create_args.extend(args)
             ret = self.exec_command("create", create_args, stdout_path=stdout_path)
@@ -327,7 +331,7 @@ def exec_install(self, args: Iterable[str], allow_local: bool = True, stdout_pat
                     continue
             if allow_local and self.use_local:
                 install_args.append("--use-local")
-            install_args.extend(self._experimental_solver_args)
+            install_args.extend(self._solver_args)
             install_args.extend(self._override_channels_args)
             install_args.extend(args)
             ret = self.exec_command("install", install_args, stdout_path=stdout_path)

lib/galaxy/tool_util/toolbox/base.py

@@ -96,7 +96,12 @@ def __init__(self, toolbox: "AbstractToolBox"):
 
     def has_tool(self, tool_id: str) -> bool:
         toolbox = self.__toolbox
-        return tool_id in toolbox._tools_by_id or tool_id in toolbox._tools_by_old_id
+        # tool_id could be full guid, old tool id (no toolshed and version info) or versionless guid.
+        return (
+            tool_id in toolbox._tools_by_id
+            or tool_id in toolbox._tools_by_old_id
+            or bool(toolbox._lineage_map.lineage_map.get(tool_id))
+        )
 
     def get_tool(self, tool_id: str):
         return self.__toolbox.get_tool(tool_id)

lib/galaxy/tool_util/toolbox/lineages/factory.py

@@ -44,7 +44,15 @@ def get(self, tool_id) -> Optional[ToolLineage]:
         if lineage:
             return lineage
         if tool_id not in self.lineage_map:
-            tool = self.app.toolbox._tools_by_id.get(tool_id)
+            toolbox = None
+            try:
+                toolbox = self.app.toolbox
+            except AttributeError:
+                # We're building the lineage map while building the toolbox,
+                # so app.toolbox may not be available.
+                # TODO: is the fallback really needed / can it be fixed by improving _get_versionless ?
+                pass
+            tool = toolbox and toolbox._tools_by_id.get(tool_id)
             if tool:
                 lineage = ToolLineage.from_tool(tool)
             if lineage:

lib/galaxy/tools/parameters/grouping.py

@@ -102,6 +102,7 @@ def title(self, value):
     def title_plural(self):
         return inflector.pluralize(self.title)
 
+    @property
     def label(self):
         return f"Repeat ({self.title})"
 
@@ -183,6 +184,7 @@ def __init__(self):
     def title_plural(self):
         return inflector.pluralize(self.title)
 
+    @property
     def label(self):
         return f"Section ({self.title})"