Merge branch 'release_24.0' into dev

.github/workflows/integration.yaml

@@ -62,7 +62,7 @@ jobs:
         id: minikube
         uses: CodingNagger/[email protected]
         with:
-          k8s-version: '1.19.16'
+          k8s-version: '1.23.0'
       - name: Launch Minikube
         run: eval ${{ steps.minikube.outputs.launcher }}
       - name: Check pods

.github/workflows/osx_startup.yaml

@@ -50,7 +50,7 @@ jobs:
           path: .tox
           key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-osx
       - name: Install miniconda  # use this job to test using Python from a conda environment
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: ''
       - name: Restore client cache

client/src/api/schema/schema.ts

@@ -3738,7 +3738,7 @@ export interface components {
              * Element Type
              * @description The type of the element. Used to interpret the `object` field.
              */
-            element_type: components["schemas"]["DCEType"];
+            element_type?: components["schemas"]["DCEType"] | null;
             /**
              * Dataset Collection Element ID
              * @example 0123456789ABCDEF
@@ -3755,10 +3755,11 @@ export interface components {
              * Object
              * @description The element's specific data depending on the value of `element_type`.
              */
-            object:
+            object?:
                 | components["schemas"]["HDAObject"]
                 | components["schemas"]["HDADetailed"]
-                | components["schemas"]["DCObject"];
+                | components["schemas"]["DCObject"]
+                | null;
         };
         /**
          * DCEType

client/src/components/Dataset/DatasetStorage/DatasetStorage.vue

@@ -59,14 +59,7 @@ watch(props, fetch, { immediate: true });
 
 <template>
     <div>
-        <h2 v-if="includeTitle" class="h-md">
-            Dataset Storage
-            <RelocateLink
-                v-if="storageInfo"
-                :dataset-id="datasetId"
-                :dataset-storage-details="storageInfo"
-                @relocated="fetch" />
-        </h2>
+        <h2 v-if="includeTitle" class="h-md">Dataset Storage</h2>
         <div v-if="errorMessage" class="error">{{ errorMessage }}</div>
         <LoadingSpan v-else-if="storageInfo == null"> </LoadingSpan>
         <div v-else-if="discarded">
@@ -84,5 +77,10 @@ watch(props, fetch, { immediate: true });
         <div v-else>
             <DescribeObjectStore what="This dataset is stored in" :storage-info="storageInfo" />
         </div>
+        <RelocateLink
+            v-if="storageInfo"
+            :dataset-id="datasetId"
+            :dataset-storage-details="storageInfo"
+            @relocated="fetch" />
     </div>
 </template>

client/src/components/Dataset/DatasetStorage/RelocateDialog.vue

@@ -13,24 +13,26 @@ defineProps<RelocateProps>();
 
 const emit = defineEmits<{
     (e: "relocate", value: string): void;
+    (e: "closeModal"): void;
 }>();
 
-const fromWhat = "This dataset location in a";
+const fromWhat = "This dataset location is";
 const toWhat = "This dataset will be relocated to";
 </script>
 
 <template>
     <div>
-        <p>Relocate the dataset's current object store of:</p>
+        <p>Currently the dataset is located in:</p>
         <b-button-group vertical size="lg" class="select-button-group">
             <ObjectStoreSelectButton
                 :key="fromObjectStore.object_store_id"
                 id-prefix="swap-target"
                 class="swap-target-object-store-select-button"
                 variant="info"
-                :object-store="fromObjectStore" />
+                :object-store="fromObjectStore"
+                @click="emit('closeModal')" />
         </b-button-group>
-        <p>Select a new object store below to relocate the dataset</p>
+        <p class="relocate-to">Select new storage location for the dataset:</p>
         <b-button-group vertical size="lg" class="select-button-group">
             <ObjectStoreSelectButton
                 v-for="objectStore in targetObjectStores"
@@ -60,4 +62,7 @@ const toWhat = "This dataset will be relocated to";
     margin: auto;
     width: 400px;
 }
+.relocate-to {
+    margin-top: 2em;
+}
 </style>

client/src/components/Dataset/DatasetStorage/RelocateLink.vue

@@ -1,4 +1,5 @@
 <script setup lang="ts">
+import { BButton } from "bootstrap-vue";
 import { storeToRefs } from "pinia";
 import { computed, ref } from "vue";
 
@@ -70,6 +71,10 @@ const emit = defineEmits<{
     (e: "relocated"): void;
 }>();
 
+function closeModal() {
+    showModal.value = false;
+}
+
 async function relocate(objectStoreId: string) {
     try {
         await updateObjectStore(props.datasetId, objectStoreId);
@@ -84,12 +89,13 @@ async function relocate(objectStoreId: string) {
 
 <template>
     <span class="storage-relocate-link">
-        <SelectModal v-if="currentObjectStore" v-model="showModal" title="Relocate Dataset Storage">
+        <SelectModal v-if="currentObjectStore" v-model="showModal" title="Relocate Dataset">
             <RelocateDialog
                 :from-object-store="currentObjectStore"
                 :target-object-stores="validTargets"
-                @relocate="relocate" />
+                @relocate="relocate"
+                @closeModal="closeModal" />
         </SelectModal>
-        <b-link v-if="relocatable" href="#" @click="showModal = true">(relocate)</b-link>
+        <BButton v-if="relocatable" @click="showModal = true">Relocate Dataset</BButton>
     </span>
 </template>

doc/source/admin/galaxy_options.rst

@@ -3030,6 +3030,17 @@
 :Type: bool
 
 
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``use_access_logging_middleware``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Log request start as well as request end. Disables uvicorn access
+    log handler.
+:Default: ``false``
+:Type: bool
+
+
 ~~~~~~~~~~~~
 ``use_lint``
 ~~~~~~~~~~~~
@@ -5495,6 +5506,3 @@
     This requires the help_forum_api_url to be set.
 :Default: ``false``
 :Type: bool
-
-
-

lib/galaxy/config/sample/galaxy.yml.sample

@@ -1743,6 +1743,10 @@ galaxy:
   # job is complete.
   #debug: false
 
+  # Log request start as well as request end. Disables uvicorn access
+  # log handler.
+  #use_access_logging_middleware: false
+
   # Check for WSGI compliance.
   #use_lint: false
 

lib/galaxy/config/sample/object_store_conf.sample.yml

@@ -61,7 +61,7 @@ backends:
 # Sample Distributed Object Store with disk backends configuration
 #
 
-# In the distributed object store, existing dataests will be located by the `object_store_id` column in the `dataset`
+# In the distributed object store, existing datasets will be located by the `object_store_id` column in the `dataset`
 # table of the Galaxy database, which corresponds to the `id` option on the backend. New datasets are created based on
 # the `weight` option: a backend with weight "2" has twice the chance of being (randomly) selected for new datasets as a
 # backend with weight "1". A weight of "0" will still allow datasets in that backend to be read, but no new datasets
@@ -299,20 +299,25 @@ extra_dirs:
 # The admin is responsible for routinely cleaning that storage using Galaxy's admin scripts - this object store
 # configuration just allows the user selection and communicates expectations to the user. Training related to Galaxy
 # cleanup scripts can be found in the Galaxy Training Network:
-# 
+#
 # Slides: https://gxy.io/GTN:S00103
 # Tutorial: https://gxy.io/GTN:T00324
 #
 # In this example, the scratch storage is marked as user-private by setting the `private` option to "true" on the
-# backend definition. This means it cannot be used in public datasets, shared between users, etc.. This is more example
+# backend definition. This means it cannot be used in public datasets, shared between users, etc.. This is for example
 # purposes - you may very well not want scratch storage to be defined as private as it prevents a lot of regular
 # functionality and Galaxy handles regularly cleaned datasets fairly gracefully when the appropriate admin scripts are
 # used.
+#
+# It is safe to just relabel the object store that a dataset belongs to if the underlying paths mapped to by the object
+# stores are the same and the dataset has not been copied. To enable users to relocate datasets this way set the
+# backends' `device` property to the same value.
 
 type: distributed
 backends:
   - id: default
     type: disk
+    device: device1
     weight: 1
     allow_selection: true
     name: Default Galaxy Storage
@@ -329,6 +334,7 @@ backends:
           found on our [Archive Tier Storage](https://www.msi.umn.edu/content/archive-tier-storage) page.
   - id: scratch
     type: disk
+    device: device2
     weight: 0
     allow_selection: true
     private: true

lib/galaxy/config/sample/object_store_conf.xml.sample

@@ -62,7 +62,7 @@
 <!--
     Sample Distributed Object Store with disk backends
 
-    In the distributed object store, existing dataests will be located by the
+    In the distributed object store, existing datasets will be located by the
     `object_store_id` column in the `dataset` table of the Galaxy database,
     which corresponds to the `id` attribute on the backend tag. New datasets are
     created based on the "weight" attribute: a backend with weight "2" has a
@@ -272,11 +272,16 @@
     of regular functionality and Galaxy handles regularly cleaned
     datasets fairly gracefully when the appropriate admin scripts
     are used.
+
+    It is safe to just relabel the object store that a dataset belongs
+    to if the underlying paths mapped to by the object stores are the
+    same and the dataset has not been copied. To enable users to relocate
+    datasets this way set the backends' `device` property to the same value.
 -->
 <!--
 <object_store type="distributed">
     <backends>
-        <backend id="default" allow_selection="true" type="disk" weight="1" name="Default Galaxy Storage">
+        <backend id="default" allow_selection="true" type="disk" device="device1" weight="1" name="Default Galaxy Storage">
             <description>This is Galaxy's default object store - this disk is regularly backed up and all user's have a default quota of 200 GB.
             </description>
             <files_dir path="database/objects/deafult"/>
@@ -286,7 +291,7 @@
                 <backed_up>Backed up to Galaxy's institutional long term tape drive nightly. More information about our tape drive can be found on our [Archive Tier Storage](https://www.msi.umn.edu/content/archive-tier-storage) page.</backed_up>
             </badges>
         </backend>
-        <backend id="scratch" allow_selection="true" type="disk" weight="0" name="Scratch Storage" private="true">
+        <backend id="scratch" allow_selection="true" type="disk" device="device2" weight="0" name="Scratch Storage" private="true">
             <quota source="second_tier" />
             <description>This object store is connected to institutional scratch storage. This disk is not backed up and private to your user and datasets belonging to this storage will be automatically deleted after one month.
 </description>

lib/galaxy/config/schemas/config_schema.yml

@@ -2193,6 +2193,13 @@ mapping:
           causes the files used by PBS/SGE (submission script, output, and error)
           to remain on disk after the job is complete.
 
+      use_access_logging_middleware:
+        type: bool
+        default: false
+        required: false
+        desc: |
+          Log request start as well as request end. Disables uvicorn access log handler.
+
       use_lint:
         type: bool
         default: false

lib/galaxy/datatypes/data.py

@@ -842,7 +842,11 @@ def convert_dataset(
         # Make the target datatype available to the converter
         params["__target_datatype__"] = target_type
         # Run converter, job is dispatched through Queue
-        job, converted_datasets, *_ = converter.execute(trans, incoming=params, set_output_hid=visible, history=history)
+        job, converted_datasets, *_ = converter.execute(
+            trans, incoming=params, set_output_hid=visible, history=history, flush_job=False
+        )
+        for converted_dataset in converted_datasets.values():
+            original_dataset.attach_implicitly_converted_dataset(trans.sa_session, converted_dataset, target_type)
         trans.app.job_manager.enqueue(job, tool=converter)
         if len(params) > 0:
             trans.log_event(f"Converter params: {str(params)}", tool_id=converter.id)

lib/galaxy/datatypes/display_applications/parameters.py

@@ -11,7 +11,6 @@
 
 from galaxy.datatypes.data import Data
 from galaxy.model import DatasetInstance
-from galaxy.model.base import transaction
 from galaxy.schema.schema import DatasetState
 from galaxy.util import string_as_bool
 from galaxy.util.template import fill_template
@@ -182,22 +181,7 @@ def prepare(self, other_values, dataset_hash, user_hash, trans):
                 if target_ext and not converted_dataset:
                     if isinstance(data, DisplayDataValueWrapper):
                         data = data.value
-                    new_data = next(
-                        iter(
-                            data.datatype.convert_dataset(
-                                trans, data, target_ext, return_output=True, visible=False
-                            ).values()
-                        )
-                    )
-                    new_data.hid = data.hid
-                    new_data.name = data.name
-                    trans.sa_session.add(new_data)
-                    assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation(
-                        parent=data, file_type=target_ext, dataset=new_data, metadata_safe=False
-                    )
-                    trans.sa_session.add(assoc)
-                    with transaction(trans.sa_session):
-                        trans.sa_session.commit()
+                    data.datatype.convert_dataset(trans, data, target_ext, return_output=True, visible=False)
                 elif converted_dataset and converted_dataset.state == DatasetState.ERROR:
                     raise Exception(f"Dataset conversion failed for data parameter: {self.name}")
         return self.get_value(other_values, dataset_hash, user_hash, trans)

lib/galaxy/datatypes/protocols.py

@@ -85,5 +85,7 @@ def has_data(self) -> bool: ...
 
     def set_peek(self) -> None: ...
 
+    def attach_implicitly_converted_dataset(self, session, new_dataset, target_ext: str) -> None: ...
+
 
 class DatasetHasHidProtocol(DatasetProtocol, HasHid, Protocol): ...

lib/galaxy/managers/collections.py

@@ -95,7 +95,7 @@ def precreate_dataset_collection_instance(
         # TODO: prebuild all required HIDs and send them in so no need to flush in between.
         dataset_collection = self.precreate_dataset_collection(
             structure,
-            allow_unitialized_element=implicit_output_name is not None,
+            allow_uninitialized_element=implicit_output_name is not None,
             completed_collection=completed_collection,
             implicit_output_name=implicit_output_name,
         )
@@ -112,10 +112,10 @@ def precreate_dataset_collection_instance(
         return instance
 
     def precreate_dataset_collection(
-        self, structure, allow_unitialized_element=True, completed_collection=None, implicit_output_name=None
+        self, structure, allow_uninitialized_element=True, completed_collection=None, implicit_output_name=None
     ):
         has_structure = not structure.is_leaf and structure.children_known
-        if not has_structure and allow_unitialized_element:
+        if not has_structure and allow_uninitialized_element:
             dataset_collection = model.DatasetCollectionElement.UNINITIALIZED_ELEMENT
         elif not has_structure:
             collection_type_description = structure.collection_type_description
@@ -143,7 +143,7 @@ def precreate_dataset_collection(
                         element = model.DatasetCollectionElement.UNINITIALIZED_ELEMENT
                     else:
                         element = self.precreate_dataset_collection(
-                            substructure, allow_unitialized_element=allow_unitialized_element
+                            substructure, allow_uninitialized_element=allow_uninitialized_element
                         )
 
                 element = model.DatasetCollectionElement(

lib/galaxy/managers/hdas.py

@@ -206,7 +206,7 @@ def copy(
             parent_id=kwargs.get("parent_id"),
             copy_hid=False,
             copy_tags=hda.tags,  # type:ignore[attr-defined]
-            flush=flush,
+            flush=False,
         )
         if hide_copy:
             copy.visible = False
@@ -227,12 +227,6 @@ def copy(
 
         return copy
 
-    def copy_ldda(self, history, ldda, **kwargs):
-        """
-        Copy this HDA as a LDDA and return.
-        """
-        return ldda.to_history_dataset_association(history, add_to_history=True)
-
     # .... deletion and purging
     def purge(self, hda, flush=True, **kwargs):
         if self.app.config.enable_celery_tasks:
@@ -569,6 +563,7 @@ def add_serializers(self):
         annotatable.AnnotatableSerializerMixin.add_serializers(self)
 
         serializers: Dict[str, base.Serializer] = {
+            "hid": lambda item, key, **context: item.hid if item.hid is not None else -1,
             "model_class": lambda item, key, **context: "HistoryDatasetAssociation",
             "history_content_type": lambda item, key, **context: "dataset",
             "hda_ldda": lambda item, key, **context: "hda",

lib/galaxy/managers/history_contents.py

@@ -590,7 +590,7 @@ def get_filter(attr, op, val):
                     if val == "__null__":
                         val = None
                     if val not in ids:
-                        raise KeyError(f"Could not find key {val} in object store keys {list(ids.keys())}")
+                        raise ValueError(f"Could not find key {val} in object store keys {list(ids.keys())}")
                     object_store_ids = ids[val]
                     return sql.column("object_store_id").in_(object_store_ids)