Merge remote-tracking branch 'upstream/release_23.1' into dev

client/src/components/User/DiskUsage/Visualizations/Charts/BarChart.vue

@@ -184,6 +184,17 @@ function createLegend() {
         .attr("fill", "black")
         .text((d) => props.labelFormatter(d));
 
+    // Set the width of the SVG to the width of the widest entry
+    let maxWidth = 0;
+    for (const node of entries.nodes()) {
+        const width = (node as HTMLElement).getBoundingClientRect().width;
+        maxWidth = Math.max(maxWidth, width);
+    }
+    const svg = container.node()?.closest("svg");
+    if (svg) {
+        svg.setAttribute("width", `${maxWidth}`);
+    }
+
     return entries;
 }
 
@@ -294,7 +305,7 @@ function setTooltipPosition(mouseX: number, mouseY: number): void {
 </script>
 
 <template>
-    <BCard class="mb-3 mx-3">
+    <BCard class="mb-3">
         <template v-slot:header>
             <h3 class="text-center my-1">
                 <slot name="title">
@@ -337,7 +348,7 @@ function setTooltipPosition(mouseX: number, mouseY: number): void {
 }
 
 .bar-chart {
-    float: right;
+    float: left;
 
     &:deep(svg) {
         overflow: visible;
@@ -349,12 +360,9 @@ function setTooltipPosition(mouseX: number, mouseY: number): void {
 }
 
 .legend {
-    float: left;
+    float: right;
     height: 400px;
-
-    &:deep(svg) {
-        overflow: visible;
-    }
+    overflow: auto;
 
     &:deep(.legend-item) {
         font-size: 14px;

client/src/components/providers/test/json/DatasetCollection.error.json

@@ -11,7 +11,7 @@
     "name": "abcdef",
     "create_time": "2020-07-02T17:33:56.567412",
     "populated_state": "new",
-    "collection_id": 44,
+    "collection_id": "b887d74393f85b6d",
     "hid": 2,
     "job_source_id": "3da1fe6d8d16a505",
     "type_id": "dataset_collection-ba03619785539f8c",

client/src/components/providers/test/json/DatasetCollection.json

@@ -35,5 +35,5 @@
     "deleted": false,
     "populated": true,
     "update_time": "2020-06-26T14:22:58.435348",
-    "collection_id": 23
-}
+    "collection_id": "f09437b8822035f7"
+}

client/src/components/providers/test/json/DatasetCollection.processing.json

@@ -19,7 +19,7 @@
     "tags": [],
     "hid": 2,
     "url": "/api/histories/f7bb1edd6b95db62/contents/dataset_collections/ba03619785539f8c",
-    "collection_id": 44,
+    "collection_id": "b887d74393f85b6d",
     "job_state_summary": {
         "running": 3,
         "waiting": 0,
@@ -36,4 +36,4 @@
         "new": 0
     },
     "name": "Unzip on data 1"
-}
+}

lib/galaxy/files/__init__.py

@@ -230,13 +230,16 @@ class ConfiguredFileSourcesConfig:
     def __init__(
         self,
         symlink_allowlist=None,
+        fetch_url_allowlist=None,
         library_import_dir=None,
         user_library_import_dir=None,
         ftp_upload_dir=None,
         ftp_upload_purge=True,
     ):
         symlink_allowlist = symlink_allowlist or []
+        fetch_url_allowlist = fetch_url_allowlist or []
         self.symlink_allowlist = symlink_allowlist
+        self.fetch_url_allowlist = fetch_url_allowlist
         self.library_import_dir = library_import_dir
         self.user_library_import_dir = user_library_import_dir
         self.ftp_upload_dir = ftp_upload_dir
@@ -248,6 +251,7 @@ def from_app_config(config):
         # for this component.
         kwds = {}
         kwds["symlink_allowlist"] = getattr(config, "user_library_import_symlink_allowlist", [])
+        kwds["fetch_url_allowlist"] = getattr(config, "fetch_url_allowlist", [])
         kwds["library_import_dir"] = getattr(config, "library_import_dir", None)
         kwds["user_library_import_dir"] = getattr(config, "user_library_import_dir", None)
         kwds["ftp_upload_dir"] = getattr(config, "ftp_upload_dir", None)
@@ -257,6 +261,7 @@ def from_app_config(config):
     def to_dict(self):
         return {
             "symlink_allowlist": self.symlink_allowlist,
+            "fetch_url_allowlist": self.fetch_url_allowlist,
             "library_import_dir": self.library_import_dir,
             "user_library_import_dir": self.user_library_import_dir,
             "ftp_upload_dir": self.ftp_upload_dir,
@@ -267,6 +272,7 @@ def to_dict(self):
     def from_dict(as_dict):
         return ConfiguredFileSourcesConfig(
             symlink_allowlist=as_dict["symlink_allowlist"],
+            fetch_url_allowlist=as_dict["fetch_url_allowlist"],
             library_import_dir=as_dict["library_import_dir"],
             user_library_import_dir=as_dict["user_library_import_dir"],
             ftp_upload_dir=as_dict["ftp_upload_dir"],

lib/galaxy/files/sources/http.py

@@ -9,6 +9,7 @@
 
 from typing_extensions import Unpack
 
+from galaxy.files.uris import validate_non_local
 from galaxy.util import (
     DEFAULT_SOCKET_TIMEOUT,
     get_charset_from_http_headers,
@@ -47,17 +48,22 @@ def __init__(self, **kwd: Unpack[FilesSourceProperties]):
         self._url_regex = re.compile(self._url_regex_str)
         self._props = props
 
+    @property
+    def _allowlist(self):
+        return self._file_sources_config.fetch_url_allowlist
+
     def _realize_to(
         self, source_path: str, native_path: str, user_context=None, opts: Optional[FilesSourceOptions] = None
     ):
         props = self._serialization_props(user_context)
         extra_props: HTTPFilesSourceProperties = cast(HTTPFilesSourceProperties, opts.extra_props or {} if opts else {})
         headers = props.pop("http_headers", {}) or {}
         headers.update(extra_props.get("http_headers") or {})
-
         req = urllib.request.Request(source_path, headers=headers)
 
         with urllib.request.urlopen(req, timeout=DEFAULT_SOCKET_TIMEOUT) as page:
+            # Verify url post-redirects is still allowlisted
+            validate_non_local(page.geturl(), self._allowlist)
             f = open(native_path, "wb")  # fd will be .close()ed in stream_to_open_named_file
             return stream_to_open_named_file(
                 page, f.fileno(), native_path, source_encoding=get_charset_from_http_headers(page.headers)

lib/galaxy/managers/hdcas.py

@@ -314,6 +314,7 @@ def add_serializers(self):
             "contents_url": self.generate_contents_url,
             "job_state_summary": self.serialize_job_state_summary,
             "elements_datatypes": self.serialize_elements_datatypes,
+            "collection_id": self.serialize_id,
         }
         self.serializers.update(serializers)
 

lib/galaxy/managers/jobs.py

@@ -420,7 +420,7 @@ def replace_dataset_ids(path, key, value):
                     c = aliased(model.HistoryDatasetAssociation)
                     d = aliased(model.JobParameter)
                     e = aliased(model.HistoryDatasetAssociationHistory)
-                    query.add_columns(a.dataset_id)
+                    query = query.add_columns(a.dataset_id)
                     used_ids.append(a.dataset_id)
                     query = query.join(a, a.job_id == model.Job.id)
                     stmt = select(model.HistoryDatasetAssociation.id).where(
@@ -513,7 +513,7 @@ def replace_dataset_ids(path, key, value):
                     e = aliased(model.HistoryDatasetAssociation)
                     query = query.add_columns(a.dataset_collection_element_id)
                     query = (
-                        query.join(a)
+                        query.join(a, a.job_id == model.Job.id)
                         .join(b, b.id == a.dataset_collection_element_id)
                         .join(
                             c,