Fix re-run with DCE inputs

client/src/mvc/ui/ui-select-content.js

@@ -424,12 +424,12 @@ const View = Backbone.View.extend({
         const select_options = { hda: [], hdca: [] };
         _.each(options, (items, src) => {
             _.each(items, (item) => {
-                self._patchValue(item);
+                self._patchValue(item, src);
                 const current_src = item.src || src;
                 const addOption = !this.model.attributes.tag || item.tags.includes(this.model.attributes.tag);
                 if (addOption) {
                     select_options[current_src].push({
-                        hid: item.hid,
+                        hid: item.hid || Infinity, // if we got no hid we have a "Selected" item
                         keep: item.keep,
                         label: `${item.hid || "Selected"}: ${item.name}`,
                         value: item.id,
@@ -455,7 +455,12 @@ const View = Backbone.View.extend({
                 list.push(value.id);
             });
             // sniff first suitable field type from config list
-            const src = new_value.values[0].src;
+            let src = new_value.values[0].src;
+            if (src === "dce") {
+                src =
+                    this.cache[`dce${new_value.values[0].id}_hda`]?.src ||
+                    this.cache[`dce${new_value.values[0].id}_hdca`]?.src;
+            }
             const multiple = new_value.values.length > 1;
             for (let i = 0; i < this.config.length; i++) {
                 const field = this.fields[i];
@@ -480,11 +485,11 @@ const View = Backbone.View.extend({
 
     /** Library datasets are displayed and selected together with history datasets,
         Dataset collection elements are displayed together with history dataset collections **/
-    _patchValue: function (v) {
-        const patchTo = { ldda: "hda", dce: "hdca" };
+    _patchValue: function (v, src) {
+        const patchTo = { ldda: "hda", dce: src };
         if (v.values) {
             _.each(v.values, (v) => {
-                this._patchValue(v);
+                this._patchValue(v, src);
             });
         } else if (patchTo[v.src]) {
             v.origin = v.src;

lib/galaxy/model/security.py

@@ -520,9 +520,7 @@ class GalaxyRBACAgent(RBACAgent):
 
         return True
 
-    def can_access_collection(
-        self, user_roles: List[galaxy.model.Role], collection: galaxy.model.DatasetCollection
-    ):
+    def can_access_collection(self, user_roles: List[galaxy.model.Role], collection: galaxy.model.DatasetCollection):
         action_tuples = collection.dataset_action_tuples
         if not self.can_access_datasets(user_roles, action_tuples):
             return False

lib/galaxy/tools/parameters/basic.py

@@ -2092,6 +2092,9 @@ class DataToolParameter(BaseDataToolParameter):
                     elif single_value["src"] == "ldda":
                         decoded_id = trans.security.decode_id(single_value["id"])
                         rval.append(trans.sa_session.query(LibraryDatasetDatasetAssociation).get(decoded_id))
+                    elif single_value["src"] == "dce":
+                        decoded_id = trans.security.decode_id(single_value["id"])
+                        rval.append(trans.sa_session.query(DatasetCollectionElement).get(decoded_id))
                     else:
                         raise ValueError(f"Unknown input source {single_value['src']} passed to job submission API.")
                 elif isinstance(
@@ -2127,6 +2130,9 @@ class DataToolParameter(BaseDataToolParameter):
             elif value["src"] == "hdca":
                 decoded_id = trans.security.decode_id(value["id"])
                 rval.append(trans.sa_session.query(HistoryDatasetCollectionAssociation).get(decoded_id))
+            elif value["src"] == "dce":
+                decoded_id = trans.security.decode_id(value["id"])
+                rval.append(trans.sa_session.query(DatasetCollectionElement).get(decoded_id))
             else:
                 raise ValueError(f"Unknown input source {value['src']} passed to job submission API.")
         elif str(value).startswith("__collection_reduce__|"):
@@ -2280,6 +2286,28 @@ class DataToolParameter(BaseDataToolParameter):
                 value["map_over_type"] = subcollection_type
             return list.append(value)
 
+        def append_dce(dce):
+            if dce.hda:
+                # well this isn't good, but what's the alternative ?
+                # we should be precise about what we're (re-)running here.
+                key = "hda"
+            else:
+                key = "hdca"
+            d["options"][key].append(
+                {
+                    "id": trans.security.encode_id(dce.id),
+                    "name": dce.element_identifier,
+                    "src": "dce",
+                    "tags": [],
+                    "keep": True,
+                }
+            )
+
+        # append DCE
+        if isinstance(other_values.get(self.name), DatasetCollectionElement):
+            dce = other_values[self.name]
+            append_dce(dce)
+
         # add datasets
         hda_list = util.listify(other_values.get(self.name))
         # Prefetch all at once, big list of visible, non-deleted datasets.
@@ -2299,6 +2327,8 @@ class DataToolParameter(BaseDataToolParameter):
                 else:
                     hda_state = "unavailable"
                 append(d["options"]["hda"], hda, f"({hda_state}) {hda.name}", "hda", True)
+            elif isinstance(hda, DatasetCollectionElement):
+                append_dce(hda)
 
         # add dataset collections
         dataset_collection_matcher = dataset_matcher_factory.dataset_collection_matcher(dataset_matcher)
@@ -2460,7 +2490,7 @@ class DataCollectionToolParameter(BaseDataToolParameter):
         # append DCE
         if isinstance(other_values.get(self.name), DatasetCollectionElement):
             dce = other_values[self.name]
-            d["options"]["dce"].append(
+            d["options"]["hdca"].append(
                 {
                     "id": trans.security.encode_id(dce.id),
                     "hid": None,