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Fix collection type drag and drop validation
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The legacy form allowed users to drag non-collection datasets into
collection inputs. The selected value wouldn't actually visibly change,
but if a user hits run the value would actually be submitted, leading to
https://sentry.galaxyproject.org/share/issue/2d1ada39ae9e4ba4952815ac07b2df47/:
```
AttributeError: 'HistoryDatasetAssociation' object has no attribute 'collection'
  File "galaxy/tools/__init__.py", line 1969, in handle_single_execution
    rval = self.execute(
  File "galaxy/tools/__init__.py", line 2066, in execute
    return self.tool_action.execute(
  File "galaxy/tools/actions/__init__.py", line 426, in execute
    ) = self._collect_inputs(tool, trans, incoming, history, current_user_roles, collection_info)
  File "galaxy/tools/actions/__init__.py", line 360, in _collect_inputs
    inp_data, all_permissions = self._collect_input_datasets(
  File "galaxy/tools/actions/__init__.py", line 300, in _collect_input_datasets
    tool.visit_inputs(param_values, visitor)
  File "galaxy/tools/__init__.py", line 1793, in visit_inputs
    visit_input_values(self.inputs, values, callback)
  File "galaxy/tools/parameters/__init__.py", line 211, in visit_input_values
    visit_input_values(
  File "galaxy/tools/parameters/__init__.py", line 227, in visit_input_values
    callback_helper(
  File "galaxy/tools/parameters/__init__.py", line 162, in callback_helper
    new_value = callback(**args)
  File "galaxy/tools/actions/__init__.py", line 246, in visitor
    collection = value.collection
```
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mvdbeek committed Aug 15, 2024
1 parent 3bcc58b commit ccfb0bf
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Showing 2 changed files with 111 additions and 8 deletions.
48 changes: 48 additions & 0 deletions client/src/components/Form/Elements/FormData/FormData.test.js
Original file line number Diff line number Diff line change
Expand Up @@ -372,6 +372,54 @@ describe("FormData", () => {
});
});

it("rejects hda on collection input", async () => {
const wrapper = createTarget({
value: null,
options: defaultOptions,
type: "data_collection",
});
eventStore.setDragData({ id: "whatever", history_content_type: "dataset" });
dispatchEvent(wrapper, "dragenter");
dispatchEvent(wrapper, "drop");
expect(wrapper.emitted().alert[0][0]).toEqual("dataset is not a valid input for dataset collection parameter.");
});

it("rejects paired collection on list collection input", async () => {
const wrapper = createTarget({
value: null,
options: defaultOptions,
type: "data_collection",
collectionTypes: ["list"],
});
eventStore.setDragData({
id: "whatever",
history_content_type: "dataset_collection",
collection_type: "paired",
});
dispatchEvent(wrapper, "dragenter");
dispatchEvent(wrapper, "drop");
expect(wrapper.emitted().alert[0][0]).toEqual(
"paired dataset collection is not a valid input for list type dataset collection parameter."
);
});

it("accepts list:list collection on list collection input", async () => {
const wrapper = createTarget({
value: null,
options: defaultOptions,
type: "data_collection",
collectionTypes: ["list"],
});
eventStore.setDragData({
id: "whatever",
history_content_type: "dataset_collection",
collection_type: "list:list",
});
dispatchEvent(wrapper, "dragenter");
dispatchEvent(wrapper, "drop");
expect(wrapper.emitted().alert[0][0]).toEqual(undefined);
});

it("linked and unlinked batch mode handling", async () => {
const wrapper = createTarget({
value: null,
Expand Down
71 changes: 63 additions & 8 deletions client/src/components/Form/Elements/FormData/FormData.vue
Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ const props = withDefaults(
values: Array<DataOption>;
};
extensions?: Array<string>;
type?: string;
type?: "data" | "data_collection";
collectionTypes?: Array<string>;
flavor?: string;
tag?: string;
Expand Down Expand Up @@ -310,6 +310,9 @@ function handleIncoming(incoming: Record<string, unknown>, partial = true) {
if (!canAcceptDatatype(extensions)) {
return false;
}
if (values.some((v) => !canAcceptSrc(v.history_content_type, v.collection_type))) {
return false;
}
if (values.length > 0) {
const incomingValues: Array<DataOption> = [];
values.forEach((v) => {
Expand Down Expand Up @@ -414,17 +417,67 @@ function canAcceptDatatype(itemDatatypes: string | Array<string>) {
return true;
}
function canAcceptSrc(historyContentType: "dataset" | "dataset_collection", collectionType?: string) {
if (historyContentType === "dataset") {
// HDA can only be fed into data parameters, not collection parameters
if (props.type === "data") {
return true;
} else {
$emit("alert", "dataset is not a valid input for dataset collection parameter.");
return false;
}
} else if (historyContentType === "dataset_collection") {
if (props.type === "data") {
// collection can always be mapped over a data input ... in theory.
// One day we should also validate the map over model
return true;
}
if (!collectionType) {
// Should always be set if item is dataset collection
throw Error("Item is a dataset collection of unknown type.");
} else if (!props.collectionTypes) {
// if no collection_type is set all collections are valid
return true;
} else {
if (props.collectionTypes.includes(collectionType)) {
return true;
}
if (props.collectionTypes.some((element) => collectionType.endsWith(element))) {
return true;
} else {
$emit(
"alert",
`${collectionType} dataset collection is not a valid input for ${orList(
props.collectionTypes
)} type dataset collection parameter.`
);
return false;
}
}
} else {
throw Error("Unknown history content type.");
}
}
// Drag/Drop event handlers
function onDragEnter(evt: MouseEvent) {
const eventData = eventStore.getDragData();
if (eventData) {
const extensions = (eventData.extension as string) || (eventData.elements_datatypes as Array<string>);
let highlightingState = "success";
if (!canAcceptDatatype(extensions)) {
currentHighlighting.value = "warning";
highlightingState = "warning";
$emit("alert", `${extensions} is not an acceptable format for this parameter.`);
} else {
currentHighlighting.value = "success";
} else if (
!canAcceptSrc(
eventData.history_content_type as "dataset" | "dataset_collection",
eventData.collection_type as string
)
) {
highlightingState = "warning";
$emit("alert", `${eventData.history_content_type} is not an acceptable input type for this parameter.`);
}
currentHighlighting.value = highlightingState;
dragTarget.value = evt.target;
dragData.value = eventData;
}
Expand Down Expand Up @@ -501,12 +554,14 @@ const formatsButtonId = useUid("form-data-formats-");
const warningListAmount = 4;
const noOptionsWarningMessage = computed(() => {
if (!props.extensions || props.extensions.length === 0) {
return "No datasets available";
const itemType = props.type === "data" ? "datasets" : "dataset collections";
const collectionTypeLabel = props.collectionTypes?.length ? `${orList(props.collectionTypes)} ` : "";
if (!props.extensions || props.extensions.length === 0 || props.extensions.includes("data")) {
return `No ${collectionTypeLabel}${itemType} available`;
} else if (props.extensions.length <= warningListAmount) {
return `No ${orList(props.extensions)} datasets available`;
return `No ${collectionTypeLabel}${itemType} with ${orList(props.extensions)} elements available`;
} else {
return "No compatible datasets available";
return `No compatible ${collectionTypeLabel}${itemType} available`;
}
});
</script>
Expand Down

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