Implement a page object accessibility dialog

[jmchilton]

This is trickier than it sounds in some ways because objects may be sources of permission in different ways. Histories need to be accessible for invocations or collections or jobs - datasets may be referenced in different ways. The APIs for histories and workflows is pretty different than for datasets also. I think I've managed to give it a unified feel though.

xref #13926 - it doesn't fix the issue yet but it is a component I want to foreground after creating a page from an invocation. I think this PR is 90% of the work.

Builds on all my markdown working branch.

How to test the changes?

(Select all options that apply)

• I've included appropriate automated tests.
• This is a refactoring of components with existing test coverage.
• Instructions for manual testing are as follows:
  1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

• I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

[jdavcs]

@jmchilton, can you resolve the conflict, please?

[davelopez]

Looks amazing! but unfortunately, I found an issue with datasets.

I created a page out of a workflow report and included a couple of markdown directives, but it seems to be an issue retrieving the dataset's name (although they show up correctly in the modal) 🤔

[jmchilton]

I've tried deleted, purged, datasets in a different history, etc... and I cannot reproduce this locally. I get a very fun error if I don't own the dataset - but it is the infinite loop that I think is being worked on elsewhere - https://github.com/galaxyproject/galaxy/pull/17818/files.

The problem with name is not the history dataset name but the name of a permission object. Your API isn't returning what mine is for some reason. The relevant block is:

function initHistoryDatasetData() {
    for (const historyDatasetId of referencedHistoryDatasetIds.value) {
        fetchDataset({ id: historyDatasetId });
        if (historyDatasetId && !(historyDatasetId in historyDatasetAccessible.value)) {
            axios
                .get(withPrefix(`/dataset/get_edit?dataset_id=${historyDatasetId}`))
                .then((response) => {
                    const permissionInputs = response.data.permission_inputs;
                    const accessPermissionInput = permissionInputs[1];
                    if (accessPermissionInput.name != "DATASET_ACCESS") {
                        throw Error("Galaxy Bug");
                    }
                    const accessible = (accessPermissionInput.value || []).length == 0;
                    Vue.set(historyDatasetAccessible.value, historyDatasetId, accessible);
                })
                .catch((e) => {
                    const errorMessage = errorMessageAsString(e);
                    const title = "Failed to fetch dataset metadata.";
                    toast.error(errorMessage, title);
                    Vue.set(historyDatasetAccessible.value, historyDatasetId, `${title} Reason: ${errorMessage}.`);
                });
        }
    }
}

The exception is being thrown here I think: if (accessPermissionInput.name != "DATASET_ACCESS") {

Is there any chance I can get you to tell me what the console is reporting the API response is for offending axios request?

axios.get(withPrefix(`/dataset/get_edit?dataset_id=${historyDatasetId}`))

Does the edit permissions page when you click the pencil in the history work for the offending datasets in your case?

[davelopez]

Unfortunately, I purged that history when testing, however I could get the response to /dataset/get_edit for one of the datasets:

{
    "display_name": "Dataset A",
    "message": null,
    "status": null,
    "dataset_id": "40002f5e6ec8c7e7",
    "metadata_disable": false,
    "attribute_inputs": [
        {
            "name": "name",
            "type": "text",
            "label": "Name",
            "value": "Dataset A"
        },
        {
            "name": "info",
            "type": "text",
            "area": true,
            "label": "Info",
            "value": "uploaded txt file"
        },
        {
            "name": "annotation",
            "type": "text",
            "area": true,
            "label": "Annotation",
            "optional": true,
            "value": null,
            "help": "Add an annotation or notes to a dataset; annotations are available when a history is viewed."
        },
        {
            "type": "select",
            "multiple": false,
            "optional": true,
            "name": "dbkey",
            "label": "Database/Build",
            "options": [
                [
                    "unspecified (?)",
                    "?",
                    true
                ],
                [
                    "A. gambiae Feb. 2003 (IAGEC MOZ2/anoGam1) (anoGam1)",
                    "anoGam1",
                    false
                ],
               ... // Trimming huge list of options for readability
            ],
            "value": "txt",
            "help": "This will change the datatype of the existing dataset but not modify its contents. Use this if Galaxy has incorrectly guessed the type of your dataset."
        }
    ],
    "datatype_disable": false,
    "permission_inputs": [
        {
            "name": "not_shareable",
            "type": "hidden",
            "label": "The dataset is stored on private storage to you and cannot be shared.",
            "readonly": true
        }
    ],
    "permission_disable": true
}

Trying with a new history it seems to work as expected, so maybe I was so unlucky I tried with a history in a "bad state"? Or maybe is the permissions_inputs because that dataset was stored in a private object store 🤔

Let me know if I can provide more info, but I don't think this should hold the PR.

Update:

That was it, relocating one of the datasets to a private object store makes the error reproducible. Which kind of makes sense 😅

[jmchilton]

Perfect - thanks for tracking that down... and frankly thanks for running with a obscure object store that should help find a lot of things. I'll revise this with a fix!

[davelopez]

and frankly thanks for running with a obscure object store that should help find a lot of things.

It was just a coincidence, but I will use it more often to test stuff 😆

[jmchilton]

[davelopez]

Awesome! Thank you very much!