Move to TypeScript

[eboileau]

A clear and concise description of what the bug is.

Branch feature/typescript, cf. 5fd9fad0eb3f8a0f308298f6415363b66a55a654

Index (Release)

• [x] The sunburst charts annotations should be sans-serif (hover is correct)
• [x] On click, we get console.trace() WARN: trace index ( undefined ) is not a number or is out of bounds

Index (Login)

• [x] A wrong passwords results in Failed to login - please try again: AxiosError: Request failed with status code 401. This should be Failed to login - please try again: Wrong user or password.
• [x] Login/Sign up: Button shading and/on hover is lost (Login, Cancel; Request Password Reset, Cancel; Ok). For some buttons, the style is wrong (there is a dark green ring around the button). In dark mode, boxes have dark inputs, it should be lighter (in fact, I would also like to get rid of the yellowish color that appears on filling the input fields). Same style problems on the Settings (change password).
• [x] Sign up: On sign up existing user, error should be Failed to register: User exists and not Failed to register: AxiosError: Request failed with status code 403. The Ok button has the same problem as above. On the other hand, the blue box is better displayed.
• [x] On reset password (login box) with a random email address, we get Sorry - something went wrong: AxiosError: Request failed with status code 404. We had previously Sorry - something went wrong: Unknown user. On sign up, this results in Failed to register: AxiosError: Request failed with status code 500, while previously this worked, i.e. a box with a success message appeared.

Search

• [x] Module "util" has been externalized for browser compatibility. Cannot access "util.debuglog" in client code.
• [x] Module "util" has been externalized for browser compatibility. Cannot access "util.inspect" in client code.
• [x] Clicking on EUFID broken [Vue Router warn]: Discarded invalid param(s) "eufid" when navigating. (also on the tables accessed with the info button).
• [x] Selection of biotype and/or feature should still trigger the query warning, i.e. the only safe queries are those with a gene or a chrom incl. start and end (not just chrom). Besides, if I select e.g. a gene, run a query, then unselect everything (optional filter) the query warning is gone and cannot be brought back, unless the primary filters are changed.
• [x] Changing from Modification to gene/Chrom does not clear the results table.
• [x] Modification: The query button does not behave correctly. In particular, it should be disabled when selection is unset, i.e. when not all 3 primary filters are present. If I unset technology, it remains enabled.
• [x] Gene/Chrom: Same problem with the query button. It should be enabled only when either gene is selected, or chrom, start, end. When everything is unselected, it remains enabled.

Browse

• [x] Info is broken. All projects are listed, and not specifically the related project.
• [x] Bam table not yet tested

Compare - this view is critical, and it is difficult to check everything, but it looks substantially broken...

• [x] On submit (3), or on going back to 1, or 2, the query criteria should be unset, to force a user to redefine them.
• [x] On reset 1, should the upload input be cleared? It was previously, but is not now. If I clear it manually, 3 remains visible, despite that there are no dataset/file selected. Even worst, if I clear the file, I can still run a query in 3 (presumable with the file?) This also happens if I select dataset, then a file, then clear a file.
• [x] On reset 1, 2 should also be cleared (dataset selection). In some cases (moving between 1 and 2, select/unselect), this seem to result in strange behaviour (passing selected dataset between 1 and 2 for conditional selection). In all case, I believe it is safer to reset 2, as soon as 1 is changed.
• [x] When there are no results, there should be a very short interval with greyed out table and spinner, at least to give the user the impression that something has happened. This is all gone now, at least on a first query (refresh).
• [x] It looks like the information on the results table is moved around and getting mixed up, e.g. select two datasets in 1, one in 2, check for closest, and the EUFIDs are all over the place! Reference EUFID should only appear on the left, while comparison EUFID on the right. I don't know if the remaining fields are correct?!
• [x] Some operations should work, but don't, it is hard to know what is happening w/o reference. Maybe we need to systematically check what bedtools return... the BE should be untouched, right? e.g. I noticed that in some cases, intersection does not return anything, which is very surprising, or comparing with production on similar sets, the results are different...
• [ ] Fix the VirtualScroller.

Project template

• [x] Some of validation is gone, e.g. PMID must be a number! Maybe we should also check for consistency e.g. do we have length criteria somewhere for DOI, PMID, etc.?

Dataset upload

• [x] Some validation is gone, e.g. SMID is required!.
• [x] The upload errors are handled differently. I don't know if this is relevant for the normal user to receive Failed to post dataset: HTTP status 500 - File upload failed. Too many skipped records. instead of just File upload failed. Too many skipped records. Same comment for all errors. Sometimes, the error message is not well formatted (very long box), e.g. Failed to post dataset: HTTP status 422 - File upload failed. Mismatch for organism and/or assembly between the file header and the selected values. Click 'Cancel'. Modify the form or the file and start again.. The console logs are slightly different, we now get Uncaught (in promise) Error: ... Previously, the error was reported using a style similar to that for validation (red color, with a cross), not it is a green box?!
• [x] On upload, the Browse view is not updated. I have to reload the application (and login again).

[HaraldWilhelmi]

The message

Module "util" has been externalized for browser compatibility. Cannot access "util.debuglog" in client code.

should only appear in DEV server setup.

[eboileau]

I fixed a few more things, but error handling is to be re-written. In short, BE should always handle errors, then send however much error handling and feedback to the FE.

I guess I don't want to touch the VirtualScroller now. We're using primevue@3.53.0, and the latest version has been rewritten using the a preprocessor approach with apply instead of pass-through (I don't know if this would still work)... updating PrimeVue will most likely break a few things...

[eboileau]

Error handling still fail to catch and backtrace unhandled errors, in particular the API throws TypeError: error.response is undefined.