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fixing some bugs with saving genecart changes
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@adkinsrs
adkinsrs committed Jan 10, 2024
1 parent 74bc116 commit 0ef733b
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Showing 2 changed files with 55 additions and 33 deletions.
16 changes: 14 additions & 2 deletions tests/test/gene_collection_manager.test.js
View file
Original file line number Diff line number Diff line change
Expand Up @@ -129,6 +129,16 @@ const mockSaveNewGeneCollection = async (page) => {
})
}

const mockSaveGeneCollectionChanges = async (page) => {
await page.route(`${gearBase}/cgi/save_genecart_changes.cgi`, async route => {
const json = {
"gene_cart": "{\"id\": 334, \"user_id\": 1, \"gctype\": \"unweighted-list\", \"label\": \"updated test\", \"organism_id\": 1, \"ldesc\": \"This is the unweighted description\", \"share_id\": \"06c1cdd3\", \"is_public\": 1, \"is_domain\": null, \"date_added\": \"2023-11-01 17:10:36\", \"genes\": [\"0610040J01Rik\", \"Zkscan1\", \"1500011K16Rik\", \"1700025G04Rik\", \"Zfp60\", \"1810037I17Rik\", \"2010111I01Rik\", \"2300009A05Rik\", \"Zfp24\", \"Zdhhc2\", \"4931406P16Rik\", \"Ypel2\", \"5031439G07Rik\", \"Wwp1\", \"Wsb2\", \"Wls\", \"Wasf1\", \"Vwc2\", \"Vwa1\", \"Aatk\", \"Vps36\", \"Vps37b\", \"Abca8a\", \"Vldlr\", \"Abhd4\", \"Vcl\", \"Utrn\", \"Acsbg1\", \"Usp1\", \"Adam10\", \"Adam17\", \"Adam23\", \"Adamts17\", \"Adamts5\", \"Ung\", \"Unc119\", \"Adgrg6\", \"Ucp2\", \"Ado\", \"Ado\", \"Uchl1\", \"Adra2c\", \"Afap1l2\", \"Ubl3\", \"Ube2e2\", \"Ube2c\", \"Ahr\", \"Ak3\", \"Ak6\", \"Tyms\", \"Akr1b8\", \"Twf1\", \"Alcam\", \"Alad\", \"Tubg1\", \"Ttyh1\", \"Ttyh2\", \"Tst\", \"Tspo\", \"Angpt2\", \"Ank3\", \"Tspan18\", \"Tspan13\", \"Tspan15\", \"Tspan17\", \"Tsc22d4\", \"Anxa2\", \"Trim2\", \"Trim13\", \"Arfip1\", \"Trappc2\", \"Arhgap19\", \"Arhgap24\", \"Arhgap32\", \"Arhgap39\", \"Arhgef10\", \"Arhgef28\", \"Tpst1\", \"Tppp3\", \"Tpp1\", \"Arid5b\", \"Tpd52\", \"Tox\", \"Arl8a\", \"Arnt2\", \"Top2a\", \"Arrdc3\", \"Art3\", \"Arvcf\", \"Arvcf\", \"Arxes2\", \"Tns3\", \"Asb8\", \"Aspa\", \"Asrgl1\", \"Atad2\", \"Asxl3\", \"Tnik\", \"Atad2\", \"Tnfrsf21\", \"Atg3\", \"Tnfaip6\", \"Tmpo\", \"Atp1b1\", \"Tmod2\", \"Tmem9b\", \"Tmem63b\", \"Atp8a1\", \"Aurkb\", \"Tmem245\", \"B4galt6\", \"Bach1\", \"Bambi\", \"Tmem117\", \"Tm7sf3\", \"Bcas1\", \"Tk1\", \"Tjp1\", \"Bcl7a\", \"Thtpa\", \"Bicd1\", \"Bin3\", \"Birc5\", \"Tgfbr3\", \"Borcs5\", \"Bpnt1\", \"Tex30\", \"Tdrkh\", \"Tead1\", \"Bzw2\", \"Tcp11l1\", \"Tcf19\", \"Tbx2\", \"Cab39l\", \"Cadm1\", \"Cadm4\", \"Camk2d\", \"Tbc1d10a\", \"Tax1bp3\", \"Capg\", \"Tanc2\", \"Capn5\", \"Taldo1\", \"Tagln2\", \"Taf13\", \"Tacc1\", \"Syt11\", \"Syngr1\", \"Cbx6\", \"Svip\", \"Ccdc13\", \"Ccdc28b\", \"Stx7\", \"Strbp\", \"Ccna2\", \"Ccnd1\", \"Ccnb2\", \"Stmn2\", \"Ccser2\"], \"folder_id\": null, \"folder_parent_id\": null, \"folder_label\": null, \"user_name\": \"Test Armstrong\", \"gene_count\": 159, \"organism\": \"Mus musculus\", \"is_owner\": false}",
"success": 1
};
await route.fulfill({ json });
});
}

/**
* Mocks the delete gene collection functionality.
* @param {Page} page - The page object.
Expand Down Expand Up @@ -281,7 +291,6 @@ const mockDownloadUnweightedGeneCollectionMembers = async (page) => {

describe('Gene Collection Manager', function () {
this.retries(3);

this.timeout(10000); // default is 2000

let browserIndex = 0;
Expand Down Expand Up @@ -498,7 +507,7 @@ describe('Gene Collection Manager', function () {

// Selecting should deselect "All"
await groupAffiliatedOption.click();
// ! This class seems to not be detected
// TODO: detecting the class seems to be flaky when all tests are run
await expect(groupAffiliatedOption).toHaveClass(/js-selected/);
await expect(yourCollectionsOption).toHaveClass(/js-selected/);
await expect(allFacet).not.toHaveClass(/js-selected/);
Expand Down Expand Up @@ -628,6 +637,9 @@ describe('Gene Collection Manager', function () {
it("should update gene collection when save button is clicked", async () => {
await page.locator("css=#result_gc_id_334 .js-edit-gc").click();
await page.locator("css=#result_gc_id_334_editable_title").fill("updated test");

await mockSaveGeneCollectionChanges(page);

await page.locator("css=#result_gc_id_334 .js-edit-gc-save").click();
await expect(page.locator("css=#result_gc_id_334_editable_title")).not.toBeVisible();
// Check that the search results were updated
Expand Down
72 changes: 41 additions & 31 deletions www/js/gene_collection_manager.js
View file
Original file line number Diff line number Diff line change
Expand Up @@ -154,7 +154,10 @@ const addGeneCollectionEventListeners = () => {
classElt.addEventListener("click", async (e) => {
const gcId = e.currentTarget.dataset.gcId;
const selectorBase = `#result_gc_id_${gcId}`;
const newVisibility = document.querySelector(`${selectorBase}_editable_visibility`).value;
//
const newVisibility = document.querySelector(`${selectorBase}_editable_visibility`).checked;
// convert "true/false" visibility to 1/0
const intNewVisibility = newVisibility ? 1 : 0;
const newTitle = document.querySelector(`${selectorBase}_editable_title`).value;
const newOrgId = document.querySelector(`${selectorBase}_editable_organism_id`).value;
const newLdesc = document.querySelector(`${selectorBase}_editable_ldesc`).value;
Expand All @@ -163,49 +166,56 @@ const addGeneCollectionEventListeners = () => {
const {data} = await axios.post('./cgi/save_genecart_changes.cgi', convertToFormData({
'session_id': CURRENT_USER.session_id,
'gc_id': gcId,
'visibility': newVisibility,
'visibility': intNewVisibility,
'title': newTitle,
'organism_id': newOrgId,
'ldesc': newLdesc || ""
}));

// Update the UI for the new values
document.querySelector(`${selectorBase}_editable_visibility`).dataset.isPublic = newVisibility;
if (newVisibility) {
document.querySelector(`${selectorBase}_display_visibility`).textContent = "Public gene collection";
document.querySelector(`${selectorBase}_table_visibility`).textContent = "Public";
document.querySelector(`${selectorBase}_display_visibility`).classList.remove("is-danger");
document.querySelector(`${selectorBase}_display_visibility`).classList.add("is-light");
} else {
document.querySelector(`${selectorBase}_display_visibility`).textContent = "Private gene collection";
document.querySelector(`${selectorBase}_table_visibility`).textContent = "Private";
document.querySelector(`${selectorBase}_display_visibility`).classList.remove("is-light");
document.querySelector(`${selectorBase}_display_visibility`).classList.add("is-danger");
}

document.querySelector(`${selectorBase}_editable_title`).dataset.originalVal = newTitle;
document.querySelector(`${selectorBase}_display_title`).textContent = newTitle;
document.querySelector(`${selectorBase}_table_title`).textContent = newTitle;

document.querySelector(`${selectorBase}_editable_ldesc`).dataset.originalVal = newLdesc;
document.querySelector(`${selectorBase}_display_ldesc`).textContent = newLdesc || "No description entered";;

document.querySelector(`${selectorBase}_display_organism`).textContent =
document.querySelector(`${selectorBase}_editable_organism_id > option[value='${newOrgId}']`).textContent;
document.querySeleector(`${selectorBase}_table_organism`).textContent = document.querySelector(`${selectorBase}_display_organism`).textContent;
document.querySelector(`${selectorBase}_editable_organism_id`).dataset.originalVal = newOrgId;

// Put interface back to view mode.
toggleEditableMode(true, selectorBase);

createToast("Gene collection changes saved", "is-success");

} catch (error) {
logErrorInConsole(error);
createToast("Failed to save gene collection changes");
return;
} finally {
document.querySelector(`${selectorBase} .js-action-links`).classList.remove("is-hidden");
}

// Update the UI for the new values
document.querySelector(`${selectorBase}_editable_visibility`).dataset.isPublic = newVisibility;
if (newVisibility) {
document.querySelector(`${selectorBase}_display_visibility`).textContent = "Public gene collection";
document.querySelector(`${selectorBase}_table_visibility`).textContent = "Public";
document.querySelector(`${selectorBase}_display_visibility`).classList.remove("is-danger");
document.querySelector(`${selectorBase}_display_visibility`).classList.add("is-light", "is-primary");
document.querySelector(`${selectorBase}_table_visibility`).classList.remove("has-background-danger");
document.querySelector(`${selectorBase}_table_visibility`).classList.add("has-background-primary-light");

} else {
document.querySelector(`${selectorBase}_display_visibility`).textContent = "Private gene collection";
document.querySelector(`${selectorBase}_table_visibility`).textContent = "Private";
document.querySelector(`${selectorBase}_display_visibility`).classList.remove("is-light", "is-primary");
document.querySelector(`${selectorBase}_display_visibility`).classList.add("is-danger");
document.querySelector(`${selectorBase}_table_visibility`).classList.remove("has-background-primary-light");
document.querySelector(`${selectorBase}_table_visibility`).classList.add("has-background-danger");
}

document.querySelector(`${selectorBase}_editable_title`).dataset.originalVal = newTitle;
document.querySelector(`${selectorBase}_display_title`).textContent = newTitle;
document.querySelector(`${selectorBase}_table_title`).textContent = newTitle;

document.querySelector(`${selectorBase}_editable_ldesc`).dataset.originalVal = newLdesc;
document.querySelector(`${selectorBase}_display_ldesc`).textContent = newLdesc || "No description entered";;

document.querySelector(`${selectorBase}_display_organism`).textContent =
document.querySelector(`${selectorBase}_editable_organism_id > option[value='${newOrgId}']`).textContent;
document.querySelector(`${selectorBase}_table_organism`).textContent = document.querySelector(`${selectorBase}_display_organism`).textContent;
document.querySelector(`${selectorBase}_editable_organism_id`).dataset.originalVal = newOrgId;

// Put interface back to view mode.
toggleEditableMode(true, selectorBase);

});
}

Expand Down

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