46a7db400ddc1280555e0bc32ed09311e19efc65
chmalee
  Thu May 7 10:53:58 2026 -0700
Reword some hubSpace assembly hub error message. Make the duration of some error message notifications longer, change some text around input about why certain inputs are disabled in certain situations, refs #37411

diff --git src/hg/js/hgMyData.js src/hg/js/hgMyData.js
index 5c23bbf4183..8bd3e531a63 100644
--- src/hg/js/hgMyData.js
+++ src/hg/js/hgMyData.js
@@ -1,2083 +1,2099 @@
 /* jshint esnext: true */
 var debugCartJson = true;
 
 function prettyFileSize(num) {
     if (!num) {return "0B";}
     if (num < (1024 * 1024)) {
         return `${(num/1024).toFixed(1)}KB`;
     } else if (num < (1024 * 1024 * 1024)) {
         return `${((num/1024)/1024).toFixed(1)}MB`;
     } else {
         return `${(((num/1024)/1024)/1024).toFixed(1)}GB`;
     }
 }
 
 function cgiEncode(value) {
     // copy of cheapgi.c:cgiEncode except we are explicitly leaving '/' characters, and
     // space becomes '+':
     let splitVal = value.split('/');
     splitVal.forEach((ele, ix) => {
         if (ele == " ") {
             splitVal[ix] = '+';
         } else {
             splitVal[ix] = encodeURIComponent(ele);
         }
     });
     return splitVal.join('/');
 }
 
 function cgiDecode(value) {
     // decode an encoded value
     return decodeURIComponent(value);
 }
 
 function setDbSelectFromAutocomplete(selectEle, item) {
     // this has been bound to the <select> we are going to add
     // a new child option to
     if (item.disabled || !item.genome) return;
     let newOpt = document.createElement("option");
     newOpt.value = item.genome;
     newOpt.label = item.label;
     newOpt.selected = true;
     selectEle.appendChild(newOpt);
     const event = new Event("change");
     selectEle.dispatchEvent(event);
 }
 
 function onSearchError(jqXHR, textStatus, errorThrown, term) {
     return [{label: 'No genomes found', value: '', genome: '', disabled: true}];
 }
 
 let autocompletes = {};
 function initAutocompleteForInput(inpIdStr, selectEle) {
     // we must set up the autocompleteCat for each input created, once per file chosen
     // override the autocompleteCat.js _renderMenu to get the menu on top
     // of the uppy widget.
     // Return true if we actually set up the autocomplete, false if we have already
     // set it up previously
     if ( !(inpIdStr in autocompletes) || autocompletes[inpIdStr] === false) {
         let selectFunction = setDbSelectFromAutocomplete.bind(null, selectEle);
         initSpeciesAutoCompleteDropdown(inpIdStr, selectFunction, null, null, null, onSearchError);
         autocompletes[inpIdStr] = true;
         return true;
     }
     return false;
 }
 
 function generateApiKey() {
     let apiKeyInstr = document.getElementById("apiKeyInstructions");
     let apiKeyDiv = document.getElementById("apiKey");
 
     if (!document.getElementById("spinner")) {
         let spinner = document.createElement("i");
         spinner.id = "spinner";
         spinner.classList.add("fa", "fa-spinner", "fa-spin");
         document.getElementById("generateApiKey").after(spinner);
     }
 
     let handleSuccess = function(reqObj) {
         apiKeyDiv.textContent = reqObj.apiKey;
         apiKeyInstr.style.display = "block";
         let revokeDiv= document.getElementById("revokeDiv");
         revokeDiv.style.display = "block";
         document.getElementById("spinner").remove();
 
         // remove the word 'already' from the message if we have just re-generated a key
         let refreshSpan = document.getElementById("removeOnGenerate");
         if (refreshSpan) {
             refreshSpan.style.display = "none";
         }
     };
 
     let cartData = {generateApiKey: {}};
     cart.setCgiAndUrl(fileListEndpoint);
     cart.send(cartData, handleSuccess);
     cart.flush();
 }
 
 function revokeApiKeys() {
     let apiKeyInstr = document.getElementById("apiKeyInstructions");
     let apiKeyDiv = document.getElementById("apiKey");
 
     if (!document.getElementById("spinner")) {
         let spinner = document.createElement("i");
         spinner.id = "spinner";
         spinner.classList.add("fa", "fa-spinner", "fa-spin");
         document.getElementById("revokeApiKeys").after(spinner);
     }
 
     let handleSuccess = function(req) {
         apiKeyInstr.style.display = "none";
         document.getElementById("spinner").remove();
         let generateDiv = document.getElementById("generateDiv");
         generateDiv.style.display = "block";
         let revokeDiv = document.getElementById("revokeDiv");
         revokeDiv.style.display = "none";
     };
 
     let cartData = {revokeApiKey: {}};
     cart.setCgiAndUrl(fileListEndpoint);
     cart.send(cartData, handleSuccess);
     cart.flush();
 }
 
 const fileNameRegex = /[0-9a-zA-Z._]+/g; // allowed characters in file names
 const fileNameFixRegex = /[^0-9a-zA-Z_]+/g; // '.' get replaced to underbars in trackHub.c. Also any files uploaded from hubtools that may have weird chars need to be escaped
 const parentDirRegex = /[0-9a-zA-Z._]+/g; // allowed characters in hub names
 
 function getTusdEndpoint() {
     // this variable is set by hgHubConnect and comes from hg.conf value
     return tusdEndpoint;
 }
 
 let uppyOptions = {
     trigger: ".uploadButton",
     showProgressDetails: true,
     note: "The UCSC Genome Browser is not a HIPAA compliant data store. Do not upload patient information or other sensitive data files here, as anyone with the URL can view them.",
     meta: {"genome": null, "fileType": null},
     restricted: {requiredMetaFields: ["genome"]},
     closeModalOnClickOutside: true,
     closeAfterFinish: true,
     theme: 'auto',
     metaFields: (file) => {
         const fields = [{
             id: 'name',
             name: 'File name',
             render: ({value, onChange, required, form}, h) => {
                 return h('input',
                     {type: "text",
                     value: value,
                     class: "uppy-u-reset uppy-c-textInput uppy-Dashboard-FileCard-input",
                     onChange: e => {
                         onChange(e.target.value);
                         file.meta.fileType = hubCreate.detectFileType(e.target.value);
                         file.meta.name = e.target.value;
                     },
                     required: required,
                     form: form,
                     }
                 );
             },
         },
         {
             id: 'genome',
             name: 'Genome',
             render: ({value, onChange}, h) => {
                 // 2bit files name a new assembly hub (editable). Other files
                 // with genomeLocked are pinned by a hub-defining sibling or
                 // the hub they were drilled into.
                 let isTwoBit = file.meta.fileType === "2bit";
+                let isHubTxt = looksLikeHubTxt(file);
                 let isLocked = !!file.meta.genomeLocked;
                 if (isTwoBit || isLocked) {
                     let editable2bit = isTwoBit && !isLocked;
+                    let batchHasHubTxt = uppy.getFiles().some(looksLikeHubTxt);
                     let label;
                     if (editable2bit) {
                         label = "Genome name for your assembly hub:";
-                    } else if (isTwoBit) {
-                        label = "Genome (set by hub.txt in this batch):";
+                    } else if (isHubTxt || (isTwoBit && batchHasHubTxt)) {
+                        label = "Genome (locked by hub.txt - edit hub.txt locally and re-add to change):";
                     } else {
-                        label = "Genome (set by the assembly hub):";
+                        label = "Genome (locked by this assembly hub):";
                     }
                     return h('div', {
                             class: "uppy-Dashboard-FileCard-label",
                             style: "display: inline-block; width: 78%"
                             },
                         label,
                         h('input', {
                             id: `${file.meta.name}AsmHubInput`,
                             type: 'text',
                             class: "uppy-u-reset uppy-c-textInput uppy-Dashboard-FileCard-input",
                             style: "margin-left: 5px",
                             value: file.meta.genome || "",
                             disabled: !editable2bit,
                             onChange: e => {
                                 let v = hubCreate.sanitizeGenomeName(e.target.value);
                                 if (!v) {
                                     // Empty input: revert rather than blank out meta.
                                     e.target.value = file.meta.genome || "";
                                     return;
                                 }
                                 onChange(v);
                                 file.meta.genome = v;
                                 file.meta.genomeLabel = v;
                             }
                         })
                     );
                 }
                 // keep these as a variable so we can init the autocompleteCat
                 // code only after the elements have actually been rendered
                 // there are multiple rendering passes and only eventually
                 // do the elements actually make it into the DOM
                 let ret = h('div', {
                         class: "uppy-Dashboard-FileCard-label",
                         style: "display: inline-block; width: 78%"
                         },
                     // first child of div
                     "Select from popular assemblies:",
                     // second div child
                     h('select', {
                         id: `${file.meta.name}DbSelect`,
                         style: "margin-left: 5px",
                         onChange: e => {
                             onChange(e.target.value);
                             file.meta.genome = e.target.value;
                             file.meta.genomeLabel = e.target.selectedOptions[0].label;
                             // If the user picked one of their own assembly hubs,
                             // flip hubType and align parentDir so the upload
                             // targets that existing hub rather than creating a
                             // new stub. If they picked a UCSC db, flip back
                             // and reset parentDir to a fresh default so they
                             // don't accidentally upload into an assembly hub.
                             let hub = hubCreate.assemblyHubByGenome(e.target.value);
                             if (hub) {
                                 file.meta.hubType = "assemblyHub";
                                 file.meta.parentDir = hub.fileName;
                             } else {
                                 file.meta.hubType = "trackHub";
                                 file.meta.parentDir = hubCreate.uiState.hubNameDefault;
                             }
                         }
                         },
                         hubCreate.makeGenomeSelectOptions(file.meta.genome, file.meta.genomeLabel).map( (genomeObj) => {
                             return h('option', {
                                 value: genomeObj.value,
                                 label: genomeObj.label,
                                 selected: file.meta.genome !== null ? genomeObj.value === file.meta.genome : genomeObj.value === hubCreate.defaultDb()
                             });
                         })
                     ),
                     h('p', {
                         class: "uppy-Dashboard-FileCard-label",
                         style: "display: block; width: 78%",
                         }, "or search for your genome:"),
                     // third div child
                     h('input', {
                         id: `${file.meta.name}DbInput`,
                         type: 'text',
                         class: "uppy-u-reset uppy-c-textInput uppy-Dashboard-FileCard-input",
                     }),
                     h('input', {
                         id: `${file.meta.name}DbSearchButton`,
                         type: 'button',
                         value: 'search',
                         style: "margin-left: 5px",
                     })
                 );
             let selectToChange = document.getElementById(`${file.meta.name}DbSelect`);
             if (selectToChange) {
                 let justInitted = initAutocompleteForInput(`${file.meta.name}DbInput`, selectToChange);
                 if (justInitted) {
                     // only do this once per file
                     document.getElementById(`${file.meta.name}DbSearchButton`)
                             .addEventListener("click", (e) => {
                                 let inp = document.getElementById(`${file.meta.name}DbInput`).value;
                                 let selector = `[id='${file.meta.name}DbInput']`;
                                 $(selector).autocompleteCat("search", inp);
                             });
                 }
             }
             return ret;
             }
         },
         {
             id: 'parentDir',
             name: 'Hub Name',
         }];
         return fields;
     },
     doneButtonHandler: function() {
         uppy.clear();
     },
 };
 
 // make our Uppy instance:
 const uppy = new Uppy.Uppy({
     debug: true,
     allowMultipleUploadBatches: false,
     onBeforeUpload: (files) => {
         // set all the fileTypes and genomes from their selects
         let doUpload = true;
         let thisQuota = 0;
         let filesToOverwrite = []; // collect files that will overwrite existing ones
 
         // Only one 2bit per hub is supported. propagateAssemblyHubMeta picks
         // the first 2bit found and overwrites every sibling's genome with it,
         // which silently orphans the second 2bit (lands on disk and in the
         // hubSpace table but is not referenced from hub.txt).
         let twoBitsInBatch = Object.values(files).filter(looksLikeTwoBit);
         if (twoBitsInBatch.length > 1) {
             let names = twoBitsInBatch.map(f => f.name).join(", ");
             uppy.info(`Error: only one 2bit file per hub is supported. ` +
                       `Found: ${names}. Upload one 2bit at a time, or split ` +
                       `them into separate hubs.`, "error", 6000);
             return false;
         }
 
         // If a 2bit is in the batch, propagate its genome/hubType to siblings.
         let batchTwoBit = twoBitsInBatch[0];
         if (batchTwoBit) {
             let asmGenome = batchTwoBit.meta.genome;
             if (!asmGenome) {
                 uppy.info(`Error: Genome name is required for ` +
                           `${batchTwoBit.name}. Open the file card and enter ` +
                           `a name for your assembly.`, "error", 5000);
                 return false;
             }
             for (let f of Object.values(files)) {
                 f.meta.genome = asmGenome;
                 f.meta.genomeLabel = asmGenome;
                 f.meta.hubType = "assemblyHub";
                 // fileType may also be stale; recompute from filename if missing
                 if (!f.meta.fileType) {
                     f.meta.fileType = hubCreate.detectFileType(f.name);
                 }
             }
         }
 
         // Tag every file so pre-finish knows a user hub.txt is coming in
         // the same batch and can skip synthesizing its own.
         let hasHubTxt = Object.values(files).some(looksLikeHubTxt);
         for (let f of Object.values(files)) {
             f.meta.batchHasHubTxt = hasHubTxt ? "true" : "false";
         }
 
         for (let [key, file] of Object.entries(files)) {
             let fileNameMatch = file.meta.name.match(fileNameRegex);
             let parentDirMatch = file.meta.parentDir.match(parentDirRegex);
             if (!fileNameMatch || fileNameMatch[0] !== file.meta.name) {
                 uppy.info(`Error: File name has special characters, please rename file: ${file.meta.name} to only include alpha-numeric characters, period, or underscore.`, 'error', 5000);
                 doUpload = false;
                 continue;
             }
             if (!parentDirMatch || parentDirMatch[0] !== file.meta.parentDir) {
                 uppy.info(`Error: Hub name has special characters, please rename hub: ${file.meta.parentDir} for file: ${file.meta.name} to only include alpha-numeric characters, period, or underscore.`, 'error', 5000);
                 doUpload = false;
                 continue;
             }
             if (!file.meta.genome) {
                 uppy.info(`Error: No genome selected for file ${file.meta.name}!`, 'error', 5000);
                 doUpload = false;
                 continue;
             }
             if  (!file.meta.fileType) {
                 uppy.info(`Error: File type not supported, file: ${file.meta.name}!`, 'error', 5000);
                 doUpload = false;
                 continue;
             }
             // check if this hub already exists and the genome is different from what was
             // just selected, if so, make the user create a new hub
             if (file.meta.parentDir in hubCreate.uiState.filesHash && hubCreate.uiState.filesHash[file.meta.parentDir].genome !== file.meta.genome) {
                 let existing = hubCreate.uiState.filesHash[file.meta.parentDir];
                 // If the existing hub is an assembly hub, adopt its genome
                 // automatically rather than erroring - the UI hid the picker
                 // for this case, so the mismatch is just stale metadata.
                 if (existing.hubType === "assemblyHub") {
                     file.meta.genome = existing.genome;
                     file.meta.genomeLabel = existing.genome;
                     file.meta.hubType = "assemblyHub";
                 } else {
                     uppy.info(`Error: the hub ${file.meta.parentDir} already exists and is for genome "${existing.genome}". Please select the correct genome, a different hub or make a new hub.`);
                     doUpload = false;
                     continue;
                 }
             }
             // check if the user is uploading a file that already exists in this hub
             if (file.meta.parentDir in hubCreate.uiState.filesHash) {
                 let hubFiles = hubCreate.uiState.filesHash[file.meta.parentDir].children;
                 for (let j = 0; j < hubFiles.length; j++) {
                     if (hubFiles[j].fileName === file.meta.name) {
                         filesToOverwrite.push(file);
                         break;
                     }
                 }
             }
 
             // Set metadata directly on the file object since we're returning a modified files object
             // (using setFileMeta would be overwritten when we return the files object)
             file.meta.fileName = file.meta.name;
             file.meta.fileSize = file.size;
             file.meta.lastModified = file.data.lastModified;
             thisQuota += file.size;
 
         }
         // If any files will overwrite existing ones, show a single confirmation dialog
         if (filesToOverwrite.length > 0) {
             let fileNames = filesToOverwrite.map(f => f.meta.name).join("\n  ");
             if (!confirm(`The following file(s) already exist and will be overwritten:\n  ${fileNames}\n\nContinue?`)) {
                 doUpload = false;
             } else {
                 // Set metadata flag to allow overwrite on backend for each file
                 filesToOverwrite.forEach(f => f.meta.allowOverwrite = "true");
             }
         }
         if (thisQuota + hubCreate.uiState.userQuota > hubCreate.uiState.maxQuota) {
             uppy.info(`Error: this file batch exceeds your quota. Please delete some files to make space or email genome-www@soe.ucsc.edu if you feel you need more space.`);
             doUpload = false;
         }
         return doUpload ? files : false;
     },
 });
 
 function extractHookErrorMessage(error, response) {
     // Our hooks exit 0 + RejectUpload=true, so the response body is the raw
     // errAbort message. tus-js-client still wraps error.message with
     // "tus: unexpected response while ..., response text: <ours>, request
     // id: n/a" when the status code is 4xx/5xx.
     if (response && response.body) return String(response.body).trim();
     let body = null;
     try { body = error && error.originalResponse && error.originalResponse.getBody(); }
     catch (e) { /* ignore */ }
     if (body) return String(body).trim();
     let msg = (error && error.message) || "Upload failed";
     // Scrape the tus wrapping off if present.
     let m = msg.match(/response text:\s*([\s\S]*?)(?:,\s*request id:|$)/);
     return m ? m[1].trim() : msg;
 }
 
 function looksLikeTwoBit(f) {
     return (f.name || "").toLowerCase().endsWith(".2bit");
 }
 
 function looksLikeHubTxt(f) {
     // Accept exact "hub.txt" or any "*.hub.txt" (e.g. "araTha1.hub.txt").
     let n = (f.name || "").toLowerCase();
     return n === "hub.txt" || n.endsWith(".hub.txt");
 }
 
 function propagateAssemblyHubMeta(uppyInstance) {
     // When a batch contains a 2bit (and/or an assembly-hub hub.txt), mirror the
     // custom genome name onto every file sharing that parentDir and mark every
     // file hubType=assemblyHub. hub.txt wins over the 2bit's default.
     //
     // We detect the hub-defining files by filename rather than by meta.fileType,
     // because setFileMeta updates Uppy's state immutably - file objects captured
     // from getFiles() earlier in this event may still carry old meta.
     let files = uppyInstance.getFiles();
     let twoBit = files.find(looksLikeTwoBit);
     let hubTxt = files.find(looksLikeHubTxt);
     if (!twoBit && !hubTxt) return;
 
     function applyGenomeToSiblings(genome, alsoLockHubDefiners) {
         // Set genome/hubType on every file in the batch. Non-hub-defining
         // files (i.e. the sibling tracks) are always locked to this genome so
         // the user can't drift them. The hub-defining files (2bit, hub.txt)
         // are locked only when alsoLockHubDefiners is true - used by the
         // hub.txt path to pin the 2bit's editable field too.
         if (!genome) return;
         // All files in this batch belong to one new hub, so they must share
         // one parentDir. Take it from the hub-defining file - its parentDir
         // came from getDefaultHubName(), while a track that was added first
         // may have been pointed at an existing assembly hub.
         let hubDefiner = hubTxt || twoBit;
         let syncParentDir = hubDefiner && hubDefiner.meta && hubDefiner.meta.parentDir;
         for (let f of uppyInstance.getFiles()) {
             let isHubDefining = looksLikeTwoBit(f) || looksLikeHubTxt(f);
             let meta = {
                 genome: genome,
                 genomeLabel: genome,
                 hubType: "assemblyHub",
                 genomeLocked: !isHubDefining || alsoLockHubDefiners,
             };
             if (syncParentDir) meta.parentDir = syncParentDir;
             uppyInstance.setFileMeta(f.id, meta);
         }
     }
 
     if (hubTxt) {
         hubCreate.readFileAsText(hubTxt.data).then((text) => {
             let parsed = hubCreate.parseHubTxt(text);
             // hub.txt is authoritative: lock the genome field so the user
             // can't edit it and drift the stored db away from what hub.txt
             // says. The user can always edit the hub.txt itself if they
             // want a different name.
             if (parsed.isAssemblyHub && parsed.genome) {
                 applyGenomeToSiblings(parsed.genome, true);
                 uppyInstance.info(`Using genome "${parsed.genome}" from hub.txt`, "info", 4000);
             } else if (parsed.genome && twoBit) {
                 let twoBitGenome = twoBit.meta.genome || hubCreate.sanitizeGenomeName(twoBit.name);
                 if (parsed.genome !== twoBitGenome) {
                     applyGenomeToSiblings(parsed.genome, true);
                     uppyInstance.info(`Using genome "${parsed.genome}" from hub.txt (overrides 2bit default)`, "warning", 5000);
                 }
             }
         }).catch((err) => {
             console.warn("Could not read hub.txt for genome detection:", err);
         });
         return;
     }
 
     let asmGenome = twoBit.meta.genome || hubCreate.sanitizeGenomeName(twoBit.name);
     applyGenomeToSiblings(asmGenome, false);
 }
 
 // create a custom uppy plugin to batch change the type and db fields
 class BatchChangePlugin extends Uppy.BasePlugin {
     constructor(uppy, opts) {
         super(uppy, opts);
         this.id = "BatchChangePlugin";
         this.type = "progressindicator";
         this.opts = opts;
     }
 
     createOptsForSelect(select, opts) {
         opts.forEach( (opt) => {
             let option = document.createElement("option");
             option.value = opt.value;
             option.label = opt.label;
             option.id = opt.id;
             option.selected = typeof opt.selected !== 'undefined' ? opt.selected : false;
             select.appendChild(option);
         });
     }
 
     addSelectsForFile(file) {
         /* create two selects for the file object, to include the db and type */
         const id = "uppy_" + file.id;
         let fileDiv = document.getElementById(id);
         // this might not exist yet depending on where we are in the render cycle
         if (fileDiv) {
             let dbSelectId = "db_select_" + file.id;
             if (!document.getElementById(dbSelectId)) {
                 let dbSelect = document.createElement("select");
                 dbSelect.id = dbSelectId;
                 let dbOpts = hubCreate.makeGenomeSelectOptions();
                 this.createOptsForSelect(dbSelect, dbOpts);
                 fileDiv.appendChild(dbSelect);
             }
         }
     }
 
     removeBatchSelectsFromDashboard() {
         let batchSelectDiv = document.getElementById("batch-selector-div");
         if (batchSelectDiv) {
             batchSelectDiv.remove();
         }
     }
 
     addBatchSelectsToDashboard() {
         if (!document.getElementById("batch-selector-div")) {
             // If the batch contains a 2bit, the UCSC genome picker makes no
             // sense - show the custom genome name read-only instead. Detect by
             // filename rather than meta.hubType because setFileMeta updates
             // Uppy state immutably and the meta may not be visible on file
             // objects captured from getFiles() earlier in this event.
             let assemblyHubGenome = null;
             for (let f of this.uppy.getFiles()) {
                 if (looksLikeTwoBit(f)) {
                     assemblyHubGenome = f.meta.genome || hubCreate.sanitizeGenomeName(f.name);
                     break;
                 }
             }
 
             let batchSelectDiv = document.createElement("div");
             batchSelectDiv.id = "batch-selector-div";
             batchSelectDiv.style.display = "grid";
             batchSelectDiv.style.width = "80%";
             // the grid syntax is 2 columns, 3 rows
             batchSelectDiv.style.gridTemplateColumns = "max-content minmax(0, 200px) max-content 1fr min-content";
             batchSelectDiv.style.gridTemplateRows = "repest(3, auto)";
             batchSelectDiv.style.margin = "10px auto"; // centers this div
             batchSelectDiv.style.fontSize = "14px";
             batchSelectDiv.style.gap = "8px";
             if (window.matchMedia("(prefers-color-scheme: dark)").matches) {
                 batchSelectDiv.style.color = "#eaeaea";
             }
 
             // first just explanatory text:
             let batchSelectText = document.createElement("div");
             batchSelectText.textContent = "Change options for all files:";
             // syntax here is rowStart / columnStart / rowEnd / columnEnd
             batchSelectText.style.gridArea = "1 / 1 / 1 / 2";
 
             let batchDbLabel = document.createElement("label");
             batchDbLabel.textContent = "Genome";
             batchDbLabel.style.gridArea = "2 / 1 / 2 / 1";
 
             let batchDbSelect = null;
             let batchDbGenomeSearchBar = null;
             let batchDbGenomeSearchButton = null;
             let batchDbSearchBarLabel = null;
 
             if (assemblyHubGenome) {
                 // Assembly hub: show the custom genome name as a locked text
                 // field, no UCSC picker or search.
                 let locked = document.createElement("input");
                 locked.type = "text";
                 locked.id = "batchAsmHubGenome";
                 locked.value = assemblyHubGenome;
                 locked.disabled = true;
                 locked.classList.add("uppy-u-reset", "uppy-c-textInput");
                 locked.style.gridArea = "2 / 2 / 2 / 2";
                 locked.style.margin = "2px";
                 batchDbLabel.for = "batchAsmHubGenome";
 
                 let note = document.createElement("div");
-                note.textContent = "(assembly hub - genome is set by the 2bit in this batch)";
+                note.textContent = "(assembly hub - genome locked; shared by all files in this batch)";
                 note.style.gridArea = "2 / 3 / 2 / 5";
                 note.style.margin = "auto 0";
                 note.style.fontStyle = "italic";
 
                 batchSelectDiv.appendChild(batchSelectText);
                 batchSelectDiv.appendChild(batchDbLabel);
                 batchSelectDiv.appendChild(locked);
                 batchSelectDiv.appendChild(note);
             } else {
                 // Track hub: the usual UCSC picker + autocomplete.
                 batchDbSelect = document.createElement("select");
                 this.createOptsForSelect(batchDbSelect, hubCreate.makeGenomeSelectOptions());
                 batchDbSelect.id = "batchDbSelect";
                 batchDbSelect.style.gridArea = "2 / 2 / 2 / 2";
                 batchDbSelect.style.margin = "2px";
                 batchDbLabel.for = "batchDbSelect";
 
                 batchDbSearchBarLabel = document.createElement("label");
                 batchDbSearchBarLabel.textContent = "or search for your genome:";
                 batchDbSearchBarLabel.style.gridArea = "2 / 3 /2 / 3";
                 batchDbSearchBarLabel.style.margin = "auto";
 
                 batchDbGenomeSearchBar = document.createElement("input");
                 batchDbGenomeSearchBar.classList.add("uppy-u-reset", "uppy-c-textInput");
                 batchDbGenomeSearchBar.type = "text";
                 batchDbGenomeSearchBar.id = "batchDbSearchBar";
                 batchDbGenomeSearchBar.style.gridArea = "2 / 4 / 2 / 4";
                 batchDbGenomeSearchButton = document.createElement("input");
                 batchDbGenomeSearchButton.type = "button";
                 batchDbGenomeSearchButton.value = "search";
                 batchDbGenomeSearchButton.id = "batchDbSearchBarButton";
                 batchDbGenomeSearchButton.style.gridArea = "2 / 5 / 2 / 5";
 
                 batchDbSelect.addEventListener("change", (ev) => {
                     let files = this.uppy.getFiles();
                     let val = ev.target.value;
                     let label = ev.target.selectedOptions[0].label;
                     let hub = hubCreate.assemblyHubByGenome(val);
                     for (let [key, file] of Object.entries(files)) {
                         let meta = {
                             genome: val,
                             genomeLabel: label,
                             hubType: hub ? "assemblyHub" : "trackHub",
                             parentDir: hub ? hub.fileName : hubCreate.uiState.hubNameDefault,
                         };
                         this.uppy.setFileMeta(file.id, meta);
                     }
                 });
 
                 batchSelectDiv.appendChild(batchSelectText);
                 batchSelectDiv.appendChild(batchDbLabel);
                 batchSelectDiv.appendChild(batchDbSelect);
                 batchSelectDiv.appendChild(batchDbSearchBarLabel);
                 batchSelectDiv.appendChild(batchDbGenomeSearchBar);
                 batchSelectDiv.appendChild(batchDbGenomeSearchButton);
             }
 
             // the batch change hub name (shown in both modes)
             let batchParentDirLabel = document.createElement("label");
             batchParentDirLabel.textContent = "Hub Name";
             batchParentDirLabel.for = "batchParentDir";
             batchParentDirLabel.style.gridArea = "3 / 1 / 3 / 1";
 
             let batchParentDirInput = document.createElement("input");
             batchParentDirInput.id = "batchParentDir";
             batchParentDirInput.value = hubCreate.getDefaultHubName();
             batchParentDirInput.style.gridArea = "3 / 2 / 3 / 2";
             batchParentDirInput.style.margin= "1px 1px auto";
             batchParentDirInput.classList.add("uppy-u-reset", "uppy-c-textInput");
 
             batchParentDirInput.addEventListener("change", (ev) => {
                 let files = this.uppy.getFiles();
                 let val = ev.target.value;
                 for (let [key, file] of Object.entries(files)) {
                     this.uppy.setFileMeta(file.id, {parentDir: val});
                 }
             });
 
             batchSelectDiv.appendChild(batchParentDirLabel);
             batchSelectDiv.appendChild(batchParentDirInput);
 
             // append the batch changes to the bottom of the file list, for some reason
             // I can't append to the actual Dashboard-files, it must be getting emptied
             // and re-rendered or something
             let uppyFilesDiv = document.querySelector(".uppy-Dashboard-progressindicators");
             if (uppyFilesDiv) {
                 uppyFilesDiv.insertBefore(batchSelectDiv, uppyFilesDiv.firstChild);
             }
 
             // autocomplete only applies in the track-hub path
             if (batchDbSelect && batchDbGenomeSearchBar && batchDbGenomeSearchButton) {
                 let justInitted = initAutocompleteForInput(batchDbGenomeSearchBar.id, batchDbSelect);
                 if (justInitted) {
                     batchDbGenomeSearchButton.addEventListener("click", (e) => {
                         let inp = document.getElementById(batchDbGenomeSearchBar.id).value;
                         let selector = "[id='"+batchDbGenomeSearchBar.id+"']";
                         $(selector).autocompleteCat("search", inp);
                     });
                 }
             }
         }
     }
 
     install() {
         this.uppy.on("file-added", (file) => {
             // Only one 2bit per hub is supported. If this batch already has
             // a 2bit, reject the new one before any meta-setting runs (which
             // would propagate the wrong genome to it). onBeforeUpload also
             // enforces this; the duplicate check here keeps the per-file card
             // UI from drifting.
             if (looksLikeTwoBit(file)) {
                 let existingTwoBits = this.uppy.getFiles().filter(
                     f => f.id !== file.id && looksLikeTwoBit(f));
                 if (existingTwoBits.length > 0) {
                     this.uppy.removeFile(file.id);
-                    // setState({error}) puts the message in the StatusBar at
-                    // the bottom of the dashboard where it stays until the
-                    // user clicks Upload (which clears state.error) or closes
-                    // the dashboard. Persistent, unlike uppy.info().
-                    this.uppy.setState({
-                        error: `Only one 2bit file per hub is supported. ` +
-                               `Already have "${existingTwoBits[0].name}"; ignoring ` +
-                               `"${file.name}". Split them into separate hubs.`
-                    });
+                    // Close the file card if it auto-opened for the first 2bit;
+                    // otherwise it covers the error banner.
+                    const dash = this.uppy.getPlugin("Dashboard");
+                    if (dash) dash.toggleFileCard(false);
+                    // Long duration so the user has time to read it; the
+                    // StatusBar (setState.error) truncates to "Upload failed"
+                    // and hides the message behind a "?" icon.
+                    this.uppy.info(
+                        `Only one 2bit file per hub is allowed. ` +
+                        `"${existingTwoBits[0].name}" was added; ` +
+                        `"${file.name}" was not. To create a separate ` +
+                        `hub for "${file.name}", upload it on its own.`,
+                        'error', 15000);
                     return;
                 }
             }
             // add default meta data for genome and fileType
             let ftype = hubCreate.detectFileType(file.name);
             let defaultMeta = {
                 "genome": hubCreate.defaultDb(),
                 "fileType": ftype,
                 "parentDir": hubCreate.getDefaultHubName(),
                 "hubType": "trackHub",
             };
             if (ftype === "2bit") {
                 // This file defines an assembly hub. Default the genome to the
                 // sanitized filename stem; the user can edit it in the file card.
                 defaultMeta.genome = hubCreate.sanitizeGenomeName(file.name);
                 defaultMeta.genomeLabel = defaultMeta.genome;
                 defaultMeta.hubType = "assemblyHub";
             }
             this.uppy.setFileMeta(file.id, defaultMeta);
 
             // When drilled into an assembly hub, inherit and lock its genome.
             let drilledIntoAsmHub = false;
             if (hubCreate.uiState.currentHub &&
                 hubCreate.uiState.currentHub === defaultMeta.parentDir) {
                 let existing = hubCreate.uiState.filesHash[defaultMeta.parentDir];
                 if (existing && existing.hubType === "assemblyHub") {
                     this.uppy.setFileMeta(file.id, {
                         genome: existing.genome,
                         genomeLabel: existing.genome,
                         hubType: "assemblyHub",
                         genomeLocked: true,
                     });
                     drilledIntoAsmHub = true;
                 }
             }
 
             // Top-level with no drilled-in hub: if the user already has an
             // assembly hub, default this file to target it so they don't have
             // to re-enter the genome + hub name. The user can still switch via
             // the dropdown. Skip this when the file itself is hub-defining
             // (2bit or hub.txt) or when any file in the batch is - in that
             // case the batch is creating a *new* hub, not adding to an
             // existing one, so the defaults should not point at the old hub.
             let fileIsHubDefining = ftype === "2bit" || ftype === "hub.txt";
             let batchHasHubDefining = this.uppy.getFiles().some(f =>
                 looksLikeTwoBit(f) || looksLikeHubTxt(f));
             if (!drilledIntoAsmHub && !fileIsHubDefining && !batchHasHubDefining) {
                 let firstHub = hubCreate.firstAssemblyHub();
                 if (firstHub) {
                     this.uppy.setFileMeta(file.id, {
                         genome: firstHub.genome,
                         genomeLabel: firstHub.genome,
                         parentDir: firstHub.fileName,
                         hubType: "assemblyHub",
                         // NOT genomeLocked - user may want a different hub/genome
                     });
                 }
             }
 
             // If a 2bit is in the batch, every sibling file in the same parentDir
             // adopts its genome and gets hubType=assemblyHub. Also handle hub.txt:
             // parse it client-side and, if it declares an assembly hub, mirror
             // those values onto every file (hub.txt wins).
             propagateAssemblyHubMeta(this.uppy);
 
             if (this.uppy.getFiles().length > 1) {
                 this.addBatchSelectsToDashboard();
             } else {
                 // only open the file editor when there is one file
                 const dash = uppy.getPlugin("Dashboard");
                 dash.toggleFileCard(true, file.id);
             }
         });
         this.uppy.on("file-removed", (file) => {
             // remove the batch change selects if now <2 files present
             if (this.uppy.getFiles().length < 2) {
                 this.removeBatchSelectsFromDashboard();
             }
         });
 
         this.uppy.on("dashboard:modal-open", () => {
             // check if there were already files chosen from before:
             if (this.uppy.getFiles().length > 2) {
                 this.addBatchSelectsToDashboard();
             }
             if (this.uppy.getFiles().length < 2) {
                 this.removeBatchSelectsFromDashboard();
             }
         });
         this.uppy.on("dashboard:modal-closed", () => {
             if (this.uppy.getFiles().length < 2) {
                 this.removeBatchSelectsFromDashboard();
             }
             let allFiles = this.uppy.getFiles();
             let completeFiles = this.uppy.getFiles().filter((f) => f.progress.uploadComplete === true);
             if (allFiles.length === completeFiles.length) {
                 this.uppy.clear();
             }
         });
         this.uppy.on("dashboard:file-edit-start", (file) => {
             autocompletes[`${file.name}DbInput`] = false;
         });
 
         this.uppy.on("dashboard:file-edit-complete", (file) => {
             // check the filename and hubname metadata and warn the user
             // to edit them if they are wrong. unfortunately I cannot
             // figure out how to force the file card to re-toggle
             // and jump back into the editor from here
             if (file) {
                 let fileNameMatch = file.meta.name.match(fileNameRegex);
                 let parentDirMatch = file.meta.parentDir.match(parentDirRegex);
                 const dash = uppy.getPlugin("Dashboard");
                 if (!fileNameMatch || fileNameMatch[0] !== file.meta.name) {
                     uppy.info(`Error: File name has special characters, please rename file: '${file.meta.name}' to only include alpha-numeric characters, period, or underscore.`, 'error', 5000);
                 }
                 if (!parentDirMatch || parentDirMatch[0] !== file.meta.parentDir) {
                     uppy.info(`Error: Hub name has special characters, please rename hub: '${file.meta.parentDir}' to only include alpha-numeric characters, period, or underscore.`, 'error', 5000);
                 }
             }
         });
     }
     uninstall() {
         // not really used because we aren't ever uninstalling the uppy instance
         this.uppy.off("file-added");
     }
 }
 
 var hubCreate = (function() {
     let uiState = { // our object for keeping track of the current UI and what to do
         userUrl: "", // the web accesible path where the uploads are stored for this user
         hubNameDefault: "",
         currentHub: "", // if the user has a hub dir open, set the name here and use it as the default
                         // hub name when uploading a new file with the dir open, otherwise hubNameDefault
         isLoggedIn: "",
         maxQuota: 0,
         userQuota: 0,
         userFiles: {}, // same as uiData.userFiles on page load
         filesHash: {}, // for each file, userFiles.fullPath is the key, and then the userFiles.fileList data as the value, with an extra key for the child fullPaths if the file is a directory
     };
 
     let extensionMap = {
         "bigBed": [".bb", ".bigbed"],
         "bam": [".bam"],
         "vcf": [".vcf"],
         "vcfTabix": [".vcf.gz", "vcf.bgz"],
         "bigWig": [".bw", ".bigwig"],
         "hic": [".hic"],
         "cram": [".cram"],
         "bigBarChart": [".bigbarchart"],
         "bigGenePred": [".bgp", ".biggenepred"],
         "bigMaf": [".bigmaf"],
         "bigInteract": [".biginteract"],
         "bigPsl": [".bigpsl"],
         "bigChain": [".bigchain"],
         "bamIndex": [".bam.bai", ".bai"],
         "tabixIndex": [".vcf.gz.tbi", "vcf.bgz.tbi"],
         "hub.txt": ["hub.txt"],
         "2bit": [".2bit"],
         "text": [".txt", ".text"],
     };
 
     function getDefaultHubName() {
         return uiState.currentHub.length > 0 ? uiState.currentHub : uiState.hubNameDefault;
     }
 
     function sanitizeGenomeName(name) {
         // Strip .2bit, replace non-alphanumeric/_/- with _, drop hub_ prefix.
         // Returns empty string if nothing usable is left.
         if (!name) return "";
         let stem = name.replace(/\.2bit$/i, "");
         stem = stem.replace(/[^A-Za-z0-9_-]/g, "_");
         stem = stem.replace(/^hub_/, "");
         return stem;
     }
 
     function hubTxtPathForHub(hubName) {
         // Return the fullPath of the hub.txt file inside hubName as recorded in
         // hubSpace, falling back to "hubName/hub.txt" if there's no row yet.
         // The user may have uploaded their own "araTha1.hub.txt" - use its
         // actual filename rather than assuming "hub.txt".
         let dir = uiState.filesHash[hubName];
         if (dir && dir.children) {
             for (let child of dir.children) {
                 if (child.fileType === "hub.txt") return child.fullPath;
             }
         }
         return hubName + "/hub.txt";
     }
 
     function assemblyHubByGenome(genome) {
         // Return the dir row of the user's assembly hub whose genome matches,
         // or null. If genome is falsy, return the first assembly hub found.
         for (let fullPath in uiState.filesHash) {
             let fd = uiState.filesHash[fullPath];
             if (fd.fileType !== "dir" || fd.hubType !== "assemblyHub" || !fd.genome) continue;
             if (!genome || fd.genome === genome) return fd;
         }
         return null;
     }
 
     function firstAssemblyHub() { return assemblyHubByGenome(null); }
     function genomeIsAssemblyHub(genome) { return !!genome && !!assemblyHubByGenome(genome); }
 
     function parseHubTxt(text) {
         // Very small hub.txt parser: extracts `genome` and `twoBitPath` lines.
         // Returns {genome, twoBitPath, isAssemblyHub} (values may be null/false).
         let ret = {genome: null, twoBitPath: null, isAssemblyHub: false};
         if (!text) return ret;
         let lines = text.split(/\r?\n/);
         for (let line of lines) {
             let trimmed = line.replace(/^\s+/, "");
             if (trimmed.startsWith("genome ") && !ret.genome) {
                 ret.genome = trimmed.substring(7).trim();
             } else if (trimmed.startsWith("twoBitPath ")) {
                 ret.twoBitPath = trimmed.substring(11).trim();
                 ret.isAssemblyHub = true;
             }
         }
         return ret;
     }
 
     function readFileAsText(fileObj) {
         // Return a Promise resolving to the file contents as text.
         return new Promise((resolve, reject) => {
             let reader = new FileReader();
             reader.onload = () => resolve(reader.result);
             reader.onerror = () => reject(reader.error);
             reader.readAsText(fileObj);
         });
     }
 
     function detectFileType(fileName) {
         let fileLower = fileName.toLowerCase();
         for (let fileType in extensionMap) {
             for (let ext of extensionMap[fileType]) {
                 if (fileLower.endsWith(ext)) {
                     return fileType;
                 }
             }
         }
         //we could alert here but instead just explicitly set the value to null
         //and let the backend reject it instead, forcing the user to rename their
         //file
         //alert(`file extension for ${fileName} not found, please explicitly select it`);
         return null;
     }
 
     function defaultDb() {
         return cartDb.split(" ").slice(-1)[0];
     }
 
     let defaultGenomeChoices = {
         "Human hg38": {value: "hg38", label: "Human hg38"},
         "Human T2T": {value: "hs1", label: "Human T2T"},
         "Human hg19": {value: "hg19", label: "Human hg19"},
         "Mouse mm39": {value: "mm39", label: "Mouse mm39"},
         "Mouse mm10": {value: "mm10", label: "Mouse mm10"}
     };
 
     function makeGenomeSelectOptions(value, label) {
         // Returns an array of options for genomes, if value and label exist, add that
         // as an additional option
         let ret = [];
         let cartChoice = {};
         cartChoice.id = cartDb;
         cartChoice.label = cartDb;
         cartChoice.value = cartDb.split(" ").slice(-1)[0];
         if (cartChoice.value.startsWith("hub_")) {
             cartChoice.label = cartDb.split(" ").slice(0,-1).join(" "); // take off the actual db value
         }
         cartChoice.selected = value && label ? false: true;
         defaultGenomeChoices[cartChoice.label] = cartChoice;
 
         // next time around our value/label pair will be a default. this time around we
         // want it selected because it was explicitly asked for, but it may not be next time
         ret = Object.values(defaultGenomeChoices);
 
         // Include the user's uploaded assembly hubs as options. One entry per
         // assembly hub (dedupe by genome name), taken from the dir row in
         // filesHash. This lets users picking a dropdown genome target a hub
         // they already created.
         let seenAsmHub = {};
         for (let fullPath in uiState.filesHash) {
             let fd = uiState.filesHash[fullPath];
             if (fd.fileType === "dir" && fd.hubType === "assemblyHub" &&
                 fd.genome && !seenAsmHub[fd.genome]) {
                 seenAsmHub[fd.genome] = true;
                 ret.push({
                     value: fd.genome,
                     label: `${fd.genome} (your assembly hub)`,
                 });
             }
         }
 
         // Cache the value/label pair so it's a default next time - but skip
         // assembly-hub genomes, those are added by the loop above with the
         // "(your assembly hub)" suffix and would otherwise show up twice.
         if (value && label && !(label in defaultGenomeChoices) &&
             !genomeIsAssemblyHub(value)) {
             defaultGenomeChoices[label] = {value: value, label: label, selected: true};
         }
         return ret;
     }
 
     function makeTypeSelectOptions() {
         let ret = [];
         let autoChoice = {};
         autoChoice.label = "Auto-detect from extension";
         autoChoice.value = "Auto-detect from extension";
         autoChoice.selected = true;
         ret.push(autoChoice);
         let choices = ["bigBed", "bam", "vcf", "vcf (bgzip or gzip compressed)", "bigWig", "hic", "cram", "bigBarChart", "bigGenePred", "bigMaf", "bigInteract", "bigPsl", "bigChain"];
         choices.forEach( (e) =>  {
             let choice = {};
             choice.id = e;
             choice.label = e;
             choice.value = e;
             ret.push(choice);
         });
         return ret;
     }
 
     function viewInGenomeBrowser(fname, ftype, genome, hubName, hubType) {
         // redirect to hgTracks with this track open in the hub
         if (typeof uiState.userUrl !== "undefined" && uiState.userUrl.length > 0) {
             if (ftype in extensionMap) {
                 // TODO: tusd should return this location in it's response after
                 // uploading a file and then we can look it up somehow, the cgi can
                 // write the links directly into the html directly for prev uploaded files maybe?
                 let hubUrl = uiState.userUrl + cgiEncode(hubTxtPathForHub(hubName));
                 // Assembly hubs use the user-defined genome name, which isn't a
                 // UCSC db - hgTracks needs 'genome=' (resolves via the hub)
                 // rather than 'db=' (looks up a native assembly).
                 let dbParam = hubType === "assemblyHub" ? "genome" : "db";
                 let url = "../cgi-bin/hgTracks?hgsid=" + getHgsid() + "&" + dbParam + "=" + genome + "&hubUrl=" + encodeURIComponent(hubUrl) + "&" + trackHubFixName(fname) + "=pack";
                 window.location.assign(url);
                 return false;
             }
         }
     }
 
     function trackHubFixName(trackName) {
         // replace everything but alphanumeric and underscore with underscore
         return encodeURIComponent(trackName.replaceAll(fileNameFixRegex, "_"));
     }
 
     function viewHubInGenomeBrowser(hubName) {
         // connect the whole hub in hgTracks, without pack'ing any specific track
         if (typeof uiState.userUrl === "undefined" || uiState.userUrl.length === 0) {
             return;
         }
         let dirRow = uiState.filesHash[hubName];
         if (!dirRow) return;
         let hubUrl = uiState.userUrl + cgiEncode(hubTxtPathForHub(hubName));
         let dbParam = dirRow.hubType === "assemblyHub" ? "genome" : "db";
         let url = "../cgi-bin/hgTracks?hgsid=" + getHgsid() + "&" + dbParam + "=" + dirRow.genome + "&hubUrl=" + encodeURIComponent(hubUrl);
         window.location.assign(url);
     }
 
     function showHubBanner(hubName) {
         let banner = document.getElementById("hubBanner");
         let nameSpan = document.getElementById("hubBannerName");
         if (!banner || !nameSpan) return;
         nameSpan.textContent = hubName;
         banner.style.display = "";
     }
 
     function hideHubBanner() {
         let banner = document.getElementById("hubBanner");
         if (banner) banner.style.display = "none";
     }
 
     // helper object so we don't need to use an AbortController to update
     // the data this function is using
     let selectedData = {};
     // track which items the user directly selected (vs children of selected directories)
     let directlySelected = {};
     function viewAllInGenomeBrowser(ev) {
         // redirect to hgTracks with these tracks/hubs open
         let data = selectedData;
         if (typeof uiState.userUrl !== "undefined" && uiState.userUrl.length > 0) {
             let url = "../cgi-bin/hgTracks?hgsid=" + getHgsid();
             let genome; // may be multiple genomes in list, just redirect to the first one
                         // TODO: this should probably raise an alert to click through
             let hubsAdded = {};
             _.forEach(data, (d) => {
                 if (!genome) {
                     genome = d.genome;
                     // Assembly hubs use 'genome=' (hub-resolved name), native
                     // UCSC assemblies use 'db='.
                     let dbParam = d.hubType === "assemblyHub" ? "genome" : "db";
                     url += "&" + dbParam + "=" + genome;
                 }
                 if (d.fileType === "hub.txt") {
                     url += "&hubUrl=" + encodeURIComponent(uiState.userUrl + cgiEncode(d.fullPath));
                 }
                 else if (d.fileType in extensionMap) {
                     // TODO: tusd should return this location in it's response after
                     // uploading a file and then we can look it up somehow, the cgi can
                     // write the links directly into the html directly for prev uploaded files maybe?
                     if (!(d.parentDir in hubsAdded)) {
                         // NOTE: hubUrls get added regardless of whether they are on this assembly
                         // or not, because multiple genomes may have been requested. If this user
                         // switches to another genome we want this hub to be connected already
                         // Resolve the actual hub.txt filename - user may have
                         // uploaded "<prefix>.hub.txt" rather than literal hub.txt.
                         let hubDir = d.parentDir.replace(/\/$/, "");
                         url += "&hubUrl=" + encodeURIComponent(uiState.userUrl + cgiEncode(hubTxtPathForHub(hubDir)));
                     }
                     hubsAdded[d.parentDir] = true;
                     if (d.genome == genome) {
                         // turn the track on if its for this db
                         url += "&" + trackHubFixName(d.fileName) + "=pack";
                     }
                 }
             });
             window.location.assign(url);
             return false;
         }
     }
 
     function deleteFileSuccess(jqXhr, textStatus) {
         deleteFileFromTable(jqXhr.deletedList);
         updateSelectedFileDiv(null);
     }
 
     function deleteFileList(ev) {
         // same as deleteFile() but acts on the selectedData variable
         let data = selectedData;
         // Block deletion of an assembly hub's defining 2bit unless the whole hub
         // is also in this batch. Removing the 2bit alone leaves hub.txt with a
         // twoBitPath pointing at a missing file and the surviving rows still
         // flagged hubType=assemblyHub. The user must delete the entire hub
         // instead, or replace the 2bit by uploading a new one with the same name.
         let selectedValues = Object.values(data);
         let selectedHubDirs = new Set(
             selectedValues.filter(x => x.fileType === "dir").map(x => x.fullPath));
         let blockedTwoBits = [];
         for (let d of selectedValues) {
             if (d.fileType !== "2bit") continue;
             let hub = uiState.filesHash[d.parentDir];
             if (!hub || hub.hubType !== "assemblyHub") continue;
             if (!selectedHubDirs.has(d.parentDir)) blockedTwoBits.push(d);
         }
         if (blockedTwoBits.length > 0) {
             let names = blockedTwoBits.map(d => d.fullPath).join("\n  ");
-            alert(`Cannot delete the following 2bit file(s) because they define ` +
+            alert(`Cannot delete the following 2bit file(s) because they are part of ` +
                   `an assembly hub:\n  ${names}\n\nDelete the whole hub instead, ` +
                   `or replace the 2bit by uploading a new one with the same name.`);
             return;
         }
         // Only warn about hub.txt deletion if the user directly selected the hub.txt file,
         // not if it's being deleted as part of selecting a whole hub/directory
         let hasDirectlySelectedHubTxt = Object.values(directlySelected).some(d => d.fileType === "hub.txt");
         if (hasDirectlySelectedHubTxt) {
             if (!confirm("Warning: Deleting a hub.txt file will remove your hub and its shareable URL. Are you sure?")) {
                 return;
             }
         }
         let cartData = {deleteFile: {fileList: []}};
         cart.setCgiAndUrl(fileListEndpoint);
         _.forEach(data, (d) => {
             cartData.deleteFile.fileList.push({
                 fileName: d.fileName,
                 fileType: d.fileType,
                 parentDir: d.parentDir,
                 genome: d.genome,
                 fullPath: d.fullPath,
             });
         });
         cart.send(cartData, deleteFileSuccess);
         cart.flush();
     }
 
     function updateSelectedFileDiv(data, isFolderSelect = false) {
         // update the div that shows how many files are selected
         let numSelected = data !== null ? data.length : 0;
         let infoDiv = document.getElementById("selectedFileInfo");
         let span = document.getElementById("numberSelectedFiles");
         let spanParentDiv = span.parentElement;
         if (numSelected > 0) {
             if (isFolderSelect || span.textContent.endsWith("hub") || span.textContent.endsWith("hubs")) {
                 span.textContent = `${numSelected} ${numSelected > 1 ? "hubs" : "hub"}`;
             } else {
                 span.textContent = `${numSelected} ${numSelected > 1 ? "files" : "file"}`;
             }
             // (re) set up the handlers for the selected file info div:
             let viewBtn = document.getElementById("viewSelectedFiles");
             viewBtn.addEventListener("click", viewAllInGenomeBrowser);
             viewBtn.textContent = "View selected";
             let deleteBtn = document.getElementById("deleteSelectedFiles");
             deleteBtn.style.display = "inline-block";
             deleteBtn.addEventListener("click", deleteFileList);
             deleteBtn.textContent = "Delete selected";
         } else {
             span.textContent = "";
         }
 
         // set the visibility of the placeholder text and info text
         spanParentDiv.style.display = numSelected === 0 ? "none": "block";
         let placeholder = document.getElementById("placeHolderInfo");
         placeholder.style.display = numSelected === 0 ? "block" : "none";
     }
 
     function handleCheckboxSelect(evtype, table, selectedRow) {
         // depending on the state of the checkbox, we will be adding information
         // to the div, or removing information. We also potentially checked/unchecked
         // all of the checkboxes if the selectAll box was clicked.
 
         // The data variable will hold all the information we want to keep visible in the info div
         let data = [];
         // The selectedData global holds the actual information needed for the view/delete buttons
         // to work, so data plus any child rows
         selectedData = {};
         // Track only the rows the user directly selected (not children)
         directlySelected = {};
 
         // get all of the currently selected rows (may be more than just the one that
         // was most recently clicked)
         table.rows({selected: true}).data().each(function(row, ix) {
             data.push(row);
             selectedData[row.fullPath] = row;
             directlySelected[row.fullPath] = row;
             // add any newly checked rows children to the selectedData structure for the view/delete
             if (row.children) {
                 row.children.forEach(function(child) {
                     selectedData[child.fullPath] = child;
                 });
             }
         });
         updateSelectedFileDiv(data, selectedRow.data().fileType === "dir");
     }
 
     function createOneCrumb(table, dirName, dirFullPath, doAddEvent) {
         // make a new span that can be clicked to nav through the table
         let newSpan = document.createElement("span");
         newSpan.id = dirName;
         newSpan.textContent = decodeURIComponent(dirName);
         newSpan.classList.add("breadcrumb");
         if (doAddEvent) {
             newSpan.addEventListener("click", function(e) {
                 dataTableShowDir(table, dirName, dirFullPath);
                 dataTableCustomOrder(table, {"fullPath": dirFullPath});
                 table.draw();
             });
         } else {
             // can't click the final crumb so don't underline it
             newSpan.style.textDecoration = "unset";
         }
         return newSpan;
     }
 
     function dataTableEmptyBreadcrumb(table) {
         let currBreadcrumb = document.getElementById("breadcrumb");
         currBreadcrumb.replaceChildren(currBreadcrumb.firstChild);
     }
 
     function dataTableCreateBreadcrumb(table, dirName, dirFullPath) {
         // Re-create the breadcrumb nav to move back through directories
         let currBreadcrumb = document.getElementById("breadcrumb");
         // empty the node but leave the first "My Data" span
         if (currBreadcrumb.children.length > 1) {
             currBreadcrumb.replaceChildren(currBreadcrumb.firstChild);
         }
         let components = dirFullPath.split("/");
         let numComponents = components.length;
         components.forEach(function(dirName, dirNameIx) {
             if (!dirName) {
                 return;
             }
             let doAddEvent = dirNameIx !== (numComponents - 1);
             let path = components.slice(0, dirNameIx+1);
             componentFullPath = path.join('/');
             let newSpan = createOneCrumb(table, dirName, componentFullPath, doAddEvent);
             currBreadcrumb.appendChild(document.createTextNode(" > "));
             currBreadcrumb.appendChild(newSpan);
         });
     }
 
     // search related functions:
     function clearSearch(table) {
         // clear any fixed searches so we can apply a new one
         let currSearches = table.search.fixed().toArray();
         currSearches.forEach((name) => table.search.fixed(name, null));
     }
 
     function dataTableShowTopLevel(table) {
         // show all the "root" files, which are files (probably mostly directories)
         // with no parentDir
         clearSearch(table);
         // deselect any selected rows like Finder et al when moving into/upto a directory
         table.rows({selected: true}).deselect();
         table.search.fixed("showRoot", function(searchStr, rowData, rowIx) {
             return !rowData.parentDir;
         });
         uiState.currentHub = "";
         hideHubBanner();
     }
 
     function dataTableShowDir(table, dirName, dirFullPath) {
         // show the directory and all immediate children of the directory
         clearSearch(table);
         // deselect any selected rows like Finder et al when moving into/upto a directory
         table.rows({selected: true}).deselect();
         // Callers must call table.draw() after this so filter + order changes
         // from showDir/customOrder render in a single redraw.
         table.search.fixed("oneHub", function(searchStr, rowData, rowIx) {
             // calculate the fullPath of this rows parentDir in case the dirName passed
             // to this function has the same name as a parentDir further up in the
             // listing. For example, consider a test/test/tmp.txt layout, where "test"
             // is the parentDir of tmp.txt and the test subdirectory
             let parentDirFull = rowData.fullPath.split("/").slice(0,-1).join("/");
             if (rowData.parentDir === dirName && parentDirFull === dirFullPath) {
                 return true;
             } else if (rowData.fullPath === dirFullPath) {
                 // also return the directory itself
                 return true;
             } else {
                 return false;
             }
         });
         uiState.currentHub = dirName;
         dataTableCreateBreadcrumb(table, dirName, dirFullPath);
         showHubBanner(dirName);
     }
 
     // when we move into a new directory, we remove the row from the table
     // and add it's html into the header, keep the row object around so
     // we can add it back in later
     let oldRowData = null;
     function dataTableCustomOrder(table, dirData) {
         // figure out the order the rows of the table should be in
         // if dirData is null, sort on  uploadTime first
         // if dirData exists, that is the first row, followed by everything else
         // in uploadTime order
         if (!dirData) {
             // make sure the old row can show up again in the table
             let thead = document.querySelector(".dt-scroll-headInner > table:nth-child(1) > thead:nth-child(1)");
             if (thead.childNodes.length > 1) {
                 let old = thead.removeChild(thead.lastChild);
                 if (oldRowData) {
                     table.row.add(oldRowData);
                     oldRowData = null;
                 }
             }
             table.order([{name: "uploadTime", dir: "desc"}]);
         } else {
             // move the dirName row into the header, then the other files can
             // sort normally
             let row = table.row((idx,data) => data.fullPath === dirData.fullPath);
             let rowNode = row.node();
             if (oldRowData) {
                 // restore the previous row, which will be not displayed by the search anyways:
                 table.row.add(oldRowData);
                 oldRowData = null;
             }
             if (!rowNode) {
                 // if we are using the breadcrumb to jump back 2 directories or doing an upload
                 // while a subdirectory is opened, we won't have a rowNode because the row will
                 // not have been rendered yet. So draw the table with the oldRowData restored
                 table.draw();
                 // and now we can try again
                 row = table.row((idx,data) => data.fullPath === dirData.fullPath);
                 rowNode = row.node();
             }
             oldRowData = row.data();
             // put the data in the header:
             let rowClone = rowNode.cloneNode(true);
             // match the background color of the normal rows:
             rowClone.style.backgroundColor = "#fff9d2";
             let thead = document.querySelector(".dt-scroll-headInner > table:nth-child(1) > thead:nth-child(1)");
             // remove the checkbox because it doesn't do anything, and replace it
             // with a back arrow 'button'
             let btn = document.createElement("button");
             btn.id = "backButton";
             $(btn).button({icon: "ui-icon-triangle-1-w"});
             btn.addEventListener("click", (e) => {
                 let parentDir = dirData.parentDir;
                 let parentDirPath = dirData.fullPath.slice(0,-dirData.fullPath.length);
                 if (parentDirPath.length) {
                     dataTableShowDir(table, parentDir, parentDirPath);
                 } else {
                     dataTableShowTopLevel(table);
                     dataTableCustomOrder(table);
                     dataTableEmptyBreadcrumb(table);
                 }
                 table.draw();
             });
             let tdBtn = document.createElement("td");
             tdBtn.appendChild(btn);
             rowClone.replaceChild(tdBtn, rowClone.childNodes[0]);
             if (thead.childNodes.length === 1) {
                 thead.appendChild(rowClone);
             } else {
                 thead.replaceChild(rowClone, thead.lastChild);
             }
             // remove the row
             row.remove();
             // now do a regular order
             table.order([{name: "uploadTime", dir: "desc"}]);
         }
     }
 
     function parseFileListIntoHash(fileList) {
         // Hash the uiState fileList by the fullPath, and also store the children
         // for each directory
         // first go through and copy all of the data and make the empty
         // children array for each directory
         fileList.forEach(function(fileData) {
             uiState.filesHash[fileData.fullPath] = fileData;
             if (fileData.fileType === "dir") {
                 uiState.filesHash[fileData.fullPath].children = [];
             }
         });
         // use a second pass to go through and set the children
         // since we may not have encountered them yet in the above loop
         fileList.forEach(function(fileData) {
             if (fileData.fileType !== "dir" || fileData.parentDir !== "") {
                 // compute the key from the fullPath:
                 let parts = fileData.fullPath.split("/");
                 let keyName = parts.slice(0,-1).join("/");
                 if (keyName in uiState.filesHash) {
                     uiState.filesHash[keyName].children.push(fileData);
                 }
             }
         });
     }
 
     function getChildRows(dirFullPath, childRowArray) {
         // Recursively return all of the child rows for a given path
         let childRows = uiState.filesHash[dirFullPath].children;
         childRows.forEach(function(rowData) {
             if (rowData.fileType !== "dir") {
                 childRowArray.push(rowData);
             } else {
                 childRowArray.concat(getChildRows(rowData.fullPath, childRowArray));
             }
         });
     }
 
     function dataTablePrintSize(data, type, row, meta) {
         if (row.fileType !== "dir") {
             return prettyFileSize(data);
         } else {
             let childRows = [];
             getChildRows(row.fullPath, childRows);
             let sum = childRows.reduce( (accumulator, currentValue) => {
                 return accumulator + currentValue.fileSize;
             }, 0);
             return prettyFileSize(sum);
         }
     }
 
     function dataTablePrintGenome(data, type, row, meta) {
         if (data.startsWith("hub_"))
             return data.split("_").slice(2).join("_");
         return data;
     }
 
     function dataTablePrintAction(rowData) {
         /* Return a node for rendering the actions column */
         if (rowData.fileType === "dir") {
             let folderIcon = document.createElement("i");
             folderIcon.style.display = "inline-block";
             folderIcon.style.backgroundImage = "url(\"../images/folderC.png\")";
             folderIcon.style.backgroundPosition = "left center";
             folderIcon.style.backgroundRepeat = "no-repeat";
             folderIcon.style.width = "24px";
             folderIcon.style.height = "24px";
             folderIcon.classList.add("folderIcon");
             folderIcon.addEventListener("click", function(e) {
                 e.stopPropagation();
                 console.log("folder click");
                 let table = $("#filesTable").DataTable();
                 let trow = $(e.target).closest("tr");
                 let row = table.row(trow);
                 dataTableShowDir(table, rowData.fileName, rowData.fullPath);
                 dataTableCustomOrder(table, rowData);
                 table.draw();
             });
             return folderIcon;
         } else {
             // only offer the button if this is a track file
             if (rowData.fileType !== "hub.txt" && rowData.fileType !== "text" && rowData.fileType !== "tabixIndex" && rowData.fileType !== "bamIndex" && rowData.fileType !== "2bit" && rowData.fileType in extensionMap) {
                 let container = document.createElement("div");
                 let viewBtn = document.createElement("button");
                 viewBtn.textContent = "View in Genome Browser";
                 viewBtn.style.whiteSpace = "nowrap";
                 viewBtn.type = 'button';
                 viewBtn.addEventListener("click", function(e) {
                     e.stopPropagation();
                     viewInGenomeBrowser(rowData.fileName, rowData.fileType, rowData.genome, rowData.parentDir, rowData.hubType);
                 });
                 container.appendChild(viewBtn);
                 return container;
             } else {
                 return null;
             }
         }
     }
 
     function deleteFileFromTable(pathList) {
         // req is an object with properties of an uploaded file, make a new row
         // for it in the filesTable
         let table = $("#filesTable").DataTable();
         let rows = table.rows((idx, data) => pathList.includes(data.fullPath));
         rows.remove().draw();
         let toKeep = (elem) => !pathList.includes(elem.fullPath);
         pathList.forEach((f) => {
             updateQuota(-uiState.filesHash[f].fileSize);
         });
         uiState.fileList = uiState.fileList.filter(toKeep);
         // Rebuild filesHash from remaining fileList to remove stale entries
         uiState.filesHash = {};
         parseFileListIntoHash(uiState.fileList);
         // If the currently viewed hub directory was deleted (its data is in oldRowData
         // because dataTableCustomOrder moved it to the header), clean up that stale state
         if (oldRowData && pathList.includes(oldRowData.fullPath)) {
             let thead = document.querySelector(
                 ".dt-scroll-headInner > table:nth-child(1) > thead:nth-child(1)");
             if (thead && thead.childNodes.length > 1) {
                 thead.removeChild(thead.lastChild);
             }
             oldRowData = null;
             dataTableShowTopLevel(table);
             dataTableEmptyBreadcrumb(table);
             table.order([{name: "uploadTime", dir: "desc"}]);
             table.draw();
         }
         history.replaceState(uiState, "", document.location.href);
     }
 
     function addFileToHub(rowData) {
         // a file has been uploaded and a hub has been created, present a modal
         // to choose which hub to associate this track to
         // backend wise: move the file into the hub directory
         //               update the hubSpace row with the hub name
         // frontend wise: move the file row into a 'child' of the hub row
         console.log(`sending addToHub req for ${rowData.fileName} to `);
         cart.setCgiAndUrl(fileListEndpoint);
         cart.send({addToHub: {hubName: "", dataFile: ""}});
         cart.flush();
     }
 
     function updateQuota(newFileSize) {
         // Change the quota displayed to the user, pass in newFileSize as a negative number
         // when deleting files
         let container = document.getElementById("quotaDiv");
         uiState.userQuota += newFileSize;
         container.textContent = `Using ${prettyFileSize(uiState.userQuota)} of ${prettyFileSize(uiState.maxQuota)}`;
     }
 
     function addNewUploadedHubToTable(hub) {
         // hub is a list of objects representing the file just uploaded, the associated
         // hub.txt, and directory. Make a new row for each in the filesTable, except for
         // maybe the hub directory row and hub.txt which we may have already seen before
         let table = $("#filesTable").DataTable();
         let justUploaded = {}; // hash of contents of hub but keyed by fullPath
         let hubDirData = {}; // the data for the parentDir of the uploaded file
         for (let obj of hub) {
             if (!obj.parentDir) {
                 hubDirData = obj;
             }
             let rowObj;
             if (!(obj.fullPath in uiState.filesHash)) {
                 justUploaded[obj.fullPath] = obj;
                 rowObj = table.row.add(obj);
                 uiState.fileList.push(obj);
                 // NOTE: we don't add the obj to the filesHash until after we're done
                 // so we don't need to reparse all files each time we add one
             } else {
                 // File already exists - update the existing row with new data (for overwrites)
                 let existingObj = uiState.filesHash[obj.fullPath];
                 existingObj.fileSize = obj.fileSize;
                 existingObj.lastModified = obj.lastModified;
                 existingObj.uploadTime = obj.uploadTime;
                 // Find and invalidate the row in DataTable to refresh display
                 let allRows = table.rows().indexes();
                 for (let j = 0; j < allRows.length; j++) {
                     let rowData = table.row(allRows[j]).data();
                     if (rowData.fullPath === obj.fullPath) {
                         table.row(allRows[j]).invalidate();
                         break;
                     }
                 }
             }
         }
 
         // show all the new rows we just added, note the double draw, we need
         // to have the new rows rendered to do the order because the order
         // will copy the actual DOM node
         parseFileListIntoHash(uiState.fileList);
         dataTableShowDir(table, hubDirData.fileName, hubDirData.fullPath);
         dataTableCustomOrder(table, hubDirData);
         table.draw();
     }
 
     function doRowSelect(evtype, table, indexes) {
         let selectedRow = table.row(indexes);
         let rowTr = selectedRow.node();
         if (rowTr) {
             handleCheckboxSelect(evtype, table, selectedRow);
         }
     }
 
     function indentActionButton(rowTr, rowData) {
         let numIndents = "0px"; //data.parentDir !== "" ? data.fullPath.split('/').length - 1: 0;
         if (rowData.fileType !== "dir") {
             numIndents = "10px";
         }
         rowTr.childNodes[1].style.textIndent = numIndents;
     }
 
     let tableInitOptions = {
         select: {
             items: 'row',
             selector: 'td:first-child',
             style: 'multi+shift', // default to a single click is all that's needed
         },
         pageLength: 25,
         autoWidth: false,     // let the browser's default table-layout:auto size columns,
                               // so they shrink/grow with the container on window resize
         scrollY: 600,
         scrollCollapse: true, // when less than scrollY height is needed, make the table shorter
         deferRender: true, // only draw into the DOM the nodes we need for each page
         orderCellsTop: true, // when viewing a subdirectory, the directory becomes a part of
                              // the header, this option prevents those cells from being used to
                              // sort the table
         layout: {
             top2Start: {
                 div: {
                     className: "",
                     id: "breadcrumb",
                     html: "<span id=\"rootBreadcrumb\" class=\"breadcrumb\">My Data</span>",
                 }
             },
             topStart: {
                 buttons: [
                     {
                         text: 'Upload',
                         action: function() {return;},
                         className: 'uploadButton',
                         enabled: false, // disable by default in case user is not logged in
                     },
                 ],
                 quota: null,
             },
         },
         columnDefs: [
             {
                 orderable: false, targets: 0,
                 render: DataTable.render.select(),
             },
             {
                 orderable: false, targets: 1,
                 data: "action", title: "",
                 render: function(data, type, row) {
                     if (type === "display") {
                         return dataTablePrintAction(row);
                     }
                     return '';
                 }
             },
             {
                 targets: 2,
                 render: function(data, type, row, meta) {
                     let decodedName = decodeURIComponent(data);
                     if (type !== "display" || row.fileType === "dir") {
                         return decodedName;
                     }
                     if (typeof uiState.userUrl === "undefined" || uiState.userUrl.length === 0) {
                         return decodedName;
                     }
                     let fileUrl = uiState.userUrl + cgiEncode(row.fullPath);
                     let copyIcon = '<svg class="copyLinkIcon" title="Copy file URL to clipboard" data-url="' + fileUrl + '" style="margin-left: 6px; cursor: pointer; vertical-align:baseline; width:0.8em" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 512 512"><path d="M502.6 70.63l-61.25-61.25C435.4 3.371 427.2 0 418.7 0H255.1c-35.35 0-64 28.66-64 64l.0195 256C192 355.4 220.7 384 256 384h192c35.2 0 64-28.8 64-64V93.25C512 84.77 508.6 76.63 502.6 70.63zM464 320c0 8.836-7.164 16-16 16H255.1c-8.838 0-16-7.164-16-16L239.1 64.13c0-8.836 7.164-16 16-16h128L384 96c0 17.67 14.33 32 32 32h47.1V320zM272 448c0 8.836-7.164 16-16 16H63.1c-8.838 0-16-7.164-16-16L47.98 192.1c0-8.836 7.164-16 16-16H160V128H63.99c-35.35 0-64 28.65-64 64l.0098 256C.002 483.3 28.66 512 64 512h192c35.2 0 64-28.8 64-64v-32h-47.1L272 448z"/></svg>';
                     return '<span style="white-space:nowrap"><a class="fileLink" href="' + fileUrl + '" target="_blank" rel="noopener">' + decodedName + '</a>' + copyIcon + '</span>';
                 }
             },
             {
                 targets: 3,
                 render: function(data, type, row, meta) {
                     if (type === "display") {
                          return dataTablePrintSize(data, type, row, meta);
                     }
                     return data;
                 }
             },
             {
                 targets: 5,
                 render: function(data, type, row) {
                     if (type === "display") {
                         return dataTablePrintGenome(data);
                     }
                     return data;
                 }
             },
             {
                 targets: 6,
                 render: function(data, type, row) {
                     if (type === "display") {
                         return cgiDecode(data);
                     }
                     return data;
                 }
             },
             {
                 targets: [7, 8],
                 className: "nowrap",
                 visible: true,
                 searchable: false,
                 orderable: true,
             },
             {
                 targets: 9,
                 visible: false,
                 searchable: false,
                 orderable: true,
             }
         ],
         columns: [
             {data: "", },
             {data: "", },
             {data: "fileName", title: "File name"},
             {data: "fileSize", title: "File size"},
             {data: "fileType", title: "File type"},
             {data: "genome", title: "Genome"},
             {data: "parentDir", title: "Hubs"},
             {data: "lastModified", title: "File Last Modified"},
             {data: "uploadTime", title: "Upload Time", name: "uploadTime"},
             {data: "fullPath", title: "fullPath", name: "fullPath"},
         ],
         drawCallback: function(settings) {
             console.log("table draw");
         },
         rowCallback: function(row, data, displayNum, displayIndex, dataIndex) {
             // row is a tr element, data is the td values
             // a row can represent one of three things:
             // a 'folder', with no parents, but with children
             // a folder with parents and children (can only come from hubtools
             // a 'file' with no children, but with parentDir
             // we assign the appropriate classes which are used later to
             // collapse/expand and select rows for viewing or deletion
             if (!data.parentDir) {
                 row.className = "topLevelRow";
             } else {
                 row.className = "childRow";
             }
             if (data.fileType === "dir") {
                 row.className += " parentRow";
             }
             indentActionButton(row, data);
         },
         initComplete: function(settings, json) {
             console.log("data loaded, only showing directories");
             let table = new $.fn.dataTable.Api(settings);
             dataTableShowTopLevel(table);
             dataTableCustomOrder(table);
             table.draw();
         }
     };
 
     function showExistingFiles(d) {
         // Make the DataTable for each file
         // make buttons have the same style as other buttons
         if ($.fn.dataTable.isDataTable("#filesTable")) {
             return $("#filesTable").DataTable();
         }
 
         $.fn.dataTable.Buttons.defaults.dom.button.className = 'button';
         tableInitOptions.data = d;
         if (uiState.isLoggedIn) {
             tableInitOptions.language = {emptyTable: "Uploaded files will appear here. Click \"Upload\" to get started"};
         } else {
             tableInitOptions.language = {emptyTable: "You are not logged in, please <a href=\"../cgi-bin/hgSession\">log in or create an account</a> to begin uploading files"};
         }
         DataTable.feature.register('quota', function(settings, opts) {
             let options = Object.assign({option1: false, option2: false}, opts);
             let container = document.createElement("div");
             container.id = "quotaDiv";
             if (uiState.isLoggedIn) {
                 container.textContent = `Using ${prettyFileSize(uiState.userQuota)} of ${prettyFileSize(uiState.maxQuota)}`;
             }
             return container;
         });
         let table = new DataTable("#filesTable", tableInitOptions);
         // Re-sync the scrollY head/body column widths after a resize settles.
         let resizeTimer = null;
         window.addEventListener("resize", function() {
             clearTimeout(resizeTimer);
             resizeTimer = setTimeout(function() {
                 table.columns.adjust();
             }, 100);
         });
         if (uiState.isLoggedIn) {
             table.buttons(".uploadButton").enable();
             document.getElementById("rootBreadcrumb").addEventListener("click", function(e) {
                 dataTableShowTopLevel(table);
                 dataTableCustomOrder(table);
                 dataTableEmptyBreadcrumb(table);
                 table.draw();
             });
         } else {
             table.buttons(".uploadButton").disable();
         }
         let hubBannerBtn = document.getElementById("hubBannerViewBtn");
         if (hubBannerBtn) {
             hubBannerBtn.addEventListener("click", function(e) {
                 viewHubInGenomeBrowser(uiState.currentHub);
             });
         }
         table.on("select", function(e, dt, type, indexes) {
             indexes.forEach(function(i) {
                 doRowSelect(e.type, dt, i);
             });
         });
         table.on("deselect", function(e, dt, type, indexes) {
             indexes.forEach(function(i) {
                 doRowSelect(e.type, dt, i);
             });
         });
         table.on("click", function(e) {
             let copyIcon = e.target.closest ? e.target.closest(".copyLinkIcon") : null;
             if (copyIcon) {
                 e.stopPropagation();
                 e.preventDefault();
                 let url = copyIcon.getAttribute("data-url");
                 navigator.clipboard.writeText(url).then(function() {
                     let feedback = document.createElement("span");
                     feedback.textContent = "copied";
                     feedback.style.marginLeft = "6px";
                     feedback.style.fontSize = "0.85em";
                     feedback.style.color = "#080";
                     copyIcon.parentNode.replaceChild(feedback, copyIcon);
                     setTimeout(function() {
                         if (feedback.parentNode) {
                             feedback.parentNode.replaceChild(copyIcon, feedback);
                         }
                     }, 1500);
                 }, function() {
                     alert("Failed to copy URL: " + url);
                 });
                 return;
             }
             if (e.target.closest && e.target.closest(".fileLink")) {
                 e.stopPropagation();
                 return;
             }
             if (e.target.className !== "dt-select-checkbox") {
                 e.stopPropagation();
                 // we've clicked somewhere not on the checkbox itself, we need to:
                 // 1. open the directory if the clicked row is a directory
                 // 2. select the file if the clicked row is a regular file
                 let row = table.row(e.target);
                 let data = row.data();
                 if (data.children && data.children.length > 0) {
                     dataTableShowDir(table, data.fileName, data.fullPath);
                     dataTableCustomOrder(table, {"fullPath": data.fullPath});
                     table.draw();
                 } else {
                     if (row.selected()) {
                         row.deselect();
                         doRowSelect("deselect", table, row.index());
                     } else {
                         row.select();
                         doRowSelect("select", table, row.index());
                     }
                 }
             }
         });
         return table;
     }
 
     function handleGetFileList(jsonData, textStatus) {
         _.assign(uiState, jsonData.userFiles);
         if (uiState.fileList) {
             parseFileListIntoHash(uiState.fileList);
         }
 
         // first add the top level directories/files
         let table = showExistingFiles(uiState.fileList);
 
         uppy.use(Uppy.Dashboard, uppyOptions);
 
         // define this in init so globals are available at runtime
         let tusOptions = {
             endpoint: getTusdEndpoint(),
             withCredentials: true,
             retryDelays: null,
             removeFingerprintOnSuccess: true, // clean up localStorage after successful upload
         };
 
         uppy.use(Uppy.Tus, tusOptions);
         uppy.use(BatchChangePlugin, {target: Uppy.Dashboard});
         uppy.on('upload-error', (file, error, response) => {
             // Replace tus's verbose default ("tus: unexpected response while
             // uploading chunk, originated from request (method: PATCH, ...)")
             // with the message our hook actually sent. Overwrite per-file
             // state, global state.error (read by the StatusBar), and the
             // info[] array (transient banner) - Uppy core populates all three
             // with the wrapped message before this handler runs.
             let cleanMsg = extractHookErrorMessage(error, response);
             if (file) {
                 uppy.setFileState(file.id, {error: cleanMsg});
             }
             uppy.setState({error: cleanMsg, info: []});
+            // Long-duration banner so the user has time to read the message;
+            // the StatusBar truncates to "Upload failed" and hides the rest
+            // behind a "?" icon.
+            uppy.info(cleanMsg, 'error', 30000);
+            // Genome-name collision is fixable in place by editing the 2bit's
+            // genome field, so reopen the file card.
+            if (file && cleanMsg && cleanMsg.includes(hubGenomeCollisionErrFrag)) {
+                const dash = uppy.getPlugin("Dashboard");
+                if (dash) dash.toggleFileCard(true, file.id);
+            }
         });
         uppy.on('upload-success', (file, response) => {
             const metadata = file.meta;
             const d = new Date(metadata.lastModified);
             const pad = (num) => String(num).padStart(2, '0');
             const dFormatted = `${d.getFullYear()}-${pad(d.getMonth() + 1)}-${pad(d.getDate())} ${pad(d.getHours())}:${pad(d.getMinutes())}:${pad(d.getSeconds())}`;
             const now = new Date(Date.now());
             const nowFormatted = `${now.getFullYear()}-${pad(now.getMonth() + 1)}-${pad(now.getDate())} ${pad(now.getHours())}:${pad(now.getMinutes())}:${pad(now.getSeconds())}`;
             let newReqObj, hubTxtObj, parentDirObj;
             let hubType = metadata.hubType || "trackHub";
             newReqObj = {
                 "fileName": cgiEncode(metadata.fileName),
                 "fileSize": metadata.fileSize,
                 "fileType": metadata.fileType,
                 "genome": metadata.genome,
                 "parentDir": cgiEncode(metadata.parentDir),
                 "lastModified": dFormatted,
                 "uploadTime": nowFormatted,
                 "fullPath": cgiEncode(metadata.parentDir) + "/" + cgiEncode(metadata.fileName),
                 "hubType": hubType,
             };
             // from what I can tell, any response we would create in the pre-finish hook
             // is completely ignored for some reason, so we have to fake the other files
             // we would have created with this one file and add them to the table if they
             // weren't already there:
             // Only fabricate a hub.txt row when the backend actually synthesized
             // one. Skip if the user supplied their own *.hub.txt (either already
             // in filesHash from a prior upload, or coming in this same batch -
             // upload-success order is arbitrary so the hub.txt row may not be
             // in filesHash yet when a sibling's upload-success fires).
             let dirHash = uiState.filesHash[cgiEncode(metadata.parentDir)];
             let hubTxtExists = !!(dirHash && dirHash.children &&
                 dirHash.children.some(c => c.fileType === "hub.txt"));
             let batchHasHubTxt = metadata.batchHasHubTxt === "true";
             if (metadata.fileType !== "hub.txt" && !hubTxtExists && !batchHasHubTxt) {
                 hubTxtObj = {
                     "uploadTime": nowFormatted,
                     "lastModified": dFormatted,
                     "fileName": "hub.txt",
                     "fileSize": 0,
                     "fileType": "hub.txt",
                     "genome": metadata.genome,
                     "parentDir": cgiEncode(metadata.parentDir),
                     "fullPath": cgiEncode(metadata.parentDir) + "/hub.txt",
                     "hubType": hubType,
                 };
             }
             parentDirObj = {
                 "uploadTime": nowFormatted,
                 "lastModified": dFormatted,
                 "fileName": cgiEncode(metadata.parentDir),
                 "fileSize": 0,
                 "fileType": "dir",
                 "genome": metadata.genome,
                 "parentDir": "",
                 "fullPath": cgiEncode(metadata.parentDir),
                 "hubType": hubType,
             };
             // package the three objects together as one "hub" and display it
             let hub = [parentDirObj, newReqObj];
             if (hubTxtObj) {
                 hub.push(hubTxtObj);
             }
             addNewUploadedHubToTable(hub);
             updateQuota(metadata.fileSize);
         });
         uppy.on('complete', (result) => {
             history.replaceState(uiState, "", document.location.href);
             console.log("replace history with uiState");
         });
         inited = true;
     }
 
     function checkJsonData(jsonData, callerName) {
         // Return true if jsonData isn't empty and doesn't contain an error;
         // otherwise complain on behalf of caller.
         if (! jsonData) {
             alert(callerName + ': empty response from server');
         } else if (jsonData.error) {
             console.error(jsonData.error);
             alert(callerName + ': error from server: ' + jsonData.error);
         } else if (jsonData.warning) {
             alert("Warning: " + jsonData.warning);
             return true;
         } else {
             if (debugCartJson) {
                 console.log('from server:\n', jsonData);
             }
             return true;
         }
         return false;
     }
 
     function handleRefreshState(jsonData, textStatus) {
         if (checkJsonData(jsonData, 'handleRefreshState')) {
             handleGetFileList(jsonData, true);
         }
     }
 
     function handleErrorState(jqXHR, textStatus) {
         cart.defaultErrorCallback(jqXHR, textStatus);
     }
 
     let inited = false; // keep track of first init for tab switching purposes
     function init() {
         cart.setCgiAndUrl(fileListEndpoint);
         cart.debug(debugCartJson);
         // get the file list immediately upon page load
         let activeTab = $("#tabs").tabs( "option", "active" );
         if (activeTab === 3) {
             let url = new URL(window.location.href);
             if (url.protocol === "http:") {
                 warn(`The hub upload feature is only available over HTTPS. Please load the HTTPS version of ` +
                         `our site: <a href="https:${url.host}${url.pathname}${url.search}">https:${url.host}${url.pathname}${url.search}</a>`);
             } else if ((url.protocol + "//" + url.host) !== loginHost) {
                 warn(`The hub upload feature is only avaiable on our US based public site (<a href="${loginHost}">${loginHost}</a>) for speed purposes. Please go there to upload your hubs, copy the links to the hub.txt files, then use the Connected Hubs tab here to view your files.`);
             } else if (!inited && isLoggedIn) {
                 cart.send({ getHubSpaceUIState: {}}, handleRefreshState, handleErrorState);
                 cart.flush();
             } else {
                 showExistingFiles([]);
             }
         }
     }
 
     return { init: init,
              uiState: uiState,
              defaultDb: defaultDb,
              makeGenomeSelectOptions: makeGenomeSelectOptions,
              getDefaultHubName: getDefaultHubName,
              detectFileType: detectFileType,
              sanitizeGenomeName: sanitizeGenomeName,
              readFileAsText: readFileAsText,
              parseHubTxt: parseHubTxt,
              firstAssemblyHub: firstAssemblyHub,
              genomeIsAssemblyHub: genomeIsAssemblyHub,
              assemblyHubByGenome: assemblyHubByGenome,
            };
 }());