c6d419ecfb6f122d7a0cb99c37f56c32c089bea3
chmalee
  Thu Jan 22 10:41:38 2026 -0800
HubSpace changes: Allow users to overwrite already uploaded files, but warn them first. When a hub.txt file is being uploaded, don't auto-generate one. Check if the tracks being uploaded already exist in the hub.txt before adding a default stanza for it. Add some more checks in the hook files to prevent faulty uploads. Have the tus client clear localStorage on successful uploads so re-uploads of the same file don't cause confusing errors

diff --git src/hg/js/hgMyData.js src/hg/js/hgMyData.js
index b639768ccff..8b80d778fe6 100644
--- src/hg/js/hgMyData.js
+++ src/hg/js/hgMyData.js
@@ -1,1531 +1,1585 @@
 /* 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
     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 processFindGenome(result, term) {
     // process the hubApi/findGenome?q= result set into somthing
     // jquery-ui autocomplete can use
     let data = [];
     let apiSkipList = new Set(["downloadTime", "downloadTimeStamp", "availableAssemblies", "browser", "elapsedTimeMs", "itemCount", "q", "totalMatchCount"]);
     _.forEach(result, function(val, key) {
         if (!(apiSkipList.has(key))) {
             let d = {
                 "genome": key,
                 "label": `${val.commonName} (${key})`,
             };
             if (val.hubUrl !== null) {
                 d.category = "UCSC GenArk - bulk annotated assemblies from NCBI GenBank / Refseq";
             } else {
                 d.category = "UCSC Genome Browser assemblies - annotation tracks curated by UCSC";
             }
             data.push(d);
         }
     });
     return data;
 }
 
 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) {
         $.widget("custom.autocompleteCat",
                  $.ui.autocomplete,
                  {
                    _renderMenu: function(ul, items) {
                        var that = this;
                        var currentCategory = "";
                        // There's no this._super as shown in the doc, so I can't override
                        // _create as shown in the doc -- just do this every time we render...
                        this.widget().menu("option", "items", "> :not(.ui-autocomplete-category)");
                        $(ul).css("z-index", "99999999");
                        $.each(items,
                               function(index, item) {
                                   // Add a heading each time we see a new category:
                                   if (item.category && item.category !== currentCategory) {
                                       ul.append("<li class='ui-autocomplete-category'>" +
                                                 item.category + "</li>" );
                                       currentCategory = item.category;
                                   }
                                   that._renderItem( ul, item );
                               });
                    },
                    _renderItem: function(ul, item) {
                      // In order to use HTML markup in the autocomplete, one has to overwrite
                      // autocomplete's _renderItem method using .html instead of .text.
                      // http://forum.jquery.com/topic/using-html-in-autocomplete
                        // Hits to assembly hub top level (not individial db names) have no item label,
                        // so use the value instead
                        return $("<li></li>")
                            .data("ui-autocomplete-item", item)
                            .append($("<a></a>").html((item.label !== null ? item.label : item.value)))
                            .appendTo(ul);
                    }
                  });
         let selectFunction = setDbSelectFromAutocomplete.bind(null, selectEle);
         autocompleteCat.init($("[id='"+inpIdStr+"']"), {
             baseUrl: "hubApi/findGenome?browser=mustExist&q=",
             //watermark: "Enter species name, common name, etc",
             onSelect: selectFunction,
             onServerReply: processFindGenome,
             enterSelectsIdentical: false
         });
         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) => {
                 // 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: `${file.meta.name}DbSelect`,
                         style: "margin-left: 5px",
                         onChange: e => {
                             onChange(e.target.value);
                             file.meta.genome = e.target.value;
                             file.meta.genomeLabel = e.target.selectedOptions[0].label;
                         }
                         },
                         hubCreate.makeGenomeSelectOptions(file.meta.genome, file.meta.genomeLabel).map( (genomeObj) => {
                             return h('option', {
                                 value: genomeObj.value,
                                 label: genomeObj.label,
                                 selected: file.meta.genome !== null ? genomeObj.value === file.meta.genome : genomeObj.value === hubCreate.defaultDb()
                             });
                         })
                     ),
                     h('p', {
                         class: "uppy-Dashboard-FileCard-label",
                         style: "display: block; width: 78%",
                         }, "or search for your genome:"),
                     // third div child
                     h('input', {
                         id: `${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
+
+        // Check if any file is a hub.txt - if so, we need to upload it first
+        // and switch to sequential uploads to prevent race conditions
+        let hasHubTxt = Object.values(files).some(f => f.meta.fileType === "hub.txt");
+        if (hasHubTxt) {
+            // Set TUS plugin to sequential uploads (limit: 1)
+            const tusPlugin = uppy.getPlugin('Tus');
+            if (tusPlugin) {
+                tusPlugin.setOptions({ limit: 1 });
+            }
+            // Reorder files so hub.txt comes first (JS objects maintain insertion order)
+            let hubTxtFiles = {};
+            let otherFiles = {};
+            for (let [key, file] of Object.entries(files)) {
+                if (file.meta.fileType === "hub.txt") {
+                    hubTxtFiles[key] = file;
+                } else {
+                    otherFiles[key] = file;
+                }
+            }
+            files = Object.assign({}, hubTxtFiles, otherFiles);
+        }
+
         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) {
                 genome = hubCreate.uiState.filesHash[file.meta.parentDir].genome;
                 uppy.info(`Error: the hub ${file.meta.parentDir} already exists and is for genome "${genome}". Please select the correct genome, a different hub or make a new hub.`);
                 doUpload = false;
                 continue;
             }
-            // check if the user is uploading a hub.txt into a hub that already has a hub.txt
+            // 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;
-                if (file.meta.fileType === "hub.txt" && hubFiles.filter((f) => f.fileType === "hub.txt").length !== 0) {
-                    uppy.info(`Error: the hub definition file (ex: hub.txt) already exists, create a new hub if you want to upload this hub definition file`);
-                    doUpload = false;
-                    continue;
+                for (let j = 0; j < hubFiles.length; j++) {
+                    if (hubFiles[j].fileName === file.meta.name) {
+                        filesToOverwrite.push(file);
+                        break;
+                    }
                 }
             }
 
-            uppy.setFileMeta(file.id, {
-                fileName: file.meta.name,
-                fileSize: file.size,
-                lastModified: file.data.lastModified,
-            });
+            // 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;
+        // Return the (possibly reordered) files object to proceed, or false to cancel
+        return doUpload ? files : 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")) {
             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";
 
             // the batch change db select
             let batchDbSelect = document.createElement("select");
             this.createOptsForSelect(batchDbSelect, hubCreate.makeGenomeSelectOptions());
             batchDbSelect.id = "batchDbSelect";
             batchDbSelect.style.gridArea = "2 / 2 / 2 / 2";
             batchDbSelect.style.margin = "2px";
             let batchDbLabel = document.createElement("label");
             batchDbLabel.textContent = "Genome";
             batchDbLabel.for = "batchDbSelect";
             batchDbLabel.style.gridArea = "2 / 1 / 2 / 1";
 
             // the search bar for db selection
             let batchDbSearchBarLabel= document.createElement("label");
             batchDbSearchBarLabel.textContent = "or search for your genome:";
             batchDbSearchBarLabel.style.gridArea = "2 / 3 /2 / 3";
             batchDbSearchBarLabel.style.margin = "auto";
 
             let 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";
             let batchDbGenomeSearchButton = document.createElement("input");
             batchDbGenomeSearchButton.type = "button";
             batchDbGenomeSearchButton.value = "search";
             batchDbGenomeSearchButton.id = "batchDbSearchBarButton";
             batchDbGenomeSearchButton.style.gridArea = "2 / 5 / 2 / 5";
 
             // the batch change hub name
             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.uiState.hubNameDefault;
             batchParentDirInput.style.gridArea = "3 / 2 / 3 / 2";
             batchParentDirInput.style.margin= "1px 1px auto";
             batchParentDirInput.classList.add("uppy-u-reset", "uppy-c-textInput");
 
             // add event handlers to change metadata, use an arrow function
             // because otherwise 'this' keyword will be the element instead of
             // our class
             batchDbSelect.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, {genome: val});
                     this.uppy.setFileMeta(file.id, {genomeLabel: ev.target.selectedOptions[0].label});
                 }
             });
             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(batchSelectText);
             batchSelectDiv.appendChild(batchDbLabel);
             batchSelectDiv.appendChild(batchDbSelect);
             batchSelectDiv.appendChild(batchDbSearchBarLabel);
             batchSelectDiv.appendChild(batchDbGenomeSearchBar);
             batchSelectDiv.appendChild(batchDbGenomeSearchButton);
             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);
             }
 
             // everything has to exist already for autocompleteCat to initialize
             let justInitted = initAutocompleteForInput(batchDbGenomeSearchBar.id, batchDbSelect);
             if (justInitted) {
                 // only do this once per batch setup
                 batchDbGenomeSearchButton.addEventListener("click", (e) => {
                     let inp = document.getElementById(batchDbSearchBar.id).value;
                     let selector = "[id='"+batchDbGenomeSearchBar.id+"']";
                     $(selector).autocompleteCat("search", inp);
                 });
             }
         }
     }
 
     install() {
         this.uppy.on("file-added", (file) => {
             // add default meta data for genome and fileType
             console.log("file-added");
             this.uppy.setFileMeta(file.id, {"genome": hubCreate.defaultDb(), "fileType": hubCreate.detectFileType(file.name), "parentDir": hubCreate.uiState.hubNameDefault});
             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: "",
         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"],
         "text": [".txt", ".text"],
     };
 
     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);
         if (value && label && !(label in defaultGenomeChoices)) {
             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) {
         // 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(hubName) + "/hub.txt";
                 let url = "../cgi-bin/hgTracks?hgsid=" + getHgsid() + "&db=" + 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, "_"));
     }
 
     // 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;
                     url += "&db=" + 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
                         url += "&hubUrl=" + encodeURIComponent(uiState.userUrl + cgiEncode(d.parentDir));
                         if (d.parentDir.endsWith("/")) {
                             url += "hub.txt";
                         } else {
                             url += "/hub.txt";
                         }
                     }
                     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;
+        // 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;
-        // if a hub.txt file is in data, disable the delete button
-        let disableDelete = false;
-        if (data) {
-            disableDelete = data.filter((obj) => obj.fileType === "hub.txt").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";
-            if (!disableDelete) {
             let deleteBtn = document.getElementById("deleteSelectedFiles");
             deleteBtn.style.display = "inline-block";
             deleteBtn.addEventListener("click", deleteFileList);
             deleteBtn.textContent = "Delete selected";
-            } else {
-                // delete the old button:
-                let deleteBtn = document.getElementById("deleteSelectedFiles");
-                deleteBtn.style.display = "none";
-            }
         } 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);
                 table.draw();
                 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;
         });
     }
 
     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();
         table.draw();
         // NOTE that the below does not actually render until the next table.draw() call
         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;
             }
         });
         dataTableCreateBreadcrumb(table, dirName, dirFullPath);
     }
 
     // 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 in extensionMap) {
                 let container = document.createElement("div");
                 let viewBtn = document.createElement("button");
                 viewBtn.textContent = "View in Genome Browser";
                 viewBtn.type = 'button';
                 viewBtn.addEventListener("click", function(e) {
                     e.stopPropagation();
                     viewInGenomeBrowser(rowData.fileName, rowData.fileType, rowData.genome, rowData.parentDir);
                 });
                 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);
         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);
         table.draw();
         dataTableCustomOrder(table, hubDirData);
         table.columns.adjust().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,
         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) {
                     return decodeURIComponent(data);
                 }
             },
             {
                 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;
                 }
             },
             {
                 // The upload time column
                 targets: 8,
                 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);
         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();
         }
         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) {
             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);
         table.columns.adjust().draw();
 
         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-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;
             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),
             };
             // 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:
             if (metadata.fileType !== "hub.txt") {
                 // if the user uploaded a hub.txt don't make a second fake object for it
                 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",
                 };
             }
             parentDirObj = {
                 "uploadTime": nowFormatted,
                 "lastModified": dFormatted,
                 "fileName": cgiEncode(metadata.parentDir),
                 "fileSize": 0,
                 "fileType": "dir",
                 "genome": metadata.genome,
                 "parentDir": "",
                 "fullPath": cgiEncode(metadata.parentDir),
             };
             // 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,
              detectFileType: detectFileType,
            };
 }());