7206132fbc62b1d3b563b67aa067ae8d6ab76e2b
chmalee
  Fri Jun 6 15:54:08 2025 -0700
Refactor hubSpace UI a little in order to make getting the initial filelist over async rather than with the CGI load, refs Max discussion

diff --git src/hg/js/hgMyData.js src/hg/js/hgMyData.js
index 70a4e3719ff..e0ab03de997 100644
--- src/hg/js/hgMyData.js
+++ src/hg/js/hgMyData.js
@@ -1,1442 +1,1472 @@
 /* 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:
     let splitVal = value.split('/');
     splitVal.forEach((ele, ix) => {
         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.setCgi("hgHubConnect");
     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.setCgi("hgHubConnect");
     cart.send(cartData, handleSuccess);
     cart.flush();
 }
 
 const fileNameRegex = /[0-9a-zA-Z._\-+]+/g; // allowed characters in file names
 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;
         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, dash, underscore or plus.`, '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, dash, underscore, or plus.`, '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;
             } else if  (!file.meta.fileType) {
                 uppy.info(`Error: File type not supported, file: ${file.meta.name}!`, 'error', 5000);
                 doUpload = false;
                 continue;
             }
             uppy.setFileMeta(file.id, {
                 fileName: file.meta.name,
                 fileSize: file.size,
                 lastModified: file.data.lastModified,
             });
             thisQuota += file.size;
         }
         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;
     },
 });
 
+// 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: '${file.meta.name}' to only include alpha-numeric characters, period, dash, underscore or plus.`, 'error', 5000);
+                }
+                if (!parentDirMatch || parentDirMatch[0] !== file.meta.parentDir) {
+                    uppy.info(`Error: Hub name has special characters, please rename hub: '${file.meta.parentDir}' to only include alpha-numeric characters, period, dash, underscore, or plus.`, '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
     };
 
-    function getTusdEndpoint() {
-        // this variable is set by hgHubConnect and comes from hg.conf value
-        return tusdEndpoint;
-    }
-
     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: "T2T", 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 url = "../cgi-bin/hgTracks?hgsid=" + getHgsid() + "&db=" + genome + "&hubUrl=" + uiState.userUrl + cgiEncode(hubName) + "/hub.txt&" + trackHubFixName(fname) + "=pack";
                 window.location.assign(url);
                 return false;
             }
         }
     }
 
     const regex = /[^A-Za-z0-9_-]/g;
     function trackHubFixName(trackName) {
         // replace everything but alphanumeric, underscore and dash with underscore
         return encodeURIComponent(trackName).replaceAll(regex, "_");
     }
 
     // helper object so we don't need to use an AbortController to update
     // the data this function is using
     let selectedData = {};
     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=" + 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=" + 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;
         let cartData = {deleteFile: {fileList: []}};
         cart.setCgi("hgHubConnect");
         _.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 = {};
 
         // 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;
             // 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 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);
         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.setCgi("hgHubConnect");
         cart.send({addToHub: {hubName: "", dataFile: ""}});
         cart.flush();
     }
 
 
     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
             }
         }
 
         // 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
-        $.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 navigate to \"My Data\" > \"My Sessions\" and log in or create an account 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");
-            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 init() {
-        cart.setCgi('hgMyData');
-        cart.debug(debugCartJson);
-        // TODO: write functions for
-        //     creating default trackDbs
-        //     editing trackDbs
-        // get the state from the history stack if it exists
-        if (typeof uiData !== 'undefined' && typeof uiState.userFiles !== 'undefined') {
-            _.assign(uiState, uiData.userFiles);
-            if (uiState.fileList) {
-                parseFileListIntoHash(uiState.fileList);
-            }
-        }
-        // first add the top level directories/files
-        let table = showExistingFiles(uiState.fileList);
-        table.columns.adjust().draw();
-        // TODO: add event handlers for editing defaults, grouping into hub
-        $("#newTrackHubDialog").dialog({
-            modal: true,
-            autoOpen: false,
-            title: "Create new track hub",
-            closeOnEscape: true,
-            minWidth: 400,
-            minHeight: 120
-        });
-
-        // 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 = 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, 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 = 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);
-                        });
+            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();
         }
+    };
 
-            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": defaultDb(), "fileType": detectFileType(file.name), "parentDir": uiState.hubNameDefault});
-                    if (this.uppy.getFiles().length > 1) {
-                        this.addBatchSelectsToDashboard();
+    function showExistingFiles(d) {
+        // Make the DataTable for each file
+        // make buttons have the same style as other buttons
+        $.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 {
-                        // only open the file editor when there is one file
-                        const dash = uppy.getPlugin("Dashboard");
-                        dash.toggleFileCard(true, file.id);
+            tableInitOptions.language = {emptyTable: "You are not logged in, please navigate to \"My Data\" > \"My Sessions\" and log in or create an account to begin uploading files"};
         }
-                });
-                this.uppy.on("file-removed", (file) => {
-                    // remove the batch change selects if now <2 files present
-                    if (this.uppy.getFiles().length < 2) {
-                        this.removeBatchSelectsFromDashboard();
+        DataTable.feature.register('quota', function(settings, opts) {
+            let options = Object.assign({option1: false, option2: false}, opts);
+            let container = document.createElement("div");
+            if (uiState.isLoggedIn) {
+                container.textContent = `Using ${prettyFileSize(uiState.userQuota)} of ${prettyFileSize(uiState.maxQuota)}`;
             }
+            return container;
         });
-
-                this.uppy.on("dashboard:modal-open", () => {
-                    // check if there were already files chosen from before:
-                    if (this.uppy.getFiles().length > 2) {
-                        this.addBatchSelectsToDashboard();
-                    }
-                    if (this.uppy.getFiles().length < 2) {
-                        this.removeBatchSelectsFromDashboard();
-                    }
+        let table = new DataTable("#filesTable", tableInitOptions);
+        if (uiState.isLoggedIn) {
+            table.buttons(".uploadButton").enable();
+            document.getElementById("rootBreadcrumb").addEventListener("click", function(e) {
+                dataTableShowTopLevel(table);
+                dataTableCustomOrder(table);
+                dataTableEmptyBreadcrumb(table);
+                table.draw();
             });
-                this.uppy.on("dashboard:modal-closed", () => {
-                    if (this.uppy.getFiles().length < 2) {
-                        this.removeBatchSelectsFromDashboard();
-                    }
-                    let allFiles = this.uppy.getFiles();
-                    let completeFiles = this.uppy.getFiles().filter((f) => f.progress.uploadComplete === true);
-                    if (allFiles.length === completeFiles.length) {
-                        this.uppy.clear();
+        } else {
+            table.buttons(".uploadButton").disable();
         }
+        table.on("select", function(e, dt, type, indexes) {
+            indexes.forEach(function(i) {
+                doRowSelect(e.type, dt, i);
             });
-                this.uppy.on("dashboard:file-edit-start", (file) => {
-                    autocompletes[`${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: '${file.meta.name}' to only include alpha-numeric characters, period, dash, underscore or plus.`, 'error', 5000);
-                        }
-                        if (!parentDirMatch || parentDirMatch[0] !== file.meta.parentDir) {
-                            uppy.info(`Error: Hub name has special characters, please rename hub: '${file.meta.parentDir}' to only include alpha-numeric characters, period, dash, underscore, or plus.`, 'error', 5000);
-                        }
-                    }
+        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());
                     }
-            uninstall() {
-                // not really used because we aren't ever uninstalling the uppy instance
-                this.uppy.off("file-added");
-            }
-        }
-        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 = 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: `${file.meta.name}DbSelect`,
-                                style: "margin-left: 5px",
-                                onChange: e => {
-                                    onChange(e.target.value);
-                                    file.meta.genome = e.target.value;
-                                    file.meta.genomeLabel = e.target.selectedOptions[0].label;
             }
-                                },
-                                makeGenomeSelectOptions(file.meta.genome, file.meta.genomeLabel).map( (genomeObj) => {
-                                    return h('option', {
-                                        value: genomeObj.value,
-                                        label: genomeObj.label,
-                                        selected: file.meta.genome !== null ? genomeObj.value === file.meta.genome : genomeObj.value === defaultDb()
-                                    });
-                                })
-                            ),
-                            h('p', {
-                                class: "uppy-Dashboard-FileCard-label",
-                                style: "display: block; width: 78%",
-                                }, "or search for your genome:"),
-                            // third div child
-                            h('input', {
-                                id: `${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']`;
-                                        $(selector).autocompleteCat("search", inp);
         });
+        return table;
     }
+
+    function handleGetFileList(jsonData, textStatus) {
+        _.assign(uiState, jsonData.userFiles);
+        if (uiState.fileList) {
+            parseFileListIntoHash(uiState.fileList);
         }
-                    return ret;
-                    }
-                },
-                {
-                    id: 'parentDir',
-                    name: 'Hub Name',
-                }];
-                return fields;
-            },
-            doneButtonHandler: function() {
-                uppy.clear();
-            },
-        };
+
+        // first add the top level directories/files
+        let table = showExistingFiles(uiState.fileList);
+        table.columns.adjust().draw();
+        uppy.use(Uppy.Dashboard, uppyOptions);
+
+        // define this in init so globals are available at runtime
         let tusOptions = {
             endpoint: getTusdEndpoint(),
             withCredentials: true,
             retryDelays: null,
         };
-        uppy.use(Uppy.Dashboard, uppyOptions);
+
         uppy.use(Uppy.Tus, tusOptions);
         uppy.use(BatchChangePlugin, {target: Uppy.Dashboard});
         uppy.on('upload-success', (file, response) => {
             const metadata = file.meta;
             const d = new Date(metadata.lastModified);
             const pad = (num) => String(num).padStart(2, '0');
             const dFormatted = `${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);
         });
         uppy.on('complete', (result) => {
             history.replaceState(uiState, "", document.location.href);
             console.log("replace history with uiState");
         });
     }
+
+    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);
+    }
+
+    function init() {
+        cart.setCgi('hgHubConnect');
+        cart.debug(debugCartJson);
+        // get the file list immediately upon page load
+        cart.send({ getHubSpaceUIState: {}}, handleRefreshState, handleErrorState);
+        cart.flush();
+    }
     return { init: init,
              uiState: uiState,
+             defaultDb: defaultDb,
+             makeGenomeSelectOptions: makeGenomeSelectOptions,
+             detectFileType: detectFileType,
            };
 }());