a2707301aa6d5239200eed6442e9e265091bde78
chmalee
  Mon Apr 8 16:35:53 2024 -0700
Add some more file extensions to allowed extension list

diff --git src/hg/js/hgMyData.js src/hg/js/hgMyData.js
index 9ca1d9e..0b11d29 100644
--- src/hg/js/hgMyData.js
+++ src/hg/js/hgMyData.js
@@ -1,545 +1,545 @@
 /* jshint esnext: true */
 debugCartJson = true;
 
 function prettyFileSize(num) {
     if (num < (1000 * 1024)) {
         return `${(num/1000).toFixed(1)}kb`;
     } else if (num < (1000 * 1000 * 1024)) {
         return `${((num/1000)/1000).toFixed(1)}mb`;
     } else {
         return `${(((num/1000)/1000)/1000).toFixed(1)}gb`;
     }
 }
 
 var hubCreate = (function() {
     let uiState = { // our object for keeping track of the current UI and what to do
         toUpload: {}, // set of file objects keyed by name
         input: null, // the hidden input element
         pickedList: null, // the <div> for displaying files in toUpload
         pendingQueue: [], // our queue of pending [tus.Upload, file], kind of like the toUpload object
         fileList: [], // the files this user has uploaded, initially populated by the server
                         // on page load, but gets updated as the user uploades/deletes files
         userUrl: "", // the web accesible path where the uploads are stored for this user
     };
 
     // We can use XMLHttpRequest if necessary or a mirror can't use tus
     var useTus = tus.isSupported && true;
 
     function getTusdEndpoint() {
         // return the port and basepath of the tusd server
         // NOTE: the port and basepath are specified in hg.conf
         //let currUrl = parseUrl(window.location.href);
         return "https://hgwdev-hubspace.gi.ucsc.edu/files";
     }
 
     function togglePickStateMessage(showMsg = false) {
         if (showMsg) {
             let para = document.createElement("p");
             para.textContent = "No files selected for upload";
             para.classList.add("noFiles");
             uiState.pickedList.prepend(para);
             removeClearSubmitButtons();
         } else {
             let msg = document.querySelector(".noFiles");
             if (msg) {
                 msg.parentNode.removeChild(msg);
             }
         }
     }
 
     function liForFile(file) {
         let liId = `${file.name}#li`;
         let li = document.getElementById(liId);
         return li;
     }
 
     function newButton(text) {
         /* Creates a new button with some text as the label */
         let newBtn = document.createElement("label");
         newBtn.classList.add("button");
         newBtn.textContent = text;
         return newBtn;
     }
 
     function createInput() {
         /* Create a new input element for a file picker */
         let input = document.createElement("input");
         //input.style.opacity = 0;
         //input.style.float = "right";
         input.multiple = true;
         input.type = "file";
         input.id = "hiddenFileInput";
         input.style = "display: none";
         input.addEventListener("change", listPickedFiles);
         return input;
     }
 
     function requestsPending() {
         /* Return true if requests are still pending, which means it needs to
          * have been sent(). aborted requests are considered done for this purpose */
         for (let [req, f] of uiState.pendingQueue) {
             if (req._req !== null) {
                 xreq = req._req._xhr;
                 if (xreq.readyState != XMLHttpRequest.DONE && xreq.readyState != XMLHttpRequest.UNSENT) {
                     return true;
                 }
             }
         }
         return false;
     }
 
     function addCancelButton(file, req) {
         /* Add a button that cancels the request req */
         let li = liForFile(file);
         let newBtn = newButton("Cancel upload");
         newBtn.addEventListener("click", (e) => {
             req.abort();
             li.removeChild(newBtn);
             // TODO: make this remove the cancel all button if it's the last pending
             // request
             stillPending = requestsPending();
             if (!stillPending) {
                 let btnRow = document.getElementById("chooseAndSendFilesRow");
                 cAllBtn = btnRow.lastChild;
                 btnRow.removeChild(cAllBtn);
             }
         });
         li.append(newBtn);
     }
 
     function removeCancelAllButton() {
         let btnRow = document.getElementById("chooseAndSendFilesRow");
         if (btnRow.lastChild.textContent === "Cancel all") {
             btnRow.removeChild(btnRow.lastChild);
         }
         togglePickStateMessage(true);
     }
 
     function addCancelAllButton() {
         let btnRow = document.getElementById("chooseAndSendFilesRow");
         let newBtn = newButton("Cancel all");
         newBtn.addEventListener("click", (e) => {
             while (uiState.pendingQueue.length > 0) {
                 let [req, f] = uiState.pendingQueue.pop();
                 // we only need to abort requests that haven't finished yet
                 if (req._req !== null) {
                     if (_req._xhr.readyState != XMLHttpRequest.DONE) {
                         req.abort(true);
                     }
                 }
                 let li = liForFile(f);
                 if (li !== null) {
                     // the xhr event handlers should handle this but just in case
                     li.removeChild(li.lastChild);
                 }
             }
         });
         btnRow.appendChild(newBtn);
     }
 
     function makeNewProgMeter(fileName) {
         // create a progress meter for this filename
         const progMeterWidth = 128;
         const progMeterHeight = 12;
         const progMeter = document.createElement("canvas");
         progMeter.classList.add("upload-progress");
         progMeter.setAttribute("width", progMeterWidth);
         progMeter.setAttribute("height", progMeterHeight);
         idStr = `${fileName}#li`;
         ele = document.getElementById(idStr);
         ele.appendChild(progMeter);
         progMeter.ctx = progMeter.getContext('2d');
         progMeter.ctx.fillStyle = 'orange';
         progMeter.updateProgress = (percent) => {
             // update the progress meter for this elem
             if (percent === 100) {
                 progMeter.ctx.fillStyle = 'green';
             }
             progMeter.ctx.fillRect(0, 0, (progMeterWidth * percent) / 100, progMeterHeight);
         };
         progMeter.updateProgress(0);
         return progMeter;
     }
 
     function submitPickedFiles() {
         let tusdServer = getTusdEndpoint();
 
         let onBeforeRequest = function(req) {
             let xhr = req.getUnderlyingObject(req);
             xhr.withCredentials = true;
         };
 
         let onSuccess = function(req) {
             // remove the selected file from the input element and the ul list
             // FileList is a read only setting, so we have to make
             // a new one without this req
             delete uiState.toUpload[req.name];
             let i, newReqObj = {};
             for (i = 0; i < uiState.pendingQueue.length; i++) {
                 fname = uiState.pendingQueue[i][1].name;
                 if (fname === req.name) {
                     // remove the successful tusUpload off
                     uiState.pendingQueue.splice(i, 1);
                 }
             }
             // remove the file from the list the user can see
             let li = document.getElementById(req.name+"#li");
             li.parentNode.removeChild(li);
             if (uiState.pendingQueue.length === 0) {
                 removeCancelAllButton();
             }
             const d = new Date(req.lastModified);
             newReqObj = {"createTime": d.toJSON(), "name": req.name, "size": req.size};
             addNewUploadedFileToTable(newReqObj);
         };
 
         let onError = function(err) {
             removeCancelAllButton();
             alert(err.originalResponse._xhr.responseText);
         };
 
         for (let f in uiState.toUpload) {
             file = uiState.toUpload[f];
             if (useTus) {
                 let tusOptions = {
                     endpoint: tusdServer,
                     metadata: {
                         filename: file.name,
                         fileType: file.type,
                         fileSize: file.size
                     },
                     onBeforeRequest: onBeforeRequest,
                     onSuccess: onSuccess.bind(null, file),
                     onError: onError,
                     retryDelays: [1000],
                 };
                 // TODO: get the uploadUrl from the tusd server
                 // use a pre-create hook to validate the user
                 // and get an uploadUrl
                 let tusUpload = new tus.Upload(file, tusOptions);
                 uiState.pendingQueue.push([tusUpload, file]);
                 tusUpload.start();
             } else {
                 // make a new XMLHttpRequest for each file, if tusd-tusclient not supported
                 new sendFile(file);
             }
         }
         addCancelAllButton();
         return;
     }
 
     function clearPickedFiles() {
         while (uiState.pickedList.firstChild) {
             uiState.pickedList.removeChild(uiState.pickedList.firstChild);
         }
         uiState.input = createInput();
         uiState.toUpload = {};
         togglePickStateMessage(true);
     }
 
     function addClearSubmitButtons() {
         let firstBtn = document.getElementById("btnForInput");
         let btnRow = document.getElementById("chooseAndSendFilesRow");
         if (!document.getElementById("clearPicked")) {
             let clearBtn = document.createElement("button");
             clearBtn.classList.add("button");
             clearBtn.id = "clearPicked";
             clearBtn.textContent = "Clear";
             clearBtn.addEventListener("click", clearPickedFiles);
             btnRow.append(clearBtn);
         }
         if (!document.getElementById("submitPicked")) {
             submitBtn = document.createElement("button");
             submitBtn.id = "submitPicked";
             submitBtn.classList.add("button");
             submitBtn.textContent = "Submit";
             submitBtn.addEventListener("click", submitPickedFiles);
             btnRow.append(submitBtn);
         }
     }
 
     function removeClearSubmitButtons() {
         let btn = document.getElementById("clearPicked");
         btn.parentNode.removeChild(btn);
         btn = document.getElementById("submitPicked");
         btn.parentNode.removeChild(btn);
     }
 
     function listPickedFiles() {
         //uiState.input.click(); // let the user choose files:
         if (uiState.input.files.length === 0) {
             console.log("not input");
             return;
             //togglePickStateMessage(true);
             //removeClearSubmitButtons();
         } else {
             let displayList = document.getElementsByClassName("pickedFiles");
             if (displayList.length === 0) {
                 displayList = document.createElement("ul");
                 displayList.classList.add("pickedFiles");
                 uiState.pickedList.appendChild(displayList);
             } else {
                 displayList = displayList[0];
             } 
             for (let file of uiState.input.files ) {
                 if (file.name in uiState.toUpload) { continue; }
                 // create a list for the user to see
                 let li = document.createElement("li");
                 li.classList.add("pickedFile");
                 li.id = `${file.name}#li`;
                 li.textContent = `File name: ${file.name}, file size: ${prettyFileSize(file.size)}`;
                 displayList.appendChild(li);
 
                 // finally add it for us
                 uiState.toUpload[file.name] = file;
             }
             togglePickStateMessage(false);
             addClearSubmitButtons();
         }
         // always clear the input element
         uiState.input = createInput();
     }
 
     function dataTablePrintSize(data, type, row, meta) {
         return prettyFileSize(data);
     }
 
     function deleteFileFromTable(rowIx, fname) {
         // req is an object with properties of an uploaded file, make a new row
         // for it in the filesTable
         let table = $("#filesTable").DataTable();
         let row = table.row((idx, data) => data.name === fname);
         row.remove().draw();
     }
 
     let pendingDeletes = {};
     function deleteFile(rowIx, fname) {
         // Send an async request to hgHubConnect to delete the file
         // Note that repeated requests, like from a bot, will return 404 as a correct response
         console.log(`sending delete req for ${fname}`);
         const endpoint = "../cgi-bin/hgHubConnect?deleteFile=" + fname;
         if (!(endpoint in pendingDeletes)) {
             const xhr = new XMLHttpRequest();
             pendingDeletes[endpoint] = xhr;
             this.xhr = xhr;
             this.xhr.open("DELETE", endpoint, true);
             this.xhr.send();
             deleteFileFromTable(rowIx, fname);
             delete pendingDeletes[endpoint];
         }
     }
 
     function viewInGenomeBrowser(rowIx, fname) {
         // redirect to hgTracks with this track as a custom track
         if (typeof uiState.userUrl !== "undefined" && uiState.userUrl.length > 0) {
-            bigBedExts = [".bb", ".bigBed"];
+            bigBedExts = [".bb", ".bigBed", ".vcf.gz", ".vcf", ".bam", ".bw", ".bigWig"];
             let i;
             for (i = 0; i < bigBedExts.length; i++) {
                 if (fname.toLowerCase().endsWith(bigBedExts[i])) {
                     // 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?
                     window.location.assign("../cgi-bin/hgTracks?db=hg38&hgt.customText=" + uiState.userUrl + fname);
                     return false;
                 }
             }
         }
     }
 
     function addNewUploadedFileToTable(req) {
         // req is an object with properties of an uploaded file, make a new row
         // for it in the filesTable
         let table = null;
         if ($.fn.dataTable.isDataTable("#filesTable")) {
             table = $("#filesTable").DataTable();
             let newRow = table.row.add(req).draw();
         } else {
             showExistingFiles([req]);
         }
     }
 
     let tableInitOptions = {
         //columnDefs: [{orderable: false, targets: [0,1]}],
         columnDefs: [
             {
                 orderable: false, targets: 0,
                 title: "<input type=\"checkbox\"></input>",
                 render: function(data, type, row) {
                     return "<input type=\"checkbox\"></input>";
                 }
             },
             {
                 orderable: false, targets: 1,
                 data: "action", title: "Action",
                 render: function(data, type, row) {
                     // TODO: add event handler on delete button
                     // click to call hgHubDelete file
                     return "<button class='deleteFileBtn'>Delete</button><button class='viewInBtn'>View In GB</button>";
                 }
             },
             {
                 targets: 3,
                 render: function(data, type, row) {
                     return dataTablePrintSize(data);
                 }
             }
         ],
         columns: [
             {data: "", },
             {data: "", },
             {data: "name", title: "File name"},
             {data: "size", title: "File size", render: dataTablePrintSize},
             {data: "createTime", title: "Creation Time"},
         ],
         order: [[4, 'desc']],
         drawCallback: function(settings) {
             let btns = document.querySelectorAll('.deleteFileBtn');
             let i;
             for (i = 0; i < btns.length; i++) {
                 let fnameNode = btns[i].parentNode.nextElementSibling.childNodes[0];
                 if (fnameNode.nodeName !== "#text") {continue;}
                 let fname = fnameNode.nodeValue;
                 btns[i].addEventListener("click", (e) => {
                     deleteFile(i, fname);
                 });
             }
             btns = document.querySelectorAll('.viewInBtn');
             for (i = 0; i < btns.length; i++) {
                 let fnameNode = btns[i].parentNode.nextElementSibling.childNodes[0];
                 if (fnameNode.nodeName !== "#text") {continue;}
                 let fname = fnameNode.nodeValue;
                 btns[i].addEventListener("click", (e) => {
                     viewInGenomeBrowser(i, fname);
                 });
             }
         },
     };
 
     function showExistingFiles(d) {
         // Make the DataTable for each file
         //$(document).on("draw.dt", function() {alert("table redrawn");});
         tableInitOptions.data = d;
         let table = $("#filesTable").DataTable(tableInitOptions);
     }
 
     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 updateStateAndPage(jsonData, doSaveHistory) {
         // Update uiState with new values and update the page.
         _.assign(uiState, jsonData);
         /*
         urlVars = {"db": db, "search": uiState.search, "showSearchResults": ""};
         // changing the url allows the history to be associated to a specific url
         var urlParts = changeUrl(urlVars);
         if (doSaveHistory)
             saveHistory(uiState, urlParts);
         changeSearchResultsLabel();
         */
     }
 
     function handleRefreshState(jsonData) {
         if (checkJsonData(jsonData, 'handleRefreshState')) {
             updateStateAndPage(jsonData, true);
         }
         $("#spinner").remove();
     }
 
     function init() {
         cart.setCgi('hgMyData');
         cart.debug(debugCartJson);
         if (!useTus) {
             console.log("tus is not supported, falling back to XMLHttpRequest");
         }
         let pickedFiles = document.getElementById("fileList");
         let inputBtn = document.getElementById("btnForInput");
         if (pickedFiles !== null) {
             // this element should be an empty div upon loading the page
             uiState.pickedList = pickedFiles;
             if (pickedFiles.children.length === 0) {
                 let para = document.createElement("p");
                 para.textContent = "No files chosen yet";
                 para.classList.add("noFiles");
                 pickedFiles.appendChild(para);
             }
         } else {
             // TODO: graceful handle of leaving the page and coming back?
         }
         let parent = document.getElementById("chooseAndSendFilesRow");
         let input = createInput();
         uiState.input = input;
         inputBtn.parentNode.appendChild(input);
 
         if (typeof cartJson !== "undefined") {
             if (typeof cartJson.warning !== "undefined") {
                 alert("Warning: " + cartJson.warning);
             }
             var urlParts = {};
             if (debugCartJson) {
                 console.log('from server:\n', cartJson);
             }
             _.assign(uiState,cartJson);
             saveHistory(cartJson, urlParts, true);
         } else {
             // no cartJson object means we are coming to the page for the first time:
             //cart.send({ getUiState: {} }, handleRefreshState);
             //cart.flush();
             // TODO: initialize buttons, check if there are already files
             // TODO: write functions for
             //     after picking files
             //     choosing file types
             //     creating default trackDbs
             //     editing trackDbs
             // TODO: make hgHubConnect respond to requests
             // TODO: initialize tus-client
             // TODO: get user name
             // TODO: send a request with username
             // TODO: have tusd respond on server
             let uploadSection = document.getElementById("chosenFilesSection");
             if (uploadSection.style.display === "none") {
                 uploadSection.style.display = "";
             }
             if (typeof userFiles !== 'undefined' && typeof userFiles.fileList !== 'undefined' &&
                     userFiles.fileList.length > 0) { 
                 uiState.fileList= userFiles.fileList;
                 uiState.userUrl = userFiles.userUrl;
                 showExistingFiles(uiState.fileList);
             }
             inputBtn.addEventListener("click", (e) => uiState.input.click());
             //uiState.input.addEventListener("change", listPickedFiles);
             // TODO: add event handler for when file is succesful upload
             // TODO: add event handlers for editing defaults, grouping into hub
             // TODO: display quota somewhere
             // TODO: customize the li to remove the picked file
         }
     }
     return { init: init,
              uiState: uiState,
            };
 
 }());
 
 
 // when a user reaches this page from the back button we can display our saved state
 // instead of sending another network request
 window.onpopstate = function(event) {
     event.preventDefault();
     hubCreate.updateStateAndPage(event.state, false);
 };