Merge pull request #11276 from assuntad23/bugfix/8488/rule-builder-fails-for-one-bad-url

Bugfix/8488/rule builder fails for one bad url

client/src/components/Upload/Collection.vue

@@ -129,6 +129,7 @@ export default {
     components: { BButton },
     data() {
         return {
+            uploadUrl: null,
             topInfo: "",
             showHelper: true,
             extension: this.app.defaultExtension,
@@ -168,7 +169,12 @@ export default {
         this.initFtpPopover();
         // file upload
         this.initUploadbox({
-            url: this.app.uploadPath,
+            initUrl: (index) => {
+                if (!this.uploadUrl) {
+                    this.uploadUrl = this.getRequestUrl([this.collection.get(index)], this.history_id);
+                }
+                return this.uploadUrl;
+            },
             announce: (index, file) => {
                 this._eventAnnounce(index, file);
             },

client/src/components/Upload/Composite.vue

@@ -141,7 +141,7 @@ export default {
             });
             $.uploadpost({
                 url: this.app.uploadPath,
-                data: this.app.toData(this.collection.filter()),
+                data: this.app.toFileUploadData(this.collection.filter()),
                 success: (message) => {
                     this._eventSuccess(message);
                 },

client/src/components/Upload/Default.vue

@@ -128,6 +128,7 @@ export default {
     },
     data() {
         return {
+            uploadUrl: null,
             topInfo: "",
             highlightBox: false,
             showHelper: true,
@@ -164,7 +165,12 @@ export default {
         this.initFtpPopover();
         // file upload
         this.initUploadbox({
-            url: this.app.uploadPath,
+            initUrl: (index) => {
+                if (!this.uploadUrl) {
+                    this.uploadUrl = this.getRequestUrl([this.collection.get(index)], this.history_id);
+                }
+                return this.uploadUrl;
+            },
             multiple: this.multiple,
             announce: (index, file) => {
                 this._eventAnnounce(index, file);

client/src/components/Upload/UploadBoxMixin.js

@@ -10,6 +10,7 @@ import UploadFtp from "mvc/upload/upload-ftp";
 import LazyLimited from "mvc/lazy/lazy-limited";
 import { findExtension } from "./utils";
 import { filesDialog } from "utils/data";
+import { getAppRoot } from "onload";
 
 const localize = _l;
 
@@ -339,5 +340,10 @@ export default {
             const models = allHids.map((hid) => Galaxy.currHistoryPanel.collection.getByHid(hid));
             return models;
         },
+        getRequestUrl: function (items, history_id) {
+            var data = this.app.toData(items, history_id);
+            const appRoot = getAppRoot();
+            return data.fetchRequest ? `${appRoot}api/tools/fetch` : this.app.uploadPath;
+        },
     },
 };

client/src/components/Upload/UploadModalContent.vue

@@ -60,6 +60,7 @@ export default {
             extensionsSet: false,
             datatypesMapper: null,
             datatypesMapperReady: true,
+            URI_PREFIXES: ["http", "https", "ftp", "file", "gxfiles", "gximport", "gxuserimport", "gxftp"],
         };
     },
     created() {
@@ -173,12 +174,44 @@ export default {
         currentFtp: function () {
             return this.currentUserId && this.ftpUploadSite;
         },
-
+        toData: function (items, history_id) {
+            const data = {
+                fetchRequest: null,
+                uploadRequest: null,
+            };
+            if (items && items.length > 0) {
+                const split = this.preprocess(items);
+                if (split.urls.length > 0) {
+                    data.fetchRequest = this.toFetchData(split.urls, history_id);
+                } else {
+                    data.uploadRequest = this.toFileUploadData(split.files, history_id);
+                }
+            }
+            return data;
+        },
+        preprocess: function (items) {
+            const data = {
+                urls: [],
+                files: [],
+            };
+            for (var index in items) {
+                var it = items[index];
+                if (it.get("file_mode") != "new" || !this.itemIsURL(it)) {
+                    data.files.push(it);
+                } else {
+                    data.urls.push(it);
+                }
+            }
+            return data;
+        },
+        itemIsURL: function (item) {
+            return this.URI_PREFIXES.some((prefix) => item.get("url_paste").startsWith(prefix));
+        },
         /**
          * Package API data from array of models
          * @param{Array} items - Upload items/rows filtered from a collection
          */
-        toData: function (items, history_id) {
+        toFileUploadData: function (items, history_id) {
             // create dictionary for data submission
             var data = {
                 payload: {
@@ -244,6 +277,38 @@ export default {
             }
             return data;
         },
+        toFetchData: function (items, history_id) {
+            var data = {
+                history_id: history_id,
+                space_to_tab: items[0].get("space_to_tab"),
+                to_posix_lines: items[0].get("to_posix_lines"),
+                targets: [
+                    {
+                        destination: { type: "hdas" },
+                        elements: [],
+                        name: "",
+                    },
+                ],
+                auto_decompress: true,
+            };
+
+            // Composite does not use the fetch API, so we can just
+            // index into the first element of items
+            const urls = items[0].get("url_paste").split("\n");
+            for (var index in urls) {
+                var url = urls[index].trim();
+                if (url != "") {
+                    var element = {
+                        url: urls[index].trim(),
+                        src: "url",
+                        dbkey: items[0].get("genome", "?"),
+                        ext: items[0].get("extension", "auto"),
+                    };
+                    data.targets[0].elements.push(element);
+                }
+            }
+            return data;
+        },
     },
 };
 </script>

client/src/utils/uploadbox.js

@@ -228,6 +228,41 @@ import { getAppRoot } from "onload/loadConfig";
             },
         });
     };
+    /**
+     *
+     * @param {*} config
+     */
+    $.datafetchpost = function (config) {
+        var cnf = $.extend(
+            {},
+            {
+                data: {},
+                success: () => {},
+                error: () => {},
+                progress: () => {},
+                url: null,
+            },
+            config
+        );
+        var data = cnf.data;
+        if (data.error_message) {
+            cnf.error(data.error_message);
+            return;
+        }
+
+        // submit request
+        _uploadrequest({
+            url: cnf.url,
+            data: JSON.stringify(cnf.data),
+            success: cnf.success,
+            error: cnf.error,
+            progress: (e) => {
+                if (e.lengthComputable) {
+                    cnf.progress(Math.round((e.loaded * 100) / e.total));
+                }
+            },
+        });
+    };
 
     /**
         Handles the upload events drag/drop etc.
@@ -391,6 +426,7 @@ import { getAppRoot } from "onload/loadConfig";
 
             // create and submit data
             var submitter = $.uploadpost;
+            var requestData = opts.initialize(index);
             if (
                 file.chunk_mode &&
                 session &&
@@ -399,10 +435,13 @@ import { getAppRoot } from "onload/loadConfig";
                 session.chunk_upload_size > 0
             ) {
                 submitter = $.uploadchunk;
+            } else if (requestData.fetchRequest) {
+                submitter = $.datafetchpost;
             }
+
             submitter({
-                url: opts.url,
-                data: opts.initialize(index),
+                url: opts.initUrl(index),
+                data: requestData.fetchRequest ? requestData.fetchRequest : requestData.uploadRequest,
                 session: session,
                 success: (message) => {
                     opts.success(index, message);