Fix ftp batch submission handler, adjust selenium tests

client/src/utils/navigation/navigation.yml

@@ -1032,35 +1032,32 @@ upload:
       close: 'div#composite div.upload-buttons button'
 
   selectors:
-    tab: '#tab-title-link-${tab}'
-    ftp_add: '#btn-ftp'
-    ftp_popup: '.upload-ftp-body'
-    ftp_items: '.upload-ftp-row'
-    ftp_close: '.popover-header .popover-close'
-    row: '#upload-row-${n}'
-    settings_button: '#upload-row-${n} .upload-settings span'
-    title: '#upload-row-${n} .upload-title'
-    paste_content: '#upload-row-${n} .upload-text-content'
-    settings: '.upload-settings-table'
-    setting_space_to_tab: '.upload-space-to-tab'
-    setting_deferred: '.upload-deferred'
-    start: '#activity-upload'
-    start_uploading: '#btn-start'
-    create: '#btn-new'
+    build_btn: '#rule-based #btn-build'
     close: '#btn-close'
-    rule_source_content: 'textarea.upload-rule-source-content'
-    rule_select_data_type: '.rule-data-type'
+    create: '#btn-new'
+    file_dialog: '#btn-remote-files'
+    file_dialog_ok: '.file-dialog-modal-ok'
+    file_source_selector:
+      type: xpath
+      selector: '//span[contains(@title, "${path}")]'
+    paste_content: '#upload-row-${n} .upload-text-content'
+    paste_new: .upload-paste
+    row: '#upload-row-${n}'
     rule_dataset_dialog: '[data-description="rules dataset dialog"]'
     rule_dataset_selector:
       selector: '.selection-dialog-modal'
     rule_dataset_selector_row:
       selector: '.selection-dialog-modal [aria-rowindex="${rowindex}"]'
-    build_btn: '#rule-based #btn-build'
-    file_source_selector:
-      type: xpath
-      selector: '//span[contains(@title, "${path}")]'
-    file_dialog_ok: '.file-dialog-modal-ok'
-    paste_new: .upload-paste
+    rule_select_data_type: '.rule-data-type'
+    rule_source_content: 'textarea.upload-rule-source-content'
+    tab: '#tab-title-link-${tab}'
+    title: '#upload-row-${n} .upload-title'
+    settings: '.upload-settings-table'
+    settings_button: '#upload-row-${n} .upload-settings span'
+    setting_deferred: '.upload-deferred'
+    setting_space_to_tab: '.upload-space-to-tab'
+    start: '#activity-upload'
+    start_uploading: '#btn-start'
 
 new_user_welcome:
   selectors:

client/src/utils/upload-queue.js

@@ -1,12 +1,8 @@
 /*
     galaxy upload utilities - requires FormData and XMLHttpRequest
 */
-
-import axios from "axios";
-import { getAppRoot } from "onload/loadConfig";
-
 import { uploadPayload } from "@/utils/upload-payload.js";
-import { uploadSubmit } from "@/utils/upload-submit.js";
+import { sendPayload, uploadSubmit } from "@/utils/upload-submit.js";
 
 export class UploadQueue {
     constructor(options) {
@@ -72,29 +68,7 @@ export class UploadQueue {
     // Initiate upload process
     start(ftpBatch = false) {
         if (ftpBatch) {
-            // package ftp files separately, and remove them from queue
-            const list = [];
-            Object.entries(this.queue).forEach(([key, model]) => {
-                if (model.status === "queued" && model.fileMode === "ftp") {
-                    this.queue.remove(model.id);
-                    list.push(this.opts.get(key));
-                }
-            });
-            if (list.length > 0) {
-                const data = uploadPayload(list, this.opts.historyId);
-                axios
-                    .post(`${getAppRoot()}api/tools/fetch`, data)
-                    .then((message) => {
-                        list.forEach((model) => {
-                            this.opts.success(model.id, message);
-                        });
-                    })
-                    .catch((message) => {
-                        list.forEach((model) => {
-                            this.opts.error(model.id, message);
-                        });
-                    });
-            }
+            this._processFtp();
         }
         if (!this.isRunning) {
             this.isRunning = true;
@@ -127,6 +101,33 @@ export class UploadQueue {
         this._processSubmit(index, data);
     }
 
+    // Submit remote files as single batch request
+    _processFtp() {
+        const list = [];
+        for (const index of this.queue.keys()) {
+            const model = this.opts.get(index);
+            if (model.status === "queued" && model.fileMode === "ftp") {
+                list.push({ index, ...model });
+                this.remove(index);
+            }
+        }
+        if (list.length > 0) {
+            const data = uploadPayload(list, this.opts.historyId);
+            sendPayload(data, {
+                success: (message) => {
+                    list.forEach((model) => {
+                        this.opts.success(model.index, message);
+                    });
+                },
+                error: (message) => {
+                    list.forEach((model) => {
+                        this.opts.error(model.index, message);
+                    });
+                },
+            });
+        }
+    }
+
     // Get next item to be processed
     _processIndex() {
         return this.queue.keys().next().value;

client/src/utils/upload-submit.js

@@ -12,7 +12,7 @@ function buildFingerprint(cnf) {
     };
 }
 
-function submitPayload(payload, cnf) {
+export function sendPayload(payload, cnf) {
     axios
         .post(`${getAppRoot()}api/tools/fetch`, payload)
         .then((response) => {
@@ -31,7 +31,7 @@ function tusUpload(uploadables, index, data, tusEndpoint, cnf) {
     if (!uploadable) {
         // We've uploaded all files or blobs; delete files from data and submit fetch payload
         delete data["files"];
-        return submitPayload(data, cnf);
+        return sendPayload(data, cnf);
     }
     console.debug(`Starting chunked upload for ${uploadable.name} [chunkSize=${chunkSize}].`);
     const upload = new tus.Upload(uploadable, {
@@ -115,7 +115,7 @@ export function uploadSubmit(config) {
         if (data.targets.length && data.targets[0].elements.length) {
             const pasted = data.targets[0].elements[0];
             if (pasted.src == "url") {
-                return submitPayload(data, cnf);
+                return sendPayload(data, cnf);
             } else {
                 const blob = new Blob([pasted.paste_content]);
                 blob.name = data.targets[0].elements[0].name || "default";

test/integration_selenium/test_upload_file_sources.py

@@ -20,7 +20,7 @@ class TestPosixFileSourceSeleniumIntegration(PosixFileSourceSetup, SeleniumInteg
     def test_upload_from_posix(self):
         self.admin_login()
         self.components.upload.start.wait_for_and_click()
-        self.components.upload.ftp_add.wait_for_and_click()
+        self.components.upload.file_dialog.wait_for_and_click()
         self.components.upload.file_source_selector(path="gxfiles://posix_test").wait_for_and_click()
         self.components.upload.file_source_selector(path="gxfiles://posix_test/a").wait_for_and_click()
         self.components.upload.file_dialog_ok.wait_for_and_click()

test/integration_selenium/test_upload_ftp.py

@@ -21,15 +21,16 @@ def handle_galaxy_config_kwds(cls, config):
     def ftp_dir(cls):
         return cls.temp_config_dir("ftp")
 
-    def _upload_all(self):
+    def _upload_all(self, n):
         self.home()
         self.components.upload.start.wait_for_and_click()
-        self.components.upload.ftp_add.wait_for_and_click()
-        self.components.upload.ftp_popup.wait_for_visible()
-        for item in self.components.upload.ftp_items().all():
-            item.click()
-        self.components.upload.ftp_close.wait_for_and_click()
-        self.components.upload.row(n=0).wait_for_visible()
+        self.components.upload.file_dialog.wait_for_and_click()
+        self.components.upload.file_source_selector(path="gxftp://").wait_for_and_click()
+        for i in range(n):
+            self.components.upload.file_source_selector(path="gxftp://%i.txt" % i).wait_for_and_click()
+        self.components.upload.file_dialog_ok.wait_for_and_click()
+        for i in range(n):
+            self.components.upload.row(n=i).wait_for_visible()
         self.upload_start()
         self.sleep_for(self.wait_types.UX_RENDER)
         self.wait_for_history()
@@ -43,18 +44,18 @@ def _create_ftp_dir(self):
     @selenium_test
     def test_upload_simplest(self):
         user_ftp_dir = self._create_ftp_dir()
-        file_path = os.path.join(user_ftp_dir, "1.txt")
+        file_path = os.path.join(user_ftp_dir, "0.txt")
         with open(file_path, "w") as f:
             f.write("Hello World!")
-        self._upload_all()
+        self._upload_all(1)
 
     @selenium_test
     def test_upload_multiple(self):
         user_ftp_dir = self._create_ftp_dir()
-        file_path = os.path.join(user_ftp_dir, "1.txt")
+        file_path = os.path.join(user_ftp_dir, "0.txt")
         with open(file_path, "w") as f:
             f.write("Hello World!")
-        file_path = os.path.join(user_ftp_dir, "2.txt")
+        file_path = os.path.join(user_ftp_dir, "1.txt")
         with open(file_path, "w") as f:
             f.write("Hello Galaxy!")
-        self._upload_all()
+        self._upload_all(2)