Don't allow checking deferred for local files.

Author: jmchilton

client/src/components/Upload/DefaultBox.vue

@@ -144,13 +144,19 @@ function addFileFromInput(eventTarget: EventTarget | null) {
 /** A new file has been announced to the upload queue */
 function eventAnnounce(index: string, file: UploadFile) {
     counterAnnounce.value++;
+    const mode = file.mode || "local";
+    let deferred: boolean | undefined = false;
+    if (mode === "local") {
+        deferred = undefined;
+    }
     const uploadModel = {
         ...defaultModel,
         id: index,
         dbKey: dbKey.value,
         extension: extension.value,
         fileData: file,
-        fileMode: file.mode || "local",
+        fileMode: mode,
+        deferred: deferred,
         fileName: file.name,
         filePath: file.path,
         fileSize: file.size,

client/src/components/Upload/DefaultRow.vue

@@ -25,7 +25,7 @@ const { isAnonymous } = storeToRefs(useUserStore());
 const fileField: Ref<HTMLInputElement | null> = ref(null);
 
 interface Props {
-    deferred?: boolean;
+    deferred?: boolean | undefined;
     extension: string;
     fileContent: string;
     fileMode: string;
@@ -44,7 +44,7 @@ interface Props {
 }
 
 const props = withDefaults(defineProps<Props>(), {
-    deferred: false,
+    deferred: undefined,
     info: "",
     listDbKeys: undefined,
     listExtensions: undefined,

client/src/components/Upload/UploadSettings.vue

@@ -11,7 +11,7 @@ library.add(faCog);
 defineProps({
     deferred: {
         type: Boolean,
-        default: null,
+        default: undefined,
     },
     disabled: {
         type: Boolean,
@@ -49,7 +49,7 @@ const emit = defineEmits(["input"]);
                         :value="toPosixLines"
                         @click="emit('input', 'toPosixLines')" />
                     <UploadOption
-                        v-if="deferred !== null"
+                        v-if="deferred !== undefined"
                         class="upload-deferred"
                         title="Defer dataset resolution"
                         :value="deferred"

client/src/components/Upload/model.ts

@@ -22,7 +22,7 @@ export interface FileStream {
 
 export interface UploadItem {
     dbKey: string;
-    deferred: boolean;
+    deferred?: boolean | undefined;
     enabled: boolean;
     extension: string;
     fileContent: string;

client/src/utils/upload-payload.js

@@ -43,7 +43,6 @@ export function uploadPayload(items, historyId, composite = false) {
                     name: fileName,
                     space_to_tab: item.spaceToTab,
                     to_posix_lines: item.toPosixLines,
-                    deferred: item.deferred,
                 };
                 // match file mode
                 switch (item.fileMode) {
@@ -59,13 +58,19 @@ export function uploadPayload(items, historyId, composite = false) {
                                     return {
                                         src: "url",
                                         url: urlTrim,
+                                        deferred: item.deferred,
                                         ...elem,
                                     };
                                 } else {
                                     throw new Error(`Invalid url: ${urlTrim}`);
                                 }
                             });
                         } else {
+                            // The researcher may have checked the deferred option and we don't know
+                            // that until here and we cannot make pasted content deferred. Idealy we would
+                            // have some sort of warning here but I don't want to import Toaster in this
+                            // utility function. This stems from the same comment above from Sam about this being
+                            // uncomfortable magic. -John
                             return {
                                 src: "pasted",
                                 paste_content: item.fileContent,
@@ -77,6 +82,7 @@ export function uploadPayload(items, historyId, composite = false) {
                             return {
                                 src: "url",
                                 url: urlContent,
+                                deferred: item.deferred,
                                 ...elem,
                             };
                         } else {

client/src/utils/upload-payload.test.js

@@ -32,7 +32,6 @@ describe("uploadPayload", () => {
                 { fileContent: " fileContent ", fileMode: "new", fileName: "1" },
                 {
                     dbKey: "dbKey2",
-                    deferred: true,
                     extension: "extension2",
                     fileData: { size: 1 },
                     fileMode: "local",
@@ -62,7 +61,6 @@ describe("uploadPayload", () => {
                 },
                 {
                     dbKey: "dbKey5",
-                    deferred: true,
                     extension: "extension5",
                     fileData: { size: 1 },
                     fileMode: "local",
@@ -83,7 +81,6 @@ describe("uploadPayload", () => {
                     elements: [
                         {
                             dbkey: "?",
-                            deferred: undefined,
                             ext: "auto",
                             name: "1",
                             paste_content: " fileContent ",
@@ -93,7 +90,6 @@ describe("uploadPayload", () => {
                         },
                         {
                             dbkey: "dbKey2",
-                            deferred: true,
                             ext: "extension2",
                             name: "2",
                             space_to_tab: true,
@@ -132,7 +128,6 @@ describe("uploadPayload", () => {
                         },
                         {
                             dbkey: "dbKey5",
-                            deferred: true,
                             ext: "extension5",
                             name: "PreviousGalaxyFile",
                             space_to_tab: true,
@@ -151,7 +146,6 @@ describe("uploadPayload", () => {
                 { fileContent: "fileContent", fileMode: "new", fileName: "1" },
                 {
                     dbKey: "dbKey",
-                    deferred: true,
                     extension: "extension",
                     fileContent: "fileContent",
                     fileData: "fileData",
@@ -162,7 +156,6 @@ describe("uploadPayload", () => {
                 },
                 {
                     dbKey: "dbKey2",
-                    deferred: true,
                     extension: "extension2",
                     fileContent: "fileContent",
                     fileData: "fileData",
@@ -188,7 +181,6 @@ describe("uploadPayload", () => {
                                 items: [
                                     {
                                         dbkey: "?",
-                                        deferred: undefined,
                                         ext: "auto",
                                         name: "1",
                                         paste_content: "fileContent",
@@ -198,7 +190,6 @@ describe("uploadPayload", () => {
                                     },
                                     {
                                         dbkey: "dbKey",
-                                        deferred: true,
                                         ext: "extension",
                                         name: "2",
                                         space_to_tab: true,
@@ -207,7 +198,6 @@ describe("uploadPayload", () => {
                                     },
                                     {
                                         dbkey: "dbKey2",
-                                        deferred: true,
                                         ext: "extension2",
                                         name: "PreviousGalaxyFile",
                                         space_to_tab: true,