From c633b981a8b1d4adb39aa922413ec52a3784e073 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Mon, 12 Dec 2022 16:00:54 +0100
Subject: [PATCH 1/5] convert datatypes to typescript

---
 .../AvailableDatatypes/AvailableDatatypes.vue |  4 +-
 client/src/composables/datatypes.js           | 51 --------------
 client/src/composables/datatypes.ts           | 70 +++++++++++++++++++
 3 files changed, 72 insertions(+), 53 deletions(-)
 delete mode 100644 client/src/composables/datatypes.js
 create mode 100644 client/src/composables/datatypes.ts

diff --git a/client/src/components/AvailableDatatypes/AvailableDatatypes.vue b/client/src/components/AvailableDatatypes/AvailableDatatypes.vue
index 079f9795680..96b6d6b286a 100644
--- a/client/src/components/AvailableDatatypes/AvailableDatatypes.vue
+++ b/client/src/components/AvailableDatatypes/AvailableDatatypes.vue
@@ -1,11 +1,11 @@
 <script setup lang="ts">
 import { ref } from "vue";
-import { useDetailedDatatypes } from "composables/datatypes";
+import { useDetailedDatatypes, type DetailedDatatypes } from "composables/datatypes";
 import { useFilterObjectArray } from "composables/utils/filter";
 import DelayedInput from "components/Common/DelayedInput.vue";
 
 const filter = ref("");
-const filterFields = ["extension"];
+const filterFields: Array<keyof DetailedDatatypes> = ["extension"];
 
 const { datatypes } = useDetailedDatatypes();
 const filteredDatatypes = useFilterObjectArray(datatypes, filter, filterFields);
diff --git a/client/src/composables/datatypes.js b/client/src/composables/datatypes.js
deleted file mode 100644
index 15aa61ce8cd..00000000000
--- a/client/src/composables/datatypes.js
+++ /dev/null
@@ -1,51 +0,0 @@
-import { ref } from "vue";
-import axios from "axios";
-import { getAppRoot } from "onload/loadConfig";
-
-/**
- * Fetches a detailed array of datatypes available on this galaxy instance.
- * Does not cache the result or use a store.
- */
-export function useDetailedDatatypes() {
-    const datatypesLoading = ref(true);
-    const datatypes = ref([]);
-
-    async function getDatatypes() {
-        try {
-            const datatypesPromise = axios.get(`${getAppRoot()}api/datatypes?extension_only=false`);
-            const datatypeEDAMFormatsPromise = axios.get(`${getAppRoot()}api/datatypes/edam_formats/detailed`);
-            const datatypeEDAMDataPromise = axios.get(`${getAppRoot()}api/datatypes/edam_data/detailed`);
-
-            const [baseTypes, datatypeEDAMFormats, datatypeEDAMData] = await Promise.all([
-                datatypesPromise,
-                datatypeEDAMFormatsPromise,
-                datatypeEDAMDataPromise,
-            ]);
-
-            datatypes.value = baseTypes.data.map((type, i) => {
-                const typeEDAMFormat = datatypeEDAMFormats.data[type.extension] ?? null;
-                const typeEDAMData = datatypeEDAMData.data[type.extension] ?? null;
-
-                return {
-                    extension: type.extension,
-                    description: type.description,
-                    descriptionUrl: type.description_url,
-                    edamFormat: typeEDAMFormat.prefix_IRI,
-                    edamFormatLabel: typeEDAMFormat.label,
-                    edamFormatDefinition: typeEDAMFormat.definition,
-                    edamData: typeEDAMData.prefix_IRI,
-                    edamDataLabel: typeEDAMData.label,
-                    edamDataDefinition: typeEDAMData.definition,
-                };
-            });
-        } catch (e) {
-            console.error("unable to fetch available datatypes\n", e);
-        } finally {
-            datatypesLoading.value = false;
-        }
-    }
-
-    getDatatypes();
-
-    return { datatypes, datatypesLoading };
-}
diff --git a/client/src/composables/datatypes.ts b/client/src/composables/datatypes.ts
new file mode 100644
index 00000000000..6140f55c12e
--- /dev/null
+++ b/client/src/composables/datatypes.ts
@@ -0,0 +1,70 @@
+import { ref } from "vue";
+import { fetcher } from "schema";
+
+import type { Ref } from "vue";
+
+const datatypesFetcher = fetcher.path("/api/datatypes").method("get").create();
+const edamFormatsFetcher = fetcher.path("/api/datatypes/edam_formats/detailed").method("get").create();
+const edamDataFetcher = fetcher.path("/api/datatypes/edam_data/detailed").method("get").create();
+
+export interface DetailedDatatypes {
+    extension: string;
+    description?: string;
+    descriptionUrl?: string;
+    edamFormat?: string;
+    edamFormatLabel?: string;
+    edamFormatDefinition?: string;
+    edamData?: string;
+    edamDataLabel?: string;
+    edamDataDefinition?: string;
+}
+
+/**
+ * Fetches a detailed array of datatypes available on this galaxy instance.
+ * Does not cache the result or use a store.
+ */
+export function useDetailedDatatypes() {
+    const datatypesLoading = ref(true);
+    const datatypes: Ref<DetailedDatatypes[]> = ref([]);
+
+    async function getDatatypes() {
+        try {
+            const datatypesPromise = datatypesFetcher({ extension_only: true });
+            const datatypeEDAMFormatsPromise = edamFormatsFetcher({});
+            const datatypeEDAMDataPromise = edamDataFetcher({});
+
+            const [baseTypes, datatypeEDAMFormats, datatypeEDAMData] = await Promise.all([
+                datatypesPromise,
+                datatypeEDAMFormatsPromise,
+                datatypeEDAMDataPromise,
+            ]);
+
+            type BaseTypes = Exclude<typeof baseTypes.data, string[]>;
+
+            datatypes.value = (baseTypes.data as BaseTypes).map((type) => {
+                const typeEDAMFormat = datatypeEDAMFormats.data[type.extension] ?? null;
+                const typeEDAMData = datatypeEDAMData.data[type.extension] ?? null;
+
+                return {
+                    extension: type.extension,
+                    description: type.description,
+                    descriptionUrl: type.description_url,
+                    edamFormat: typeEDAMFormat?.prefix_IRI,
+                    edamFormatLabel: typeEDAMFormat?.label,
+                    edamFormatDefinition: typeEDAMFormat?.definition,
+                    edamData: typeEDAMData?.prefix_IRI,
+                    edamDataLabel: typeEDAMData?.label,
+                    edamDataDefinition: typeEDAMData?.definition,
+                };
+            });
+        } catch (e) {
+            console.error("unable to fetch available datatypes\n", e);
+        } finally {
+            datatypesLoading.value = false;
+        }
+    }
+
+    getDatatypes();
+
+    return { datatypes, datatypesLoading };
+}

From f2f3a84c5f558e9dbf234d30b7f0224097b8a987 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Mon, 12 Dec 2022 16:13:03 +0100
Subject: [PATCH 2/5] fix tsconfig name

---
 tsconfig.js => tsconfig.json | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename tsconfig.js => tsconfig.json (100%)

diff --git a/tsconfig.js b/tsconfig.json
similarity index 100%
rename from tsconfig.js
rename to tsconfig.json

From d1d31d9523009eecccaa66c511093c6e12120b73 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Mon, 12 Dec 2022 16:31:11 +0100
Subject: [PATCH 3/5] convert toast composable to ts

---
 client/src/composables/toast.js | 34 ----------------------------
 client/src/composables/toast.ts | 39 +++++++++++++++++++++++++++++++++
 2 files changed, 39 insertions(+), 34 deletions(-)
 delete mode 100644 client/src/composables/toast.js
 create mode 100644 client/src/composables/toast.ts

diff --git a/client/src/composables/toast.js b/client/src/composables/toast.js
deleted file mode 100644
index 0f19ef6a240..00000000000
--- a/client/src/composables/toast.js
+++ /dev/null
@@ -1,34 +0,0 @@
-import { ref } from "vue";
-
-let toastRef = ref(null);
-
-export const setToastComponentRef = (newRef) => {
-    // eslint-disable-next-line vue/no-ref-as-operand
-    toastRef = newRef;
-};
-
-/**
- * Direct export to simplify usage in Options Api component.
- * Use 'useToast' for the Composition Api instead.
- */
-export const Toast = {
-    success(message, title = "Success") {
-        toastRef.value.showToast(message, title, "success");
-    },
-
-    info(message, title = "Info") {
-        toastRef.value.showToast(message, title, "info");
-    },
-
-    warning(message, title = "Warning") {
-        toastRef.value.showToast(message, title, "warning");
-    },
-
-    error(message, title = "Error") {
-        toastRef.value.showToast(message, title, "error");
-    },
-};
-
-export function useToast() {
-    return { ...Toast };
-}
diff --git a/client/src/composables/toast.ts b/client/src/composables/toast.ts
new file mode 100644
index 00000000000..7ebb50cd8fc
--- /dev/null
+++ b/client/src/composables/toast.ts
@@ -0,0 +1,39 @@
+import { ref, type Ref } from "vue";
+
+import type Vue from "vue";
+import type ToastComponentFile from "components/Toast";
+
+export type ToastComponent = Vue & typeof ToastComponentFile.methods;
+
+let toastRef: Ref<ToastComponent | null> = ref(null);
+
+export const setToastComponentRef = (newRef: typeof toastRef) => {
+    // eslint-disable-next-line vue/no-ref-as-operand
+    toastRef = newRef;
+};
+
+/**
+ * Direct export to simplify usage in Options Api component.
+ * Use 'useToast' for the Composition Api instead.
+ */
+export const Toast = {
+    success(message: string, title = "Success") {
+        toastRef.value?.showToast(message, title, "success");
+    },
+
+    info(message: string, title = "Info") {
+        toastRef.value?.showToast(message, title, "info");
+    },
+
+    warning(message: string, title = "Warning") {
+        toastRef.value?.showToast(message, title, "warning");
+    },
+
+    error(message: string, title = "Error") {
+        toastRef.value?.showToast(message, title, "error");
+    },
+};
+
+export function useToast() {
+    return { ...Toast };
+}

From 0dad02fbdb65e575b3d0372d331b2b91256a839f Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Mon, 12 Dec 2022 17:03:14 +0100
Subject: [PATCH 4/5] convert FormElement to ts

---
 client/src/components/Form/FormElement.vue    | 175 +++++++-----------
 .../src/components/Form/parameterTypes.d.ts   |  30 +++
 2 files changed, 100 insertions(+), 105 deletions(-)
 create mode 100644 client/src/components/Form/parameterTypes.d.ts

diff --git a/client/src/components/Form/FormElement.vue b/client/src/components/Form/FormElement.vue
index 85a1a78ddd2..8a686211162 100644
--- a/client/src/components/Form/FormElement.vue
+++ b/client/src/components/Form/FormElement.vue
@@ -1,95 +1,66 @@
-<script setup>
-import FormBoolean from "./Elements/FormBoolean";
-import FormHidden from "./Elements/FormHidden";
-import FormInput from "./Elements/FormInput";
-import FormParameter from "./Elements/FormParameter";
-import FormSelection from "./Elements/FormSelection";
-import FormColor from "./Elements/FormColor";
-import FormDirectory from "./Elements/FormDirectory";
-import FormNumber from "./Elements/FormNumber";
-import FormRulesEdit from "./Elements/FormRulesEdit";
+<script setup lang="ts">
+import FormBoolean from "./Elements/FormBoolean.vue";
+import FormHidden from "./Elements/FormHidden.vue";
+import FormInput from "./Elements/FormInput.vue";
+import FormParameter from "./Elements/FormParameter.vue";
+import FormSelection from "./Elements/FormSelection.vue";
+import FormColor from "./Elements/FormColor.vue";
+import FormDirectory from "./Elements/FormDirectory.vue";
+import FormNumber from "./Elements/FormNumber.vue";
+import FormRulesEdit from "./Elements/FormRulesEdit.vue";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { ref, computed, useAttrs } from "vue";
+import { library } from "@fortawesome/fontawesome-svg-core";
+import { faExclamation, faTimes, faArrowsAltH } from "@fortawesome/free-solid-svg-icons";
+import { faCaretSquareDown, faCaretSquareUp } from "@fortawesome/free-regular-svg-icons";
 
-const props = defineProps({
-    id: {
-        type: String,
-        default: "identifier",
-    },
-    type: {
-        type: String,
-        default: null,
-    },
-    value: {
-        default: null,
-    },
-    title: {
-        type: String,
-        default: null,
-    },
-    refreshOnChange: {
-        type: Boolean,
-        default: false,
-    },
-    help: {
-        type: String,
-        default: null,
-    },
-    error: {
-        type: String,
-        default: null,
-    },
-    backbonejs: {
-        type: Boolean,
-        default: false,
-    },
-    disabled: {
-        type: Boolean,
-        default: false,
-    },
-    attributes: {
-        type: Object,
-        default: null,
-    },
-    collapsedEnableText: {
-        type: String,
-        default: "Enable",
-    },
-    collapsedDisableText: {
-        type: String,
-        default: "Disable",
-    },
-    collapsedEnableIcon: {
-        type: String,
-        default: "far fa-caret-square-down",
-    },
-    collapsedDisableIcon: {
-        type: String,
-        default: "far fa-caret-square-up",
-    },
-    connectedEnableText: {
-        type: String,
-        default: "Remove connection from module.",
-    },
-    connectedDisableText: {
-        type: String,
-        default: "Add connection to module.",
-    },
-    connectedEnableIcon: {
-        type: String,
-        default: "fa fa-times",
-    },
-    connectedDisableIcon: {
-        type: String,
-        default: "fa fa-arrows-alt-h",
-    },
-    workflowBuildingMode: {
-        type: Boolean,
-        default: false,
-    },
+import type { ComputedRef } from "vue";
+import type { FormParameterTypes, FormParameterAttributes, FormParameterValue } from "./parameterTypes";
+
+export interface FormElementProps {
+    id?: string;
+    type?: FormParameterTypes;
+    value?: FormParameterValue;
+    title?: string;
+    refreshOnChange?: boolean;
+    help?: string;
+    error?: string;
+    backbonejs?: boolean;
+    attributes?: FormParameterAttributes;
+    collapsedEnableText?: string;
+    collapsedDisableText?: string;
+    collapsedEnableIcon?: string;
+    collapsedDisableIcon?: string;
+    connectedEnableText?: string;
+    connectedDisableText?: string;
+    connectedEnableIcon?: string;
+    connectedDisableIcon?: string;
+    workflowBuildingMode?: boolean;
+}
+
+const props = withDefaults(defineProps<FormElementProps>(), {
+    id: "identifier",
+    refreshOnChange: false,
+    backbonejs: false,
+    disabled: false,
+    collapsedEnableText: "Enable",
+    collapsedDisableText: "Disable",
+    collapsedEnableIcon: "far fa-caret-square-down",
+    collapsedDisableIcon: "far fa-caret-square-up",
+    connectedEnableText: "Remove connection from module.",
+    connectedDisableText: "Add connection to module.",
+    connectedEnableIcon: "fa fa-times",
+    connectedDisableIcon: "fa fa-arrows-alt-h",
+    workflowBuildingMode: false,
 });
 
-const emit = defineEmits(["input", "change"]);
+const emit = defineEmits<{
+    (e: "input", value: FormParameterValue, id: string): void;
+    (e: "change", shouldRefresh: boolean): void;
+}>();
+
+//@ts-ignore bad library types
+library.add(faExclamation, faTimes, faArrowsAltH, faCaretSquareDown, faCaretSquareUp);
 
 /** TODO: remove attrs computed.
  useAttrs is *not* reactive, and does not play nice with type safety.
@@ -97,15 +68,15 @@ const emit = defineEmits(["input", "change"]);
  but should be removed as soon as that component is removed.
  */
 const attrs = computed(() => props.attributes || useAttrs());
-const collapsibleValue = computed(() => attrs.value["collapsible_value"]);
-const defaultValue = computed(() => attrs.value["default_value"]);
-const connectedValue = { __class__: "ConnectedValue" };
+const collapsibleValue: ComputedRef<FormParameterValue> = computed(() => attrs.value["collapsible_value"]);
+const defaultValue: ComputedRef<FormParameterValue> = computed(() => attrs.value["default_value"]);
+const connectedValue: FormParameterValue = { __class__: "ConnectedValue" };
 
 const connected = ref(false);
 const collapsed = ref(false);
 
 const collapsible = computed(() => !props.disabled && collapsibleValue.value !== undefined);
-const connectable = computed(() => collapsible.value && attrs.value["connectable"]);
+const connectable = computed(() => collapsible.value && Boolean(attrs.value["connectable"]));
 
 // Determines to wether expand or collapse the input
 {
@@ -118,7 +89,7 @@ const connectable = computed(() => collapsible.value && attrs.value["connectable
 }
 
 /** Submits a changed value. */
-function setValue(value) {
+function setValue(value: FormParameterValue) {
     emit("input", value, props.id);
     emit("change", props.refreshOnChange);
 }
@@ -154,7 +125,7 @@ const showField = computed(() => !collapsed.value && !props.disabled);
 const previewText = computed(() => attrs.value["text_value"]);
 const helpText = computed(() => {
     const helpArgument = attrs.value["argument"];
-    if (helpArgument && !props.help.includes(`(${helpArgument})`)) {
+    if (helpArgument && !props.help?.includes(`(${helpArgument})`)) {
         return `${props.help} (${helpArgument})`;
     } else {
         return props.help;
@@ -171,7 +142,9 @@ const currentValue = computed({
 });
 
 const isHiddenType = computed(
-    () => ["hidden", "hidden_data", "baseurl"].includes(props.type) || (props.attributes && props.attributes.titleonly)
+    () =>
+        ["hidden", "hidden_data", "baseurl"].includes(props.type ?? "") ||
+        (props.attributes && props.attributes.titleonly)
 );
 
 const collapseText = computed(() => (collapsed.value ? props.collapsedEnableText : props.collapsedDisableText));
@@ -182,7 +155,7 @@ const isEmpty = computed(() => {
         return true;
     }
 
-    if (["text", "integer", "float", "password"].includes(props.type) && currentValue.value === "") {
+    if (["text", "integer", "float", "password"].includes(props.type ?? "") && currentValue.value === "") {
         return true;
     }
 
@@ -194,14 +167,6 @@ const isRequiredType = computed(() => props.type !== "boolean");
 const isOptional = computed(() => !isRequired.value && attrs.value["optional"] !== undefined);
 </script>
 
-<script>
-import { library } from "@fortawesome/fontawesome-svg-core";
-import { faExclamation, faTimes, faArrowsAltH } from "@fortawesome/free-solid-svg-icons";
-import { faCaretSquareDown, faCaretSquareUp } from "@fortawesome/free-regular-svg-icons";
-
-library.add(faExclamation, faTimes, faArrowsAltH, faCaretSquareDown, faCaretSquareUp);
-</script>
-
 <template>
     <div
         v-show="!isHidden"
@@ -258,7 +223,7 @@ library.add(faExclamation, faTimes, faArrowsAltH, faCaretSquareDown, faCaretSqua
                 v-model="currentValue"
                 :max="attrs.max"
                 :min="attrs.min"
-                :type="type"
+                :type="props.type ?? 'float'"
                 :workflow-building-mode="workflowBuildingMode" />
             <FormSelection
                 v-else-if="props.type == 'select' && attrs.display == 'radio'"
@@ -277,7 +242,7 @@ library.add(faExclamation, faTimes, faArrowsAltH, faCaretSquareDown, faCaretSqua
                 :id="props.id"
                 v-model="currentValue"
                 :data-label="props.title"
-                :type="props.type"
+                :type="props.type ?? 'text'"
                 :attributes="attrs" />
             <FormInput v-else :id="props.id" v-model="currentValue" :area="attrs['area']" />
         </div>
diff --git a/client/src/components/Form/parameterTypes.d.ts b/client/src/components/Form/parameterTypes.d.ts
new file mode 100644
index 00000000000..e3c7ca53574
--- /dev/null
+++ b/client/src/components/Form/parameterTypes.d.ts
@@ -0,0 +1,30 @@
+// TODO: stricter types
+export type FormParameterValue = any;
+export type FormParameterAttributes = {
+    [attribute: string]: any;
+};
+
+export type FormParameterTypes =
+    | "boolean"
+    | "hidden"
+    | "hidden_data"
+    | "baseurl"
+    | "integer"
+    | "float"
+    | "radio"
+    | "color"
+    | "directory_uri"
+    | "text"
+    | "password"
+    | "select"
+    | "data_column"
+    | "genomebuild"
+    | "data"
+    | "data_collection"
+    | "drill_down"
+    | "group_tag"
+    | "library_data"
+    | "ftpfile"
+    | "upload"
+    | "rules"
+    | "data_dialog";

From 07a9927cd769449843ceffce58896658e4e3b627 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Mon, 12 Dec 2022 17:08:35 +0100
Subject: [PATCH 5/5] fix missing typedef

---
 client/src/components/Form/FormElement.vue | 1 +
 1 file changed, 1 insertion(+)

diff --git a/client/src/components/Form/FormElement.vue b/client/src/components/Form/FormElement.vue
index 8a686211162..c353530abb4 100644
--- a/client/src/components/Form/FormElement.vue
+++ b/client/src/components/Form/FormElement.vue
@@ -26,6 +26,7 @@ export interface FormElementProps {
     help?: string;
     error?: string;
     backbonejs?: boolean;
+    disabled?: boolean;
     attributes?: FormParameterAttributes;
     collapsedEnableText?: string;
     collapsedDisableText?: string;