diff --git a/src/components/parameter-schema/ParameterSchemaFormComponent.vue b/src/components/parameter-schema/ParameterSchemaFormComponent.vue
index e7e5232af42607426b973700113e0c5ba6eb6b77..b80fd1eb59bcedf639a898f81065ad497ae78be6 100644
--- a/src/components/parameter-schema/ParameterSchemaFormComponent.vue
+++ b/src/components/parameter-schema/ParameterSchemaFormComponent.vue
@@ -2,38 +2,95 @@
import { computed, ref, reactive, watch, onMounted } from "vue";
import ParameterGroupForm from "@/components/parameter-schema/form-mode/ParameterGroupForm.vue";
import FontAwesomeIcon from "@/components/FontAwesomeIcon.vue";
+import { WorkflowExecutionService } from "@/client/workflow";
+import type { ApiError } from "@/client/workflow";
import Ajv from "ajv";
import type { ValidateFunction } from "ajv";
+import ParameterStringInput from "@/components/parameter-schema/form-mode/ParameterStringInput.vue";
+import { Toast } from "bootstrap";
-const launchForm = ref<HTMLFormElement | null>(null);
-const schemaCompiler = new Ajv({
- strict: false,
-});
-
-let validateSchema: ValidateFunction;
-
+// Props
+// =============================================================================
const props = defineProps({
schema: {
type: Object,
required: true,
},
+ workflowVersionId: {
+ type: String,
+ required: true,
+ },
});
+// Bootstrap Elements
+// =============================================================================
+let errorToast: Toast | null = null;
+
+// Types
+// =============================================================================
type ParameterGroup = {
group: string;
title: string;
icon?: string;
};
+// JSON Schema package
+// =============================================================================
+const schemaCompiler = new Ajv({
+ strict: false,
+});
+
+let validateSchema: ValidateFunction;
+
+// Reactive State
+// =============================================================================
+const launchForm = ref<HTMLFormElement | null>(null);
+
const formState = reactive<{
// eslint-disable-next-line @typescript-eslint/no-explicit-any
formInput: Record<string, any>;
validated: boolean;
+ pipelineNotes: string;
+ report_bucket?: string;
+ loading: boolean;
+ errorType?: string;
}>({
formInput: {},
validated: false,
+ pipelineNotes: "",
+ report_bucket: undefined,
+ loading: false,
+ errorType: undefined,
});
+// Computed Properties
+// =============================================================================
+const parameterGroups = computed<Record<string, never>>(
+ () => props.schema["definitions"]
+);
+
+// Create a list with the names of all parameter groups
+const navParameterGroups = computed<ParameterGroup[]>(() =>
+ Object.keys(parameterGroups.value)
+ .map((group) => {
+ return {
+ group: group,
+ title: parameterGroups.value[group]["title"],
+ icon: parameterGroups.value[group]["fa_icon"],
+ };
+ })
+ .filter(
+ // filter all groups that have only hidden parameters
+ (group) =>
+ Object.keys(parameterGroups.value[group.group]["properties"]).filter(
+ (key) =>
+ !parameterGroups.value[group.group]["properties"][key]["hidden"]
+ ).length > 0
+ )
+);
+
+// Watchers
+// =============================================================================
watch(
() => props.schema,
(newValue) => {
@@ -41,6 +98,8 @@ watch(
}
);
+// Functions
+// =============================================================================
/* eslint-disable @typescript-eslint/no-explicit-any, @typescript-eslint/ban-ts-comment, @typescript-eslint/no-unused-vars */
function updateSchema(schema: Record<string, any>) {
validateSchema = schemaCompiler.compile(props.schema);
@@ -61,33 +120,6 @@ function updateSchema(schema: Record<string, any>) {
}
/* eslint-disable @typescript-eslint/no-explicit-any, @typescript-eslint/ban-ts-comment, @typescript-eslint/no-unused-vars */
-onMounted(() => {
- updateSchema(props.schema);
-});
-
-const parameterGroups = computed<Record<string, never>>(
- () => props.schema["definitions"]
-);
-
-const navParameterGroups = computed<ParameterGroup[]>(() =>
- Object.keys(parameterGroups.value)
- .map((group) => {
- return {
- group: group,
- title: parameterGroups.value[group]["title"],
- icon: parameterGroups.value[group]["fa_icon"],
- };
- })
- .filter(
- // filter all groups that have only hidden parameters
- (group) =>
- Object.keys(parameterGroups.value[group.group]["properties"]).filter(
- (key) =>
- !parameterGroups.value[group.group]["properties"][key]["hidden"]
- ).length > 0
- )
-);
-
function startWorkflow() {
formState.validated = true;
if (launchForm.value?.checkValidity()) {
@@ -96,15 +128,70 @@ function startWorkflow() {
});
const schemaValid = validateSchema(realInput);
- console.log(realInput);
- if (!schemaValid) console.log(validateSchema.errors);
- } else {
- console.log("invalid");
+ if (!schemaValid) {
+ console.error(validateSchema.errors);
+ errorToast?.show();
+ } else {
+ formState.errorType = undefined;
+ formState.loading = true;
+ WorkflowExecutionService.workflowExecutionStartWorkflow({
+ workflow_version_id: props.workflowVersionId,
+ parameters: realInput,
+ notes: formState.pipelineNotes,
+ report_output_bucket: formState.report_bucket,
+ })
+ .then(() => {
+ console.log("Started Workflow");
+ })
+ .catch((err: ApiError) => {
+ console.error(err);
+ if (err.body["detail"].includes("workflow execution limit")) {
+ formState.errorType = "limit";
+ }
+ errorToast?.show();
+ })
+ .finally(() => {
+ formState.loading = false;
+ });
+ }
}
}
+
+// Lifecycle Events
+// =============================================================================
+onMounted(() => {
+ updateSchema(props.schema);
+ errorToast = new Toast("#workflowExecutionErrorToast");
+});
</script>
<template>
+ <div class="toast-container position-fixed top-toast end-0 p-3">
+ <div
+ role="alert"
+ aria-live="assertive"
+ aria-atomic="true"
+ class="toast text-bg-danger align-items-center border-0"
+ data-bs-autohide="true"
+ id="workflowExecutionErrorToast"
+ >
+ <div class="d-flex p-2">
+ <div v-if="formState.errorType === 'limit'" class="toast-body">
+ You have too many active workflow executions to start a new one
+ </div>
+ <div v-else>
+ There was an error with starting the workflow execution. Look in the
+ console for more information
+ </div>
+ <button
+ type="button"
+ class="btn-close btn-close-white m-auto"
+ data-bs-dismiss="toast"
+ aria-label="Close"
+ ></button>
+ </div>
+ </div>
+ </div>
<div class="row mb-5 align-items-start">
<form
class="col-9"
@@ -112,7 +199,56 @@ function startWorkflow() {
ref="launchForm"
:class="{ 'was-validated': formState.validated }"
>
- <div v-for="(group, groupName) in parameterGroups" :key="groupName">
+ <div class="card bg-dark mb-3">
+ <h2 class="card-header" id="pipelineGeneralOptions">
+ <font-awesome-icon icon="fa-solid fa-gear" class="me-2" />
+ Pipeline Options
+ </h2>
+ <div class="card-body">
+ <h5 class="card-title">
+ General Options about the pipeline execution
+ </h5>
+ <div class="input-group">
+ <span class="input-group-text" id="pipelineNotes">
+ <font-awesome-icon
+ class="me-2 text-dark"
+ icon="fa-solid fa-sticky-note"
+ />
+ <code>--notes</code>
+ </span>
+ <textarea
+ class="form-control"
+ rows="2"
+ v-model="formState.pipelineNotes"
+ />
+ </div>
+ <label class="mb-3"
+ >Personal notes about the pipeline execution</label
+ >
+ <div class="input-group">
+ <span class="input-group-text" id="pipelineNotes">
+ <font-awesome-icon
+ class="me-2 text-dark"
+ icon="fa-solid fa-sticky-note"
+ />
+ <code>--report_output_bucket</code>
+ </span>
+ <parameter-string-input
+ parameter-name="report_output_bucket"
+ v-model="formState.report_bucket"
+ :parameter="{
+ format: 'directory-path',
+ type: 'string',
+ }"
+ />
+ </div>
+ <label class="mb-3">
+ Directory in bucket where to save the Nextflow report about the
+ pipeline execution
+ </label>
+ </div>
+ </div>
+ <template v-for="(group, groupName) in parameterGroups" :key="groupName">
<parameter-group-form
:modelValue="formState.formInput[groupName]"
@update:model-value="
@@ -122,25 +258,42 @@ function startWorkflow() {
:parameter-group-name="groupName"
:parameter-group="group"
/>
- </div>
+ </template>
</form>
<div
class="col-3 sticky-top bg-dark rounded-1 px-0"
style="top: 70px !important; max-height: calc(100vh - 150px)"
>
- <div class="d-grid gap-2 col-6">
+ <div class="d-flex pt-2">
<button
type="submit"
form="launchWorkflowForm"
@click.prevent="startWorkflow"
- class="btn btn-success"
+ class="btn btn-success w-50 mx-2"
+ :disabled="formState.loading"
>
+ <font-awesome-icon icon="fa-solid fa-rocket" class="me-2" />
Launch
</button>
+ <router-link
+ role="button"
+ class="btn btn-success w-50 mx-2"
+ target="_blank"
+ :to="{ name: 'buckets' }"
+ >
+ <font-awesome-icon icon="fa-solid fa-upload" class="me-2" />
+ Upload files
+ </router-link>
</div>
<nav class="h-100">
<nav class="nav">
<ul class="ps-0">
+ <li class="nav-link">
+ <a href="#pipelineGeneralOptions"
+ ><font-awesome-icon icon="fa-solid fa-gear" class="me-2" />
+ General Pipeline Options
+ </a>
+ </li>
<li
class="nav-link"
v-for="group in navParameterGroups"
diff --git a/src/components/parameter-schema/form-mode/ParameterGroupForm.vue b/src/components/parameter-schema/form-mode/ParameterGroupForm.vue
index 3043606ade85c4c241b45ad151de2e0545f668b8..c68eb662a236b5fbaf1583530267492f189cb7ed 100644
--- a/src/components/parameter-schema/form-mode/ParameterGroupForm.vue
+++ b/src/components/parameter-schema/form-mode/ParameterGroupForm.vue
@@ -37,7 +37,7 @@ const parameters = computed<Record<string, never>>(
() => props.parameterGroup["properties"]
);
-const modelStuff = computed(() => props.modelValue);
+const formInput = computed(() => props.modelValue);
const emit = defineEmits<{
(
e: "update:modelValue",
@@ -45,8 +45,21 @@ const emit = defineEmits<{
): void;
}>();
+function parameterRequired(
+ // eslint-disable-next-line @typescript-eslint/no-explicit-any
+ parameterGroup: Record<string, any>,
+ parameterName: string
+): boolean {
+ return (
+ parameterGroup["required"]?.includes(parameterName) || // parameter is required
+ parameterGroup["dependentRequired"]?.[parameterName] // parameter is required when another parameter is set
+ ?.map((param: string) => formInput.value[param])
+ ?.reduce((acc: boolean, val: string) => acc || val, false)
+ );
+}
+
watch(
- modelStuff,
+ formInput,
(newVal) => {
//console.log("Group", props.parameterGroupName, newVal);
emit("update:modelValue", newVal);
@@ -87,10 +100,10 @@ watch(
:parameter-name="parameterName"
:parameter="parameter"
:help-id="parameterName + '-help'"
- :required="parameterGroup['required']?.includes(parameterName)"
- :model-value="modelStuff[parameterName]"
+ :required="parameterRequired(parameterGroup, parameterName)"
+ :model-value="formInput[parameterName]"
@update:model-value="
- (newValue) => (modelStuff[parameterName] = newValue)
+ (newValue) => (formInput[parameterName] = newValue)
"
/>
<parameter-boolean-input
@@ -98,9 +111,9 @@ watch(
:parameter-name="parameterName"
:parameter="parameter"
:help-id="parameterName + '-help'"
- :model-value="modelStuff[parameterName]"
+ :model-value="formInput[parameterName]"
@update:model-value="
- (newValue) => (modelStuff[parameterName] = newValue)
+ (newValue) => (formInput[parameterName] = newValue)
"
/>
<template v-else-if="parameter['type'] === 'string'">
@@ -108,20 +121,20 @@ watch(
v-if="parameter['enum']"
:parameter-name="parameterName"
:parameter="parameter"
- :model-value="modelStuff[parameterName]"
- :required="parameterGroup['required']?.includes(parameterName)"
+ :model-value="formInput[parameterName]"
+ :required="parameterRequired(parameterGroup, parameterName)"
@update:model-value="
- (newValue) => (modelStuff[parameterName] = newValue)
+ (newValue) => (formInput[parameterName] = newValue)
"
/>
<parameter-string-input
v-else
:parameter-name="parameterName"
:parameter="parameter"
- :model-value="modelStuff[parameterName]"
- :required="parameterGroup['required']?.includes(parameterName)"
+ :model-value="formInput[parameterName]"
+ :required="parameterRequired(parameterGroup, parameterName)"
@update:model-value="
- (newValue) => (modelStuff[parameterName] = newValue)
+ (newValue) => (formInput[parameterName] = newValue)
"
/>
</template>
@@ -151,6 +164,9 @@ watch(
class="helpTextCode"
:markdown="parameter['help_text']"
/>
+ <p v-if="parameter['pattern']">
+ Pattern: <code>{{ parameter["pattern"] }}</code>
+ </p>
</div>
</template>
</template>
diff --git a/src/components/parameter-schema/form-mode/ParameterNumberInput.vue b/src/components/parameter-schema/form-mode/ParameterNumberInput.vue
index 345deb5b75aa39a21f64cf4c931d08c0be6c481b..513b783282e6b08ce8e78b4dd4360ddd4fe963ce 100644
--- a/src/components/parameter-schema/form-mode/ParameterNumberInput.vue
+++ b/src/components/parameter-schema/form-mode/ParameterNumberInput.vue
@@ -39,6 +39,7 @@ function updateValue() {
ref="numberInput"
:max="props.parameter['maximum']"
:min="props.parameter['minimum']"
+ step="0.01"
:value="props.modelValue"
:required="props.required"
:aria-describedby="props.helpId"
diff --git a/src/components/parameter-schema/form-mode/ParameterStringInput.vue b/src/components/parameter-schema/form-mode/ParameterStringInput.vue
index d247cbc5b9da04dc1ca068cfd9509b5f2e63833c..b6be2cb88238b1e10ead54d2a32c37cd99ac0505 100644
--- a/src/components/parameter-schema/form-mode/ParameterStringInput.vue
+++ b/src/components/parameter-schema/form-mode/ParameterStringInput.vue
@@ -1,5 +1,9 @@
<script setup lang="ts">
-import { computed, watch, ref } from "vue";
+import { computed, watch, ref, onMounted, reactive } from "vue";
+import { useBucketStore } from "@/stores/buckets";
+import { ObjectService } from "@/client/s3proxy";
+
+const bucketRepository = useBucketStore();
const props = defineProps({
parameter: {
@@ -22,14 +26,41 @@ const props = defineProps({
},
});
+const randomIDSuffix = Math.random().toString(16).substr(2, 8);
+
const defaultValue = computed<string>(() => props.parameter["default"]);
+const s3Path = reactive<{
+ bucket: string | undefined;
+ key: string | undefined;
+}>({
+ bucket: undefined,
+ key: undefined,
+});
+
+const keysInBucket = ref<string[]>([]);
+
watch(defaultValue, (newVal, oldVal) => {
if (newVal != oldVal && newVal != undefined) {
emit("update:modelValue", newVal);
}
});
+watch(s3Path, () => {
+ if (format.value) {
+ updateValue();
+ }
+});
+
+watch(
+ () => s3Path.bucket,
+ (newVal, oldVal) => {
+ if (newVal !== oldVal) {
+ updateKeysInBucket(newVal);
+ }
+ }
+);
+
const pattern = computed<string>(() => props.parameter["pattern"]);
const emit = defineEmits<{
@@ -38,16 +69,112 @@ const emit = defineEmits<{
const stringInput = ref<HTMLInputElement | undefined>(undefined);
+const format = computed<string | undefined>(() => props.parameter["format"]);
+
+const filesInBucket = computed<string[]>(() =>
+ keysInBucket.value.filter(
+ (obj) => !obj.endsWith("/") && !obj.endsWith(".s3keep")
+ )
+);
+
+const foldersInBucket = computed<string[]>(() =>
+ keysInBucket.value
+ .map((obj) => {
+ const parts = obj.split("/");
+ return parts
+ .slice(0, parts.length - 1)
+ .map((part, index) =>
+ parts.slice(0, index + 1).reduce((acc, val) => `${acc}/${val}`)
+ );
+ })
+ .flat()
+ .filter((val, index, array) => array.indexOf(val) === index)
+);
+
+const filesAndFoldersInBucket = computed<string[]>(() =>
+ filesInBucket.value.concat(foldersInBucket.value)
+);
+
+const keyDataList = computed<string[]>(() => {
+ switch (format.value) {
+ case "file-path":
+ return filesInBucket.value;
+ case "directory-path":
+ return foldersInBucket.value;
+ case "path":
+ return filesAndFoldersInBucket.value;
+ default:
+ return [];
+ }
+});
+
function updateValue() {
- emit(
- "update:modelValue",
- stringInput.value?.value ? stringInput.value?.value : undefined
- );
+ if (format.value) {
+ emit(
+ "update:modelValue",
+ !s3Path.bucket && s3Path.key
+ ? undefined
+ : `s3://${s3Path.bucket}/${s3Path.key}`
+ );
+ } else {
+ emit(
+ "update:modelValue",
+ stringInput.value?.value ? stringInput.value?.value : undefined
+ );
+ }
+}
+
+const helpTextPresent = computed<boolean>(() => props.parameter["help_text"]);
+
+function updateKeysInBucket(bucketName?: string) {
+ if (bucketName != null) {
+ ObjectService.objectGetBucketObjects(bucketName).then((objs) => {
+ keysInBucket.value = objs.map((obj) => obj.key);
+ });
+ } else {
+ keysInBucket.value = [];
+ }
}
+
+onMounted(() => {
+ bucketRepository.fetchBuckets();
+ if (format.value) {
+ s3Path.key = defaultValue.value;
+ }
+});
</script>
<template>
+ <template v-if="format">
+ <select
+ class="form-select"
+ :required="props.required"
+ v-model="s3Path.bucket"
+ >
+ <option selected disabled value="">Please select a bucket</option>
+ <option
+ v-for="bucket in bucketRepository.ownBucketsAndFullPermissions"
+ :key="bucket"
+ :value="bucket"
+ >
+ {{ bucket }}
+ </option>
+ </select>
+ <input
+ class="form-control"
+ :class="{ 'rounded-end': !helpTextPresent }"
+ :list="'datalistOptions2' + randomIDSuffix"
+ placeholder="Type to search in bucket..."
+ :required="props.required && format === 'file-path'"
+ v-model="s3Path.key"
+ :pattern="pattern"
+ />
+ <datalist :id="'datalistOptions2' + randomIDSuffix">
+ <option v-for="obj in keyDataList" :value="obj" :key="obj" />
+ </datalist>
+ </template>
<input
+ v-else
ref="stringInput"
class="form-control"
type="text"
diff --git a/src/stores/buckets.ts b/src/stores/buckets.ts
index e3ab60b32801feb038b904a8293c0ec9cf6502e9..c95040f8eeee280d35e822af6ed3fdb2f55cb4af 100644
--- a/src/stores/buckets.ts
+++ b/src/stores/buckets.ts
@@ -3,6 +3,7 @@ import {
BucketPermissionService,
BucketService,
Constraint,
+ Permission,
} from "@/client/s3proxy";
import type {
BucketOut,
@@ -10,6 +11,7 @@ import type {
BucketPermissionOut,
} from "@/client/s3proxy";
import { useAuthStore } from "@/stores/auth";
+import type { CancelablePromise } from "@/client/auth";
export const useBucketStore = defineStore({
id: "buckets",
@@ -17,11 +19,27 @@ export const useBucketStore = defineStore({
({
buckets: [],
ownPermissions: {},
+ _lastFetchBucketPromise: undefined,
+ _bla: 0,
} as {
buckets: BucketOut[];
ownPermissions: Record<string, BucketPermissionOut>;
+ _lastFetchBucketPromise?: CancelablePromise<never>;
+ _bla: number;
}),
getters: {
+ ownBucketsAndFullPermissions(): string[] {
+ const names = this.buckets
+ .map((bucket) => bucket.name)
+ .concat(
+ Object.values(this.ownPermissions)
+ .filter((perm) => perm.permission === Permission.READWRITE)
+ .map((perm) => perm.bucket_name)
+ );
+ names.sort();
+ return names;
+ },
+
permissionFeatureAllowed(): (bucketName: string) => boolean {
return (bucketName) => {
// If a permission for the bucket exist, then false
@@ -131,15 +149,27 @@ export const useBucketStore = defineStore({
onRejected: ((reason: any) => void) | null | undefined = null,
onFinally: (() => void) | null | undefined = null
) {
- const authStore = useAuthStore();
- BucketService.bucketListBuckets(authStore.currentUID)
- .then((buckets) => {
- this.buckets = buckets;
- onFulfilled?.(buckets);
- })
- .catch(onRejected)
- .finally(onFinally);
- this._fetchOwnPermissions();
+ /* If the time between two calls to this function is less than 5 seconds,
+ * then no API call will be made and the last one reused
+ */
+ const currentTime = new Date().getTime();
+ if (currentTime - this._bla > 5000) {
+ this._bla = currentTime;
+ const authStore = useAuthStore();
+ BucketService.bucketListBuckets(authStore.currentUID)
+ .then((buckets) => {
+ this.buckets = buckets;
+ onFulfilled?.(buckets);
+ })
+ .catch(onRejected)
+ .finally(onFinally);
+ this._fetchOwnPermissions();
+ } else {
+ this._lastFetchBucketPromise
+ ?.then(onFulfilled)
+ .catch(onRejected)
+ .finally(onFinally);
+ }
},
fetchBucket(
bucketName: string,
diff --git a/src/views/workflows/WorkflowVersionView.vue b/src/views/workflows/WorkflowVersionView.vue
index a769f3f992f153274d5ad979fd11f13331c7eb17..c450386da0df32cdc98e00c1c072ae6fcac951b6 100644
--- a/src/views/workflows/WorkflowVersionView.vue
+++ b/src/views/workflows/WorkflowVersionView.vue
@@ -4,7 +4,7 @@ import { WorkflowVersionService } from "@/client/workflow";
import type { WorkflowVersionFull } from "@/client/workflow";
import axios from "axios";
import MarkdownRenderer from "@/components/MarkdownRenderer.vue";
-import ParameterSchemaFormComponent from "@/components/parameter-schema/ParameterSchemaFormComponent.vue";
+import ParameterSchemaDescriptionComponent from "@/components/parameter-schema/ParameterSchemaDescriptionComponent.vue";
const props = defineProps<{
versionId: string;
@@ -132,7 +132,7 @@ onMounted(() => {
<p v-if="props.activeTab === 'description'">
<markdown-renderer :markdown="versionState.descriptionMarkdown" />
</p>
- <parameter-schema-form-component
+ <parameter-schema-description-component
v-else-if="props.activeTab === 'parameters'"
:schema="versionState.parameterSchema"
/>