From 81ef48978ad10dfb90596e702f9b71b7b1200346 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daniel=20G=C3=B6bel?= <dgoebel@techfak.uni-bielefeld.de>
Date: Wed, 19 Jun 2024 14:11:11 +0000
Subject: [PATCH] Add option to select the nextflow version for workflow
versions
#131
---
src/client/index.ts | 1 +
src/client/models/DevWorkflowExecutionIn.ts | 5 +++
src/client/models/NextflowVersion.ts | 18 +++++++++
src/client/models/UserOutExtended.ts | 2 +-
src/client/models/WorkflowIn.ts | 5 +++
src/client/models/WorkflowUpdate.ts | 5 +++
src/client/models/WorkflowVersion.ts | 5 +++
src/components/AppHeader.vue | 7 ----
.../workflows/WorkflowWithVersionsCard.vue | 6 ++-
.../modals/ArbitraryWorkflowModal.vue | 26 ++++++++++++-
.../workflows/modals/CreateWorkflowModal.vue | 30 ++++++++++++++-
.../workflows/modals/UpdateWorkflowModal.vue | 37 +++++++++++++++----
src/views/admin/AdminUsersView.vue | 6 ---
src/views/workflows/ArbitraryWorkflowView.vue | 4 +-
src/views/workflows/MyWorkflowsView.vue | 10 ++++-
15 files changed, 138 insertions(+), 29 deletions(-)
create mode 100644 src/client/models/NextflowVersion.ts
diff --git a/src/client/index.ts b/src/client/index.ts
index 98752ac..77aaffd 100644
--- a/src/client/index.ts
+++ b/src/client/index.ts
@@ -26,6 +26,7 @@ export type { ErrorDetail } from './models/ErrorDetail';
export { FileTree } from './models/FileTree';
export type { HTTPValidationError } from './models/HTTPValidationError';
export type { IconUpdateOut } from './models/IconUpdateOut';
+export { NextflowVersion } from './models/NextflowVersion';
export { OIDCProvider } from './models/OIDCProvider';
export type { ParameterExtension } from './models/ParameterExtension';
export { Permission } from './models/Permission';
diff --git a/src/client/models/DevWorkflowExecutionIn.ts b/src/client/models/DevWorkflowExecutionIn.ts
index f65f6eb..e075238 100644
--- a/src/client/models/DevWorkflowExecutionIn.ts
+++ b/src/client/models/DevWorkflowExecutionIn.ts
@@ -2,6 +2,7 @@
/* istanbul ignore file */
/* tslint:disable */
/* eslint-disable */
+import type { NextflowVersion } from './NextflowVersion';
import type { WorkflowModeIn } from './WorkflowModeIn';
export type DevWorkflowExecutionIn = {
/**
@@ -36,5 +37,9 @@ export type DevWorkflowExecutionIn = {
* Mode of the workflow with an alternative entrypoint
*/
mode?: (WorkflowModeIn | null);
+ /**
+ * The version of Nextflow this workflow execution requires
+ */
+ nextflow_version: NextflowVersion;
};
diff --git a/src/client/models/NextflowVersion.ts b/src/client/models/NextflowVersion.ts
new file mode 100644
index 0000000..e16dfe9
--- /dev/null
+++ b/src/client/models/NextflowVersion.ts
@@ -0,0 +1,18 @@
+/* generated using openapi-typescript-codegen -- do not edit */
+/* istanbul ignore file */
+/* tslint:disable */
+/* eslint-disable */
+export enum NextflowVersion {
+ _23_04_0 = '23.04.0',
+ _23_04_1 = '23.04.1',
+ _23_04_2 = '23.04.2',
+ _23_04_3 = '23.04.3',
+ _23_04_4 = '23.04.4',
+ _23_04_5 = '23.04.5',
+ _23_10_0 = '23.10.0',
+ _23_10_1 = '23.10.1',
+ _23_10_2 = '23.10.2',
+ _23_10_3 = '23.10.3',
+ _24_04_1 = '24.04.1',
+ _24_04_2 = '24.04.2',
+}
diff --git a/src/client/models/UserOutExtended.ts b/src/client/models/UserOutExtended.ts
index a05ecb6..709361b 100644
--- a/src/client/models/UserOutExtended.ts
+++ b/src/client/models/UserOutExtended.ts
@@ -27,6 +27,6 @@ export type UserOutExtended = {
/**
* URL to the gravatar avatar based on the users email
*/
- gravatar_url?: (string | null);
+ gravatar_url: string;
};
diff --git a/src/client/models/WorkflowIn.ts b/src/client/models/WorkflowIn.ts
index acc74b5..f433bf9 100644
--- a/src/client/models/WorkflowIn.ts
+++ b/src/client/models/WorkflowIn.ts
@@ -2,6 +2,7 @@
/* istanbul ignore file */
/* tslint:disable */
/* eslint-disable */
+import type { NextflowVersion } from './NextflowVersion';
import type { WorkflowModeIn } from './WorkflowModeIn';
export type WorkflowIn = {
/**
@@ -32,5 +33,9 @@ export type WorkflowIn = {
* List of modes with alternative entrypoint the new workflow has
*/
modes?: Array<WorkflowModeIn>;
+ /**
+ * The version of Nextflow this workflow version requires
+ */
+ nextflow_version: NextflowVersion;
};
diff --git a/src/client/models/WorkflowUpdate.ts b/src/client/models/WorkflowUpdate.ts
index 9b3dac3..a67749a 100644
--- a/src/client/models/WorkflowUpdate.ts
+++ b/src/client/models/WorkflowUpdate.ts
@@ -2,6 +2,7 @@
/* istanbul ignore file */
/* tslint:disable */
/* eslint-disable */
+import type { NextflowVersion } from './NextflowVersion';
import type { WorkflowModeIn } from './WorkflowModeIn';
export type WorkflowUpdate = {
/**
@@ -20,5 +21,9 @@ export type WorkflowUpdate = {
* Delete modes for the new workflow version.
*/
delete_modes?: Array<string>;
+ /**
+ * The version of Nextflow this new workflow version requires.
+ */
+ nextflow_version: NextflowVersion;
};
diff --git a/src/client/models/WorkflowVersion.ts b/src/client/models/WorkflowVersion.ts
index 1974ff1..3e3138e 100644
--- a/src/client/models/WorkflowVersion.ts
+++ b/src/client/models/WorkflowVersion.ts
@@ -2,6 +2,7 @@
/* istanbul ignore file */
/* tslint:disable */
/* eslint-disable */
+import type { NextflowVersion } from './NextflowVersion';
import type { ParameterExtension } from './ParameterExtension';
import type { WorkflowVersionStatus } from './WorkflowVersionStatus';
export type WorkflowVersion = {
@@ -37,5 +38,9 @@ export type WorkflowVersion = {
* Parameter extension specific for this CloWM instance
*/
parameter_extension?: (ParameterExtension | null);
+ /**
+ * The version of Nextflow this workflow version requires
+ */
+ nextflow_version: NextflowVersion;
};
diff --git a/src/components/AppHeader.vue b/src/components/AppHeader.vue
index 97d73da..331c790 100644
--- a/src/components/AppHeader.vue
+++ b/src/components/AppHeader.vue
@@ -3,7 +3,6 @@ import { useUserStore } from "@/stores/users";
import { useRoute, useRouter } from "vue-router";
import { watch, ref, computed } from "vue";
import { OpenAPI } from "@/client";
-import FontAwesomeIcon from "@/components/FontAwesomeIcon.vue";
const userRepository = useUserStore();
const route = useRoute();
@@ -266,18 +265,12 @@ watch(
>
<strong class="me-2">{{ userRepository.user.display_name }}</strong>
<img
- v-if="userRepository.user.gravatar_url"
:src="userRepository.user.gravatar_url + '?d=mp&s=32'"
class="rounded-circle"
height="32"
width="32"
alt="profile picture"
/>
- <font-awesome-icon
- v-else
- icon="fa-solid fa-circle-user"
- class="text-secondary fs-4"
- />
</a>
<ul
class="dropdown-menu text-small shadow"
diff --git a/src/components/workflows/WorkflowWithVersionsCard.vue b/src/components/workflows/WorkflowWithVersionsCard.vue
index cae0ee5..a5a95f2 100644
--- a/src/components/workflows/WorkflowWithVersionsCard.vue
+++ b/src/components/workflows/WorkflowWithVersionsCard.vue
@@ -215,6 +215,7 @@ onMounted(() => {
<th scope="col">Version</th>
<th scope="col">Status</th>
<th scope="col">Updated at</th>
+ <th scope="col">Nextflow version</th>
<th scope="col" class="text-align-center">Usage</th>
<th scope="col" class="text-align-center">Icon</th>
<th scope="col"></th>
@@ -246,6 +247,9 @@ onMounted(() => {
<td>
{{ dayjs.unix(version.created_at).format("DD MMM YYYY") }}
</td>
+ <td class="text-align-center">
+ {{ version.nextflow_version }}
+ </td>
<td class="text-align-center">
<span
class="text-success me-1"
@@ -351,7 +355,7 @@ onMounted(() => {
</tr>
<tr>
<th scope="row" class="fw-bold">Overall</th>
- <td colspan="2"></td>
+ <td colspan="3"></td>
<td class="text-align-center">
<span
class="text-success me-1"
diff --git a/src/components/workflows/modals/ArbitraryWorkflowModal.vue b/src/components/workflows/modals/ArbitraryWorkflowModal.vue
index 6399ce3..749dcd9 100644
--- a/src/components/workflows/modals/ArbitraryWorkflowModal.vue
+++ b/src/components/workflows/modals/ArbitraryWorkflowModal.vue
@@ -10,7 +10,7 @@ import {
} from "@/utils/GitRepository";
import { Collapse, Modal } from "bootstrap";
import { useWorkflowStore } from "@/stores/workflows";
-import type { WorkflowModeOut } from "@/client";
+import { NextflowVersion, type WorkflowModeOut } from "@/client";
import { environment } from "@/environment";
import { useS3KeyStore } from "@/stores/s3keys";
import { useResourceStore } from "@/stores/resources";
@@ -38,9 +38,12 @@ const resourceStore = useResourceStore();
const workflow = reactive<{
repository_url: string;
git_commit_hash: string;
+ nextflow_version: NextflowVersion;
}>({
repository_url: "",
git_commit_hash: "",
+ nextflow_version:
+ Object.values(NextflowVersion)[Object.values(NextflowVersion).length - 1],
});
const repositoryCredentials = reactive<{
@@ -504,7 +507,7 @@ onMounted(() => {
/>
</div>
<div id="gitRepoProviderHelp" class="form-text">
- We support Github and GitLab Repositories
+ We support Github and (self-hosted) GitLab Repositories
</div>
<div class="text-danger">
<div v-if="formState.unsupportedRepository">
@@ -555,6 +558,25 @@ onMounted(() => {
</li>
</ul>
</div>
+ <div class="mb-3">
+ <label for="workflowNextflowVersionInput" class="form-label"
+ >Nextflow version</label
+ >
+ <select
+ class="form-select"
+ id="workflowNextflowVersionInput"
+ required
+ v-model="workflow.nextflow_version"
+ >
+ <option
+ v-for="version in Object.values(NextflowVersion).reverse()"
+ :key="version"
+ :value="version"
+ >
+ {{ version }}
+ </option>
+ </select>
+ </div>
<div class="mb-3">
<div class="form-check fs-5">
<input
diff --git a/src/components/workflows/modals/CreateWorkflowModal.vue b/src/components/workflows/modals/CreateWorkflowModal.vue
index 61398ea..c1ec15a 100644
--- a/src/components/workflows/modals/CreateWorkflowModal.vue
+++ b/src/components/workflows/modals/CreateWorkflowModal.vue
@@ -1,7 +1,12 @@
<script setup lang="ts">
import { computed, onMounted, reactive, ref, watch } from "vue";
import { Modal, Toast, Collapse, Tooltip } from "bootstrap";
-import type { WorkflowIn, WorkflowOut, WorkflowModeOut } from "@/client";
+import {
+ type WorkflowIn,
+ type WorkflowOut,
+ type WorkflowModeOut,
+ NextflowVersion,
+} from "@/client";
import BootstrapModal from "@/components/modals/BootstrapModal.vue";
import FontAwesomeIcon from "@/components/FontAwesomeIcon.vue";
import { ApiError } from "@/client";
@@ -61,6 +66,8 @@ const workflow = reactive<WorkflowIn>({
initial_version: undefined,
token: undefined,
modes: [],
+ nextflow_version:
+ Object.values(NextflowVersion)[Object.values(NextflowVersion).length - 1],
});
const formState = reactive<{
@@ -410,7 +417,7 @@ onMounted(() => {
</div>
</div>
<div id="gitRepoProviderHelp" class="form-text">
- We support GitHub and GitLab Repositories
+ We support GitHub and (self-hosted) GitLab Repositories
</div>
<div class="text-danger">
<div v-if="formState.unsupportedRepository">
@@ -501,6 +508,25 @@ onMounted(() => {
</div>
</div>
</div>
+ <div class="mb-3">
+ <label for="createWorkflowNextflowVersionInput" class="form-label"
+ >Nextflow version</label
+ >
+ <select
+ class="form-select"
+ id="createWorkflowNextflowVersionInput"
+ required
+ v-model="workflow.nextflow_version"
+ >
+ <option
+ v-for="version in Object.values(NextflowVersion).reverse()"
+ :key="version"
+ :value="version"
+ >
+ {{ version }}
+ </option>
+ </select>
+ </div>
<div class="mb-3">
<div class="form-check fs-5">
<input
diff --git a/src/components/workflows/modals/UpdateWorkflowModal.vue b/src/components/workflows/modals/UpdateWorkflowModal.vue
index 55d13e7..7347855 100644
--- a/src/components/workflows/modals/UpdateWorkflowModal.vue
+++ b/src/components/workflows/modals/UpdateWorkflowModal.vue
@@ -1,13 +1,14 @@
<script setup lang="ts">
import { computed, onMounted, reactive, ref, watch } from "vue";
import { Collapse, Modal, Toast } from "bootstrap";
-import type {
- WorkflowUpdate,
- WorkflowOut,
- WorkflowModeIn,
- WorkflowModeOut,
- WorkflowVersion,
- ApiError,
+import {
+ type WorkflowUpdate,
+ type WorkflowOut,
+ type WorkflowModeIn,
+ type WorkflowModeOut,
+ type WorkflowVersion,
+ type ApiError,
+ NextflowVersion,
} from "@/client";
import BootstrapModal from "@/components/modals/BootstrapModal.vue";
import FontAwesomeIcon from "@/components/FontAwesomeIcon.vue";
@@ -59,6 +60,8 @@ const workflowUpdate = reactive<WorkflowUpdate>({
git_commit_hash: "",
delete_modes: [],
append_modes: [],
+ nextflow_version:
+ Object.values(NextflowVersion)[Object.values(NextflowVersion).length - 1],
});
const workflowModes = reactive<{
@@ -96,6 +99,7 @@ watch(
() => {
resetForm();
formState.modesEnabled = (latestVersion.value.modes ?? []).length > 0;
+ workflowUpdate.nextflow_version = latestVersion.value.nextflow_version;
if (props.workflow.private) {
formState.loadCredentials = true;
WorkflowCredentialsService.workflowCredentialsGetWorkflowCredentials(
@@ -431,6 +435,25 @@ onMounted(() => {
</div>
</div>
</div>
+ <div class="mb-3">
+ <label for="updateWorkflowNextflowVersionInput" class="form-label"
+ >Nextflow version</label
+ >
+ <select
+ class="form-select"
+ id="updateWorkflowNextflowVersionInput"
+ required
+ v-model="workflowUpdate.nextflow_version"
+ >
+ <option
+ v-for="version in Object.values(NextflowVersion).reverse()"
+ :key="version"
+ :value="version"
+ >
+ {{ version }}
+ </option>
+ </select>
+ </div>
<div class="mb-3">
<div class="form-check fs-5">
<input
diff --git a/src/views/admin/AdminUsersView.vue b/src/views/admin/AdminUsersView.vue
index 69fa6ea..498e36f 100644
--- a/src/views/admin/AdminUsersView.vue
+++ b/src/views/admin/AdminUsersView.vue
@@ -213,18 +213,12 @@ onMounted(() => {
<tr v-for="(user, index) in userState.users" :key="user.uid">
<th scope="row">
<img
- v-if="user.gravatar_url"
:src="user.gravatar_url + '?d=mp&s=32'"
class="rounded-circle"
height="32"
width="32"
alt="profile picture"
/>
- <font-awesome-icon
- v-else
- icon="fa-solid fa-circle-user"
- class="text-secondary fs-4"
- />
<span class="ms-2">{{ user.display_name }}</span>
</th>
<td>{{ user.uid }}</td>
diff --git a/src/views/workflows/ArbitraryWorkflowView.vue b/src/views/workflows/ArbitraryWorkflowView.vue
index 45f1b3e..3a58992 100644
--- a/src/views/workflows/ArbitraryWorkflowView.vue
+++ b/src/views/workflows/ArbitraryWorkflowView.vue
@@ -121,6 +121,7 @@ function startWorkflow(
debug_s3_path: metaParameters.debug_s3_path,
provenance_s3_path: metaParameters.provenance_s3_path,
repository_url: workflowState.workflow.repository_url,
+ nextflow_version: workflowState.workflow.nextflow_version,
token: workflowState.workflow.token ?? undefined,
mode:
(workflowState.workflow.modes ?? []).length > 0
@@ -185,8 +186,9 @@ onMounted(() => {
workflowState.workflow?.repository_url
}}</a>
</h5>
+ <h5>Git Commit Hash: {{ workflowState.workflow?.git_commit_hash }}</h5>
<h5 :class="{ 'mb-5': workflowState.workflow.modes!.length < 1 }">
- Git Commit Hash: {{ workflowState.workflow?.git_commit_hash }}
+ Nextflow version: {{ workflowState.workflow?.nextflow_version }}
</h5>
<template v-if="workflowState.workflow.modes!.length > 0">
<h5>Entrypoint: {{ workflowState.workflow?.modes?.[0].entrypoint }}</h5>
diff --git a/src/views/workflows/MyWorkflowsView.vue b/src/views/workflows/MyWorkflowsView.vue
index 9ad162d..7ccfeb4 100644
--- a/src/views/workflows/MyWorkflowsView.vue
+++ b/src/views/workflows/MyWorkflowsView.vue
@@ -1,7 +1,11 @@
<script setup lang="ts">
import { computed, onMounted, reactive } from "vue";
-import type { WorkflowOut, WorkflowVersion } from "@/client";
-import { WorkflowVersionStatus } from "@/client";
+import {
+ NextflowVersion,
+ type WorkflowOut,
+ type WorkflowVersion,
+ WorkflowVersionStatus,
+} from "@/client";
import WorkflowWithVersionsCard from "@/components/workflows/WorkflowWithVersionsCard.vue";
import CreateWorkflowModal from "@/components/workflows/modals/CreateWorkflowModal.vue";
import CardTransitionGroup from "@/components/transitions/CardTransitionGroup.vue";
@@ -37,6 +41,7 @@ const workflowsState = reactive<{
workflow_id: "",
icon_url: "",
modes: [],
+ nextflow_version: NextflowVersion._24_04_2,
},
],
repository_url: "",
@@ -52,6 +57,7 @@ const workflowsState = reactive<{
icon_url: null,
created_at: 0,
status: WorkflowVersionStatus.CREATED,
+ nextflow_version: NextflowVersion._24_04_2,
},
});
--
GitLab