mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 13:50:20 +08:00
Merge remote-tracking branch 'upstream/release_23.0' into dev
This commit is contained in:
Dannon Baker
@@ -51,6 +51,7 @@
|
||||
"csv-parse": "^5.3.0",
|
||||
"d3": "^7.8.0",
|
||||
"d3-zoom": "^3.0.0",
|
||||
"d3v3": "npm:d3@3",
|
||||
"date-fns": "^2.28.0",
|
||||
"date-fns-tz": "^1.3.3",
|
||||
"decode-uri-component": "^0.2.1",
|
||||
|
||||
@@ -97,6 +97,10 @@ export default {
|
||||
type: Boolean,
|
||||
default: false,
|
||||
},
|
||||
sortItems: {
|
||||
type: Boolean,
|
||||
default: true,
|
||||
},
|
||||
},
|
||||
setup() {
|
||||
const { config, isLoaded } = useConfig();
|
||||
@@ -135,6 +139,7 @@ export default {
|
||||
if (
|
||||
this.isLoaded &&
|
||||
this.config.toolbox_auto_sort === true &&
|
||||
this.sortItems === true &&
|
||||
!this.category.elems.some((el) => el.text !== undefined && el.text !== "")
|
||||
) {
|
||||
const elements = [...this.category.elems];
|
||||
|
||||
@@ -59,6 +59,7 @@
|
||||
:key="workflowSection.name"
|
||||
:category="workflowSection"
|
||||
section-name="workflows"
|
||||
:sort-items="false"
|
||||
operation-icon="fa fa-files-o"
|
||||
operation-title="Insert individual steps."
|
||||
:query-filter="query"
|
||||
|
||||
@@ -84,7 +84,6 @@
|
||||
import FormCard from "@/components/Form/FormCard";
|
||||
import FormElement from "@/components/Form/FormElement";
|
||||
import FormOutputLabel from "@/components/Workflow/Editor/Forms/FormOutputLabel";
|
||||
import { Step } from "@/stores/workflowStepStore";
|
||||
|
||||
const actions = [
|
||||
"RenameDatasetAction__newname",
|
||||
@@ -129,7 +128,8 @@ export default {
|
||||
required: true,
|
||||
},
|
||||
step: {
|
||||
type: Step,
|
||||
// type Step from "@/stores/workflowStepStore";
|
||||
type: Object,
|
||||
required: true,
|
||||
},
|
||||
},
|
||||
|
||||
@@ -52,9 +52,13 @@ describe("FormOutputLabel", () => {
|
||||
const inputOther = wrapperOther.find("input");
|
||||
await input.setValue("new-label");
|
||||
expect(wrapper.find(".ui-form-error").exists()).toBe(false);
|
||||
expect(wrapperOther.find(".ui-form-error").exists()).toBe(false);
|
||||
await inputOther.setValue("other-label");
|
||||
expect(wrapper.find(".ui-form-error").exists()).toBe(false);
|
||||
expect(wrapperOther.find(".ui-form-error").exists()).toBe(false);
|
||||
await input.setValue("other-label");
|
||||
expect(wrapper.find(".ui-form-error").text()).toBe("Duplicate output label 'other-label' will be ignored.");
|
||||
expect(wrapperOther.find(".ui-form-error").exists()).toBe(false);
|
||||
expect(stepStore.workflowOutputs["new-label"].outputName).toBe("output-name");
|
||||
});
|
||||
});
|
||||
|
||||
@@ -45,7 +45,8 @@ const label = computed(() => {
|
||||
});
|
||||
|
||||
function onInput(newLabel: string) {
|
||||
if (!stepStore.workflowOutputs[newLabel]) {
|
||||
const existingWorkflowOutput = stepStore.workflowOutputs[newLabel];
|
||||
if (!existingWorkflowOutput) {
|
||||
const newWorkflowOutputs = [...(props.step.workflow_outputs || [])].filter(
|
||||
(workflowOutput) => workflowOutput.output_name !== props.name
|
||||
);
|
||||
@@ -55,7 +56,7 @@ function onInput(newLabel: string) {
|
||||
});
|
||||
stepStore.updateStep({ ...props.step, workflow_outputs: newWorkflowOutputs });
|
||||
error.value = undefined;
|
||||
} else {
|
||||
} else if (existingWorkflowOutput.stepId !== props.step.id) {
|
||||
error.value = `Duplicate output label '${newLabel}' will be ignored.`;
|
||||
}
|
||||
}
|
||||
|
||||
@@ -30,7 +30,6 @@
|
||||
<script>
|
||||
import FormElement from "@/components/Form/FormElement";
|
||||
import FormOutput from "@/components/Workflow/Editor/Forms/FormOutput";
|
||||
import { Step } from "@/stores/workflowStepStore";
|
||||
|
||||
export default {
|
||||
components: {
|
||||
@@ -51,7 +50,8 @@ export default {
|
||||
required: true,
|
||||
},
|
||||
step: {
|
||||
type: Step,
|
||||
// type Step from "@/stores/workflowStepStore";
|
||||
type: Object,
|
||||
required: true,
|
||||
},
|
||||
datatypes: {
|
||||
|
||||
@@ -1,27 +0,0 @@
|
||||
<script lang="ts" setup>
|
||||
import { useWorkflowStateStore } from "@/stores/workflowEditorStateStore";
|
||||
import type { Step } from "@/stores/workflowStepStore";
|
||||
import { computed } from "vue";
|
||||
|
||||
const props = defineProps<{
|
||||
step: Step;
|
||||
}>();
|
||||
|
||||
const stateStore = useWorkflowStateStore();
|
||||
const nodePosition = computed(() => stateStore.stepPosition[props.step.id]);
|
||||
|
||||
const nodeClass = computed(() => {
|
||||
const stateClass = props.step.errors ? "error" : "ok";
|
||||
|
||||
const highlightClass = stateStore.activeNodeId == props.step.id ? "highlight" : "";
|
||||
return [stateClass, highlightClass];
|
||||
});
|
||||
</script>
|
||||
<template>
|
||||
<rect
|
||||
:class="nodeClass"
|
||||
:x="step.position.left"
|
||||
:y="step.position.top"
|
||||
:width="nodePosition.width"
|
||||
:height="nodePosition.height" />
|
||||
</template>
|
||||
@@ -176,7 +176,12 @@ const connectionStore = useConnectionStore();
|
||||
const stateStore = useWorkflowStateStore();
|
||||
const stepStore = useWorkflowStepStore();
|
||||
const isLoading = computed(() => Boolean(stateStore.getStepLoadingState(props.id)?.loading));
|
||||
useNodePosition(el, props.id, stateStore);
|
||||
useNodePosition(
|
||||
el,
|
||||
props.id,
|
||||
stateStore,
|
||||
computed(() => props.scale)
|
||||
);
|
||||
const title = computed(() => props.step.label || props.step.name);
|
||||
const idString = computed(() => `wf-node-step-${props.id}`);
|
||||
const showRule = computed(() => props.step.inputs?.length > 0 && props.step.outputs?.length > 0);
|
||||
|
||||
@@ -17,6 +17,13 @@
|
||||
@click="onRemove"
|
||||
@keyup.delete="onRemove" />
|
||||
{{ label }}
|
||||
<span
|
||||
v-if="!input.optional && !hasTerminals"
|
||||
v-b-tooltip.hover
|
||||
class="input-required"
|
||||
title="Input is required">
|
||||
*
|
||||
</span>
|
||||
</div>
|
||||
</template>
|
||||
|
||||
@@ -25,7 +32,6 @@ import { useCoordinatePosition } from "./composables/useCoordinatePosition";
|
||||
import { useConnectionStore } from "@/stores/workflowConnectionStore";
|
||||
import { computed } from "vue";
|
||||
import { inject, ref, toRefs, watchEffect } from "vue";
|
||||
import { UseElementBoundingReturn } from "@vueuse/core";
|
||||
import { storeToRefs } from "pinia";
|
||||
import { useTerminal } from "./composables/useTerminal";
|
||||
import { DatatypesMapperModel } from "@/components/Datatypes/model";
|
||||
@@ -51,7 +57,8 @@ export default {
|
||||
required: true,
|
||||
},
|
||||
rootOffset: {
|
||||
type: UseElementBoundingReturn,
|
||||
// type UseElementBoundingReturn from "@vueuse/core";
|
||||
type: Object,
|
||||
required: true,
|
||||
},
|
||||
scale: {
|
||||
@@ -214,3 +221,16 @@ export default {
|
||||
},
|
||||
};
|
||||
</script>
|
||||
|
||||
<style lang="scss" scoped>
|
||||
@import "theme/blue.scss";
|
||||
@import "~@fortawesome/fontawesome-free/scss/_variables";
|
||||
|
||||
.input-required {
|
||||
margin-top: $margin-v * 0.25;
|
||||
margin-bottom: $margin-v * 0.25;
|
||||
color: $brand-danger;
|
||||
font-weight: 300;
|
||||
cursor: default;
|
||||
}
|
||||
</style>
|
||||
|
||||
@@ -29,10 +29,10 @@
|
||||
<workflow-minimap
|
||||
v-if="elementBounding"
|
||||
:steps="steps"
|
||||
:root-offset="elementBounding"
|
||||
:scale="scale"
|
||||
:pan="transform"
|
||||
@pan-by="panBy"
|
||||
:viewport-bounds="elementBounding"
|
||||
:viewport-scale="scale"
|
||||
:viewport-pan="transform"
|
||||
@panBy="panBy"
|
||||
@moveTo="moveTo" />
|
||||
</div>
|
||||
</template>
|
||||
@@ -68,7 +68,7 @@ const canvas: Ref<HTMLElement | null> = ref(null);
|
||||
|
||||
const elementBounding = useElementBounding(canvas, { windowResize: false, windowScroll: false });
|
||||
const scroll = useScroll(canvas);
|
||||
const { transform, panBy, setZoom, moveTo } = useD3Zoom(1, minZoom, maxZoom, canvas, scroll);
|
||||
const { transform, panBy, setZoom, moveTo } = useD3Zoom(1, minZoom, maxZoom, canvas, scroll, { x: 20, y: 20 });
|
||||
|
||||
const isDragging = ref(false);
|
||||
provide("isDragging", isDragging);
|
||||
|
||||
@@ -1,171 +1,296 @@
|
||||
<script lang="ts" setup>
|
||||
import { computed, onMounted, ref, unref, watch } from "vue";
|
||||
import { useAnimationFrame } from "@/composables/sensors/animationFrame";
|
||||
import { useWorkflowStateStore } from "@/stores/workflowEditorStateStore";
|
||||
import { AxisAlignedBoundingBox, Transform } from "./modules/geometry";
|
||||
import { useDraggable, type UseElementBoundingReturn } from "@vueuse/core";
|
||||
|
||||
import type { Step, Steps } from "@/stores/workflowStepStore";
|
||||
import type { Ref } from "vue";
|
||||
|
||||
const props = defineProps<{
|
||||
steps: Steps;
|
||||
viewportBounds: UseElementBoundingReturn;
|
||||
viewportPan: { x: number; y: number };
|
||||
viewportScale: number;
|
||||
}>();
|
||||
|
||||
const emit = defineEmits<{
|
||||
(e: "panBy", offset: { x: number; y: number }): void;
|
||||
(e: "moveTo", position: { x: number; y: number }): void;
|
||||
}>();
|
||||
|
||||
const stateStore = useWorkflowStateStore();
|
||||
|
||||
/** bounding box following the viewport */
|
||||
const viewportBounds = computed(() => {
|
||||
const bounds = new AxisAlignedBoundingBox();
|
||||
bounds.x = -props.viewportPan.x / props.viewportScale;
|
||||
bounds.y = -props.viewportPan.y / props.viewportScale;
|
||||
bounds.width = unref(props.viewportBounds.width) / props.viewportScale;
|
||||
bounds.height = unref(props.viewportBounds.height) / props.viewportScale;
|
||||
|
||||
return bounds;
|
||||
});
|
||||
|
||||
/** reference to the main canvas element */
|
||||
const canvas: Ref<HTMLCanvasElement | null> = ref(null);
|
||||
let redraw = false;
|
||||
|
||||
/** bounding box encompassing all nodes in the workflow */
|
||||
const aabb = new AxisAlignedBoundingBox();
|
||||
let aabbChanged = false;
|
||||
|
||||
/** transform mapping workflow coordinates to minimap coordinates */
|
||||
let canvasTransform = new Transform();
|
||||
|
||||
function recalculateAABB() {
|
||||
aabb.reset();
|
||||
|
||||
Object.values(props.steps).forEach((step) => {
|
||||
const rect = stateStore.stepPosition[step.id];
|
||||
aabb.fitRectangle({
|
||||
x: step.position!.left,
|
||||
y: step.position!.top,
|
||||
width: rect.width,
|
||||
height: rect.height,
|
||||
});
|
||||
});
|
||||
|
||||
aabb.squareCenter();
|
||||
aabb.expand(120);
|
||||
|
||||
// transform canvas to show entire workflow bounding box
|
||||
if (canvas.value) {
|
||||
const scale = canvas.value.width / aabb.width;
|
||||
canvasTransform = new Transform().translate([-aabb.x * scale, -aabb.y * scale]).scale([scale, scale]);
|
||||
}
|
||||
}
|
||||
|
||||
// redraw if any of these props change
|
||||
watch(viewportBounds, () => (redraw = true));
|
||||
watch(
|
||||
props.steps,
|
||||
() => {
|
||||
redraw = true;
|
||||
aabbChanged = true;
|
||||
},
|
||||
{ deep: true }
|
||||
);
|
||||
|
||||
// these settings are controlled via css, so they can be defined in one common place
|
||||
// this ensures future style changes wont break the minimap's behavior
|
||||
const colors = {
|
||||
node: "#000",
|
||||
error: "#000",
|
||||
selectedOutline: "#000",
|
||||
view: "#000",
|
||||
viewOutline: "#000",
|
||||
};
|
||||
|
||||
const size = {
|
||||
default: 150,
|
||||
min: 50,
|
||||
max: 300,
|
||||
padding: 5,
|
||||
border: 0,
|
||||
};
|
||||
|
||||
onMounted(() => {
|
||||
const element = canvas.value!;
|
||||
const style = getComputedStyle(element);
|
||||
|
||||
colors.node = style.getPropertyValue("--node-color");
|
||||
colors.error = style.getPropertyValue("--error-color");
|
||||
colors.selectedOutline = style.getPropertyValue("--selected-outline-color");
|
||||
colors.view = style.getPropertyValue("--view-color");
|
||||
colors.viewOutline = style.getPropertyValue("--view-outline-color");
|
||||
|
||||
size.default = parseInt(style.getPropertyValue("--workflow-overview-size"));
|
||||
size.min = parseInt(style.getPropertyValue("--workflow-overview-min-size"));
|
||||
size.max = parseInt(style.getPropertyValue("--workflow-overview-max-size"));
|
||||
size.padding = parseInt(style.getPropertyValue("--workflow-overview-padding"));
|
||||
size.border = parseInt(style.getPropertyValue("--workflow-overview-border"));
|
||||
|
||||
recalculateAABB();
|
||||
redraw = true;
|
||||
});
|
||||
|
||||
// for performance reasons, only draw and calculate on animation frames.
|
||||
useAnimationFrame(() => {
|
||||
if (aabbChanged) {
|
||||
recalculateAABB();
|
||||
aabbChanged = false;
|
||||
}
|
||||
|
||||
if (redraw && canvas.value) {
|
||||
renderMinimap();
|
||||
redraw = false;
|
||||
}
|
||||
});
|
||||
|
||||
/** Renders the entire minimap to the canvas */
|
||||
function renderMinimap() {
|
||||
const ctx = canvas.value!.getContext("2d") as CanvasRenderingContext2D;
|
||||
ctx.resetTransform();
|
||||
ctx.clearRect(0, 0, ctx.canvas.width, ctx.canvas.height);
|
||||
|
||||
// apply global to local transform
|
||||
canvasTransform.applyToContext(ctx);
|
||||
|
||||
const allSteps = Object.values(props.steps);
|
||||
const okSteps: Step[] = [];
|
||||
const errorSteps: Step[] = [];
|
||||
let selectedStep: Step | undefined;
|
||||
|
||||
// sort steps into different arrays
|
||||
allSteps.forEach((step) => {
|
||||
if (stateStore.activeNodeId === step.id) {
|
||||
selectedStep = step;
|
||||
}
|
||||
|
||||
if (step.errors) {
|
||||
errorSteps.push(step);
|
||||
} else {
|
||||
okSteps.push(step);
|
||||
}
|
||||
});
|
||||
|
||||
// draw rects
|
||||
ctx.beginPath();
|
||||
ctx.fillStyle = colors.node;
|
||||
okSteps.forEach((step) => {
|
||||
const rect = stateStore.stepPosition[step.id];
|
||||
ctx.rect(step.position!.left, step.position!.top, rect.width, rect.height);
|
||||
});
|
||||
ctx.fill();
|
||||
|
||||
ctx.beginPath();
|
||||
ctx.fillStyle = colors.error;
|
||||
errorSteps.forEach((step) => {
|
||||
const rect = stateStore.stepPosition[step.id];
|
||||
ctx.rect(step.position!.left, step.position!.top, rect.width, rect.height);
|
||||
});
|
||||
ctx.fill();
|
||||
|
||||
// draw selected
|
||||
if (selectedStep) {
|
||||
const edge = 2 / canvasTransform.scaleX;
|
||||
|
||||
ctx.beginPath();
|
||||
ctx.strokeStyle = colors.selectedOutline;
|
||||
ctx.lineWidth = edge;
|
||||
const rect = stateStore.stepPosition[selectedStep.id];
|
||||
ctx.rect(
|
||||
selectedStep.position!.left - edge,
|
||||
selectedStep.position!.top - edge,
|
||||
rect.width + edge * 2,
|
||||
rect.height + edge * 2
|
||||
);
|
||||
ctx.stroke();
|
||||
}
|
||||
|
||||
// draw viewport
|
||||
ctx.beginPath();
|
||||
ctx.strokeStyle = colors.viewOutline;
|
||||
ctx.fillStyle = colors.view;
|
||||
ctx.lineWidth = 1 / canvasTransform.scaleX;
|
||||
ctx.rect(viewportBounds.value.x, viewportBounds.value.y, viewportBounds.value.width, viewportBounds.value.height);
|
||||
ctx.fill();
|
||||
ctx.stroke();
|
||||
}
|
||||
|
||||
// -- Resizing --
|
||||
const minimap: Ref<HTMLCanvasElement | null> = ref(null);
|
||||
const { position: dragHandlePosition, isDragging: isHandleDragging } = useDraggable(minimap, {
|
||||
preventDefault: true,
|
||||
exact: true,
|
||||
});
|
||||
const minimapSize = ref(parseInt(localStorage.getItem("overview-size") || size.default.toString()));
|
||||
|
||||
watch(dragHandlePosition, () => {
|
||||
// resize
|
||||
minimapSize.value = Math.max(
|
||||
unref(props.viewportBounds.right) - dragHandlePosition.value.x,
|
||||
unref(props.viewportBounds.bottom) - dragHandlePosition.value.y
|
||||
);
|
||||
|
||||
// clamp
|
||||
minimapSize.value = Math.min(Math.max(minimapSize.value, size.min), size.max);
|
||||
});
|
||||
|
||||
watch(isHandleDragging, () => {
|
||||
if (!isHandleDragging.value) {
|
||||
localStorage.setItem("overview-size", minimapSize.value.toString());
|
||||
}
|
||||
});
|
||||
|
||||
// -- Repositioning Viewport --
|
||||
|
||||
/** Scaling factor of the canvas element. Draw size in relation to actual size on screen */
|
||||
const scaleFactor = computed(() => size.max / minimapSize.value);
|
||||
let dragViewport = false;
|
||||
|
||||
useDraggable(canvas, {
|
||||
onStart: (position, event) => {
|
||||
// minimap coordinates to global coordinates
|
||||
const [x, y] = canvasTransform
|
||||
.inverse()
|
||||
.scale([scaleFactor.value, scaleFactor.value])
|
||||
.apply([event.offsetX, event.offsetY]);
|
||||
|
||||
if (viewportBounds.value.isPointInBounds({ x, y })) {
|
||||
dragViewport = true;
|
||||
}
|
||||
},
|
||||
onMove: (position, event) => {
|
||||
if (!dragViewport || Object.values(props.steps).length === 0) {
|
||||
return;
|
||||
}
|
||||
|
||||
// minimap coordinates to global coordinates, without translation
|
||||
const [x, y] = canvasTransform
|
||||
.resetTranslation()
|
||||
.inverse()
|
||||
.scale([scaleFactor.value, scaleFactor.value])
|
||||
.apply([-event.movementX, -event.movementY]);
|
||||
|
||||
emit("panBy", { x, y });
|
||||
},
|
||||
onEnd(position, event) {
|
||||
// minimap coordinates to global coordinates
|
||||
const [x, y] = canvasTransform
|
||||
.inverse()
|
||||
.scale([scaleFactor.value, scaleFactor.value])
|
||||
.apply([event.offsetX, event.offsetY]);
|
||||
|
||||
if (!dragViewport && Object.values(props.steps).length > 0) {
|
||||
emit("moveTo", { x, y });
|
||||
}
|
||||
|
||||
dragViewport = false;
|
||||
},
|
||||
});
|
||||
</script>
|
||||
|
||||
<template>
|
||||
<div ref="overview" class="workflow-overview" :style="style" aria-hidden="true">
|
||||
<div class="workflow-overview-body" @click="onClick">
|
||||
<svg width="100%" height="100%" :viewBox="viewBox">
|
||||
<MinimapNode v-for="step of Object.values(steps)" :key="step.id" class="mini-node" :step="step" />
|
||||
<rect
|
||||
ref="rect"
|
||||
class="viewport"
|
||||
:x="visible.x"
|
||||
:y="visible.y"
|
||||
:width="visible.width"
|
||||
:height="visible.height"
|
||||
stroke-width="1%"
|
||||
rx="1%"
|
||||
fill="white"
|
||||
fill-opacity="0.5"
|
||||
@click.stop />
|
||||
</svg>
|
||||
</div>
|
||||
<div
|
||||
ref="minimap"
|
||||
class="workflow-overview"
|
||||
:style="{ '--workflow-overview-size': `${minimapSize + size.padding + size.border}px` }">
|
||||
<canvas ref="canvas" class="workflow-overview-body" :width="size.max" :height="size.max" />
|
||||
</div>
|
||||
</template>
|
||||
<script>
|
||||
import MinimapNode from "./MinimapNode.vue";
|
||||
import { computed, reactive, ref } from "vue";
|
||||
import { useDraggable, UseElementBoundingReturn } from "@vueuse/core";
|
||||
import { useWorkflowStateStore } from "@/stores/workflowEditorStateStore";
|
||||
|
||||
export default {
|
||||
components: {
|
||||
MinimapNode,
|
||||
},
|
||||
props: {
|
||||
steps: {
|
||||
type: Object,
|
||||
required: true,
|
||||
},
|
||||
width: {
|
||||
type: Number,
|
||||
default: 200,
|
||||
},
|
||||
height: {
|
||||
type: Number,
|
||||
default: 200,
|
||||
},
|
||||
scale: {
|
||||
type: Number,
|
||||
default: 1,
|
||||
},
|
||||
pan: {
|
||||
type: Object,
|
||||
default() {
|
||||
return { x: 0, y: 0 };
|
||||
},
|
||||
},
|
||||
rootOffset: {
|
||||
type: UseElementBoundingReturn,
|
||||
required: true,
|
||||
},
|
||||
},
|
||||
setup(props, { emit }) {
|
||||
const overview = ref(null);
|
||||
const overviewPosition = reactive(useDraggable(overview, { preventDefault: true, exact: true }));
|
||||
const size = ref(parseInt(localStorage.getItem("overview-size")) || 150);
|
||||
const visible = computed(() => {
|
||||
const x = props.pan.x / -props.scale;
|
||||
const y = props.pan.y / -props.scale;
|
||||
const width = props.rootOffset.width / props.scale;
|
||||
const height = props.rootOffset.bottom / props.scale;
|
||||
const rval = { x, y, width, height };
|
||||
return rval;
|
||||
});
|
||||
const stepStore = useWorkflowStateStore();
|
||||
const bounds = computed(() => {
|
||||
let left = props.pan.x * -1;
|
||||
let right = props.rootOffset.width;
|
||||
let top = props.pan.y * -1;
|
||||
let bottom = props.rootOffset.bottom;
|
||||
Object.values(props.steps).forEach((step) => {
|
||||
const stepPosition = stepStore.stepPosition[step.id];
|
||||
left = Math.min(left, step.position.left);
|
||||
right = Math.max(right, stepPosition.right);
|
||||
top = Math.min(top, step.position.top);
|
||||
bottom = Math.max(bottom, stepPosition.bottom);
|
||||
});
|
||||
<style lang="scss" scoped>
|
||||
@import "~bootstrap/scss/_functions.scss";
|
||||
@import "theme/blue.scss";
|
||||
|
||||
return {
|
||||
left: left / props.scale,
|
||||
right: right / props.scale,
|
||||
top: top / props.scale,
|
||||
bottom: bottom / props.scale,
|
||||
};
|
||||
});
|
||||
const scaleFactorX = computed(() => {
|
||||
return (bounds.value.right - bounds.value.left) / size.value;
|
||||
});
|
||||
const scaleFactorY = computed(() => {
|
||||
return (bounds.value.bottom - bounds.value.top) / size.value;
|
||||
});
|
||||
const rect = ref(null);
|
||||
let startX = null;
|
||||
let startY = null;
|
||||
const rectPosition = reactive(
|
||||
useDraggable(rect, {
|
||||
onStart: (position, event) => {
|
||||
startX = event.clientX;
|
||||
startY = event.clientY;
|
||||
},
|
||||
onMove: (position, event) => {
|
||||
const offsetX = event.clientX - startX;
|
||||
const offsetY = event.clientY - startY;
|
||||
emit("pan-by", { x: -offsetX * scaleFactorX.value, y: -offsetY * scaleFactorY.value });
|
||||
startX = event.clientX;
|
||||
startY = event.clientY;
|
||||
},
|
||||
})
|
||||
);
|
||||
return {
|
||||
overview,
|
||||
overviewPosition,
|
||||
rect,
|
||||
rectPosition,
|
||||
size,
|
||||
visible,
|
||||
bounds,
|
||||
scaleFactorX,
|
||||
scaleFactorY,
|
||||
startX,
|
||||
startY,
|
||||
};
|
||||
},
|
||||
data() {
|
||||
return {
|
||||
maxSize: 300,
|
||||
minSize: 50,
|
||||
};
|
||||
},
|
||||
computed: {
|
||||
style() {
|
||||
if (this.overviewPosition.x) {
|
||||
let newSize = Math.max(
|
||||
this.rootOffset.right - this.overviewPosition.x,
|
||||
this.rootOffset.bottom - this.overviewPosition.y
|
||||
);
|
||||
if (newSize > this.maxSize) {
|
||||
newSize = this.maxSize;
|
||||
} else if (newSize < this.minSize) {
|
||||
newSize = this.minSize;
|
||||
}
|
||||
if (!this.overviewPosition.isDragging) {
|
||||
localStorage.setItem("overview-size", newSize);
|
||||
}
|
||||
this.setSize(newSize);
|
||||
}
|
||||
return { width: `${this.size}px`, height: `${this.size}px` };
|
||||
},
|
||||
viewBox() {
|
||||
return `${this.bounds.left} ${this.bounds.top} ${this.bounds.right} ${this.bounds.bottom}`;
|
||||
},
|
||||
},
|
||||
methods: {
|
||||
setSize(size) {
|
||||
this.size = size;
|
||||
},
|
||||
onClick(e) {
|
||||
const x = e.offsetX * this.scaleFactorX;
|
||||
const y = e.offsetY * this.scaleFactorY;
|
||||
this.$emit("moveTo", { x, y });
|
||||
},
|
||||
},
|
||||
};
|
||||
</script>
|
||||
.workflow-overview-body {
|
||||
--node-color: #{$brand-primary};
|
||||
--error-color: #{$state-danger-bg};
|
||||
--selected-outline-color: #{$brand-primary};
|
||||
--view-color: #{fade-out($brand-dark, 0.8)};
|
||||
--view-outline-color: #{$brand-info};
|
||||
}
|
||||
</style>
|
||||
|
||||
@@ -17,9 +17,10 @@ export function useD3Zoom(
|
||||
minZoom: number,
|
||||
maxZoom: number,
|
||||
targetRef: Ref<HTMLElement | null>,
|
||||
scroll: UseScrollReturn
|
||||
scroll: UseScrollReturn,
|
||||
initialPan: XYPosition = { x: 0, y: 0 }
|
||||
) {
|
||||
const transform = ref({ x: 0, y: 0, k: k });
|
||||
const transform = ref({ x: initialPan.x, y: initialPan.y, k: k });
|
||||
const d3Zoom = zoom<HTMLElement, unknown>().filter(filter).scaleExtent([minZoom, maxZoom]);
|
||||
|
||||
watch(targetRef, () => {
|
||||
|
||||
@@ -1,14 +1,33 @@
|
||||
import { useElementBounding } from "@vueuse/core";
|
||||
import { onUnmounted, reactive, type Ref } from "vue";
|
||||
import { onUnmounted, unref, watch, type ComputedRef, type Ref } from "vue";
|
||||
import type { useWorkflowStateStore } from "@/stores/workflowEditorStateStore";
|
||||
|
||||
export function useNodePosition(
|
||||
nodeRef: Ref<HTMLElement | null>,
|
||||
stepId: number,
|
||||
workflowStateStore: ReturnType<typeof useWorkflowStateStore>
|
||||
workflowStateStore: ReturnType<typeof useWorkflowStateStore>,
|
||||
scale: ComputedRef<number> | Ref<number>
|
||||
) {
|
||||
const position = useElementBounding(nodeRef, { windowResize: false });
|
||||
workflowStateStore.setStepPosition(stepId, reactive(position));
|
||||
|
||||
watch(
|
||||
Object.values(position),
|
||||
() => {
|
||||
workflowStateStore.setStepPosition(stepId, {
|
||||
height: unref(position.height) / scale.value,
|
||||
width: unref(position.width) / scale.value,
|
||||
left: unref(position.left) / scale.value,
|
||||
right: unref(position.right) / scale.value,
|
||||
top: unref(position.top) / scale.value,
|
||||
bottom: unref(position.bottom) / scale.value,
|
||||
x: unref(position.x) / scale.value,
|
||||
y: unref(position.y) / scale.value,
|
||||
update: position.update,
|
||||
});
|
||||
},
|
||||
{ immediate: true }
|
||||
);
|
||||
|
||||
onUnmounted(() => {
|
||||
workflowStateStore.deleteStepPosition(stepId);
|
||||
});
|
||||
|
||||
@@ -0,0 +1,202 @@
|
||||
/** simple rectangle without rotation */
|
||||
export interface Rectangle {
|
||||
x: number;
|
||||
y: number;
|
||||
width: number;
|
||||
height: number;
|
||||
}
|
||||
|
||||
/**
|
||||
* Class compatible with rectangle interface.
|
||||
* Provides additional properties and methods specific to bounding boxes.
|
||||
* Useful to calculate the bounds of multiple rectangles,
|
||||
* using the `fitRectangle` method.
|
||||
*/
|
||||
export class AxisAlignedBoundingBox implements Rectangle {
|
||||
/** x coordinate of left edge */
|
||||
x = Infinity;
|
||||
|
||||
/** y coordinate of upper edge */
|
||||
y = Infinity;
|
||||
|
||||
/** x coordinate of right edge */
|
||||
endX = -Infinity;
|
||||
|
||||
/** y coordinate of lower edge */
|
||||
endY = -Infinity;
|
||||
|
||||
get width() {
|
||||
const width = this.endX - this.x;
|
||||
return width > 0 ? width : 0;
|
||||
}
|
||||
|
||||
set width(value) {
|
||||
this.endX = this.x + value;
|
||||
}
|
||||
|
||||
get height() {
|
||||
const height = this.endY - this.y;
|
||||
return height > 0 ? height : 0;
|
||||
}
|
||||
|
||||
set height(value) {
|
||||
this.endY = this.y + value;
|
||||
}
|
||||
|
||||
reset() {
|
||||
this.x = Infinity;
|
||||
this.y = Infinity;
|
||||
this.endX = -Infinity;
|
||||
this.endY = -Infinity;
|
||||
}
|
||||
|
||||
/** expand bounding box to fit a rectangle */
|
||||
fitRectangle(rect: Readonly<Rectangle>) {
|
||||
if (this.x > rect.x) {
|
||||
this.x = rect.x;
|
||||
}
|
||||
|
||||
if (this.y > rect.y) {
|
||||
this.y = rect.y;
|
||||
}
|
||||
|
||||
if (this.endX < rect.x + rect.width) {
|
||||
this.endX = rect.x + rect.width;
|
||||
}
|
||||
|
||||
if (this.endY < rect.y + rect.height) {
|
||||
this.endY = rect.y + rect.height;
|
||||
}
|
||||
}
|
||||
|
||||
/** make width and height the same, maintaining the center of the bounding box */
|
||||
squareCenter() {
|
||||
if (this.width > this.height) {
|
||||
const difference = this.width - this.height;
|
||||
this.y -= difference * 0.5;
|
||||
this.endY += difference * 0.5;
|
||||
} else {
|
||||
const difference = this.height - this.width;
|
||||
this.x -= difference * 0.5;
|
||||
this.endX += difference * 0.5;
|
||||
}
|
||||
}
|
||||
|
||||
/** expand bounding box in every direction */
|
||||
expand(by: number) {
|
||||
this.x -= by;
|
||||
this.y -= by;
|
||||
this.endX += by;
|
||||
this.endY += by;
|
||||
}
|
||||
|
||||
/** check if a point is inside the bounding box */
|
||||
isPointInBounds(point: { x: number; y: number }) {
|
||||
if (point.x > this.x && point.y > this.y && point.x < this.endX && point.y < this.endY) {
|
||||
return true;
|
||||
} else {
|
||||
return false;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* Format
|
||||
[a b
|
||||
c d
|
||||
e f]
|
||||
as used by canvas: https://developer.mozilla.org/en-US/docs/Web/API/CanvasRenderingContext2D/transform
|
||||
*/
|
||||
// prettier-ignore
|
||||
export type Matrix = [
|
||||
number, number,
|
||||
number, number,
|
||||
number, number,
|
||||
];
|
||||
|
||||
/** vector as a tuple */
|
||||
export type Vector = [number, number];
|
||||
|
||||
/**
|
||||
* Wraps basic transform operations.
|
||||
* Each operation returns a new instance, so method calls can be chained
|
||||
* without mutating the initial transform.
|
||||
*/
|
||||
export class Transform {
|
||||
matrix: Matrix;
|
||||
|
||||
constructor(matrix: Matrix = [1, 0, 0, 1, 0, 0]) {
|
||||
this.matrix = matrix;
|
||||
}
|
||||
|
||||
/** returns a new transform with a translation vector added */
|
||||
translate(vector: Vector) {
|
||||
// prettier-ignore
|
||||
return new Transform([
|
||||
this.matrix[0], this.matrix[1],
|
||||
this.matrix[2], this.matrix[3],
|
||||
this.matrix[4] + vector[0], this.matrix[5] + vector[1]
|
||||
]);
|
||||
}
|
||||
|
||||
/** returns a new transform scaled by a given vector */
|
||||
scale(vector: Vector) {
|
||||
// prettier-ignore
|
||||
return new Transform([
|
||||
this.matrix[0] * vector[0], this.matrix[1] * vector[1],
|
||||
this.matrix[2] * vector[0], this.matrix[3] * vector[1],
|
||||
this.matrix[4], this.matrix[5]
|
||||
]);
|
||||
}
|
||||
|
||||
/** Returns the inverse vector. Can be used to un-transform things */
|
||||
inverse() {
|
||||
const m = this.matrix;
|
||||
// https://www.wolframalpha.com/input?i=Inverse+%5B%7B%7Ba%2Cc%2Ce%7D%2C%7Bb%2Cd%2Cf%7D%2C%7B0%2C0%2C1%7D%7D%5D
|
||||
const denominator = m[0] * m[3] - m[1] * m[2];
|
||||
|
||||
const a = m[3] / denominator;
|
||||
const b = m[1] / -denominator;
|
||||
const c = m[2] / -denominator;
|
||||
const d = m[0] / denominator;
|
||||
const e = (m[3] * m[4] - m[2] * m[5]) / -denominator;
|
||||
const f = (m[1] * m[4] - m[0] * m[5]) / denominator;
|
||||
|
||||
// prettier-ignore
|
||||
return new Transform([
|
||||
a, b,
|
||||
c, d,
|
||||
e, f
|
||||
]);
|
||||
}
|
||||
|
||||
/** applies this transform to a rendering context */
|
||||
applyToContext(ctx: CanvasRenderingContext2D): void {
|
||||
ctx.transform(...this.matrix);
|
||||
}
|
||||
|
||||
/** returns a vector transformed by this transform */
|
||||
apply(vector: Vector): Vector {
|
||||
return [
|
||||
this.matrix[0] * vector[0] + this.matrix[2] * vector[1] + this.matrix[4],
|
||||
this.matrix[1] * vector[0] + this.matrix[3] * vector[1] + this.matrix[5],
|
||||
];
|
||||
}
|
||||
|
||||
/** removes the translation portion of the transform */
|
||||
resetTranslation(): Transform {
|
||||
// prettier-ignore
|
||||
return new Transform ([
|
||||
this.matrix[0], this.matrix[1],
|
||||
this.matrix[2], this.matrix[3],
|
||||
0, 0
|
||||
]);
|
||||
}
|
||||
|
||||
get scaleX() {
|
||||
return this.matrix[0];
|
||||
}
|
||||
|
||||
get scaleY() {
|
||||
return this.matrix[3];
|
||||
}
|
||||
}
|
||||
@@ -252,7 +252,11 @@ export const useWorkflowStepStore = defineStore("workflowStepStore", {
|
||||
},
|
||||
removeConnection(connection: Connection) {
|
||||
const inputStep = this.getStep(connection.input.stepId);
|
||||
Vue.delete(inputStep.input_connections, connection.input.name);
|
||||
if (this.getStepExtraInputs(inputStep.id).find((input) => connection.input.name === input.name)) {
|
||||
inputStep.input_connections[connection.input.name] = undefined;
|
||||
} else {
|
||||
Vue.delete(inputStep.input_connections, connection.input.name);
|
||||
}
|
||||
this.updateStep(inputStep);
|
||||
},
|
||||
removeStep(this: State, stepId: number) {
|
||||
|
||||
@@ -209,45 +209,51 @@
|
||||
@extend .mr-1;
|
||||
}
|
||||
.workflow-overview {
|
||||
--workflow-overview-size: 150px;
|
||||
--workflow-overview-min-size: 50px;
|
||||
--workflow-overview-max-size: 300px;
|
||||
--workflow-overview-padding: 7px;
|
||||
--workflow-overview-border: 1px;
|
||||
|
||||
border-top-left-radius: 0.3rem;
|
||||
cursor: pointer;
|
||||
cursor: nwse-resize;
|
||||
position: absolute;
|
||||
width: 150px;
|
||||
height: 150px;
|
||||
width: var(--workflow-overview-size);
|
||||
height: var(--workflow-overview-size);
|
||||
right: 0px;
|
||||
bottom: 0px;
|
||||
border-top: solid $border-color 1px;
|
||||
border-left: solid $border-color 1px;
|
||||
padding: 7px 0 0 7px;
|
||||
border-top: solid $border-color var(--workflow-overview-border);
|
||||
border-left: solid $border-color var(--workflow-overview-border);
|
||||
background: $workflow-overview-bg no-repeat url("../../assets/images/resizable.png");
|
||||
z-index: 20000;
|
||||
overflow: hidden;
|
||||
max-width: 300px;
|
||||
max-height: 300px;
|
||||
min-width: 50px;
|
||||
min-height: 50px;
|
||||
.viewport {
|
||||
stroke: #25537b;
|
||||
}
|
||||
padding: var(--workflow-overview-padding) 0 0 var(--workflow-overview-padding);
|
||||
|
||||
// account for padding and border
|
||||
max-width: calc(
|
||||
var(--workflow-overview-max-size) + var(--workflow-overview-padding) +
|
||||
var(--workflow-overview-border)
|
||||
);
|
||||
max-height: calc(
|
||||
var(--workflow-overview-max-size) + var(--workflow-overview-padding) +
|
||||
var(--workflow-overview-border)
|
||||
);
|
||||
min-width: calc(
|
||||
var(--workflow-overview-min-size) + var(--workflow-overview-padding) +
|
||||
var(--workflow-overview-border)
|
||||
);
|
||||
min-height: calc(
|
||||
var(--workflow-overview-min-size) + var(--workflow-overview-padding) +
|
||||
var(--workflow-overview-border)
|
||||
);
|
||||
|
||||
.workflow-overview-body {
|
||||
cursor: pointer;
|
||||
position: relative;
|
||||
overflow: hidden;
|
||||
width: 100%;
|
||||
height: 100%;
|
||||
}
|
||||
.mini-node {
|
||||
+ .ok {
|
||||
// this is $primary-brand / #25537b
|
||||
filter: invert(26%) sepia(75%) saturate(489%) hue-rotate(166deg) brightness(90%) contrast(89%);
|
||||
}
|
||||
+ .error {
|
||||
// this is #e31a1e
|
||||
filter: invert(16%) sepia(86%) saturate(3962%) hue-rotate(350deg) brightness(96%) contrast(97%);
|
||||
}
|
||||
+ .highlight {
|
||||
filter: invert(14%) sepia(38%) saturate(1544%) hue-rotate(321deg) brightness(84%) contrast(117%);
|
||||
}
|
||||
}
|
||||
}
|
||||
#input-choices-menu {
|
||||
color: black;
|
||||
|
||||
@@ -615,6 +615,11 @@ workflow_editor:
|
||||
type: xpath
|
||||
selector: >
|
||||
//div[@id='form-element-__annotation']//textarea
|
||||
step_when:
|
||||
type: xpath
|
||||
selector: >
|
||||
//div[@id='form-element-__conditional']//input
|
||||
param_type_form: '#parameter_definition\|parameter_type'
|
||||
configure_output:
|
||||
type: xpath
|
||||
selector: >
|
||||
|
||||
@@ -4,8 +4,8 @@ import Backbone from "backbone";
|
||||
import { getAppRoot } from "onload/loadConfig";
|
||||
import { getGalaxyInstance } from "app";
|
||||
import _l from "utils/localization";
|
||||
import * as d3 from "d3";
|
||||
import { event as currentEvent } from "d3";
|
||||
import * as d3 from "d3v3";
|
||||
import { event as currentEvent } from "d3v3";
|
||||
import visualization from "viz/visualization";
|
||||
import mod_utils from "utils/utils";
|
||||
import config from "utils/config";
|
||||
|
||||
@@ -1,7 +1,7 @@
|
||||
import $ from "jquery";
|
||||
import Backbone from "backbone";
|
||||
import _l from "utils/localization";
|
||||
import * as d3 from "d3";
|
||||
import * as d3 from "d3v3";
|
||||
import visualization_mod from "viz/visualization";
|
||||
import { Dataset } from "mvc/dataset/data";
|
||||
import mod_icon_btn from "mvc/ui/icon-button";
|
||||
|
||||
@@ -8,7 +8,7 @@ import $ from "jquery";
|
||||
import Backbone from "backbone";
|
||||
import { getAppRoot } from "onload/loadConfig";
|
||||
import _l from "utils/localization";
|
||||
import * as d3 from "d3";
|
||||
import * as d3 from "d3v3";
|
||||
import visualization from "viz/visualization";
|
||||
import tracks from "viz/trackster/tracks";
|
||||
import tools from "viz/tools";
|
||||
|
||||
@@ -3,7 +3,7 @@
|
||||
*/
|
||||
import _ from "underscore";
|
||||
import $ from "jquery";
|
||||
import * as d3 from "d3";
|
||||
import * as d3 from "d3v3";
|
||||
import Backbone from "backbone";
|
||||
import { getAppRoot } from "onload/loadConfig";
|
||||
import util from "viz/trackster/util";
|
||||
|
||||
@@ -4515,6 +4515,11 @@ d3@^7.8.0:
|
||||
d3-transition "3"
|
||||
d3-zoom "3"
|
||||
|
||||
"d3v3@npm:d3@3":
|
||||
version "3.5.17"
|
||||
resolved "https://registry.yarnpkg.com/d3/-/d3-3.5.17.tgz#bc46748004378b21a360c9fc7cf5231790762fb8"
|
||||
integrity sha512-yFk/2idb8OHPKkbAL8QaOaqENNoMhIaSHZerk3oQsECwkObkCpJyjYwCe+OHiq6UEdhe1m8ZGARRRO3ljFjlKg==
|
||||
|
||||
d@1, d@^1.0.1:
|
||||
version "1.0.1"
|
||||
resolved "https://registry.npmjs.org/d/-/d-1.0.1.tgz"
|
||||
|
||||
@@ -537,7 +537,7 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin):
|
||||
reset_user, prt = self.get_reset_token(trans, email)
|
||||
if prt:
|
||||
host = self.__get_host(trans)
|
||||
reset_url = url_for(controller="root", action="login", token=prt.token)
|
||||
reset_url = url_for(controller="login", action="start", token=prt.token)
|
||||
body = PASSWORD_RESET_TEMPLATE % (
|
||||
host,
|
||||
prt.expiration_time.strftime(trans.app.config.pretty_datetime_format),
|
||||
|
||||
@@ -65,7 +65,7 @@ def load_edam_tree_from_tsv_stream(tsv_stream: TextIO, *included_terms: str):
|
||||
|
||||
parents = fields[parents_column].split("|")
|
||||
edam[term_id] = {
|
||||
"label": fields[label_column],
|
||||
"label": fields[label_column].strip('"'),
|
||||
"definition": fields[definition_column].strip('"'),
|
||||
"parents": [x[len(EDAM_PREFIX) :] for x in parents if x.startswith(EDAM_PREFIX)],
|
||||
}
|
||||
|
||||
@@ -1,4 +1,7 @@
|
||||
"""This module contains a linting function for a tool's help."""
|
||||
|
||||
from typing import Union
|
||||
|
||||
from galaxy.util import (
|
||||
rst_to_html,
|
||||
unicodify,
|
||||
@@ -30,10 +33,22 @@ def lint_help(tool_xml, lint_ctx):
|
||||
if "TODO" in help_text:
|
||||
lint_ctx.warn("Help contains TODO text.", node=helps[0])
|
||||
|
||||
try:
|
||||
rst_to_html(help_text, error=True)
|
||||
except Exception as e:
|
||||
lint_ctx.warn(f"Invalid reStructuredText found in help - [{unicodify(e)}].", node=helps[0])
|
||||
return
|
||||
invalid_rst = rst_invalid(help_text)
|
||||
if invalid_rst:
|
||||
lint_ctx.warn(f"Invalid reStructuredText found in help - [{invalid_rst}].", node=helps[0])
|
||||
else:
|
||||
lint_ctx.valid("Help contains valid reStructuredText.", node=helps[0])
|
||||
|
||||
lint_ctx.valid("Help contains valid reStructuredText.", node=helps[0])
|
||||
|
||||
def rst_invalid(text: str) -> Union[bool, str]:
|
||||
"""
|
||||
Predicate to determine if text is invalid reStructuredText.
|
||||
Return False if the supplied text is valid reStructuredText or
|
||||
a string indicating the problem.
|
||||
"""
|
||||
invalid_rst: Union[bool, str] = False
|
||||
try:
|
||||
rst_to_html(text, error=True)
|
||||
except Exception as e:
|
||||
invalid_rst = unicodify(e)
|
||||
return invalid_rst
|
||||
|
||||
@@ -109,7 +109,7 @@ PARAMETER_VALIDATOR_TYPE_COMPATIBILITY = {
|
||||
}
|
||||
|
||||
PARAM_TYPE_CHILD_COMBINATIONS = [
|
||||
("./options", ["select", "drill_down"]),
|
||||
("./options", ["data", "select", "drill_down"]),
|
||||
("./options/option", ["drill_down"]),
|
||||
("./column", ["data_column"]),
|
||||
]
|
||||
@@ -186,6 +186,37 @@ def lint_inputs(tool_xml, lint_ctx):
|
||||
lint_ctx.warn(
|
||||
f"Param input [{param_name}] with no format specified - 'data' format will be assumed.", node=param
|
||||
)
|
||||
options = param.findall("./options")
|
||||
has_options_filter_attribute = False
|
||||
if len(options) == 1:
|
||||
for oa in options[0].attrib:
|
||||
if oa == "options_filter_attribute":
|
||||
has_options_filter_attribute = True
|
||||
else:
|
||||
lint_ctx.error(f"Data parameter [{param_name}] uses invalid attribute: {oa}", node=param)
|
||||
elif len(options) > 1:
|
||||
lint_ctx.error(f"Data parameter [{param_name}] contains multiple options elements.", node=options[1])
|
||||
# for data params only filters with key='build' of type='data_meta' are allowed
|
||||
filters = param.findall("./options/filter")
|
||||
for f in filters:
|
||||
if not f.get("ref"):
|
||||
lint_ctx.error(
|
||||
f"Data parameter [{param_name}] filter needs to define a ref attribute",
|
||||
node=f,
|
||||
)
|
||||
if has_options_filter_attribute:
|
||||
if f.get("type") != "data_meta":
|
||||
lint_ctx.error(
|
||||
f'Data parameter [{param_name}] for filters only type="data_meta" is allowed, found type="{f.get("type")}"',
|
||||
node=f,
|
||||
)
|
||||
else:
|
||||
if f.get("key") != "dbkey" or f.get("type") != "data_meta":
|
||||
lint_ctx.error(
|
||||
f'Data parameter [{param_name}] for filters only type="data_meta" and key="dbkey" are allowed, found type="{f.get("type")}" and key="{f.get("key")}"',
|
||||
node=f,
|
||||
)
|
||||
|
||||
elif param_type == "select":
|
||||
# get dynamic/statically defined options
|
||||
dynamic_options = param.get("dynamic_options", None)
|
||||
|
||||
@@ -190,7 +190,7 @@ def looks_like_a_data_manager_xml(path):
|
||||
|
||||
def as_dict_if_looks_like_yaml_or_cwl_with_class(path, classes):
|
||||
"""
|
||||
get a dict from yaml file if it contains `class: CLASS`, where CLASS is
|
||||
get a dict from yaml file if it contains a line `class: CLASS`, where CLASS is
|
||||
any string given in CLASSES. must appear in the first 5k and also load
|
||||
properly in total.
|
||||
"""
|
||||
@@ -199,7 +199,7 @@ def as_dict_if_looks_like_yaml_or_cwl_with_class(path, classes):
|
||||
start_contents = f.read(5 * 1024)
|
||||
except UnicodeDecodeError:
|
||||
return False, None
|
||||
if re.search(rf"\nclass:\s+({'|'.join(classes)})\s*\n", start_contents) is None:
|
||||
if re.search(rf"^class:\s+{'|'.join(classes)}\s*$", start_contents, re.MULTILINE) is None:
|
||||
return False, None
|
||||
|
||||
with open(path) as f:
|
||||
|
||||
@@ -3999,14 +3999,17 @@ dataset for the contained input of the type specified using the ``type`` tag.
|
||||
<xs:complexType name="ParamOptions">
|
||||
<xs:annotation>
|
||||
<xs:documentation xml:lang="en"><
|
||||
for an example of how to use this tag set. This tag set is optionally contained
|
||||
within the ``<param>`` tag when the ``type`` attribute value is ``select`` or
|
||||
``data`` and used to dynamically generated lists of options. This tag set
|
||||
dynamically creates a list of options whose values can be
|
||||
obtained from a predefined file stored locally or a dataset selected from the
|
||||
current history.
|
||||
``data`` and used to dynamically generated lists of options.
|
||||
|
||||
For data parameters this tag can be used to restrict possible input datasets to datasets that match the ``dbkey`` of another data input by including a ``data_meta`` filter. See for
|
||||
instance here: [/tools/maf/interval2maf.xml](https://github.com/galaxyproject/galaxy/blob/master/tools/maf/interval2maf.xml)
|
||||
|
||||
For select parameters this tag set dynamically creates a list of options whose
|
||||
values can be obtained from a predefined file stored locally or a dataset
|
||||
selected from the current history.
|
||||
|
||||
There are at least five basic ways to use this tag - four of these correspond to
|
||||
a ``from_XXX`` attribute on the ``options`` directive and the other is to
|
||||
|
||||
@@ -747,6 +747,67 @@ steps:
|
||||
workflow = self.workflow_populator.download_workflow(workflow_id)
|
||||
assert len(workflow["steps"]) == 3
|
||||
|
||||
@selenium_test
|
||||
def test_editor_create_conditional_step(self):
|
||||
editor = self.components.workflow_editor
|
||||
self.workflow_create_new(annotation="simple when step definition")
|
||||
# Insert a boolean parameter
|
||||
self.workflow_editor_add_input(item_name="parameter_input")
|
||||
param_type_element = editor.param_type_form.wait_for_present()
|
||||
self.switch_param_type(param_type_element, "Boolean")
|
||||
editor.label_input.wait_for_and_send_keys("param_input")
|
||||
editor.tool_menu.wait_for_visible()
|
||||
# Insert cat tool
|
||||
self.tool_open("cat")
|
||||
self.sleep_for(self.wait_types.UX_RENDER)
|
||||
editor.label_input.wait_for_and_send_keys("downstream_step")
|
||||
# Insert head tool
|
||||
self.tool_open("head")
|
||||
self.workflow_editor_click_option("Auto Layout")
|
||||
self.sleep_for(self.wait_types.UX_RENDER)
|
||||
editor.label_input.wait_for_and_send_keys("conditional_step")
|
||||
# Connect head to cat
|
||||
self.workflow_editor_connect("conditional_step#out_file1", "downstream_step#input1")
|
||||
self.assert_connected("conditional_step#out_file1", "downstream_step#input1")
|
||||
# Make head tool conditional
|
||||
conditional_node = editor.node._(label="conditional_step")
|
||||
conditional_node.input_terminal(name="input").wait_for_present()
|
||||
# Assert no when input before making step conditional
|
||||
conditional_node.input_terminal(name="when").wait_for_absent()
|
||||
conditional_toggle = editor.step_when.wait_for_present()
|
||||
self.action_chains().move_to_element(conditional_toggle).click().perform()
|
||||
# Toggling conditional should cause when input to appear
|
||||
conditional_node.input_terminal(name="when").wait_for_present()
|
||||
self.action_chains().move_to_element(conditional_toggle).click().perform()
|
||||
# Toggling conditional should cause when input to disappear
|
||||
conditional_node.input_terminal(name="when").wait_for_absent()
|
||||
self.action_chains().move_to_element(conditional_toggle).click().perform()
|
||||
conditional_node.input_terminal(name="when").wait_for_present()
|
||||
# Output connection should be invalid, as output from conditional step is potentially null
|
||||
self.assert_connection_invalid("conditional_step#out_file1", "downstream_step#input1")
|
||||
downstream_step = editor.node._(label="downstream_step")
|
||||
downstream_step.destroy.wait_for_and_click()
|
||||
downstream_step.wait_for_absent()
|
||||
# Connect boolean input to when
|
||||
self.workflow_editor_connect("param_input#output", "conditional_step#when")
|
||||
self.assert_connected("param_input#output", "conditional_step#when")
|
||||
# Change boolean input parameter to invalid parameter type
|
||||
editor.node._(label="param_input").wait_for_and_click()
|
||||
param_type_element = editor.param_type_form.wait_for_present()
|
||||
self.switch_param_type(param_type_element, "Text")
|
||||
self.assert_connection_invalid("param_input#output", "conditional_step#when")
|
||||
self.workflow_editor_destroy_connection("conditional_step#when")
|
||||
# Make sure the when input is still shown
|
||||
conditional_node.input_terminal(name="when").wait_for_present()
|
||||
# Assert save button is disabled because of disconnected when
|
||||
save_button = self.components.workflow_editor.save_button
|
||||
save_button.wait_for_visible()
|
||||
# TODO: hook up best practice panel, disable save when "when" not connected
|
||||
# assert save_button.has_class("disabled")
|
||||
|
||||
def switch_param_type(self, element, param_type):
|
||||
self.action_chains().move_to_element(element).click().send_keys(param_type).send_keys(Keys.ENTER).perform()
|
||||
|
||||
@selenium_test
|
||||
def test_editor_invalid_tool_state(self):
|
||||
workflow_populator = self.workflow_populator
|
||||
|
||||
@@ -0,0 +1,24 @@
|
||||
import tempfile
|
||||
|
||||
from galaxy.tool_util.loader_directory import is_a_yaml_with_class
|
||||
|
||||
|
||||
def test_is_a_yaml_with_class():
|
||||
with tempfile.NamedTemporaryFile("w", suffix=".yaml") as tf:
|
||||
fname = tf.name
|
||||
tf.write(
|
||||
"""class: GalaxyWorkflow
|
||||
name: "Test Workflow"
|
||||
inputs:
|
||||
- id: input1
|
||||
outputs:
|
||||
- id: wf_output_1
|
||||
outputSource: first_cat/out_file1
|
||||
steps:
|
||||
- tool_id: cat
|
||||
label: first_cat
|
||||
in:
|
||||
input1: input1"""
|
||||
)
|
||||
tf.flush()
|
||||
assert is_a_yaml_with_class(fname, ["GalaxyWorkflow"])
|
||||
@@ -192,6 +192,43 @@ INPUTS_DATA_PARAM = """
|
||||
</tool>
|
||||
"""
|
||||
|
||||
INPUTS_DATA_PARAM_OPTIONS = """
|
||||
<tool>
|
||||
<inputs>
|
||||
<param name="valid_name" type="data" format="txt">
|
||||
<options>
|
||||
<filter type="data_meta" key="dbkey" ref="input"/>
|
||||
</options>
|
||||
</param>
|
||||
</inputs>
|
||||
</tool>
|
||||
"""
|
||||
|
||||
INPUTS_DATA_PARAM_OPTIONS_FILTER_ATTRIBUTE = """
|
||||
<tool>
|
||||
<inputs>
|
||||
<param name="valid_name" type="data" format="txt">
|
||||
<options options_filter_attribute="metadata.foo">
|
||||
<filter type="data_meta" key="foo" ref="input"/>
|
||||
</options>
|
||||
</param>
|
||||
</inputs>
|
||||
</tool>
|
||||
"""
|
||||
|
||||
INPUTS_DATA_PARAM_INVALIDOPTIONS = """
|
||||
<tool>
|
||||
<inputs>
|
||||
<param name="valid_name" type="data" format="txt">
|
||||
<options/>
|
||||
<options from_file="blah">
|
||||
<filter type="expression"/>
|
||||
</options>
|
||||
</param>
|
||||
</inputs>
|
||||
</tool>
|
||||
"""
|
||||
|
||||
INPUTS_CONDITIONAL = """
|
||||
<tool>
|
||||
<inputs>
|
||||
@@ -1099,6 +1136,42 @@ def test_inputs_data_param(lint_ctx):
|
||||
assert not lint_ctx.error_messages
|
||||
|
||||
|
||||
def test_inputs_data_param_options(lint_ctx):
|
||||
tool_source = get_xml_tool_source(INPUTS_DATA_PARAM_OPTIONS)
|
||||
run_lint(lint_ctx, inputs.lint_inputs, tool_source)
|
||||
assert not lint_ctx.valid_messages
|
||||
assert "Found 1 input parameters." in lint_ctx.info_messages
|
||||
assert len(lint_ctx.info_messages) == 1
|
||||
assert not lint_ctx.warn_messages
|
||||
assert not lint_ctx.error_messages
|
||||
|
||||
|
||||
def test_inputs_data_param_options_filter_attribute(lint_ctx):
|
||||
tool_source = get_xml_tool_source(INPUTS_DATA_PARAM_OPTIONS_FILTER_ATTRIBUTE)
|
||||
run_lint(lint_ctx, inputs.lint_inputs, tool_source)
|
||||
assert not lint_ctx.valid_messages
|
||||
assert "Found 1 input parameters." in lint_ctx.info_messages
|
||||
assert len(lint_ctx.info_messages) == 1
|
||||
assert not lint_ctx.warn_messages
|
||||
assert not lint_ctx.error_messages
|
||||
|
||||
|
||||
def test_inputs_data_param_invalid_options(lint_ctx):
|
||||
tool_source = get_xml_tool_source(INPUTS_DATA_PARAM_INVALIDOPTIONS)
|
||||
run_lint(lint_ctx, inputs.lint_inputs, tool_source)
|
||||
assert not lint_ctx.valid_messages
|
||||
assert "Found 1 input parameters." in lint_ctx.info_messages
|
||||
assert len(lint_ctx.info_messages) == 1
|
||||
assert not lint_ctx.warn_messages
|
||||
assert "Data parameter [valid_name] contains multiple options elements." in lint_ctx.error_messages
|
||||
assert "Data parameter [valid_name] filter needs to define a ref attribute" in lint_ctx.error_messages
|
||||
assert (
|
||||
'Data parameter [valid_name] for filters only type="data_meta" and key="dbkey" are allowed, found type="expression" and key="None"'
|
||||
in lint_ctx.error_messages
|
||||
)
|
||||
assert len(lint_ctx.error_messages) == 3
|
||||
|
||||
|
||||
def test_inputs_conditional(lint_ctx):
|
||||
tool_source = get_xml_tool_source(INPUTS_CONDITIONAL)
|
||||
run_lint(lint_ctx, inputs.lint_inputs, tool_source)
|
||||
@@ -1284,7 +1357,7 @@ def test_inputs_type_child_combinations(lint_ctx):
|
||||
assert not lint_ctx.valid_messages
|
||||
assert not lint_ctx.warn_messages
|
||||
assert (
|
||||
"Parameter [text_param] './options' tags are only allowed for parameters of type ['select', 'drill_down']"
|
||||
"Parameter [text_param] './options' tags are only allowed for parameters of type ['data', 'select', 'drill_down']"
|
||||
in lint_ctx.error_messages
|
||||
)
|
||||
assert (
|
||||
|
||||
Reference in New Issue
Block a user