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Replace jquery for each with es6 methods in workflow manager client
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@guerler
guerler committed Mar 23, 2020
1 parent 13990d6 commit 3fbc2d9
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Showing 10 changed files with 68 additions and 56 deletions.
8 changes: 4 additions & 4 deletions client/galaxy/scripts/components/Panels/ToolBoxWorkflow.vue
View file
Expand Up @@ -77,16 +77,16 @@ export default {
},
workflows: {
type: Array,
required: true
required: true,
},
dataManagers: {
type: Array,
required: true
required: true,
},
moduleSections: {
type: Array,
required: true
}
required: true,
},
},
computed: {
workflowSection() {
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17 changes: 13 additions & 4 deletions client/galaxy/scripts/components/Workflow/Editor/Index.vue
View file
Expand Up @@ -4,8 +4,8 @@
<template v-slot:panel>
<ToolBoxWorkflow
:toolbox="toolbox"
:module-sections="module_sections"
:data-managers="data_managers"
:module-sections="moduleSections"
:data-managers="dataManagers"
:workflows="workflows"
@onInsertTool="onInsertTool"
@onInsertModule="onInsertModule"
Expand Down Expand Up @@ -110,30 +110,39 @@ export default {
props: {
id: {
type: String,
required: true,
},
version: {
type: Number,
required: true,
},
name: {
type: String,
required: true,
},
tags: {
type: Array,
required: true,
},
annotation: {
type: String,
required: true,
},
module_sections: {
moduleSections: {
type: Array,
required: true,
},
data_managers: {
dataManagers: {
type: Array,
required: true,
},
workflows: {
type: Array,
required: true,
},
toolbox: {
type: Array,
required: true,
},
},
data() {
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2 changes: 1 addition & 1 deletion client/galaxy/scripts/components/Workflow/Editor/Node.vue
View file
Expand Up @@ -59,7 +59,7 @@ export default {
node: {
type: Object,
default: null,
}
},
},
computed: {
iconClass() {
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7 changes: 4 additions & 3 deletions client/galaxy/scripts/components/Workflow/Editor/utilities.js
View file
Expand Up @@ -144,9 +144,9 @@ export function getWorkflowParameters(nodes) {
});
}
if (node.post_job_actions) {
Object.entries(node.post_job_actions).forEach(([k, pja]) => {
Object.values(node.post_job_actions).forEach((pja) => {
if (pja.action_arguments) {
Object.entries(pja.action_arguments).forEach(([k, action_argument]) => {
Object.values(pja.action_arguments).forEach((action_argument) => {
if (typeof action_argument === "string") {
const arg_matches = action_argument.match(parameter_re);
if (arg_matches) {
Expand Down Expand Up @@ -198,7 +198,8 @@ export function saveAs(workflow) {
window.location = `${getAppRoot()}workflow/editor?id=${id}`;
hide_modal();
})
.fail(() => {
.fail((err) => {
console.debug(err);
hide_modal();
alert("Saving this workflow failed. Please contact this site's administrator.");
});
Expand Down
2 changes: 1 addition & 1 deletion client/galaxy/scripts/mvc/tool/tool-form-base.js
View file
Expand Up @@ -39,7 +39,7 @@ export default FormBase.extend({
},

/** Allows tool form variation to update tool model */
_update: function() {
_update: function () {
var self = this;
var callback = this.model.get("buildmodel");
if (callback) {
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18 changes: 9 additions & 9 deletions client/galaxy/scripts/mvc/workflow/workflow-forms.js
View file
Expand Up @@ -21,13 +21,13 @@ export class DefaultForm {
id: node.id,
type: node.type,
content_id: node.content_id,
inputs: self.form.data.create()
inputs: self.form.data.create(),
})
.then(response => {
.then((response) => {
const data = response.data;
node.update_field_data(data);
});
}
},
});
}
}
Expand All @@ -54,12 +54,12 @@ export class ToolForm {
tool_id: options.id,
tool_version: options.version,
type: "tool",
inputs: Object.assign({}, form.data.create())
inputs: Object.assign({}, form.data.create()),
};
Galaxy.emit.debug("tool-form-workflow::postchange()", "Sending current state.", current_state);
axios
.post(`${getAppRoot()}api/workflows/build_module`, current_state)
.then(response => {
.then((response) => {
const data = response.data;
self._customize(data);
self.form.model.set(data.config_form);
Expand All @@ -73,16 +73,16 @@ export class ToolForm {
Galaxy.emit.debug("tool-form-workflow::postchange()", "Received new model.", data);
process.resolve();
})
.catch(response => {
.catch((response) => {
Galaxy.emit.debug("tool-form-workflow::postchange()", "Refresh request failed.", response);
process.reject();
});
}
},
});
}
_customize(node) {
const inputs = node.config_form.inputs;
Utils.deepeach(inputs, input => {
Utils.deepeach(inputs, (input) => {
if (input.type) {
if (["data", "data_collection"].indexOf(input.type) != -1) {
input.type = "hidden";
Expand Down Expand Up @@ -145,7 +145,7 @@ function _addLabelAnnotation(self, node) {
duplicate && "Duplicate label. Please fix this before saving the workflow."
);
self.form.trigger("change");
}
},
});
}

Expand Down
62 changes: 31 additions & 31 deletions client/galaxy/scripts/mvc/workflow/workflow-manager.js
View file
Expand Up @@ -49,7 +49,7 @@ class Workflow extends EventEmitter {
set_node(node, data) {
node.init_field_data(data);
node.update_field_data(data);
$.each(node.output_terminals, (ot_id, ot) => {
Object.values(node.output_terminals).forEach((ot) => {
node.addWorkflowOutput(ot.name);
node.markWorkflowOutput(ot.name);
});
Expand Down Expand Up @@ -195,47 +195,47 @@ class Workflow extends EventEmitter {
}
remove_all() {
var wf = this;
$.each(this.nodes, (k, v) => {
v.destroy();
wf.remove_node(v);
Object.values(this.nodes).forEach((node) => {
node.destroy();
wf.remove_node(node);
});
}
rectify_workflow_outputs() {
// Find out if we're using workflow_outputs or not.
var using_workflow_outputs = false;
var has_existing_pjas = false;
$.each(this.nodes, (k, node) => {
Object.values(this.nodes).forEach((node) => {
if (node.type === "tool" && node.workflow_outputs && node.workflow_outputs.length > 0) {
using_workflow_outputs = true;
}
$.each(node.post_job_actions, (pja_id, pja) => {
Object.values(node.post_job_actions).forEach((pja) => {
if (pja.action_type === "HideDatasetAction") {
has_existing_pjas = true;
}
});
});
if (using_workflow_outputs !== false || has_existing_pjas !== false) {
// Using workflow outputs, or has existing pjas. Remove all PJAs and recreate based on outputs.
$.each(this.nodes, (k, node) => {
Object.values(this.nodes).forEach((node) => {
var node_changed = false;
if (node.post_job_actions === null) {
node.post_job_actions = {};
node_changed = true;
}
var pjas_to_rem = [];
$.each(node.post_job_actions, (pja_id, pja) => {
Object.entries(node.post_job_actions).forEach(([pja_id, pja]) => {
if (pja.action_type == "HideDatasetAction") {
pjas_to_rem.push(pja_id);
}
});
if (pjas_to_rem.length > 0) {
$.each(pjas_to_rem, (i, pja_name) => {
pjas_to_rem.forEach((pja_name) => {
node_changed = true;
delete node.post_job_actions[pja_name];
});
}
if (using_workflow_outputs) {
$.each(node.output_terminals, (ot_id, ot) => {
Object.values(node.output_terminals).forEach((ot) => {
var create_pja = !node.isWorkflowOutput(ot.name);
if (create_pja === true) {
node_changed = true;
Expand All @@ -258,14 +258,14 @@ class Workflow extends EventEmitter {
}
to_simple() {
var nodes = {};
$.each(this.nodes, (i, node) => {
Object.values(this.nodes).forEach((node) => {
var input_connections = {};
$.each(node.input_terminals, (k, t) => {
Object.values(node.input_terminals).forEach((t) => {
input_connections[t.name] = null;
// There should only be 0 or 1 connectors, so this is
// really a sneaky if statement
var cons = [];
$.each(t.connectors, (i, c) => {
t.connectors.forEach((c, i) => {
if (c.handle1) {
var con_dict = {
id: c.handle1.node.id,
Expand All @@ -282,8 +282,8 @@ class Workflow extends EventEmitter {
});
var post_job_actions = {};
if (node.post_job_actions) {
$.each(node.post_job_actions, (i, act) => {
var pja = {
Object.values(node.post_job_actions).forEach((act) => {
const pja = {
action_type: act.action_type,
output_name: act.output_name,
action_arguments: act.action_arguments,
Expand Down Expand Up @@ -329,13 +329,13 @@ class Workflow extends EventEmitter {
var using_workflow_outputs = false;
wf.workflow_version = data.version;
wf.report = data.report || {};
$.each(data.steps, (id, step) => {
Object.entries(data.steps).forEach(([id, step]) => {
var node = wf.prebuildNode(step.type, step.name, step.content_id);
// If workflow being copied into another, wipe UUID and let
// Galaxy assign new ones.
if (!initialImport) {
step.uuid = null;
$.each(step.workflow_outputs, (name, workflow_output) => {
step.workflow_outputs.forEach((workflow_output) => {
workflow_output.uuid = null;
});
}
Expand All @@ -357,7 +357,7 @@ class Workflow extends EventEmitter {
if (node.workflow_outputs.length > 0) {
using_workflow_outputs = true;
} else {
$.each(node.post_job_actions || [], (pja_id, pja) => {
Object.values(node.post_job_actions).forEach((pja) => {
if (pja.action_type === "HideDatasetAction") {
using_workflow_outputs = true;
}
Expand All @@ -367,14 +367,14 @@ class Workflow extends EventEmitter {
});
wf.id_counter = max_id + 1;
// Second pass, connections
$.each(data.steps, (id, step) => {
Object.entries(data.steps).forEach(([id, step]) => {
const node = wf.nodes[parseInt(id) + offset];
$.each(step.input_connections, (k, v) => {
Object.entries(step.input_connections).forEach(([k, v]) => {
if (v) {
if (!$.isArray(v)) {
if (!Array.isArray(v)) {
v = [v];
}
$.each(v, (l, x) => {
v.forEach((x) => {
const other_node = wf.nodes[parseInt(x.id) + offset];
const c = new Connector(this.canvas_manager);
c.connect(other_node.output_terminals[x.output_name], node.input_terminals[k]);
Expand All @@ -384,7 +384,7 @@ class Workflow extends EventEmitter {
});
if (using_workflow_outputs) {
// Ensure that every output terminal has a WorkflowOutput or HideDatasetAction.
$.each(node.output_terminals, (ot_id, ot) => {
Object.values(node.output_terminals).forEach((ot) => {
if (node.post_job_actions[`HideDatasetAction${ot.name}`] === undefined) {
node.addWorkflowOutput(ot.name);
node.markWorkflowOutput(ot.name);
Expand Down Expand Up @@ -450,7 +450,7 @@ class Workflow extends EventEmitter {
var n_pred = {};
var successors = {};
// First pass to initialize arrays even for nodes with no connections
$.each(this.nodes, (id, node) => {
Object.keys(this.nodes).forEach((id) => {
if (n_pred[id] === undefined) {
n_pred[id] = 0;
}
Expand All @@ -459,9 +459,9 @@ class Workflow extends EventEmitter {
}
});
// Second pass to count predecessors and successors
$.each(this.nodes, (id, node) => {
$.each(node.input_terminals, (j, t) => {
$.each(t.connectors, (k, c) => {
Object.values(this.nodes).forEach((node) => {
Object.values(node.input_terminals).forEach((t) => {
t.connectors.forEach((c) => {
// A connection exists from `other` to `node`
var other = c.handle1.node;
// node gains a predecessor
Expand Down Expand Up @@ -504,14 +504,14 @@ class Workflow extends EventEmitter {
var h_pad = 80;
var v_pad = 30;
var left = h_pad;
$.each(node_ids_by_level, (i, ids) => {
node_ids_by_level.forEach((ids) => {
// We keep nodes in the same order in a level to give the user
// some control over ordering
ids.sort((a, b) => $(all_nodes[a].element).position().top - $(all_nodes[b].element).position().top);
// Position each node
var max_width = 0;
var top = v_pad;
$.each(ids, (j, id) => {
ids.forEach((id) => {
var node = all_nodes[id];
var element = $(node.element);
$(element).css({ top: top, left: left });
Expand All @@ -521,7 +521,7 @@ class Workflow extends EventEmitter {
left += max_width + h_pad;
});
// Need to redraw all connectors
$.each(all_nodes, (_, node) => {
Object.values(all_nodes).forEach((node) => {
node.redraw();
});
}
Expand All @@ -531,7 +531,7 @@ class Workflow extends EventEmitter {
var ymin = Infinity;
var ymax = -Infinity;
var p;
$.each(this.nodes, (id, node) => {
Object.values(this.nodes).forEach((node) => {
var e = $(node.element);
p = e.position();
xmin = Math.min(xmin, p.left);
Expand Down
1 change: 1 addition & 0 deletions client/galaxy/scripts/utils/simple-error.js
View file
Expand Up @@ -9,5 +9,6 @@ export function errorMessageAsString(e) {
}

export function rethrowSimple(e) {
console.debug(e);
throw errorMessageAsString(e);
}

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