Allow option overrides with global flow variables

front-end/src/API.js

@@ -60,10 +60,12 @@ export async function deleteNode(node) {
  * Update configuration of node in server-side workflow
  * @param {CustomNodeModel} node - JS node to remove
  * @param {Object} config - configuration from options form
+ * @param {Object} flowConfig - flow variable configuration options
  * @returns {Promise<Object>} - server response (serialized node)
  */
-export async function updateNode(node, config) {
+export async function updateNode(node, config, flowConfig) {
     node.config = config;
+    node.options.option_replace = flowConfig;
     const payload = {...node.options, options: node.config};
     const options = {
         method: "POST",
@@ -212,9 +214,11 @@ export async function downloadDataFile(node) {
         .then(async resp => {
             if (!resp.ok) return Promise.reject(await resp.json());
             contentType = resp.headers.get("content-type");
+            let filename = resp.headers.get("Content-Disposition");
+
             if (contentType.startsWith("text")) {
                 resp.text().then(data => {
-                    downloadFile(data, contentType, node.config["file"]);
+                    downloadFile(data, contentType, filename);
                 })
             }
         }).catch(err => console.log(err));

front-end/src/components/CustomNode/CustomNodeWidget.js

@@ -37,8 +37,8 @@ export default class CustomNodeWidget extends React.Component {
         }).catch(err => console.log(err));
     }
 
-    acceptConfiguration(formData) {
-        API.updateNode(this.props.node, formData).then(() => {
+    acceptConfiguration(optionsData, flowData) {
+        API.updateNode(this.props.node, optionsData, flowData).then(() => {
             this.props.node.setStatus("configured");
             this.forceUpdate();
             this.props.engine.repaintCanvas();
@@ -77,6 +77,7 @@ export default class CustomNodeWidget extends React.Component {
                 <div className="custom-node" style={{ borderColor: this.props.node.options.color, width: width }}>
                     <div className="custom-node-configure" onClick={this.toggleConfig}>{String.fromCharCode(this.icon)}</div>
                     <NodeConfig node={this.props.node}
+                        globals={this.props.engine.model.globals || []}
                         show={this.state.showConfig}
                         toggleShow={this.toggleConfig}
                         onDelete={this.handleDelete}

front-end/src/components/CustomNode/NodeConfig.js

@@ -1,16 +1,18 @@
 import React, { useRef, useState, useEffect } from 'react';
-import { Modal, Button, Form } from 'react-bootstrap';
+import { Col, Modal, Button, Form } from 'react-bootstrap';
 import propTypes from 'prop-types';
 import * as _ from 'lodash';
-import * as API from "../../API";
+import * as API from '../../API';
+import '../../styles/NodeConfig.css';
 
 export default class NodeConfig extends React.Component {
 
     constructor(props) {
         super(props);
         this.state = {
             disabled: false,
-            data: {}
+            data: {},
+            flowData: {}
         };
         this.updateData = this.updateData.bind(this);
         this.handleDelete = this.handleDelete.bind(this);
@@ -19,15 +21,26 @@ export default class NodeConfig extends React.Component {
 
     // callback to update form data in state;
     // resulting state will be sent to node config callback
-    updateData(key, value) {
-        this.setState((prevState) => ({
-                ...prevState,
-                data: {
-                    ...prevState.data,
-                    [key]: value
-                }
-            })
-        );
+    updateData(key, value, flow = false) {
+        if (flow) {
+            this.setState((prevState) => ({
+                    ...prevState,
+                    flowData: {
+                        ...prevState.flowData,
+                        [key]: value
+                    }
+                })
+            );
+        } else {
+            this.setState((prevState) => ({
+                    ...prevState,
+                    data: {
+                        ...prevState.data,
+                        [key]: value
+                    }
+                })
+            );
+        }
     };
 
     // confirm, fire delete callback, close modal
@@ -42,15 +55,21 @@ export default class NodeConfig extends React.Component {
     handleSubmit(e) {
         e.preventDefault();
         console.log(this.state.data);
-        this.props.onSubmit(this.state.data);
+        // remove items from flow vars if null
+        const flowData = {...this.state.flowData};
+        for (let key in flowData) {
+            if (flowData[key] === null) delete flowData[key];
+        }
+        this.props.onSubmit(this.state.data, flowData);
         this.props.toggleShow();
     };
 
     render() {
         if (!this.props.node) return null;
         return (
             <Modal show={this.props.show} onHide={this.props.toggleShow} centered
-                onWheel={e => e.stopPropagation()}>
+                   dialogClassName="NodeConfig"
+                   onWheel={e => e.stopPropagation()}>
                 <Form onSubmit={this.handleSubmit}>
                     <Modal.Header>
                         <Modal.Title><b>{this.props.node.options.name}</b> Configuration</Modal.Title>
@@ -61,6 +80,9 @@ export default class NodeConfig extends React.Component {
                                          onChange={this.updateData}
                                          node={this.props.node}
                                          value={this.props.node.config[key]}
+                                         flowValue={this.props.node.options.option_replace ?
+                                            this.props.node.options.option_replace[key] : null}
+                                         globals={this.props.globals}
                                          disableFunc={(v) => this.setState({disabled: v})}/>
                         )}
                         <Form.Group>
@@ -96,27 +118,61 @@ NodeConfig.propTypes = {
  */
 function OptionInput(props) {
 
+    const [isFlow, setIsFlow] = useState(props.flowValue ? true : false);
+
+    const handleFlowCheck = (bool) => {
+        // if un-checking, fire callback with null so no stale value is in `option_replace`
+        if (!bool) props.onChange(props.keyName, null, true);
+        setIsFlow(bool);
+    };
+
+    // fire callback to update `option_replace` with flow node info
+    const handleFlowVariable = (value) => {
+        props.onChange(props.keyName, value, true);
+    };
+
     let inputComp;
     if (props.type === "file") {
-        inputComp = <FileUploadInput {...props} />
+        inputComp = <FileUploadInput {...props} disabled={isFlow} />
     } else if (props.type === "string") {
+<<<<<<< HEAD
+        inputComp = <SimpleInput {...props} type="text" disabled={isFlow} />
+=======
         inputComp = <SimpleInput {...props} type="text" />
     } else if (props.type === "text") {
         inputComp = <SimpleInput {...props} type="textarea"/>
+>>>>>>> master
     } else if (props.type === "int") {
-        inputComp = <SimpleInput {...props} type="number" />
+        inputComp = <SimpleInput {...props} type="number" disabled={isFlow} />
     } else if (props.type === "boolean") {
+<<<<<<< HEAD
+        inputComp = <BooleanInput {...props} disabled={isFlow} />
+=======
         inputComp = <BooleanInput {...props} />
     } else if (props.type === "select") {
         inputComp = <SelectInput {...props} />
+>>>>>>> master
     } else {
         return (<></>)
     }
+
+    const hideFlow = props.node.options.is_global
+                        || props.type === "file" || props.globals.length === 0
     return (
         <Form.Group>
-                <Form.Label>{props.label}</Form.Label>
-                <div style={{fontSize: '0.7rem'}}>{props.docstring}</div>
-                { inputComp }
+            <Form.Label>{props.label}</Form.Label>
+            <div className="option-docstring">{props.docstring}</div>
+            <Form.Row>
+                <Col xs={hideFlow ? 12 : 8}>{ inputComp }</Col>
+                {hideFlow ? null :
+                    <FlowVariableOverride keyName={props.keyName}
+                                          flowValue={props.flowValue || {}}
+                                          flowNodes={props.globals || []}
+                                          checked={isFlow}
+                                          onFlowCheck={handleFlowCheck}
+                                          onChange={handleFlowVariable} />
+                }
+            </Form.Row>
         </Form.Group>
     )
 }
@@ -236,8 +292,44 @@ function BooleanInput(props) {
 
     return  (
         <Form.Check type="checkbox" name={props.keyName}
-                      checked={value}
-                      onChange={handleChange} />
+                    disabled={props.disabled}
+                    checked={value}
+                    onChange={handleChange} />
+    )
+}
+
+
+function FlowVariableOverride(props) {
+
+    const handleSelect = (event) => {
+        const uuid = event.target.value;
+        const flow = props.flowNodes.find(d => d.id === uuid);
+        const obj = {
+            node_id: uuid,
+            is_global: flow.is_global
+        };
+        props.onChange(obj);
+    };
+    const handleCheck = (event) => { props.onFlowCheck(event.target.checked) };
+
+    return  (
+        <Col>
+            <Form.Check type="checkbox" inline
+                        label="Use Flow Variable"
+                        checked={props.checked} onChange={handleCheck} />
+            {props.checked ?
+                <Form.Control as="select" name={props.keyName} onChange={handleSelect}
+                              value={props.flowValue.node_id}>
+                    <option/>
+                    {props.flowNodes.map(gfv =>
+                        <option  key={gfv.id} value={gfv.id}>
+                            {gfv.options.var_name}
+                        </option>
+                    )}
+                </Form.Control>
+                : null
+            }
+        </Col>
     )
 }
 

front-end/src/components/Workspace.js

@@ -51,7 +51,10 @@ class Workspace extends React.Component {
 
     getGlobalVars() {
         API.getGlobalVars()
-            .then(vars => this.setState({globals: vars}))
+            .then(vars => {
+                this.setState({globals: vars});
+                this.model.globals = vars;
+            })
             .catch(err => console.log(err));
     }
 

front-end/src/styles/NodeConfig.css

@@ -0,0 +1,7 @@
+.option-docstring {
+    font-size: 0.7rem;
+}
+
+.NodeConfig {
+    min-width: 50%;
+}

front-end/src/styles/Workspace.css

@@ -1,9 +1,6 @@
-.Workspace {
-    border: 1px solid grey;
-}
 .NodeMenu, .GlobalFlowMenu {
     padding: 1rem;
-    margin: 0.5rem 0;
+    margin-bottom: 1rem;
     box-shadow: 0px 3px 6px grey;
 }
 .NodeMenu ul {
@@ -23,7 +20,8 @@
     font-size: 1rem;
 }
 .diagram-canvas {
-    height: 75vh;
+    box-shadow: 0px 2px 4px grey;
+    height: 100vh;
     background-size: 20px 20px;
     background-image:
         linear-gradient(to right, rgba(54, 169, 231, 0.1) 1px, transparent 1px),

pyworkflow/pyworkflow/node.py

@@ -28,15 +28,19 @@ def __init__(self, node_info):
     def execute(self, predecessor_data, flow_vars):
         raise NotImplementedError()
 
-    def get_execution_options(self, flow_nodes):
+    def get_execution_options(self, workflow, flow_nodes):
         """Replace Node options with flow variables.
 
         If the user has specified any flow variables to replace Node options,
         perform the replacement and return a dict with all options to use for
         execution. If no flow variables are included, this method will return
-        a copy of all Node options unchanged.
+        a copy of all Node options.
+
+        For any 'file' options, the value will be replaced with a path based on
+        the Workflow's root directory.
 
         Args:
+            workflow: Workflow object to construct file paths
             flow_nodes: dict of FlowNodes used to replace options
 
         Returns:
@@ -49,7 +53,12 @@ def get_execution_options(self, flow_nodes):
         for key, option in self.options.items():
 
             if key in flow_nodes:
-                option.set_value(flow_nodes[key].get_replacement_value())
+                replacement_value = flow_nodes[key].get_replacement_value()
+            else:
+                replacement_value = option.get_value()
+
+            if key == 'file':
+                option.set_value(workflow.path(replacement_value))
 
             execution_options[key] = option
 
@@ -64,8 +73,9 @@ def validate(self):
         Raises:
             ParameterValidationError: invalid Parameter value
         """
-        for option in self.options.values():
-            option.validate()
+        for key, option in self.options.items():
+            if key not in self.option_replace:
+                option.validate()
 
     def validate_input_data(self, num_input_data):
         """Validate Node input data.

pyworkflow/pyworkflow/workflow.py

@@ -304,7 +304,7 @@ def execute(self, node_id):
         try:
             # Validate input data, and replace flow variables
             node_to_execute.validate_input_data(len(preceding_data))
-            execution_options = node_to_execute.get_execution_options(flow_nodes)
+            execution_options = node_to_execute.get_execution_options(self, flow_nodes)
 
             # Pass in data to current Node to use in execution
             output = node_to_execute.execute(preceding_data, execution_options)
@@ -353,7 +353,7 @@ def load_flow_nodes(self, option_replace):
                 else:
                     flow_node = self.get_node(flow_node_id)
 
-                if flow_node is None or flow_node.node_type != 'FlowNode':
+                if flow_node is None or flow_node.node_type != 'flow_control':
                     raise WorkflowException('load flow vars', 'The workflow does not contain FlowNode %s' % flow_node_id)
 
                 flow_nodes[key] = flow_node
@@ -419,8 +419,15 @@ def download_file(self, node_id):
             return None
 
         try:
-            # TODO: Change to generic "file" option to allow for more than WriteCsv
-            to_open = self.path(node.options['file'].get_value())
+            # Check if file option is overridden by flow variable
+            if 'file' in node.option_replace:
+                flow_node = self.load_flow_nodes({'file': node.option_replace['file']})
+                filename = flow_node['file'].get_replacement_value()
+            else:
+                filename = node.options['file'].get_value()
+
+            # Construct path to file in Workflow dir
+            to_open = self.path(filename)
             return open(to_open)
         except KeyError:
             raise WorkflowException('download_file', '%s does not have an associated file' % node_id)

vp/node/views.py

@@ -264,13 +264,9 @@ def create_node(request):
     """Pass all request info to Node Factory.
 
     """
+    # Any filenames/paths passed through as-is
+    # A Workflow-specific path is constructed at execution
     json_data = json.loads(request.body)
-    # for options with type 'file', replace value with FileStorage path
-    for field, info in json_data.get("option_types", dict()).items():
-        if info["type"] == "file" or info["label"] == "Filename":
-            opt_value = json_data["options"][field]
-            if opt_value is not None:
-                json_data["options"][field] = request.pyworkflow.path(opt_value)
 
     try:
         return node_factory(json_data)