Parameter classes

front-end/src/API.js

@@ -189,7 +189,7 @@ export async function downloadDataFile(node) {
             contentType = resp.headers.get("content-type");
             if (contentType.startsWith("text")) {
                 resp.text().then(data => {
-                    downloadFile(data, contentType, node.config["path_or_buf"]);
+                    downloadFile(data, contentType, node.config["file"]);
                 })
             }
         }).catch(err => console.log(err));

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

@@ -85,8 +85,8 @@ function OptionInput(props) {
     }
     return (
         <Form.Group>
-                <Form.Label>{props.name}</Form.Label>
-                <div style={{fontSize: '0.7rem'}}>{props.desc}</div>
+                <Form.Label>{props.label}</Form.Label>
+                <div style={{fontSize: '0.7rem'}}>{props.docstring}</div>
                 { inputComp }
         </Form.Group>
     )

pyworkflow/pyworkflow/node.py

@@ -1,11 +1,16 @@
 import pandas as pd
 
+from .parameters import *
+
 
 class Node:
     """Node object
 
     """
-    def __init__(self, node_info, options=None):
+    options = Options()
+    option_types = OptionTypes()
+
+    def __init__(self, node_info):
         self.name = node_info.get('name')
         self.node_id = node_info.get('node_id')
         self.node_type = node_info.get('node_type')
@@ -14,12 +19,9 @@ def __init__(self, node_info, options=None):
 
         self.is_global = node_info.get('is_global') is True
 
-        # Execution options are passed up from children
-        self.options = options or dict()
-
-        # User-override takes precedence
+        self.option_values = dict()
         if node_info.get("options"):
-            self.options.update(node_info["options"])
+            self.option_values.update(node_info["options"])
 
     def execute(self, predecessor_data, flow_vars):
         pass
@@ -35,12 +37,6 @@ class FlowNode(Node):
     """FlowNode object
     """
     display_name = "Flow Control"
-    DEFAULT_OPTIONS = {
-
-    }
-
-    def __init__(self, node_info, options=dict()):
-        super().__init__(node_info, {**FlowNode.DEFAULT_OPTIONS, **options})
 
 
 class StringNode(FlowNode):
@@ -53,27 +49,13 @@ class StringNode(FlowNode):
     num_out = 1
     color = 'purple'
 
-    DEFAULT_OPTIONS = {
-        'default_value': None,
-        'var_name': 'my_var',
+    OPTIONS = {
+        "default_value": StringParameter("Default Value",
+                                         docstring="Value this node will pass as a flow variable"),
+        "var_name": StringParameter("Variable Name", default="my_var",
+                                    docstring="Name of the variable to use in another Node")
     }
 
-    OPTION_TYPES = {
-        'default_value': {
-            "type": "string",
-            "name": "Default Value",
-            "desc": "Value this Node will pass as a flow variable"
-        },
-        'var_name': {
-            "type": "string",
-            "name": "Variable Name",
-            "desc": "Name of the variable to use in another Node"
-        }
-    }
-
-    def __init__(self, node_info):
-        super().__init__(node_info)
-
 
 class IONode(Node):
     """IONodes deal with file-handling in/out of the Workflow.
@@ -85,13 +67,6 @@ class IONode(Node):
     color = 'black'
     display_name = "I/O"
 
-    DEFAULT_OPTIONS = {
-        # 'file': None,
-    }
-
-    def __init__(self, node_info, options=dict()):
-        super().__init__(node_info, {**IONode.DEFAULT_OPTIONS, **options})
-
     def execute(self, predecessor_data, flow_vars):
         pass
 
@@ -112,49 +87,24 @@ class ReadCsvNode(IONode):
     num_in = 0
     num_out = 1
 
-    DEFAULT_OPTIONS = {
-        'filepath_or_buffer': None,
-        'sep': ',',
-        'header': 'infer',
-        'index_col': None
-    }
-
-    OPTION_TYPES = {
-        'filepath_or_buffer': {
-            "type": "file",
-            "name": "File",
-            "desc": "CSV File"
-        },
-        'sep': {
-            "type": "string",
-            "name": "Delimiter",
-            "desc": "column delimiter, default ','"
-        },
-        'header': {
-            "type": "string",
-            "name": "Column Name Row",
-            "desc": "Row number with column names (0-indexed) or 'infer'"
-        },
-        'index_col': {
-            "type": "string",
-            "name": "Index Column Name",
-            "desc": "Column to use as index (facilitates joining)"
-        }
+    OPTIONS = {
+        "file": FileParameter("File", docstring="CSV File"),
+        "sep": StringParameter("Delimiter", default=",", docstring="Column delimiter"),
+        # user-specified headers are probably integers, but haven't figured out
+        # arguments with multiple possible types
+        "header": StringParameter("Header Row", default="infer",
+                                   docstring="Row number containing column names (0-indexed)"),
     }
 
-    def __init__(self, node_info, options=dict()):
-        super().__init__(node_info, {**self.DEFAULT_OPTIONS, **options})
-
     def execute(self, predecessor_data, flow_vars):
         try:
-            # TODO: FileStorage implemented in Django to store in /tmp
-            #       Better filename/path handling should be implemented.
             # Read CSV needs exactly 0 input DataFrame
             NodeUtils.validate_predecessor_data(len(predecessor_data), self.num_in, self.node_key)
             NodeUtils.replace_flow_vars(self.options, flow_vars)
-            opts = self.options
-            df = pd.read_csv(opts["filepath_or_buffer"], sep=opts["sep"],
-                             header=opts["header"])
+            fname = self.options["file"].get_value()
+            sep = self.options["sep"].get_value()
+            hdr = self.options["header"].get_value()
+            df = pd.read_csv(fname, sep=sep, header=hdr)
             return df.to_json()
         except Exception as e:
             raise NodeException('read csv', str(e))
@@ -177,34 +127,12 @@ class WriteCsvNode(IONode):
     num_out = 0
     download_result = True
 
-    DEFAULT_OPTIONS = {
-        'path_or_buf': None,
-        'sep': ',',
-        'index': True,
-    }
-
-    OPTION_TYPES = {
-        "path_or_buf": {
-            "type": "string",
-            "name": "Filename",
-            "desc": "Filename to write"
-        },
-        "sep": {
-            "type": "string",
-            "name": "Delimiter",
-            "desc": "column delimiter, default ','"
-        },
-        "index": {
-            "type": "boolean",
-            "name": "Index",
-            "desc": "Write index column or not"
-        }
-
+    OPTIONS = {
+        "file": StringParameter("Filename", docstring="CSV file to write"),
+        "sep": StringParameter("Delimiter", default=",", docstring="Column delimiter"),
+        "index": BooleanParameter("Write Index", default=True, docstring="Write index as column?"),
     }
 
-    def __init__(self, node_info, options=dict()):
-        super().__init__(node_info, {**self.DEFAULT_OPTIONS, **options})
-
     def execute(self, predecessor_data, flow_vars):
         try:
             # Write CSV needs exactly 1 input DataFrame
@@ -214,8 +142,10 @@ def execute(self, predecessor_data, flow_vars):
             df = pd.DataFrame.from_dict(predecessor_data[0])
 
             # Write to CSV and save
-            opts = self.options
-            df.to_csv(opts["path_or_buf"], sep=opts["sep"], index=opts["index"])
+            fname = self.options["file"].get_value()
+            sep = self.options["sep"].get_value()
+            index = self.options["index"].get_value()
+            df.to_csv(fname, sep=sep, index=index)
             return df.to_json()
         except Exception as e:
             raise NodeException('write csv', str(e))
@@ -232,11 +162,6 @@ class ManipulationNode(Node):
     display_name = "Manipulation"
     color = 'goldenrod'
 
-    DEFAULT_OPTIONS = {}
-
-    def __init__(self, node_info, options=dict()):
-        super().__init__(node_info, {**ManipulationNode.DEFAULT_OPTIONS, **options})
-
     def execute(self, predecessor_data, flow_vars):
         pass
 
@@ -310,9 +235,6 @@ class PivotNode(ManipulationNode):
         }
     }
 
-    def __init__(self, node_info, options=dict()):
-        super().__init__(node_info, {**self.DEFAULT_OPTIONS, **options})
-
     def execute(self, predecessor_data, flow_vars):
         try:
             NodeUtils.validate_predecessor_data(len(predecessor_data), self.num_in, self.node_key)
@@ -328,29 +250,19 @@ class JoinNode(ManipulationNode):
     num_in = 2
     num_out = 1
 
-    DEFAULT_OPTIONS = {
-        "on": None,
+    OPTIONS = {
+        "on": StringParameter("Join Column", docstring="Name of column to join on")
     }
 
-    OPTION_TYPES = {
-        "on": {
-            "type": "string",
-            "name": "Join Column",
-            "desc": "Name of column to join on"
-        }
-    }
-
-    def __init__(self, node_info, options=dict()):
-        super().__init__(node_info, {**self.DEFAULT_OPTIONS, **options})
-
     def execute(self, predecessor_data, flow_vars):
         # Join cannot accept more than 2 input DataFrames
         # TODO: Add more error-checking if 1, or no, DataFrames passed through
         try:
             NodeUtils.validate_predecessor_data(len(predecessor_data), self.num_in, self.node_key)
             first_df = pd.DataFrame.from_dict(predecessor_data[0])
             second_df = pd.DataFrame.from_dict(predecessor_data[1])
-            combined_df = pd.merge(first_df, second_df, on=self.options["on"])
+            combined_df = pd.merge(first_df, second_df,
+                                   on=self.options["on"].get_value())
             return combined_df.to_json()
         except Exception as e:
             raise NodeException('join', str(e))
@@ -437,6 +349,9 @@ def validate_predecessor_data(predecessor_data_len, num_in, node_key):
 
     @staticmethod
     def replace_flow_vars(node_options, flow_vars):
+        # TODO: this will no longer work with the Node.options descriptor,
+        #       which uses Node.option_values to populate the Parameter
+        #       class values upon access
         for var in flow_vars:
             node_options[var['var_name']] = var['default_value']