Merge pull request #69 from matthew-t-smith/dev/cli

Reads to stdin and writes to stdout, batch execution of workflows

CLI/cli.py

@@ -1,6 +1,11 @@
+import sys
+
 import click
+import os
+import uuid
 
 from pyworkflow import Workflow
+from pyworkflow import NodeException
 
 
 class Config(object):
@@ -10,16 +15,47 @@ def __init__(self):
 pass_config = click.make_pass_decorator(Config, ensure=True)
 
 @click.group()
-@click.option('--file-directory', type=click.Path())
-@pass_config
-def cli(config, file_directory):
-    if file_directory is None:
-        file_directory = '.'
-    config.file_directory = file_directory
+def cli():
+    pass
 
 
 @cli.command()
-@pass_config
-def execute(config):
-    click.echo('Loading workflow file form %s' % config.file_directory)
-    Workflow.execute_workflow(config.file_directory)
+@click.argument('filename', type=click.Path(exists=True), nargs=-1)
+def execute(filename):
+
+    write_to_stdout = not click.get_text_stream('stdout').isatty()
+
+    #execute each one of the workflows in the ar
+    for workflow_file in filename:
+
+        stdin_files = []
+
+        if not click.get_text_stream('stdin').isatty():
+            stdin_text = click.get_text_stream('stdin')
+
+            # write standard in to a new file in local filesystem
+            file_name = str(uuid.uuid4())
+
+            # TODO small issue here, might be better to upload this file to the workflow directory instead of cwd
+            new_file_path = os.path.join(os.getcwd(), file_name)
+
+            # read from std in and upload a new file in project directory
+            with open(new_file_path, 'w') as f:
+                f.write(stdin_text.read())
+
+            stdin_files.append(file_name)
+
+
+
+        if workflow_file is None:
+            click.echo('Please specify a workflow to run')
+            return
+        try:
+            if not write_to_stdout:
+                click.echo('Loading workflow file from %s' % workflow_file)
+            Workflow.execute_workflow(workflow_file, stdin_files, write_to_stdout)
+
+
+        except NodeException as ne:
+            click.echo("Issues during node execution")
+            click.echo(ne)

README.md

@@ -65,7 +65,11 @@ data from `localhost:8000` **where the Django app must be running**.
 ## CLI
 1. Run pipenv shell.
 2. Create a workflow using UI and save it. 
-3. Run it as: pyworkflow --file-directory (path-to-json-workflow-file) execute
+3. Run it as: pyworkflow execute workflow-file
+
+Also accepts reading input from std (i.e < file.csv) and writing to sdt out (i.e > output.csv)
+
+
 
 ---
 ## Tests

pyworkflow/pyworkflow/nodes/io/read_csv.py

@@ -46,3 +46,13 @@ def execute(self, predecessor_data, flow_vars):
             return df.to_json()
         except Exception as e:
             raise NodeException('read csv', str(e))
+
+    def execute_for_read(self, predecessor_data, flow_vars, file_to_read):
+        try:
+            fname = file_to_read
+            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))

pyworkflow/pyworkflow/workflow.py

@@ -8,6 +8,8 @@
 from collections import OrderedDict
 from modulefinder import ModuleFinder
 
+from pyworkflow.nodes import ReadCsvNode, WriteCsvNode
+
 from .node import Node, NodeException
 from .node_factory import node_factory
 
@@ -547,8 +549,60 @@ def to_session_dict(self):
         except nx.NetworkXError as e:
             raise WorkflowException('to_session_dict', str(e))
 
+    def execute_read_csv(self, node_id, csv_location):
+        # TODO: some duplicated code here from execute common method. Need to refactor.
+        """Execute read_csv from a file specified to standard input.
+                  Current use case: CLI.
+        """
+        preceding_data = list()
+        flow_vars = list()
+        node_to_execute = self.get_node(node_id)
+        if node_to_execute is None:
+            raise WorkflowException('execute', 'The workflow does not contain node %s' % node_id)
+        # Pass in data to current Node to use in execution
+        output = node_to_execute.execute_for_read(preceding_data.append(None), flow_vars.append(None), csv_location)
+
+        # Save new execution data to disk
+        node_to_execute.data = Workflow.store_node_data(self, node_id, output)
+
+        if node_to_execute.data is None:
+            raise WorkflowException('execute', 'There was a problem saving node output.')
+
+        return node_to_execute
+
+    def execute_write_csv(self, node_id):
+        node_to_execute = self.get_node(node_id)
+
+        if node_to_execute is None:
+            raise WorkflowException('execute', 'The workflow does not contain node %s' % node_id)
+
+        # Load predecessor data and FlowNode values
+        preceding_data = self.load_input_data(node_to_execute.node_id)
+        flow_nodes = self.load_flow_nodes(node_to_execute.option_replace)
+
+        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)
+
+            # Pass in data to current Node to use in execution
+            output = node_to_execute.execute(preceding_data, execution_options)
+
+            #printing the output in order to include in std_out
+            print(output)
+
+            # Save new execution data to disk
+            node_to_execute.data = Workflow.store_node_data(self, node_id, output)
+        except NodeException as e:
+            raise e
+
+        if node_to_execute.data is None:
+            raise WorkflowException('execute', 'There was a problem saving node output.')
+
+        return node_to_execute
+
     @staticmethod
-    def execute_workflow(workflow_location):
+    def execute_workflow(workflow_location, stdin_files, write_to_stdout):
         """Execute entire workflow at a certain location.
            Current use case: CLI.
         """
@@ -565,7 +619,17 @@ def execute_workflow(workflow_location):
         #execute each node in the order returned by execution order method
         #TODO exception handling: stop and provide details on which node failed to execute
         for node in execution_order:
-            workflow_instance.execute(node)
+            if type(workflow_instance.get_node(node)) is ReadCsvNode and len(stdin_files) > 0:
+                csv_location = stdin_files[0]
+                executed_node = workflow_instance.execute_read_csv(node, csv_location)
+                # delete file at index 0
+                del stdin_files[0]
+            elif type(workflow_instance.get_node(node)) is WriteCsvNode and write_to_stdout:
+                executed_node = workflow_instance.execute_write_csv(node)
+            else:
+                executed_node = workflow_instance.execute(node)
+
+            workflow_instance.update_or_add_node(executed_node)
 
 
 class WorkflowUtils: